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Data from: Moderation is best: effects of grazing intensity on plant-flower visitor networks in Mediterranean communities
09-03-2015 08-04-2016
The structure of pollination networks is an important indicator of ecosystem stability and functioning. Livestock grazing is a frequent land use practice that directly affects the abundance and diversity of flowers and pollinators and, therefore, may indirectly affect the structure of pollination networks. Here we studied how grazing intensity affected the structure of plant-flower visitor networks along a wide range of grazing intensities by sheep and goats, using data from 11 Mediterranean plant-flower visitor communities from Lesvos Island, Greece. We hypothesized that intermediate grazing might result in higher diversity as predicted by the Intermediate Disturbance Hypothesis, which could in turn confer more stability to the networks. Indeed, we found that networks at intermediate grazing intensities were larger, more generalized, more modular, and contained more diverse and even interactions. Despite general responses at the network level, the number of interactions and selectiveness of particular flower visitor and plant taxa in the networks responded differently to grazing intensity, presumably as a consequence of variation in the abundance of different taxa with grazing. Our results highlight the benefit of maintaining moderate levels of livestock grazing by sheep and goats to preserve the complexity and biodiversity of the rich Mediterranean communities, which have a long history of grazing by these domestic animals.
Data from: Socially selected ornaments and fitness: signals of fighting ability in paper wasps are positively associated with survival, reproductive success, and rank
10-12-2015 11-21-2015
Many animals have ornaments that mediate choice and competition in social and sexual contexts. Individuals with elaborate sexual ornaments typically have higher fitness than those with less elaborate ornaments, but less is known about whether socially selected ornaments are associated with fitness. Here, we test the relationship between fitness and facial patterns that are a socially-selected signal of fighting ability in Polistes dominula wasps. We found wasps that signal higher fighting ability have larger nests, are more likely to survive harsh winters, and obtain higher dominance rank than wasps that signal lower fighting ability. In comparison, body weight was not associated with fitness. Larger wasps were dominant over smaller wasps, but showed no difference nest size or survival. Overall, the positive relationship between wasp facial patterns and fitness indicates that receivers can obtain diverse information about a signaler's phenotypic quality by paying attention to socially selected ornaments. Therefore, there are surprisingly strong parallels between the information conveyed by socially and sexually selected signals. Similar fitness relationships in social and sexually selected signals may be one reason it can be difficult to distinguish the role of social versus sexual selection in ornament evolution.
Data from: Species turnover (β diversity) in ectomycorrhizal fungi linked to NH4+ uptake capacity
10-28-2015 02-29-2016
Ectomycorrhizal (EcM) fungal communities may be shaped by both deterministic and stochastic processes, potentially influencing ecosystem development and function. We evaluated community assembly processes for EcM fungi of Pseudotsuga menziesii among 12 sites up to 400 km apart in southwest British Columbia (Canada) by investigating species turnover (β diversity) in relation to soil nitrogen (N) availability and physical distance. We then examined functional traits for an N-related niche by quantifying net fluxes of NH4+, NO3- and protons on excised root tips from three contrasting sites using a microelectrode ion flux measurement system. EcM fungal communities were well aligned with soil N availability and pH, with no effect of site proximity (distance-decay curve) on species assemblages. Species turnover was significant (β1/2 = 1.48) along soil N gradients, with many more Tomentella species on high-N than low-N soils, in contrast to Cortinarius species. Ammonium uptake was greatest in the spring on the medium and rich sites, and averaged over 190 nmol m−2 s−1 for Tomentella species. The lowest uptake rates of NH4+ were by non-mycorrhizal roots of axenically grown seedlings (10 nmol m−2 s−1), followed by Cortinarius species (60 nmol m−2 s−1). EcM roots from all sites displayed only marginal uptake of nitrate (8.3 nmol m−2 s−1). These results suggest NH4+ uptake capacity is an important functional trait influencing the assembly of EcM fungal communities. The diversity of EcM fungal species across the region arguably provides critical belowground adaptations to organic and inorganic N supply that are integral to temperate rainforest ecology.
Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species
10-22-2015 12-28-2015
Two common approaches for estimating phylogenies in species-rich groups are to: (i) sample many loci for few species (e.g. phylogenomic approach), or (ii) sample many species for fewer loci (e.g. supermatrix approach). In theory, these approaches can be combined to simultaneously resolve both higher-level relationships (with many genes) and species-level relationships (with many taxa). However, fundamental questions remain unanswered about this combined approach. First, will higher-level relationships more closely resemble those estimated from many genes or those from many taxa? Second, will branch support increase for higher-level relationships (relative to the estimate from many taxa)? Here, we address these questions in squamate reptiles. We combined two recently published datasets, one based on 44 genes for 161 species, and one based on 12 genes for 4161 species. The likelihood-based tree from the combined matrix (52 genes, 4162 species) shared more higher-level clades with the 44-gene tree (90% vs. 77% shared). Branch support for higher level-relationships was marginally higher than in the 12-gene tree, but lower than in the 44-gene tree. Relationships were apparently not obscured by the abundant missing data (92% overall). We provide a time-calibrated phylogeny based on extensive sampling of genes and taxa as a resource for comparative studies.
Data from: Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic acanthisittid wrens
05-31-2016 07-27-2016
The New Zealand acanthisittid wrens are the sister-taxon to all other “perching birds” (Passeriformes) and – including recently extinct species – represent the most diverse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) diverged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall’s wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.
Data from: Vervet monkeys use paths consistent with context-specific spatial movement heuristics
10-05-2015 10-28-2015
Animal foraging routes are analogous to the computationally demanding “traveling salesman problem” (TSP), where individuals must find the shortest path among several locations before returning to the start. Humans approximate solutions to TSPs using simple heuristics or “rules of thumb,” but our knowledge of how other animals solve multidestination routing problems is incomplete. Most nonhuman primate species have shown limited ability to route plan. However, captive vervets were shown to solve a TSP for six sites. These results were consistent with either planning three steps ahead or a risk-avoidance strategy. I investigated how wild vervet monkeys (Chlorocebus pygerythrus) solved a path problem with six, equally rewarding food sites; where site arrangement allowed assessment of whether vervets found the shortest route and/or used paths consistent with one of three simple heuristics to navigate. Single vervets took the shortest possible path in fewer than half of the trials, usually in ways consistent with the most efficient heuristic (the convex hull). When in competition, vervets' paths were consistent with different, more efficient heuristics dependent on their dominance rank (a cluster strategy for dominants and the nearest neighbor rule for subordinates). These results suggest that, like humans, vervets may solve multidestination routing problems by applying simple, adaptive, context-specific “rules of thumb.” The heuristics that were consistent with vervet paths in this study are the same as some of those asserted to be used by humans. These spatial movement strategies may have common evolutionary roots and be part of a universal mental navigational toolkit. Alternatively, they may have emerged through convergent evolution as the optimal way to solve multidestination routing problems.
Data from: The selective myosin II inhibitor blebbistatin reversibly eliminates gastrovascular flow and stolon tip pulsations in the colonial hydroid Podocoryna carnea
11-25-2015 12-22-2015
Blebbistatin reversibly disrupted both stolon tip pulsations and gastrovascular flow in the colonial hydroid Podocoryna carnea. Epithelial longitudinal muscles of polyps were unaffected by blebbistatin, as polyps contracted when challenged with a pulse of KCl. Latrunculin B, which sequesters G actin preventing F actin assembly, caused stolons to retract, exposing focal adhesions where the tip epithelial cells adhere to the substratum. These results are consistent with earlier suggestions that non-muscle myosin II provides the motive force for stolon tip pulsations and further suggest that tip oscillations are functionally coupled to hydrorhizal axial muscle contraction.
Data from: Continuous theta burst stimulation over the left dorsolateral prefrontal cortex decreases medium load working memory performance in healthy humans
03-17-2015 09-23-2015
The dorsolateral prefrontal cortex (DLPFC) plays a key role in working memory. Evidence indicates that transcranial magnetic stimulation (TMS) over the DLPFC can interfere with working memory performance. Here we investigated for how long continuous theta-burst stimulation (cTBS) over the DLPFC decreases working memory performance and whether the effect of cTBS on performance depends on working memory load. Forty healthy young subjects received either cTBS over the left DLPFC or sham stimulation before performing a 2-, and 3-back working memory letter task. An additional 0-back condition served as a non-memory-related control, measuring general attention. cTBS over the left DLPFC significantly impaired 2-back working memory performance for about 15 min, whereas 3-back and 0-back performances were not significantly affected. Our results indicate that the effect of left DLPFC cTBS on working memory performance lasts for roughly 15 min and depends on working memory load.
Data from: Perceptual expertise in forensic facial image comparison
09-02-2015 09-24-2015
Forensic facial identification examiners are required to match the identity of faces in images that vary substantially, owing to changes in viewing conditions and in a person's appearance. These identifications affect the course and outcome of criminal investigations and convictions. Despite calls for research on sources of human error in forensic examination, existing scientific knowledge of face matching accuracy is based, almost exclusively, on people without formal training. Here, we administered three challenging face matching tests to a group of forensic examiners with many years' experience of comparing face images for law enforcement and government agencies. Examiners outperformed untrained participants and computer algorithms, thereby providing the first evidence that these examiners are experts at this task. Notably, computationally fusing responses of multiple experts produced near-perfect performance. Results also revealed qualitative differences between expert and non-expert performance. First, examiners' superiority was greatest at longer exposure durations, suggestive of more entailed comparison in forensic examiners. Second, experts were less impaired by image inversion than non-expert students, contrasting with face memory studies that show larger face inversion effects in high performers. We conclude that expertise in matching identity across unfamiliar face images is supported by processes that differ qualitatively from those supporting memory for individual faces.
Data from: Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait-specificity in Drosophila
10-06-2015 02-24-2016
Cryptic genetic variation (CGV) is defined as the genetic variation that has little effect on phenotypic variation under a normal condition, but contributes to heritable variation under environmental or genetic perturbations. Genetic buffering systems that suppress the expression of CGV and store it in a population are called genetic capacitors, and the opposite systems are called genetic potentiators. One of the best-known candidates for a genetic capacitor and potentiator is the molecular chaperone protein, HSP90, and one of its characteristics is that it affects the genetic variation in various morphological traits. However, it remains unclear whether the wide-ranging effects of HSP90 on a broad range of traits are a general feature of genetic capacitors and potentiators. In the current study, I searched for novel genetic capacitors and potentiators for quantitative bristle traits of Drosophila melanogaster, and then investigate the trait-specificity of their genetic buffering effect. Three bristle traits of D. melanogaster were used as the target traits, and the genomic regions with genetic buffering effects were screened using the 61 genomic deficiencies examined previously for genetic buffering effects in wing shape. As a result, four and six deficiencies with significant effects on increasing and decreasing the broad-sense heritability of the bristle traits were identified, respectively. Of the 18 deficiencies with significant effects detected in the current study and/or by the previous study, 14 showed trait-specific effects, and four affected the genetic buffering of both bristle traits and wing shape. This suggests that most genetic capacitors and potentiators exert trait-specific effects, but that general capacitors and potentiators with effects on multiple traits also exist.
Data from: Lack of spatial immunogenetic structure among wolverine (Gulo gulo) populations suggestive of broad scale balancing selection
10-08-2015 10-16-2015
Elucidating the adaptive genetic potential of wildlife populations to environmental selective pressures is fundamental for species conservation. Genes of the major histocompatibility complex (MHC) are highly polymorphic, and play a key role in the adaptive immune response against pathogens. MHC polymorphism has been linked to balancing selection or heterogeneous selection promoting local adaptation. However, spatial patterns of MHC polymorphism are also influenced by gene flow and drift. Wolverines are highly vagile, inhabiting varied ecoregions that include boreal forest, taiga, tundra, and high alpine ecosystems. Here, we investigated the immunogenetic variation of wolverines in Canada as a surrogate for identifying local adaptation by contrasting the genetic structure at MHC relative to the structure at 11 neutral microsatellites to account for gene flow and drift. Evidence of historical positive selection was detected at MHC using maximum likelihood codon-based methods. Bayesian and multivariate cluster analyses revealed weaker population genetic differentiation at MHC relative to the increasing microsatellite genetic structure towards the eastern wolverine distribution. Mantel correlations of MHC against geographical distances showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9), whereas for microsatellites we found a relatively strong and significant IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation between microsatellite allelic richness and the mean number of MHC alleles, but we did not observe low MHC diversity in small populations. Overall these results suggest that MHC polymorphism has been influenced primarily by balancing selection and to a lesser extent by neutral processes such as genetic drift, with no clear evidence for local adaptation. This study contributes to our understanding of how vulnerable populations of wolverines may respond to selective pressures across their range.
Data from: Selection on bristle length has the ability to drive the evolution of male abdominal appendages in the sepsid fly Themira biloba
10-05-2015 07-07-2016
Many exaggerated and novel traits are strongly influenced by sexual selection. Although sexual selection is a powerful evolutionary force, underlying genetic interactions can constrain evolutionary outcomes. The relative strength of selection vs. constraint has been a matter of debate for the evolution of male abdominal appendages in sepsid flies. These abdominal appendages are involved in courtship and mating, but their function has not been directly tested. We performed mate choice experiments to determine whether sexual selection acts on abdominal appendages in the sepsid Themira biloba. We tested whether appendage bristle length influenced successful insemination by surgically trimming the bristles. Females paired with males that had shortened bristles laid only unfertilized eggs, indicating that long bristles are necessary for successful insemination. We also tested whether the evolution of bristle length was constrained by phenotypic correlations with other traits. Analyses of phenotypic covariation indicated that bristle length was highly correlated with other abdominal appendage traits, but was not correlated with abdominal sternite size. Thus, abdominal appendages are not exaggerated traits like many sexual ornaments, but vary independently from body size. At the same time, strong correlations between bristle length and appendage length suggest that selection on bristle length is likely to result in a correlated increase in appendage length. Bristle length is under sexual selection in T. biloba and has the potential to evolve independently from abdomen size.
Data from: Phylogenetic placement of the unusual jumping spider Depreissia Lessert, and a new synapomorphy uniting Hisponinae and Salticinae (Araneae, Salticidae)
01-05-2016 01-08-2016
The relationships of the unusual salticid spider Depreissia from central Africa and Borneo have been difficult to resolve, obscured by its highly modified ant-like body. Phylogenetic analysis of the gene 28S strongly supports its placement outside the major clade Salticinae and within the clade of cocalodines, spartaeines and lapsiines, with weaker support for a relationship with the cocalodines in particular. Excluding the genus from the Salticinae is supported also by the presence of a median apophysis on the male palp, and by the lack of a cymbial apical groove cradling the tip of embolus, which is newly presented here as a synapomorphy of Hisponinae plus Salticinae.
Data from: Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum
12-23-2015 01-14-2016
Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation has been important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analyzed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signaling molecules. This study provides insight into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was likely present in the last common ancestor of animals.
Data from: Phylogeographic pattern of range expansion provides evidence for cryptic species lineages in Silene nutans in Western Europe
12-09-2015 03-09-2016
As a result of recent or past evolutionary processes, a single species might consist of distinct Evolutionary Significant Units (ESUs), even corresponding to cryptic species. Determining the underlying mechanisms of range shifts and the processes at work in the build-up of divergent ESUs requires elucidating the factors that contribute to population genetic divergence across a species’ range. We investigated the large-scale patterns of genetic structure in the perennial herbaceous plant species Silene nutans (Caryophyllaceae) in Western Europe. We sampled and genotyped 111 populations using 13 nuclear microsatellite loci and 6 plastid single-nucleotide polymorphisms. Broad-scale spatial population genetic structure was examined using Bayesian clustering, spatial multivariate analyses and measures of hierarchical genetic differentiation. The genotypic structure of S. nutans was typical of a predominantly allogamous mating system. We also identified plastid lineages with no intra-population polymorphism, mirroring two genetically differentiated nuclear lineages. No evidence of admixture was found. Spatial trends in genetic diversity further suggested independent leading-edge expansion associated with founding events and subsequent genetic erosion. Overall, our findings suggested speciation processes in S. nutans and highlighted striking patterns of distinct stepwise recolonisation of Western Europe shaped by Quaternary climate oscillations. Two main potential ESUs can be defined in Western Europe, corresponding to Eastern and Western nuclear-plastid lineages. In situ preservation of populations and genetic rescue implying ex situ conservation techniques should take the lineage identity into account. This is particularly true in Great Britain, northern France and Belgium, where S. nutans is rare and where distinct lineages co-occur in close contact.
Data from: Estimating cranial musculoskeletal constraints in theropod dinosaurs
11-04-2015 12-08-2015
Many inferences on the biology, behaviour and ecology of extinct vertebrates are based on the reconstruction of the musculature and rely considerably on its accuracy. Although the advent of digital reconstruction techniques has facilitated the creation and testing of musculoskeletal hypotheses in recent years, muscle strain capabilities have rarely been considered. Here, a digital modelling approach using the freely available visualization and animation software BLENDER is applied to estimate cranial muscle length changes and optimal and maximal possible gape in different theropod dinosaurs. Models of living archosaur taxa (Alligator mississippiensis, Buteo buteo) were used in an extant phylogenetically bracketed framework to validate the method. Results of this study demonstrate that Tyrannosaurus rex, Allosaurus fragilis and Erlikosaurus andrewsi show distinct differences in the recruitment of the jaw adductor musculature and resulting gape, confirming previous dietary and ecological assumptions. While the carnivorous taxa T. rex and Allo. fragilis were capable of a wide gape and sustained muscle force, the herbivorous therizinosaurian E. andrewsi was constrained to small gape angles.
Data from: Camouflaged or tanned: plasticity in freshwater snail pigmentation
09-18-2013 09-30-2015
By having phenotypically plastic traits, such as morphology, behaviour and life history, many organisms optimise their fitness in response to fluctuating threats. Freshwater snails with translucent shells, e.g. snails from the Radix genus, differ considerably in their mantle pigmentation patterns, with snails from the same water body ranging from completely dark pigmented to only a few dark patterns. These pigmentation differences have previously been suggested to be genetically fixed, but we suggest that this polymorphism is due to phenotypic plasticity in response to a fluctuating environment. Hence, we here aimed at assessing if common stressors, including ultraviolet radiation (UVR) and predation, induce a plastic response in mantle pigmentation patterns of Radix balthica. We show, in contrast to previous studies, that snails are plastic in their expression of mantle pigmentation in response to changes in UVR and predator threats, i.e. differences among species or populations are not genetically fixed. When exposed to cues from visually hunting fish, R. balthica increased the proportion of their dark pigmentation, suggesting a crypsis strategy. Snails increased their pigmentation even further in response to UVR, but this also lead to reduced complexity of the patterns. Furthermore, when exposed to UVR and fish, snails responded in the same way as in the UVR treatment, suggesting a trade-off between photoprotection and crypsis.
Data from: The evolution of bat nucleic acid sensing Toll-like receptors
10-21-2015 02-26-2016
We characterized the nucleic acid sensing Toll-like receptors (TLR) of a New World bat species, the common vampire bat (Desmodus rotundus), and through a comparative molecular evolutionary approach searched for general adaptation patterns among the nucleic acid sensing TLRs of eight different bats species belonging to three families (Pteropodidae, Vespertilionidae and Phyllostomidae). We found that the bat TLRs are evolving slowly and mostly under purifying selection and that the divergence pattern of such receptors is overall congruent with the species tree, consistent with the evolution of many other mammalian nuclear genes. However, the chiropteran TLRs exhibited unique mutations fixed in ligand binding sites, some of which involved non-conservative amino acid changes and/or targets of positive selection. Such changes could potentially modify protein function and ligand biding properties, as some changes were predicted to alter nucleic acid binding motifs in TLR 9. Moreover, evidence for episodic diversifying selection acting specifically upon the bat lineage and sub lineages was detected. Thus, the long-term adaptation of chiropterans to a wide variety of environments and ecological niches with different pathogen profiles is likely to have shaped the evolution of the bat TLRs in an order-specific manner. The observed evolutionary patterns provide evidence for potential functional differences between bat and other mammalian TLRs in terms of resistance to specific pathogens or recognition of nucleic acids in general.
Data from: Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus)
10-28-2015 09-27-2016
Variation in resource availability commonly exerts strong effects on fitness-related traits in wild animals. However, we know little about the molecular mechanisms that mediate these effects, or about their persistence over time. To address these questions, we profiled genome-wide whole blood DNA methylation levels in two sets of wild baboons: (i) ‘wild-feeding’ baboons that foraged naturally in a savanna environment and (ii) ‘Lodge’ baboons that had ready access to spatially concentrated human food scraps, resulting in high feeding efficiency and low daily travel distances. We identified 1,014 sites (0.20% of sites tested) that were differentially methylated between wild-feeding and Lodge baboons, providing the first evidence that resource availability shapes the epigenome in a wild mammal. Differentially methylated sites tended to occur in contiguous stretches (i.e., in differentially methylated regions or DMRs), in promoters and enhancers, and near metabolism-related genes, supporting their functional importance in gene regulation. In agreement, reporter assay experiments confirmed that methylation at the largest identified DMR, located in the promoter of a key glycolysis-related gene, was sufficient to causally drive changes in gene expression. Intriguingly, all dispersing males carried a consistent epigenetic signature of their membership in a wild-feeding group, regardless of whether males dispersed into or out of this group as adults. Together, our findings support a role for DNA methylation in mediating ecological effects on phenotypic traits in the wild, and emphasize the dynamic environmental sensitivity of DNA methylation levels across the life course.
Data from: Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens
10-10-2015 02-24-2016
Diapause is the key adaptation allowing insects to survive unfavorable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species, and are hypothesized to be regulated by a conserved suite of genes (a “toolkit”). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens we examined the physiological and transcriptomic changes associated with diapause and CO2 treatment, which causes queens to bypass diapause. We performed comparative analyses with genes previously identified to be associated with diapause in the Dipteran Sarcophaga crassipalpis and with caste differentiation in bumble bees. As in Diptera, diapause in bumble bees is associated with physiological and transcriptional changes related to nutrient storage, stress resistance and core metabolic pathways. There is a significant overlap, both at the level of transcript and gene ontology, between the genetic mechanisms mediating diapause in B. terrestris and S. crassipalpis, reaffirming the existence of a conserved insect diapause genetic toolkit. However, a substantial proportion (10%) of the differentially regulated transcripts in diapausing queens have no clear orthologs in other species, and key players regulating diapause in Diptera (juvenile hormone and vitellogenin) appear to have distinct functions in bumble bees. We also found a substantial overlap between genes related to caste determination and diapause in bumble bees. Thus, our studies demonstrate an intriguing interplay between pathways underpinning adaptation to environmental extremes and the evolution of sociality in insects.
Data from: Quantitative analysis of the ecological dominance of benthic disaster taxa in the aftermath of the end-Permian mass extinction
10-21-2015 08-12-2016
The end-Permian mass extinction, the largest extinction of the Phanerozoic, led to a severe reduction in both taxonomic richness and ecological complexity of marine communities in its aftermath, eventually culminating in a dramatic ecological restructuring of communities. During the Early Triassic recovery interval, disaster taxa proliferated and numerically dominated many marine benthic invertebrate assemblages. These disaster taxa include the bivalve genera Claraia, Unionites, Eumorphotis and Promyalina, and the inarticulate brachiopod Lingularia. The exact nature and extent of their dominance remains uncertain. Here, a quantitative analysis of the dominance of these taxa within the fossil communities of Panthalassa and Tethys benthic realms is undertaken for the stages of the Early Triassic to examine temporal and regional changes in disaster taxon dominance as recovery progresses. Community dominance and disaster taxon abundance is markedly different between Panthalassic and Tethyan communities. In Panthalassa, community evenness is low in the Induan stage, but increases significantly in the Smithian and Spathian. This is coincident with a significant decrease in the relative abundance and occurrence frequency of the disaster taxa, most notably of low-oxygen affinity taxa Claraia and Lingularia. While the disaster taxa are present in post-Induan assemblages, other taxa, including two articulate brachiopod genera, outrank the disaster taxa in relative abundance. In the Tethys, assemblages are generally more even than contemporaneous Panthalassic assemblages. We observe an averaged trend towards more even communities with fewer disaster taxa in both Panthalassic and Tethyan assemblages over time.
Data from: Sex ratio variation shapes the ecological effects of a globally introduced freshwater fish
10-21-2015 10-26-2015
Sex ratio and sexual dimorphism have long been of interest in population and evolutionary ecology, but consequences for communities and ecosystems remain untested. Sex ratio could influence ecological conditions whenever sexual dimorphism is associated with ecological dimorphism in species with strong ecological interactions. We tested for ecological implications of sex ratio variation in the sexually dimorphic western mosquitofish, Gambusia affinis. This species causes strong pelagic trophic cascades and exhibits substantial variation in adult sex ratios. We found that female-biased populations induced stronger pelagic trophic cascades compared with male-biased populations, causing larger changes to key community and ecosystem responses, including zooplankton abundance, phytoplankton abundance, productivity, pH and temperature. The magnitude of such effects indicates that sex ratio is important for mediating the ecological role of mosquitofish. Because both sex ratio variation and sexual dimorphism are common features of natural populations, our findings should encourage broader consideration of the ecological significance of sex ratio variation in nature, including the relative contributions of various sexually dimorphic traits to these effects.
Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
11-07-2015 02-29-2016
Closely related species with divergent life-history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and north-eastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale we found a high genetic structure within the brooders (COI: 0.07
Data from: Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats
06-03-2016 11-16-2016
Aim: Ecologically driven diversification can create spectacular diversity in both species numbers and form. However, the prediction that the match between intrinsic (e.g. functional trait) and extrinsic (e.g. climatic niche) variables may lead to evolutionary radiation has not been critically tested. Here, we test this hypothesis in the Southern Hemisphere plant family Proteaceae, which shows a spectacular diversity in open mediterranean shrublands in the Southwest Australian Floristic Region (SWAFR) and the Cape Floristic Region (CFR). Species in the Proteaceae family occupy habitats ranging from tropical rain forests to deserts and are remarkably variable in leaf morphology. Location: Southern Hemisphere. Methods: We built a phylogenetic tree for 337 Proteaceae species (21% of the total), representing all main clades, climatic tolerances and morphologies, and collected leaf functional traits (leaf area, sclerophylly, leaf shape) for 261 species and climatic niche data for 1645 species. Phylogenetic generalized least squares regression and quantitative-trait evolutionary model testing were used to investigate the evolutionary pathways of traits and climatic niches, and their effect on diversification rates. Results: We found that divergent selection may have caused lineages in open vegetation types to evolve towards trait and climatic niche optima distinct from those in closed forests. Furthermore, we show that the interaction between open habitats, dry, warm and/or mediterranean climates, and small, sclerophyllous, toothed leaves increases net diversification rates in Proteaceae. Main conclusions: Our results suggest that the evolution of specific leaf adaptations may have allowed Proteaceae to adapt to variable climatic niches and diversify extensively in open ecosystems such as those in the CFR and SWAFR. This match between morphology and environment may therefore more generally lead to evolutionary radiation.
Data from: Nature of the coupling between neural drive and force-generating capacity in the human quadriceps muscle
11-25-2015 01-14-2016
The force produced by a muscle depends on both the neural drive it receives and several biomechanical factors. When multiple muscles act on a single joint the nature of the relationship between the neural drive and force-generating capacity of the synergistic muscles is largely unknown. This study aimed to determine the relationship between the ratio of neural drive and the ratio of muscle force-generating capacity between two synergist muscles (vastus lateralis[VL] and medialis[VM]) in humans. Twenty-one participants performed isometric knee extensions at 20% and 50% of maximal voluntary contractions (MVC). Myoelectric activity (surface electromyography [EMG]) provided an index of neural drive. Physiological cross-sectional area (PCSA) was estimated from measurements of muscle volume (magnetic resonance imaging) and muscle fascicle length (3D ultrasound imaging) to represent the muscles’ force-generating capacities. Neither PCSA nor neural drive was balanced between VL and VM. There was a large (r=0.68) and moderate (r=0.43) correlation between the ratio of VL/VM EMG amplitude and the ratio of VL/VM PCSA at 20% and 50% of MVC, respectively. This study provides evidence that neural drive is biased by muscle force-generating capacity, the greater the force generating capacity of VL compared to VM, the stronger bias of drive to the VL.
Data from: Asplenium pifongiae (Aspleniaceae: Polypodiales), a new species from Taiwan
02-11-2016 03-17-2016
We describe and illustrate a new species, Asplenium pifongia., currently known only from Taiwan. Although superficially similar to A. monanthe., this species is a sexual diploid and has little perforation on its spore surfaces. Phylogenetic analyses demonstrate that A. pifongia. is not closely related to A. monanthe., and is instead sister to the A. normal. complex. Asplenium pifongia. differs from A. normal. in having sori mostly only on, and parallel to, the basiscopic side of pinnae, a common feature in A. monanthes.
Data from: The divergence and positive selection of the plant-specific BURP-containing protein family
11-02-2015 12-10-2015
BURP domain-containing proteins belong to a plant-specific protein family and have diverse roles in plant development and stress responses. However, our understanding about the genetic divergence patterns and evolutionary rates of these proteins remain inadequate. In this study, 15 plant genomes were explored to elucidate the genetic origins, divergence, and functions of these proteins. One hundred and twenty-five BURP protein-encoding genes were identified from four main plant lineages, including 13 higher plant species. The absence of BURP family genes in unicellular and multicellular algae suggests that this family (1) appeared when plants shifted from relatively stable aquatic environments to land, where conditions are more variable and stressful, and (2) is critical in the adaptation of plants to adverse environments. Promoter analysis revealed that several responsive elements to plant hormones and external environment stresses are concentrated in the promoter region of BURP protein-encoding genes. This finding confirms that these genes influence plant stress responses. Several segmentally and tandem-duplicated gene pairs were identified from eight plant species. Thus, in general, BURP domain-containing genes have been subject to strong positive selection, even though these genes have conformed to different expansion models in different species. Our study also detected certain critical amino acid sites that may have contributed to functional divergence among groups or subgroups. Unexpectedly, all of the critical amino acid residues of functional divergence and positive selection were exclusively located in the C-terminal region of the BURP domain. In conclusion, our results contribute novel insights into the genetic divergence patterns and evolutionary rates of BURP proteins.
Data from: Macroevolution of leaf defenses and secondary metabolites across the genus Helianthus
11-19-2015 03-03-2016
Leaf defenses are widely recognized as key adaptations and drivers of plant evolution. Across environmentally diverse habitats, the macroevolution of leaf defenses can be predicted by the univariate trade-off model, which predicts that defenses are functionally redundant and thus trade off, and the resource availability hypothesis, which predicts that defense investment is determined by inherent growth rate and that higher defense will evolve in lower resource environments. Here, we examined the evolution of leaf physical and chemical defenses and secondary metabolites in relation to environmental characteristics and leaf economic strategy across 28 species of Helianthus (the sunflowers). Using a phylogenetic comparative approach, we found few evolutionary trade-offs among defenses and no evidence for defense syndromes. We also found that leaf defenses are strongly related to leaf economic strategy, with higher defense in more resource-conservative species, although there is little support for the evolution of higher defense in low-resource habitats. A wide variety of physical and chemical defenses predict resistance to different insect herbivores, fungal pathogens, and a parasitic plant, suggesting that most sunflower defenses are not redundant in function and that wild Helianthus represents a rich source of variation for the improvement of crop sunflower.
Data from: Ground ice melt in the high Arctic leads to greater ecological heterogeneity
10-19-2015 12-14-2015
1. The polar desert biome of the Canadian high Arctic Archipelago is currently experiencing some of the greatest mean annual air temperature increases on the planet, threatening the stability of ecosystems residing above temperature-sensitive permafrost. 2. Ice wedges are the most widespread form of ground ice, occurring in up to 25% of the world's terrestrial near-surface, and their melting (thermokarst) may catalyze a suite of biotic and ecological changes, facilitating major ecosystem shifts. 3. These unknown ecosystem shifts raise serious questions as to how permafrost stability, vegetation diversity, and edaphic conditions will change with a warming high Arctic. Ecosystem and thermokarst processes tend to be examined independently, limiting our understanding of a coupled system whereby the effect of climate change on one will affect the outcome of the other. 4. Using in-depth, comprehensive field observations and a space-for-time approach, we investigate the highly structured landscape that has emerged due to the thermokarst-induced partitioning of microhabitats. We examine differences in vegetation diversity, community composition, and soil conditions on the Fosheim Peninsula, Ellesmere Island, Nunavut. We hypothesize that: (i) greater ice wedge subsidence results in increased vegetation cover due to elevated soil moisture, thereby decreasing the seasonal depth of thaw and restricting groundwater outflow; (ii) thermokarst processes result in altered vegetation richness, turnover, and dispersion, with greater microhabitat diversity at the landscape scale; (iii) shifts in hydrology and plant community structure alter soil chemistry. 5. We found that the disturbance caused by melting ice wedges catalyzes a suite of environmental and biotic effects: topographical changes, a new hydrological balance, significant species richness and turnover changes, and distinct soil chemistries. Thermokarst areas favour a subset of species unique from the polar desert and are characterized by greater species turnover (β-diversity) across the landscape. 6. Synthesis. Our findings suggest that projected increases of thermokarst in the polar desert will lead to the increased partitioning of microhabitats, creating a more heterogeneous high arctic landscape through diverging vegetation communities and edaphic conditions, resulting in a wetland-like biome in the high Arctic that could replace much of the ice-rich polar desert.
Data from: Body size, swimming speed, or thermal sensitivity? Predator-imposed selection on amphibian larvae
11-02-2015 11-04-2015
Background: Many animals rely on their escape performance during predator encounters. Because of its dependence on body size and temperature, escape velocity is fully characterized by three measures, absolute value, size-corrected value, and its response to temperature (thermal sensitivity). The primary target of the selection imposed by predators is poorly understood. We examined predator (dragonfly larva)-imposed selection on prey (newt larvae) body size and characteristics of escape velocity using replicated and controlled predation experiments under seminatural conditions. Specifically, because these species experience a wide range of temperatures throughout their larval phases, we predict that larvae achieving high swimming velocities across temperatures will have a selective advantage over more thermally sensitive individuals. Results: Nonzero selection differentials indicated that predators selected for prey body size and both absolute and size-corrected maximum swimming velocity. Comparison of selection differentials with control confirmed selection only on body size, i.e., dragonfly larvae preferably preyed on small newt larvae. Maximum swimming velocity and its thermal sensitivity showed low group repeatability, which contributed to non-detectable selection on both characteristics of escape performance. Conclusions: In the newt-dragonfly larvae interaction, body size plays a more important role than maximum values and thermal sensitivity of swimming velocity during predator escape. This corroborates the general importance of body size in predator–prey interactions. The absence of an appropriate control in predation experiments may lead to potentially misleading conclusions about the primary target of predator-imposed selection. Insights from predation experiments contribute to our understanding of the link between performance and fitness, and further improve mechanistic models of predator–prey interactions and food web dynamics.
Data from: The aggregate site frequency spectrum (aSFS) for comparative population genomic inference
11-03-2015 02-29-2016
Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, and an endeavor that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to gain complex demographic inference at unprecedented resolution across assemblages of non-model species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) datasets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multi-species demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a dataset consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent post-glacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multi-level statistical frameworks to test models involving assemblages and/or communities and as large-scale SNP data from non-model species become routine, the aSFS expands the potential for powerful next-generation comparative population genomic inference.
Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress
02-10-2016 06-03-2016
Corals are among the most active producers of dimethylsulfoniopropionate (DMSP), a key molecule in marine sulfur cycling, yet the specific physiological role of DMSP in corals remains elusive. Here, we examine the oxidative stress response of three coral species (Acropora millepora, Stylophora pistillata and Pocillopora damicornis) and explore the antioxidant role of DMSP and its breakdown products under short-term hyposalinity stress. Symbiont photosynthetic activity declined with hyposalinity exposure in all three reef-building corals. This corresponded with the upregulation of superoxide dismutase and glutathione in the animal host of all three species. For the symbiont component, there were differences in antioxidant regulation, demonstrating differential responses to oxidative stress between the Symbiodinium subclades. Of the three coral species investigated, only A. millepora provided any evidence of the role of DMSP in the oxidative stress response. Our study reveals variability in antioxidant regulation in corals and highlights the influence life-history traits, and the subcladal differences can have on coral physiology. Our data expand on the emerging understanding of the role of DMSP in coral stress regulation and emphasizes the importance of exploring both the host and symbiont responses for defining the threshold of the coral holobiont to hyposalinity stress.
Data from: Joint torques in a freely walking insect reveal distinct functions of leg joints in propulsion and posture control
01-20-2016 08-31-2016
Determining the mechanical output of limb joints is critical for understanding the control of complex motor behaviours such as walking. In the case of insect walking, the neural infrastructure for single-joint control is well described. However, a detailed description of the motor output in form of time-varying joint torques is lacking. Here, we determine joint torques in the stick insect to identify leg joint function in the control of body height and propulsion. Torques were determined by measuring whole-body kinematics and ground reaction forces in freely walking animals. We demonstrate that despite strong differences in morphology and posture, stick insects show a functional division of joints similar to other insect model systems. Propulsion was generated by strong depression torques about the coxa-trochanter joint, not by retraction or flexion/extension torques. Torques about the respective thorax-coxa and femur-tibia joints were often directed opposite to fore-aft forces and joint movements. This suggests a posture-dependent mechanism that counteracts collapse of the leg under body load and directs the resultant force vector such that strong depression torques can control both body height and propulsion. Our findings parallel propulsive mechanisms described in other walking, jumping, and flying insects and challenge current control models of insect walking.
Data from: Artificial selection on introduced Asian haplotypes shaped the genetic architecture in European commercial pigs
12-23-2015 12-28-2015
Early pig farmers in Europe imported Asian pigs to cross with their local breeds in order to improve traits of commercial interest. Current genomics techniques enabled genome-wide identification of these Asian introgressed haplotypes in modern European pig breeds. We propose that the Asian variants are still present because they affect phenotypes that were important for ancient traditional, as well as recent, commercial pig breeding. Genome-wide introgression levels were only weakly correlated with gene content and recombination frequency. However, regions with an excess or absence of Asian haplotypes (AS) contained genes that were previously identified as phenotypically important such as FASN, ME1, and KIT. Therefore, the Asian alleles are thought to have an effect on phenotypes that were historically under selection. We aimed to estimate the effect of AS in introgressed regions in Large White pigs on the traits of backfat (BF) and litter size. The majority of regions we tested that retained Asian deoxyribonucleic acid (DNA) showed significantly increased BF from the Asian alleles. Our results suggest that the introgression in Large White pigs has been strongly determined by the selective pressure acting upon the introgressed AS. We therefore conclude that human-driven hybridization and selection contributed to the genomic architecture of these commercial pigs.
Data from: Utility of geometric morphometrics for inferring feeding habit from mouthpart morphology in insects: tests with larval Carabidae (Insecta: Coleoptera)
12-21-2015 04-20-2016
Feeding habits are important life-history traits in animals; however, methods for their determination are not well established in many species. The larvae of the beetle family Carabidae are an example. The present study tested the utility of geometric morphometrics of mouthpart morphology to infer the feeding habits of carabid larvae. Using Pterostichus thunbergi as a model system, larval feeding habits were inferred using geometric morphometrics of mouthparts and the results were compared with those obtained from rearing experiments. The rearing experiments indicated that P. thunbergi larvae are carnivores that require snails as an essential part of the diet. Through geometric morphometrics, associations between mouthpart morphology and larval feeding habits were confirmed for species in which these two traits are known. A discriminant analysis using these associations classified P. thunbergi larvae as snail/slug feeders, which is a result compatible with the rearing experiments. Geometric morphometrics also revealed that morphological integration and ontogenetic shape change might play roles in the diversification of mouthpart morphology. Overall, these results demonstrate the utility of the geometric morphometrics of mouthparts to infer feeding habit and to clarify the mechanisms of mouthpart morphological diversification in the study group, and the results also serve as a basis for future studies of other insect groups.
Data from: Simulating the distribution of individual livestock farms and their populations in the united states: an example using domestic swine (Sus scrofa domesticus) farms
11-16-2015 11-20-2015
Livestock distribution in the United States (U.S.) can only be mapped at a county-level or worse resolution. We developed a spatial microsimulation model called the Farm Location and Agricultural Production Simulator (FLAPS) that simulated the distribution and populations of individual livestock farms throughout the conterminous U.S. Using domestic pigs (Sus scrofa domesticus) as an example species, we customized iterative proportional-fitting algorithms for the hierarchical structure of the U.S. Census of Agriculture and imputed unpublished state- or county-level livestock population totals that were redacted to ensure confidentiality. We used a weighted sampling design to collect data on the presence and absence of farms and used them to develop a national-scale distribution model that predicted the distribution of individual farms at a 100 m resolution. We implemented microsimulation algorithms that simulated the populations and locations of individual farms using output from our imputed Census of Agriculture dataset and distribution model. Approximately 19% of county-level pig population totals were unpublished in the 2012 Census of Agriculture and needed to be imputed. Using aerial photography, we confirmed the presence or absence of livestock farms at 10,238 locations and found livestock farms were correlated with open areas, cropland, and roads, and also areas with cooler temperatures and gentler topography. The distribution of swine farms was highly variable, but cross-validation of our distribution model produced an area under the receiver-operating characteristics curve value of 0.78, which indicated good predictive performance. Verification analyses showed FLAPS accurately imputed and simulated Census of Agriculture data based on absolute percent difference values of < 0.01% at the state-to-national scale, 3.26% for the county-to-state scale, and 0.03% for the individual farm-to-county scale. Our output data have many applications for risk management of agricultural systems including epidemiological studies, food safety, biosecurity issues, emergency-response planning, and conflicts between livestock and other natural resources.
Data from: Wavelet domain radiofrequency pulse design applied to magnetic resonance imaging
10-30-2015 10-30-2015
A new method for designing radiofrequency (RF) pulses with numerical optimization in the wavelet domain is presented. Numerical optimization may yield solutions that might otherwise have not been discovered with analytic techniques alone. Further, processing in the wavelet domain reduces the number of unknowns through compression properties inherent in wavelet transforms, providing a more tractable optimization problem. This algorithm is demonstrated with simultaneous multi-slice (SMS) spin echo refocusing pulses because reduced peak RF power is necessary for SMS diffusion imaging with high acceleration factors. An iterative, nonlinear, constrained numerical minimization algorithm was developed to generate an optimized RF pulse waveform. Wavelet domain coefficients were modulated while iteratively running a Bloch equation simulator to generate the intermediate slice profile of the net magnetization. The algorithm minimizes the L2-norm of the slice profile with additional terms to penalize rejection band ripple and maximize the net transverse magnetization across each slice. Simulations and human brain imaging were used to demonstrate a new RF pulse design that yields an optimized slice profile and reduced peak energy deposition when applied to a multiband single-shot echo planar diffusion acquisition. This method may be used to optimize factors such as magnitude and phase spectral profiles and peak RF pulse power for multiband simultaneous multi-slice (SMS) acquisitions. Wavelet-based RF pulse optimization provides a useful design method to achieve a pulse waveform with beneficial amplitude reduction while preserving appropriate magnetization response for magnetic resonance imaging.
Data from: New evidence for hybrid zones of forest and savanna elephants in Central and West Africa
11-17-2015 02-29-2016
The African elephant consists of forest and savanna subspecies. Both subspecies are highly endangered due to severe poaching and habitat loss, and knowledge of their population structure is vital to their conservation. Previous studies have demonstrated marked genetic and morphological differences between forest and savanna elephants and despite extensive sampling, genetic evidence of hybridization between them has been restricted largely to a few hybrids in the Garamba region of northeastern Democratic Republic of Congo (DRC). Here we present new genetic data on hybridization from previously unsampled areas of Africa. Novel statistical methods applied to these data identify 46 hybrid samples - many more than have been previously identified - only two of which are from the Garamba region. The remaining 44 are from three other geographically-distinct locations: a major hybrid zone along the border of the DRC and Uganda, a second potential hybrid zone in Central African Republic, and a smaller fraction of hybrids in the Pendjari-Arli complex of West Africa. Most of the hybrids show evidence of interbreeding over more than one generation, demonstrating that hybrids are fertile. Mitochondrial and Y chromosome data demonstrate that the hybridization is bidirectional, involving males and females from both subspecies. We hypothesize that the hybrid zones may have been facilitated by poaching and habitat modification. The localized geography and rarity of hybrid zones, their possible facilitation from human pressures, and the high divergence and genetic distinctness of forest and savanna elephants throughout their ranges, are consistent with calls for separate species classification.
Data from: Global mammal betadiversity show parallel assemblage structure in similar but isolated environments
08-24-2016 02-28-2017
The taxonomic, phylogenetic and trait dimensions of betadiversity each provide unique insight into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait betadiversity. Conversely, we expect lower phylogenetic diversity but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of ~110x110 km grid-cells across the globe for ~5,000 mammal species (~70 million comparisons). We considered realms as units representing geographic distance and historical isolation and biomes as units with similar environmental conditions. While betadiversity dimensions were generally correlated, we highlight geographic regions of decoupling among betadiversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic betadiversity was significantly higher than expected, suggesting potential convergent evolution. Low trait betadiversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale.
Data from: Drift, not selection, shapes toll-like receptor variation among oceanic island populations
10-28-2015 02-29-2016
Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analyzed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here we focused on diversity at toll-like receptor (TLR) loci, which play a key role in the vertebrate innate immune system and, therefore, are expected to be under pathogen-mediated selection. We assessed TLR variation within and among 13 island populations (grouped into three archipelagos) of Berthelot's pipit, Anthus berthelotii, for which detailed population history has previously been ascertained. We also compared the variation observed with that found in its widespread sister species, the tawny pipit, Anthus campestris. We found strong evidence for positive selection at specific codons in TLR1LA, TLR3 and TLR4. Despite this, we found that at the allele frequency level, demographic history has played the major role in shaping patterns of TLR variation in Berthelot's pipit. Levels of diversity and differentiation within and across archipelagos at all TLR loci corresponded very closely with neutral microsatellite variation, and with the severity of the bottlenecks that occurred during colonization. Our study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales.
Data from: Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil?
10-23-2015 12-14-2015
1. Fine roots and mycorrhiza often represent the largest input of carbon (C) into soils, and are therefore of primary relevance to the soil C balance. Arbuscular mycorrhizal (AM) fungi have previously been found to increase litter decomposition which may lead to reduced soil C stocks, but these studies have focused on immediate decomposition of relatively high amounts of high-quality litter and may therefore not hold in many ecological settings over longer terms. 2. Here we assessed the effect of mycorrhizal fungi on the fate of C and nitrogen (N) contained within a realistic amount of highly 13C/15N labelled root-litter in soil. This litter was either added fresh or after a 3-month incubation period under field conditions to a hyphal in-growth core where mycorrhizal abundance was either reduced or not through rotation. After three months of incubation with a plant under greenhouse conditions, the effect of turning cores on residual 13C and 15N inside the cores was measured, as well as 13C incorporation in microbial signature fatty acids and 15N incorporation of plants. 3. Turning of cores increased abundance of fungal decomposers and 13C loss from cores, while 15N content of cores and plants was unaffected. Despite the difference in disturbance that turning the cores could have caused, the results suggest that mycorrhizal fungi and field incubation of litter acted to additively increase proportion of 13C left in cores. 4. Synthesis. Apart from stimulating litter decomposition as previously shown, mycorrhizas can also stabilize C during litter decomposition and this effect is persistent through time.
Data from: Environmental heterogeneity has a weak effect on diversity during community assembly in tallgrass prairie
11-06-2015 03-14-2016
Understanding what constrains the persistence of species in communities is at the heart of community assembly theory and its application to conserving and enhancing biodiversity. The “environmental heterogeneity hypothesis” predicts greater species coexistence in habitats with greater resource variability. In the context of community assembly, environmental heterogeneity may influence the variety and strength of abiotic conditions and competitive interactions (environmental filters) to affect the relative abundance of species and biodiversity. We manipulated key resources that influence plant diversity in tallgrass prairie (i.e., soil depth and nitrogen availability) to increase environmental heterogeneity prior to sowing native prairie species into a former agricultural field. We compared variability in nutrient availability, aboveground annual net primary productivity (ANPP), and the composition of species between replicate plots containing soil heterogeneity manipulations and plots with no resource manipulations (n = 4 per treatment) during the first 15 yr of community assembly as a test of the “environmental heterogeneity hypothesis.” The manipulations increased environmental heterogeneity, measured as the coefficient of variation in NO3-N availability and ANPP. Plant diversity, however, was similar and decayed exponentially and indiscriminately over time between the heterogeneity treatments. Species richness declined linearly over time in both heterogeneity treatments, but richness was higher in the more heterogeneous soil 2 yr following a second propagule addition 8 yr after the initial sowing. As a result, there was a lower rate of species loss over time in the more heterogeneous soil (0.60 species yr−1) relative to the control soil (0.96 species yr−1). Communities in each treatment exhibited strong convergence over time resulting from a shift in dominant species across all treatments and a gradual increase in the clonal C4 grass, Andropogon gerardii. We attribute the weak effect of heterogeneity on diversity to increasing dominance of a clonal species, which decreased the scale of soil treatments relative to plant size, dispersal limitation, and absence of a key driver (grazing) known to increase plant diversity under a frequent fire regime. Thus, steering community assembly to attain high biodiversity may depend more on manipulating processes that reduce dominance and facilitate the arrival of new species than promoting environmental heterogeneity.
Data from: Effect of winter cold duration on spring phenology of the orange tip butterfly, Anthocharis cardamines
11-07-2015 12-10-2015
The effect of spring temperature on spring phenology is well understood in a wide range of taxa. However, studies on how winter conditions may affect spring phenology are underrepresented. Previous work on Anthocharis cardamines (orange tip butterfly) has shown population-specific reaction norms of spring development in relation to spring temperature and a speeding up of post-winter development with longer winter durations. In this experiment, we examined the effects of a greater and ecologically relevant range of winter durations on post-winter pupal development of A. cardamines of two populations from the United Kingdom and two from Sweden. By analyzing pupal weight loss and metabolic rate, we were able to separate the overall post-winter pupal development into diapause duration and post-diapause development. We found differences in the duration of cold needed to break diapause among populations, with the southern UK population requiring a shorter duration than the other populations. We also found that the overall post-winter pupal development time, following removal from winter cold, was negatively related to cold duration, through a combined effect of cold duration on diapause duration and on post-diapause development time. Longer cold durations also lead to higher population synchrony in hatching. For current winter durations in the field, the A. cardamines population of southern UK could have a reduced development rate and lower synchrony in emergence because of short winters. With future climate change, this might become an issue also for other populations. Differences in winter conditions in the field among these four populations are large enough to have driven local adaptation of characteristics controlling spring phenology in response to winter duration. The observed phenology of these populations depends on a combination of winter and spring temperatures; thus, both must be taken into account for accurate predictions of phenology.
Data from: The global antigenic diversity of swine influenza A viruses
04-15-2016 05-04-2016
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the risk profile of swine influenza viruses in terms of their epizootic and pandemic potential. Here, using the most comprehensive set of swine influenza virus antigenic data compiled to date, we quantify the antigenic diversity of swine influenza viruses on a multi-continental scale. The substantial antigenic diversity of recently circulating viruses in different parts of the world adds complexity to the risk profiles for the movement of swine and the potential for swine-derived infections in humans.
Data from: De novo sequencing and assembly of Azadirachta indica fruit transcriptome
12-01-2011 10-13-2015
Azadirachta indica (neem) is a unique, versatile and important tree species. Many parts of the plant are traditionally used as pesticide, insecticide, fungicide and for other medicinal purposes. Azadirachta fruits and seeds, a good source of oil, are widely used for agriculturally important pest management. Neem oil and its derivatives also support multiple cottage industries in India. Past efforts have been mostly concentrated towards identifying, characterizing and synthesizing one of its principal components, i.e. azadirachtin from seed kernels. Despite diverse use of the neem plant, a modern drug-development programme which systematically exploits the therapeutic ability of Azadirachta fruits remains to be fully established. Next generation sequencing technology that helps decode genomes and transcriptomes has transformational impact on medicine, agriculture, bio-fuel and biodiversity studies. Here, we report sequencing, assembly and analysis of Azadirachta fruit transcriptome using next-generation sequencing technology. We believe that our study shall offer valuable insights towards realizing the larger vision of understanding the key medicinally active compounds and their pathways.
Data from: Ecology drives natural variation in an extreme antipredator trait: a cost-benefits analysis integrating modeling and field data
10-24-2015 06-15-2016
Autotomy, or the voluntary shedding of body parts, is an extreme antipredator behaviour used by species in more than 100 animal families. Despite the long-standing observation that the propensity for autotomy can vary extensively among populations, how ecology might drive such variation is still poorly understood. We tested the hypothesis that the variation in this extreme behaviour reflects the balance between costs and benefits determined by the local ecological environment. We focused on three ecological factors that can influence the cost–benefit dynamics of autotomy: predation, male–male competition, and food abundance. Using tail autotomy in lizards as the study system, we first built an individual-based model to show that environments with high predation, high food abundance, and low male–male competition favoured individuals that autotomized more readily. Moreover, predation likely maintained the ability to autotomize, whereas male–male competition and food abundance fine-tuned the propensity for autotomy. We used field data from five side-blotched lizard populations to verify model results, as well as to test the explanatory power of our model. Field data supported simulation results regarding the roles predation, male–male competition and food abundance. Our model also successfully explained the variation in the propensity for tail autotomy among those five lizard populations. Our approach can be easily extended to examine how ecology might drive adaptive variation in autotomy in other taxa, as well as any traits that share similar cost–benefit dynamics.
Data from: Phylogeny of the polybotryoid fern clade (Dryopteridaceae)
10-20-2015 11-18-2015
Premise of research. The polybotryoid fern clade is completely Neotropical and consists of Cyclodium, Maxonia, Olfersia, Polybotrya, and Polystichopsis. It has never received a detailed phylogenetic analysis. We performed such an analysis to examine the relationships among species and genera and to map the evolution of their morphological and anatomical characters.Methodology. Our study included 46 (77%) of the 60 species in the clade. It also included 37 outgroup species from 19 genera. We sequenced four plastid DNA markers (rbcL, rps4-trnS, trnG-trnR, and trnL-trnF) and analyzed the data with maximum likelihood and Bayesian inference. One anatomical and 11 morphological characters were mapped on the resulting phylogenetic trees using the criterion of maximum parsimony.Pivotal results. The polybotryoid clade was strongly supported as monophyletic, as were its component genera. Nearly all its species have long-creeping rhizomes. Polystichopsis was resolved sister to the other polybotryoid genera. Its monophyly is supported by the morphological synapomorphies of distichous phyllotaxy, long straightish white hairs on the leaves, and tuberculate perines. Two species currently classified in Arachniodes (Arachniodes macrostegia and Arachniodes ochropteroides) form a clade with Olfersia. No known morphological characters support this clade. Olfersia, however, is highly distinct from all other polybotryoids by the combination of its imparipinnate laminae, submarginal connecting vein, strong sterile-fertile leaf dimorphy, loss of indusia, and evolution of acrostichoid sori. Maxonia is defined by its terrestrial root-climbing habit and dimorphic sterile and fertile leaves. Cyclodium and Polybotrya were resolved as sister. The presence of peltate indusia is synapomorphic for Cyclodium. Polybotrya is defined by several morphological synapomorphies: a rhizome anatomy unique among dryopteroid ferns (each individual meristele is surrounded by a dark sclerenchymatous sheath), strong sterile-fertile dimorphy, and loss of indusia. A possible synapomorphy for Polybotrya is the terrestrial root-climbing habit. Within Polybotrya, anastomosing veins and round discrete sori have evolved more than once.Conclusions. This is the first phylogenetic analysis of the polybotryoid ferns. The clade was resolved as monophyletic, as were its genera. An unexpected result was that two species currently classified in Arachniodes (A. macrostegia and A. ochropteroides) were resolved sister to Olfersia. Most of the main clades of polybotryoids were supported by morphological and/or anatomical characters.
Data from: Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa
09-11-2015 12-15-2015
Antibiotic resistance is a growing concern to public health. New treatment strategies may alleviate the situation by slowing down the evolution of resistance. Here, we evaluated sequential treatment protocols using two fully independent laboratory-controlled evolution experiments with the human pathogen Pseudomonas aeruginosa PA14 and two pairs of clinically relevant antibiotics (doripenem/ciprofloxacin and cefsulodin/gentamicin). Our results consistently show that the sequential application of two antibiotics decelerates resistance evolution relative to monotherapy. Sequential treatment enhanced population extinction although we applied antibiotics at sub-lethal dosage. In both experiments, we identified an order-effect of the antibiotics used in the sequential protocol, leading to significant variation in the long-term efficacy of the tested protocols. These variations appear to be caused by asymmetric evolutionary constraints, whereby adaptation to one drug slowed down adaptation to the other drug, but not vice versa. An understanding of such asymmetric constraints may help future development of evolutionary robust treatments against infectious disease.
Data from: Characterizing driver-response relationships in marine pelagic ecosystems for improved ocean management
08-20-2015 05-04-2016
Scientists and resources managers often use methods and tools that assume ecosystem components respond linearly to environmental drivers and human stressor. However, a growing body of literature demonstrates that many relationships are non-linear, where small changes in a driver prompt a disproportionately large ecological response. Here we aim to provide a comprehensive assessment of the relationships between drivers and ecosystem components to identify where and when non-linearities are likely to occur. We focus our analyses on one of the best-studied marine systems, pelagic ecosystems, which allowed us to apply robust statistical techniques on a large pool of previously published studies. In this synthesis, we (1) conduct a wide literature review on single driver-response relationships in pelagic systems, (2) use statistical models to identify the degree of non-linearity in these relationships, and (3) assess whether general patterns exist in the strengths and shapes of non-linear relationships across drivers. Overall we found that non-linearities are common in pelagic ecosystems, comprising at least 52% of all driver-response relationships. This is likely an underestimate, as papers with higher quality data and analytical approaches reported non-linear relationships at a higher frequency - on average 11% more. Consequently, in the absence of evidence for a linear relationship, it is safer to assume a relationship is non-linear. Strong non-linearities can lead to greater ecological and socio-economic consequences if they are unknown (and/or unanticipated), but if known they may provide clear thresholds to inform management targets. In pelagic systems, strongly non-linear relationships are often driven by climate and trophodynamic variables, but are also associated with local stressors such as overfishing and pollution that can be more easily controlled by managers. Even when marine resource managers cannot influence ecosystem change, they can use information about threshold responses to guide how other stressors are managed and to adapt to new ocean conditions. As methods to detect and reduce uncertainty around threshold values improve, managers will be able to better understand and account for ubiquitous non-linear relationships.
Data from: Human punishment is not primarily motivated by inequality
02-10-2017 05-11-2017
Previous theorizing about punishment has suggested that humans desire to punish inequality per se. However, the research supporting such an interpretation contains important methodological confounds. The main objective of the current experiment was to remove those confounds in order to test whether generating inequality per se is punished. Participants were recruited from an online market to take part in a wealth-alteration game with an ostensible second player. The participants were given an option to deduct from the other player’s payment as punishment for their behavior during the game. The results suggest that human punishment does not appear to be motivated by inequality per se, as inequality that was generated without inflicting costs on others was not reliably punished. Instead, punishment seems to respond primarily to the infliction of costs, with inequality only becoming relevant as a secondary input for punishment decisions. The theoretical significance of this finding is discussed in the context of its possible adaptive value.
Data from: Effects of increased flight on the energetics and life history of the butterfly Speyeria mormonia
10-28-2015 10-29-2015
Movement uses resources that may otherwise be allocated to somatic maintenance or reproduction. How does increased energy expenditure affect resource allocation? Using the butterfly Speyeria mormonia, we tested whether experimentally increased flight affects fecundity, lifespan or flight capacity. We measured body mass (storage), resting metabolic rate and lifespan (repair and maintenance), flight metabolic rate (flight capacity), egg number and composition (reproduction), and food intake across the adult lifespan. The flight treatment did not affect body mass or lifespan. Food intake increased sufficiently to offset the increased energy expenditure. Total egg number did not change, but flown females had higher early-life fecundity and higher egg dry mass than control females. Egg dry mass decreased with age in both treatments. Egg protein, triglyceride or glycogen content did not change with flight or age, but some components tracked egg dry mass. Flight elevated resting metabolic rate, indicating increased maintenance costs. Flight metabolism decreased with age, with a steeper slope for flown females. This may reflect accelerated metabolic senescence from detrimental effects of flight. These effects of a drawdown of nutrients via flight contrast with studies restricting adult nutrient input. There, fecundity was reduced, but flight capacity and lifespan were unchanged. The current study showed that when food resources were abundant, wing-monomorphic butterflies living in a continuous meadow landscape resisted flight-induced stress, exhibiting no evidence of a flight-fecundity or flight-longevity trade-off. Instead, flight changed the dynamics of energy use and reproduction as butterflies adopted a faster lifestyle in early life. High investment in early reproduction may have positive fitness effects in the wild, as long as food is available. Our results help to predict the effect of stressful conditions on the life history of insects living in a changing world.
Data from: Transcontinental dispersal, ecological opportunity and origins of an adaptive radiation in the Neotropical catfish genus Hypostomus (Siluriformes: Loricariidae)
02-08-2016 05-27-2016
Ecological opportunity is often proposed as a driver of accelerated diversification, but evidence has been largely derived from either contemporary island radiations or the fossil record. Here, we investigate the potential influence of ecological opportunity on a transcontinental radiation of South American freshwater fishes. We generate a species-dense, time-calibrated molecular phylogeny for the suckermouth armored catfish subfamily Hypostominae, with a focus on the species-rich and geographically widespread genus Hypostomus. We use the resulting chronogram to estimate ancestral geographic ranges, infer historical rates of cladogenesis and diversification in habitat and body size and shape, and test the hypothesis that invasions of previously unoccupied river drainages accelerated evolution and contributed to adaptive radiation. Both the subfamily Hypostominae and the included genus Hypostomus originated in the Amazon/Orinoco ecoregion. Hypostomus subsequently dispersed throughout tropical South America east of the Andes Mountains. Consequent to invasion of the peripheral, low-diversity Paraná River basin in southeastern Brazil approximately 12.5 Mya, Paraná lineages of Hypostomus experienced increased rates of cladogenesis and ecological and morphological diversification. Contemporary lineages of Paraná Hypostomus are less species rich but more phenotypically diverse than their congeners elsewhere. Accelerated speciation and morphological diversification rates within Paraná basin Hypostomus are consistent with adaptive radiation. The geographical remoteness of the Paraná River basin, its recent history of marine incursion, and its continuing exclusion of many species that are widespread in other tropical South American rivers suggest that ecological opportunity played an important role in facilitating the observed accelerations in diversification.
Data from: A within-animal comparison of skilled forelimb assessments in rats
10-27-2015 10-29-2015
A variety of skilled reaching tasks have been developed to evaluate forelimb function in rodent models. The single pellet skilled reaching task and pasta matrix task have provided valuable insight into recovery of forelimb function in models of neurological injury and disease. Recently, several automated measures have been developed to reduce the cost and time burden of forelimb assessment in rodents. Here, we provide a within-subject comparison of three common forelimb assessments to allow direct evaluation of sensitivity and efficiency across tasks. Rats were trained to perform the single pellet skilled reaching task, the pasta matrix task, and the isometric pull task. Once proficient on all three tasks, rats received an ischemic lesion of motor cortex and striatum to impair use of the trained limb. On the second week post-lesion, all three tasks measured a significant deficit in forelimb function. Performance was well-correlated across tasks. By the sixth week post-lesion, only the isometric pull task measured a significant deficit in forelimb function, suggesting that this task is more sensitive to chronic impairments. The number of training days required to reach asymptotic performance was longer for the isometric pull task, but the total experimenter time required to collect and analyze data was substantially lower. These findings suggest that the isometric pull task represents an efficient, sensitive measure of forelimb function to facilitate preclinical evaluation in models of neurological injury and disease.
Data from: Eye coding mechanisms in early human face event-related potentials
11-01-2014 10-23-2015
In humans, the N170 event-related potential (ERP) is an integrated measure of cortical activity that varies in amplitude and latency across trials. Researchers often conjecture that N170 variations reflect cortical mechanisms of stimulus coding for recognition. Here, to settle the conjecture and understand cortical information processing mechanisms, we unraveled the coding function of N170 latency and amplitude variations in possibly the simplest socially important natural visual task: face detection. On each experimental trial, 16 observers saw face and noise pictures sparsely sampled with small Gaussian apertures. Reverse-correlation methods coupled with information theory revealed that the presence of the eye specifically covaries with behavioral and neural measurements: the left eye strongly modulates reaction times and lateral electrodes represent mainly the presence of the contralateral eye during the rising part of the N170, with maximum sensitivity before the N170 peak. Furthermore, single-trial N170 latencies code more about the presence of the contralateral eye than N170 amplitudes and early latencies are associated with faster reaction times. The absence of these effects in control images that did not contain a face refutes alternative accounts based on retinal biases or allocation of attention to the eye location on the face. We conclude that the rising part of the N170, roughly 120–170 ms post-stimulus, is a critical time-window in human face processing mechanisms, reflecting predominantly, in a face detection task, the encoding of a single feature: the contralateral eye.
Data from: Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex
11-25-2015 03-09-2016
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
Data from: Intensifying drought eliminates the expected benefits of elevated carbon dioxide for soybean
09-05-2016 11-29-2016
Stimulation of C3 crop yield by rising concentrations of atmospheric carbon dioxide ([CO2]) is widely expected to counteract crop losses that are due to greater drought this century. But these expectations come from sparse field trials that have been biased towards mesic growth conditions. This eight-year study used precipitation manipulation and year-to-year variation in weather conditions at a unique open-air field facility to show that the stimulation of soybean yield by elevated [CO2] diminished to zero as drought intensified. Contrary to the prevalent expectation in the literature, rising [CO2] did not counteract the effect of strong drought on photosynthesis and yield because elevated [CO2] interacted with drought to modify stomatal function and canopy energy balance. This new insight from field experimentation under hot and dry conditions, which will become increasingly prevalent in the coming decades, highlights the likelihood of negative impacts from interacting global change factors on a key global commodity crop in its primary region of production.
Data from: Individual learning performance and exploratory activity are linked to colony foraging success in a mass-recruiting ant
06-23-2016 12-19-2016
Learning plays an important role in the life of many animals. In social insects, colony foraging success depends on the combined actions of many individuals and learning contributes to individual foraging success. In many ants, for example, route learning helps foragers to navigate between the nest and a food source. Here, we studied if the foraging success of a colony depends on the route-learning performance of its individuals. We used a doubly bifurcating T-maze to assess the route-learning performance of ants from 12 Lasius niger colonies. We also measured the propensity of workers to deposit trail pheromone and to explore the surrounding of their nest. We then tested colony foraging performance in a complex maze, set up either as a poor environment (one food source at the end of one tip), or a rich environment (a food source at the end of each tip). We found that individual learning performance was linked to colony foraging success in the rich, but not the poor environment. The propensity of individual ants to lay pheromone correlated negatively with their learning performance and only predicted colony foraging success in colonies with poor learning abilities in a rich environment. The strongest predictor of colony foraging success was exploratory activity, which differed consistently between colonies. Our results suggest that the importance of individual learning for colony foraging success depends on the environment and that explorative activity is an important factor for colony foraging success.
Data from: Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall subsp. n. (Perciformes: Mullidae), a new subspecies of goatfish from the Red Sea and Arabian Sea
07-14-2016 08-05-2016
The number of goatfish sp­­ecies has increased recently, thanks in part to the application of molecular approaches to the taxonomy of a family with conservative morphology and widespread intraspecific color variation. A new subspecies Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall subsp. n. is described from the Red Sea and Arabian Sea, including Socotra and Gulf of Oman. The two subspecies are distinguished by 1.7% sequence divergence at the mitochondrial cytochrome b gene, a yellow caudal fin, 25-28 gill rakers, and 37-38 lateral-line scales. The morphometric examination of specimens of M. flavolineatus flavolineatus revealed variation in head length, eye diameter, and barbel length, in western direction from the Hawaiian Islands, South Pacific, Micronesia, and the East Indies to the Indian Ocean.  The population of the subspecies in the Gulf of Aqaba is distinguished from that of the remaining Red Sea by shorter barbels, smaller eyes, shorter heads, and shorter pelvic fins. We present a list of 26 endemic fishes from the Gulf of Aqaba and discuss and discuss the probable basis for the endemism in the light of the geological history of this region.
Data from: Applying SNP-derived molecular coancestry estimates to captive breeding programs
05-10-2016 11-30-2016
Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate two options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84 – 0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (p >>0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs.
Data from: Indications for three independent domestication events for the tea plant (Camellia sinensis (L.) O. Kuntze) and new insights into the origin of tea germplasm in China and India revealed by nuclear microsatellites
05-24-2016 05-26-2016
Background: Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking. Methodology/Principal Findings: Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and domestication history of cultivated tea in both China and India. Based on a total of 392 samples, high levels of genetic diversity were observed for all tea types in both countries. The cultivars clustered into three distinct genetic groups (i.e. China tea, Chinese Assam tea and Indian Assam tea) based on STRUCTURE, PCoA and UPGMA analyses with significant pairwise genetic differentiation, corresponding well with their geographical distribution. A high proportion (30%) of the studied tea samples were shown to possess genetic admixtures of different tea types suggesting a hybrid origin for these samples, including the Cambod type. Conclusions: We demonstrate that Chinese Assam tea is a distinct genetic lineage from Indian Assam tea, and that China tea sampled from India was likely introduced from China directly. Our results further indicate that China type tea, Chinese Assam type tea and Indian Assam type tea are likely the result of three independent domestication events from three separate regions across China and India. Our findings have important implications for the conservation of genetic stocks, as well as future breeding programs.
Data from: Evolution determines how global warming and pesticide exposure will shape predator–prey interactions with vector mosquitoes
06-15-2016 08-15-2016
How evolution may mitigate the effects of global warming and pesticide exposure on predator–prey interactions is directly relevant for vector control. Using a space-for-time substitution approach, we addressed how 4°C warming and exposure to the pesticide endosulfan shape the predation on Culex pipiens mosquitoes by damselfly predators from replicated low- and high-latitude populations. Although warming was only lethal for the mosquitoes, it reduced predation rates on these prey. Possibly, under warming escape speeds of the mosquitoes increased more than the attack efficiency of the predators. Endosulfan imposed mortality and induced behavioral changes (including increased filtering and thrashing and a positional shift away from the bottom) in mosquito larvae. Although the pesticide was only lethal for the mosquitoes, it reduced predation rates by the low-latitude predators. This can be explained by the combination of the evolution of a faster life history and associated higher vulnerabilities to the pesticide (in terms of growth rate and lowered foraging activity) in the low-latitude predators and pesticide-induced survival selection in the mosquitoes. Our results suggest that predation rates on mosquitoes at the high latitude will be reduced under warming unless predators evolve toward the current low-latitude phenotype or low-latitude predators move poleward.
Data from: Flap or soar? How a flight generalist responds to its aerial environment
08-15-2016 08-15-2016
The aerial environment is heterogeneous in space and time and directly influences the costs of animal flight. Volant animals can reduce these costs by using different flight modes, each with their own benefits and constraints. However, the extent to which animals alter their flight modes in response to environmental conditions has rarely been studied in the wild. To provide insight into how a flight generalist can reduce the energetic cost of movement, we studied flight behaviour in relation to the aerial environmental and landscape using hundreds of hours of global positioning system and triaxial acceleration measurements of the lesser black-backed gull (Larus fuscus). Individuals differed largely in the time spent in flight, which increased linearly with the time spent in flight at sea. In general, flapping was used more frequently than more energetically efficient soaring flight. The probability of soaring increased with increasing boundary layer height and time closer to midday, reflecting improved convective conditions supportive of thermal soaring. Other forms of soaring flight were also used, including fine-scale use of orographic lift. We explore the energetic consequences of behavioural adaptations to the aerial environment and underlying landscape and implications for individual energy budgets, foraging ecology and reproductive success.
Data from: Constraints on geographic variation in fiddler crabs (Ocypodidae: Uca) from the western Atlantic
08-08-2016 11-23-2016
A key question in evolutionary biology is how intraspecific variation biases the evolution of a population and its divergence from other populations. Such constraints potentially limit the extent to which populations respond to selection, but may endure long enough to have macroevolutionary consequences. Previous studies have focused on the association between covariation patterns and divergence among isolated populations. Few have focused on geographic variation among semi-connected populations, however, even though this may be indicative of early selective pressures that could lead to long-term divergence and speciation. Here, we test whether covariation in the shape of the carapace of fiddler crabs (genus Uca Leach, 1814) is important for structuring geographic variation. We find that morphological divergence among populations is associated with evolvability in the direction of divergence in only a few species. The shape of the ancestral covariation matrix in these species differs from other species in having notably more variation concentrated along fewer directions (i.e., higher eccentricity). For most species, there is some evidence that covariation has constrained the range of directions into which populations have diverged but not the degree of divergence. These results suggest that even though fiddler crab populations have diverged morphologically in directions predicted by covariation, constraints on the extent to which divergence has occurred may only be manifested in species where variation patterns are eccentric enough to limit populations’ ability to respond effectively in many directions.
Data from: Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?
05-12-2016 09-29-2016
Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.
Data from: Investigating the impacts of field-realistic exposure to a neonicotinoid pesticide on bumblebee foraging, homing ability and colony growth
05-10-2016 05-16-2017
The ability to forage and return home is essential to the success of bees as both foragers and pollinators. Pesticide exposure may cause behavioural changes that interfere with these processes, with consequences for colony persistence and delivery of pollination services. We investigated the impact of chronic exposure (5–43 days) to field-realistic levels of a neonicotinoid insecticide (2·4 ppb thiamethoxam) on foraging ability, homing success and colony size using radio frequency identification (RFID) technology in free-flying bumblebee colonies. Individual foragers from pesticide-exposed colonies carried out longer foraging bouts than untreated controls (68 vs. 55 min). Pesticide-exposed bees also brought back pollen less frequently than controls indicating reduced foraging performance. A higher proportion of bees from pesticide-exposed colonies returned when released 1 km from their nests; this is potentially related to increased orientation experience during longer foraging bouts. We measured no impact of pesticide exposure on homing ability for bees released from 2 km, or when data were analysed overall. Despite a trend for control colonies to produce more new workers earlier, we found no overall impacts of pesticide exposure on whole colony size. Synthesis and applications. This study shows that field-realistic neonicotinoid exposure can have impacts on both foraging ability and homing success of bumblebees, with implications for the success of bumblebee colonies in agricultural landscapes and their ability to deliver crucial pollination services. Pesticide risk assessments should include bee species other than honeybees and assess a range of behaviours to elucidate the impact of sublethal effects. This has relevance for reviews of neonicotinoid risk assessment and usage policy world-wide.
Data from: Coupled range dynamics of brood parasites and their hosts responding to climate and vegetation changes
05-07-2016 08-16-2016
As populations shift their ranges in response to global change, local species assemblages can change, setting the stage for new ecological interactions, community equilibria, and evolutionary responses. Here we focus on the range dynamics of four avian brood parasite species and their hosts in southern Africa, in a context of bush encroachment (increase in woody vegetation density in places previously occupied by savanna-grassland mosaics) favouring some species at the expense of others. We first tested whether hosts and parasites constrained each other's ability to expand or maintain their ranges. Second, we investigated whether range shifts represented an opportunity for new host-parasite and parasite-parasite interactions. We used multi-species dynamic occupancy models with interactions, fitted to citizen-science data, to estimate the contribution of interspecific interactions to range shifts and to quantify the change in species co-occurrence probability over a 25-year period. Parasites were able to track their hosts’ range shifts. We detected no deleterious effect of the parasites’ presence on either the local population viability of host species or the hosts’ ability to colonize newly suitable areas. In the recently diversified indigobird radiation (Vidua spp.), following bush encroachment, the new assemblages presented more potential opportunities for speciation via host switch, but also more potential for hybridization between extant lineages, also via host switch. Multi-species dynamic occupancy models with interactions brought new insights into the feedbacks between range shifts, biotic interactions, and local demography: brood parasitism had little detected impact on extinction or colonization processes, but inversely the latter processes affected biotic interactions via the modification of co-occurrence patterns.
Data from: Taxonomic and functional diversity in Mediterranean pastures: Insights on the biodiversity-productivity trade-off
05-03-2016 09-23-2016
Agricultural intensification is one of the main causes of biodiversity loss world-wide. The inclusion of semi-natural features in agricultural landscapes is suggested as a means of enhancing farm biodiversity, but this practice may have potential negative effects on yield production. Moreover, little evidence exists for effects of semi-natural features on other components of biodiversity, such as functional diversity. Yet this could provide a more comprehensive understanding of biodiversity–productivity trade-offs. Here, we report the effects of semi-natural woody vegetation on taxonomic and functional diversity, and biomass production of herbaceous species at the field and farm scales by sampling 50 fields, ranging from 0 to 90% woody vegetation cover, on nine similarly managed farms in central-western Spain. We found significant differences in herbaceous species richness among farms. Both taxonomic and functional β-diversity exhibited significant negative relationships with herbage production, highlighting the trade-off between biodiversity and productivity in these agroecosystems. Woody vegetation cover had a significant negative relationship with biomass production and a unimodal relationship with species richness at the field scale. At high values of woody vegetation cover, species richness and functional diversity indices were decoupled, suggesting that at this extreme of the woody vegetation gradient, only herbaceous species with contrasting trait values were present. Our results showed both convergent and divergent patterns of trait values, suggesting that different assembly processes are acting concurrently along the gradient of woody vegetation. Synthesis and applications. Our result indicates that management of woody vegetation may indeed increase both taxonomic and functional diversity, but this may come at the expense of key ecosystem services or other management goals, namely herbage production. Optimization of the trade-off between herbage diversity and productivity can be reached with a woody vegetation cover of c. 30% at the field scale.
Data from: Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass
06-04-2016 10-31-2016
Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. FST and principal components analysis revealed striking divergence between South-East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South-East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South-East Asia during mid-Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid-Pleistocene.
Data from: Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals
06-15-2016 11-18-2016
Aim: To test whether phylogeographical barriers in the brooding sponge Callyspongia vaginalis match breaks previously identified in the Caribbean. We also compared patterns of subdivision in the sponge to those of three of its commensals, the broadcast spawning brittle star Ophiothrix suensonii and the brooding amphipods Leucothoe ashleyae and L. kensleyi, and tested whether any shared breaks arose simultaneously. Location: Florida, Bahamas and the Caribbean. Methods: Subdivision of C. vaginalis populations was inferred from one mitochondrial (COI) and six nuclear loci using clustering analyses. We identified phylogeographical breaks in the sponge and its invertebrate commensals by determining geographical patterns of genetic variation and tested simultaneous population divergence across barriers shared among taxa using hierarchical approximate Bayesian computation. Results: Sponge populations were partitioned into western and eastern groups across the Caribbean, with hierarchical subdivision within regions. The sponge and its commensals shared barriers across their ranges despite differences in dispersal strategy: C. vaginalis, L. ashleyae and O. suensonii populations in Central America were isolated from the remainder of the Caribbean, and all four taxa shared a break between Florida and the Bahamas, although simultaneous population divergence could not be inferred with statistical certainty. Our results also suggest cryptic speciation within C. vaginalis. Main conclusions: Phylogeographical patterns in C. vaginalis largely matched barriers previously identified at the Florida Straits, Mona Passage and Bay of Honduras in other Caribbean taxa. Oceanographic features such as deep water between locations, strong currents, and eddies are likely mechanisms responsible for these breaks.
Data from: Direct and indirect effects of native range expansion on soil microbial community structure and function
05-30-2016 09-28-2016
Analogous to the spread of non-native species, shifts in native species’ ranges resulting from climate and land use change are also creating new combinations of species in many ecosystems. These native range shifts may be facilitated by similar mechanisms that provide advantages for non-native species and may also have comparable impacts on the ecosystems they invade. Soil biota, in particular bacteria and fungi, are important regulators of plant community composition and below-ground ecosystem function. Compared to non-native plant invasions, there have been relatively few studies examining how soil biota influence – or are influenced by – native species range shifts. Here, we examined how a native range-expanding sagebrush species (Artemisia rothrockii) affects below-ground abiotic conditions and microbial community structure and function using next-generation sequencing coupled with other biotic and abiotic soil analyses. We utilized a range-expansion gradient, together with a shrub removal experiment and structural equation models, to determine the direct and indirect drivers of these interconnected processes. Sagebrush colonization increased bacterial and archaeal richness and diversity and altered community composition across the expansion gradient. Soil organic C and N and soil moisture increased with sagebrush presence; however, results varied across the expansion gradient. We found no relationship between sagebrush and soil pH; however, pH strongly influenced microbial richness and diversity. Microbial (substrate-induced) respiration was influenced by soil organic N, as well as microbial diversity and functional group relative abundances, highlighting direct and indirect effects of sagebrush on microbial community structure and function. Microbial community composition of soils after 4 years of sagebrush removal was more similar to communities in shrub interspaces than underneath shrubs, suggesting microbial community resilience. Synthesis. Our results suggest that native range expansions can have important impacts on soil biological communities, soil chemistry and hydrology which can further impact below-ground ecosystem processes such as nutrient cycling and litter decomposition. The combination of high-throughput sequencing and structural equation modelling used here offers an exciting yet underutilized approach to understanding how both native and non-native species’ range expansions may affect the structure and function of soil ecosystems.
Data from: A revision of the Leptogium saturninum group in North America
09-23-2016 10-11-2016
A revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.
Data from: Biparental care is predominant and beneficial to parents in the burying beetle Nicrophorus orbicollis (Coleoptera: Silphidae)
05-26-2016 12-14-2016
Parenting strategies can be flexible within a species and may have varying fitness effects. Understanding this flexibility and its fitness consequences is important for understanding why parenting strategies evolve. In the present study, we investigate the fitness consequences of flexible parenting in the burying beetle Nicrophorus orbicollis, a species known for its advanced provisioning behaviour of regurgitated vertebrate carrion to offspring by both sexes. We show that, even when a parent is freely allowed to abandon the carcass at any point in time, biparental post-hatching care is the most common pattern of care adopted in N. orbicollis. Furthermore, two parents together raised more offspring than single parents of either sex, showing that the presence of the male can directly influence parental fitness even in the absence of competitors. This contrasts with studies in other species of burying beetle, where biparental families do not differ in offspring number. This may explain why biparental care is more common in N. orbicollis than in other burying beetles. We suggest how the fitness benefits of two parents may play a role in the evolution and maintenance of flexible biparental care in N. orbicollis.
Data from: Communication value of mistakes in dark-eyed junco song
07-08-2016 08-15-2016
Sexual signals contain information on individual quality or motivation, and most explanations for their reliability are based on signal costs. A recent suggestion is that signaling mistakes, defined as deviations from typical signal design, provide cues on individual quality, contributing to reliable communication even when signal design is not costly. We describe several atypical song traits in dark-eyed juncos (Junco hyemalis) that may be mistakes during song production or development and occur in up to 6% of songs. These putative mistakes were more frequent in an urban versus a wildland population, and individuals differed in their frequency of mistakes. Some atypical signals were more frequent in younger males or were negatively related to paternity success, supporting the hypothesis that fewer mistakes indicate individual quality. We also discuss unexpected results, such as some atypical signals being more frequent in more ornamented males and in songs with lower performance demands. Song consistency (similarity across syllable renditions) was positively related to male age and paternity success; nonetheless, relations with paternity were stronger when looking at the most deviant syllable renditions, suggesting that the perceptual salience of large mistakes may mediate receiver responses to song consistency. Results indicate that signaling mistakes reveal relevant information to play a role in communication.
Data from: Abundance inequality in freshwater communities has an ecological origin
03-03-2016 05-16-2017
The hollow-shaped species abundance distribution (SAD) and its allied rank abundance distribution (RAD)—showing that abundance is unevenly distributed among species—are some of the most studied patterns in ecology. To explain the nature of abundance inequality, I developed a novel framework identifying environmental favorability, which controls the balance between reproduction and immigration, as the ultimate source and species stress tolerance as a proximate factor. Thus, under harsh conditions, only a few tolerant species can reproduce, while some sensitive species can be present in low numbers due to chance immigration. This would lead to high abundance inequality between the two groups of species. Under benign conditions, both groups can reproduce and give rise to higher abundance equality. To test these ideas, I examined the variability in the parameters of a Poisson lognormal fit of the SAD and a square root fit of the RAD in diatom and fish communities across US streams. Indeed, as environmental favorability increased, more sensitive forms were able to establish large populations, diminishing the abundance disparity between locally common and rare species. Finally, it was demonstrated that in diatoms, the RAD belonged to the same family of relationships as those of population density with body size and regional distribution.
Data from: Assessment of markers of antimalarial drug resistance in Plasmodium falciparum isolates from pregnant women in Lagos, Nigeria
01-25-2016 02-25-2016
Background: The use of antimalarial drugs for prevention and treatment is a major strategy in the prevention of malaria in pregnancy. Although sulphadoxine-pyrimethamine (SP) is currently recommended for intermittent preventive treatment of malaria during pregnancy in Nigeria, previously used drugs for prophylaxis such as chloroquine (CQ) and pyrimethamine are accessible as they are purchased over the counter. This study describes the markers of absence or presence of resistance to quinoline (Pfcrt and Pfmdr 1) and type 1 antifolate antimalarial medicines (Pfdhfr). Methods: Plasmodium falciparum-positive dried blood spots from pregnant women attending antenatal clinics for the first time during current pregnancy were investigated for the presence of mutations at codons 72–76 of Plasmodium falciparum chloroquine resistance transporter (Pfcrt) gene by real time polymerase chain reaction (PCR) using haplotype-specific probes. PCR followed by sequence analysis was used to identify mutations at codons 86, 184, 1034, 1042 and 1246 of P. falciparum multi-drug resistance-1 (Pfmdr1) gene; and codons 16, 50, 51, 59, 108, 140 and 164 of Pfdhfr gene. Results: Two haplotypes of Pfcrt (n = 54) were observed: CVMNK 13(24.2%) and CVIET 41 (75.9%) of the samples. The SVMNT haplotype was absent in this population. The Pfmdr1 (n = 28) haplotypes were NYSND 15(53.6%), YYSND 5(17.9%), NFSND 6(21.4%) and YFSND 2(7.1%). The Pfdhfr (n = 15) were ACNCSVI 4(26.7%), and ACICNSVI 1(6.7%) and ACIRNVI 10 (66.7%). The rate of occurrence of Pfcrt 76T, Pfdhfr108N, Pfmdr186Yand184F were 75.9%, 73.3%, 25% and 28.1% respectively. The Pfmdr1 86Y was associated with low parasitaemia (median = 71 parasites/μl, P = 0.024) while Pfcrt 76T was associated with young maternal age (mean 24.1 ± 4.5 years; P = 0.006). The median parasitaemia were similar (P>0.05) in wild and mutant strains of Pfcrt 76, Pfmdr1 184 and Pfdhfr 108. There was no association between gravidity or gestational age of the women and presence of mutations in the Pfcrt, Pfmdr1 or Pfdhfr genes (P>0.05). Conclusion: Markers of resistance to chloroquine and pyrimethamine were high, whereas cycloguanil-resistance marker was not present in the studied population. The low level of mutations in the Pfmdr1gene indicates likely efficacy of amodiaquine against malaria in pregnancy.
Data from: A phylogenetic analysis of egg size, clutch size, spawning mode, adult body size, and latitude in reef fishes
12-10-2015 05-13-2016
Theoretical treatments of egg size in fishes suggest that constraints on reproductive output should create trade-offs between the size and number of eggs produced per spawn. For marine reef fishes, the observation of distinct reproductive care strategies (demersal guarding, egg scattering, and pelagic spawning) has additionally prompted speculation that these strategies reflect alternative fitness optima with selection on egg size differing by reproductive mode and perhaps latitude. Here, we aggregate data from 278 reef fish species and test whether clutch size, reproductive care, adult body size, and latitudinal bands (i.e., tropical, subtropical, and temperate) predict egg size, using a statistically unified framework that accounts for phylogenetic correlations among traits. We find no inverse relationship between species egg size and clutch size, but rather that egg size differs by reproductive mode (mean volume for demersal eggs = 1.22 mm3, scattered eggs = 0.18 mm3, pelagic eggs = 0.52 mm3) and that clutch size is strongly correlated with adult body size. Larger eggs were found in temperate species compared with tropical species in both demersal guarders and pelagic spawners, but this difference was not strong when accounting for phylogenetic correlations, suggesting that differences in species composition underlies regional differences in egg size. In summary, demersal guarders are generally small fishes with small clutch sizes that produce large eggs. Pelagic spawners and egg scatterers are variable in adult and clutch size. Although pelagic spawned eggs are variable in size, those of scatterers are consistently small.
Data from: European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?
12-07-2015 01-22-2016
Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average ФST = 0.159, rst = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average ФST = 0.103, rst = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene–early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored.
Data from: Warming alters food web-driven changes in the CO2 flux of experimental pond ecosystems
12-02-2015 12-07-2015
Evidence shows the important role biota play in the carbon cycle, and strategic management of plant and animal populations could enhance CO2 uptake in aquatic ecosystems. However, it is currently unknown how management-driven changes to community structure may interact with climate warming and other anthropogenic perturbations to alter CO2 fluxes. Here we showed that under ambient water temperatures, predators (three-spined stickleback) and nutrient enrichment synergistically increased primary producer biomass, resulting in increased CO2 uptake by mesocosms in early dawn. However, a 3°C increase in water temperatures counteracted positive effects of predators and nutrients, leading to reduced primary producer biomass and a switch from CO2 influx to efflux. This confounding effect of temperature demonstrates that climate scenarios must be accounted for when undertaking ecosystem management actions to increase biosequestration.
Data from: When does intraspecific trait variation contribute to functional beta-diversity?
11-27-2015 03-04-2016
1. Intraspecific trait variation (ITV) is hypothesized to play an important role in community assembly and the maintenance of biodiversity. However, fundamental gaps remain in our understanding of how ITV contributes to mechanisms that create spatial variation in the functional-trait composition of communities (functional β-diversity). Importantly, ITV may influence the perceived importance of environmental filtering across spatial scales. 2. We examined how ITV contributes to functional β-diversity and environmental filtering in woody plant communities in a temperate forest in the Ozark ecoregion, Missouri, USA. To test the hypothesis that ITV contributes to changes in the perceived importance of environmental filtering across scales, we compared patterns of functional β-diversity across soil-resource and topographic gradients at three spatial grains and three spatial extents. To quantify the contribution of ITV to functional β-diversity, we compared patterns that included ITV in five traits (leaf area, specific leaf area, leaf water content, leaf toughness, and chlorophyll content) to patterns based on species-mean trait values. 3. Functional β-diversity that included ITV increased with spatial extent and decreased with spatial grain, suggesting stronger environmental filtering within spatially extensive landscapes that contain populations locally adapted to different habitats. In contrast, functional β-diversity based on species-mean trait values increased with spatial extent but did not change with spatial grain, suggesting weaker environmental filtering among larger communities which each contain a variety of habitats and locally adapted populations. 4. Synthesis. Although studies typically infer community assembly mechanisms from species-mean trait values, our study suggests that mean trait values may mask the strength of assembly mechanisms such as environmental filtering, especially in landscape-scale studies that encompass strong environmental gradients and locally adapted populations. Our study highlights the utility of integrating ITV into studies of functional β-diversity to better understand the ecological conditions under which trait variation within and among species contributes most strongly to patterns of biodiversity across spatial scales.
Data from: High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement
06-03-2011 10-05-2015
Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted of adaptations that involve sets of high dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining by high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection.
Data from: The length of adaptive walks is insensitive to starting fitness in Aspergillus nidulans
06-07-2011 11-17-2011
Adaptation involves the successive substitution of beneficial mutations by selection, a process known as an adaptive walk. Gradualist models of adaptation, which assume that all mutations are small relative to the distance to a fitness optimum, predict that adaptive walks should be longer when the founding genotype is less well adapted. More recent work modelling adaptation as a sequence of moves in phenotype or genotype space predicts, by contrast, much shorter adaptive walks irrespective of the fitness of the founding genotype. Here we provide what is, to the best of our knowledge, the first direct test of these alternative models, measuring the length of adaptive walks in evolving lineages of fungus that differ initially in fitness. Contrary to the gradualist view, we show that the length of adaptive walks in the fungus Aspergillus nidulans is insensitive to starting fitness and involves just two mutations on average. This arises because poorly adapted populations tend to fix mutations of larger average effect than those of better-adapted populations. Our results suggest that the length of adaptive walks may be independent of the fitness of the founding genotype and, moreover, that poorly adapted populations can quickly adapt to novel environments.
Data from: A history of phenotypic plasticity accelerates adaptation to a new environment
06-08-2011 05-31-2017
Can a history of phenotypic plasticity increase the rate of adaptation to a new environment? Theory suggests it can through two different mechanisms. Phenotypically plastic organisms can adapt rapidly to new environments through genetic assimilation, or the fluctuating environments that result in phenotypic plasticity can produce evolvable genetic architectures. In this article, I studied a model of a gene regulatory network that determined a phenotypic character in one population selected for phenotypic plasticity and a second population in a constant environment. A history of phenotypic plasticity increased the rate of adaptation in a new environment, but the amount of this increase was dependent on the strength of selection in the original environment. Phenotypic variance in the original environment predicted the adaptive capacity of the trait within, but not between, plastic and non-plastic populations. These results have implications for invasive species, and ecological studies of rapid adaptation.
Data from: Genetic evidence for a Janzen-Connell recruitment pattern in reproductive offspring of Pinus halepensis trees.
07-29-2011 06-01-2017
Effective seed dispersal, combining both dispersal and post-dispersal (establishment) processes, determines population dynamics and colonization ability in plants. According to the Janzen-Connell (JC) model, high mortality near the mother plant shifts the offspring establishment distribution farther away from the mother plant relative to the seed dispersal distribution. Yet, extending this prediction to the distribution of mature (reproductive) offspring remains a challenge for long-living plants. To address this challenge we selected an isolated natural Aleppo pine (Pinus halepensis) population in Mt. Pithulim (Israel), expanded from five ancestor trees in the beginning of the 20th century into ~2000 trees today. Using nine microsatellite markers, we assigned parents to trees established during the early stages of population expansion. To elucidate the effect of the distance from mother plant on post-dispersal survival, we compared the effective seed dispersal kernel, constructed based on the distribution of mother-offspring distances, to the seed dispersal kernel, computed based on simulations of a mechanistic wind dispersal model. We found that the mode of the effective dispersal kernel is shifted farther away than the mode of the seed dispersal kernel, reflecting increased survival with increasing distance from the mother plant. The parentage analysis demonstrated a highly skewed reproductive success and a strong directionality in effective dispersal corresponding to the wind regime. We thus provide the first evidence that JC effects act also on offspring that become reproductive and persisted as adults for many decades, a key requirement in assessing the role of post-dispersal processes in shaping population and community dynamics.
Data from: Levels of clonal mixing in the black bean aphid Aphis fabae, a facultative ant mutualist
07-21-2011 10-02-2015
Aphids are a worldwide pest and an important model in ecology and evolution. Little is known, however, of the genetic structure of their colonies at a microgeographic level. For example, it remains largely unknown whether most species form monoclonal or polyclonal colonies. Here, we present the first detailed study on levels of clonal mixing in a nonsocial facultative ant mutualist, the black bean aphid Aphis fabae. In contrast to the earlier suggestion that colonies of this species are generally monoclonal, we found that across two subspecies of the black bean aphid, A. fabae cirsiiacanthoidis and A. fabae fabae, 32% and 77% of the aphid colonies were in fact polyclonal, consisting of a mix of up to 4 different clones, which resulted in an overall average relatedness within colonies of 0.90 and 0.79 in the two subspecies. Data further show that the average relatedness in A. f. cirsiiacanthoidis remained relatively constant throughout the season, which means that clonal erosion due to clonal selection more or less balanced with the influx of new clones from elsewhere. Nevertheless, relatedness tended to decrease over the lifetime of a given colony, implying that clonal mixing primarily resulted from the joining of preexisting colonies as opposed to via simultaneous host colonisation by several foundresses. Widespread clonal mixing is argued to affect the ecology and evolution of the aphids in various important ways, for example with respect to the costs and benefits of group living, the evolution of dispersal and the interaction with predators as well as with the ant mutualists.
Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
08-02-2011 05-31-2017
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognised as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study the sequence of eIF4E was analysed in 1090 barley landraces and non-current cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eIF4E haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 out of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest eIF4E may play a role in barley adaptation to local habitats.
Data from: Clonal genetic variation in a Wolbachia-infected asexual wasp: horizontal transmission or historical sex?
06-14-2011 06-01-2017
Wolbachia are endocellular bacteria known for manipulating the reproductive systems of many of their invertebrate hosts. Wolbachia are transmitted vertically from mother to offspring. In addition, new infections result from horizontal transmission between different host species. However, to what extent horizontal transmission plays a role in the spread of a new infection through the host population is unknown. Here, we investigate whether horizontal transmission of Wolbachia can explain clonal genetic variation in natural populations of Leptopilina clavipes, a parasitoid wasp infected with a parthenogenesis-inducing Wolbachia. We assessed variance of markers on the nuclear, mitochondrial and Wolbachia genomes. The nuclear and mitochondrial markers displayed significant and congruent variation among thelytokous wasp lineages, showing that multiple lineages have become infected with Wolbachia. The alternative hypothesis in which a single female became infected, the daughters of which mated with males (thus introducing nuclear genetic variance) cannot account for the presence of concordant variance in mtDNA. All Wolbachia markers, including the hypervariable wsp gene, were invariant, suggesting that only a single strain of Wolbachia is involved. These results show that Wolbachia has transferred horizontally to infect multiple female lineages during the early spread through L. clavipes. Remarkably, multiple thelytokous lineages have persisted side-by-side in the field for tens of thousands of generations.
Data from: Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations
07-25-2011 09-14-2012
Currently there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during four years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life-cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only one year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were very low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programs into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.
Data from: Mechanical reproductive isolation facilitates parallel speciation in western North American scincid lizards
07-28-2011 06-01-2017
Mechanical reproductive barriers have been dismissed as a major driver of animal speciation, yet the extent to which such barriers cause reproductive isolation in most animal groups is largely unknown and rarely tested. In this study, we used hierarchical Bayesian modeling of mate compatibility experiments to show that body size divergence in lizards of the Plestiodon skiltonianus complex contributes to reproductive isolation in at least three ways: males preferably court females that are more similar in size, females reject males that are highly divergent in size, and that the size difference of a male and female in copula constrains the ability to align the genitalia for intromission. We used a predictive model to estimate the contributions of behavioral and mechanical barriers to reproductive isolation between populations with differing degrees of size divergence. This model shows that the mechanical barrier is more important than the behavioral barriers at small and intermediate degrees of size divergence, suggesting that it acts earlier during speciation. As correlated divergence in size and ecology is common in animals, similar constraints imposed by the geometry of the mating posture may apply to a variety of major animal lineages and merit further attention in speciation research.
Data from: Population genomics of wild and laboratory zebrafish (Danio rerio)
09-16-2011 10-25-2011
Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mtDNA clades with an average of 5.8% among-clade sequence divergence. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105 - 0.254). Evolutionarily distinct groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4 %) and nine loci (0.5%) with significantly low FST values. Valleys of reduced variation of up to 10 Mb in size surrounding divergent outliers were consistent with selective sweeps. The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analyzed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations will be essential to understand the full range of genetic influences on phenotypic variation in this species.
Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation
07-13-2011 05-31-2017
Little is known about the genetic diversity of coho salmon in Alaska, although this area represents half of the species’ North American range. In this study, nine microsatellite loci were used to genotype 32 putative coho salmon populations from seven regions of Alaska. The primary objectives were to estimate and evaluate the degree and spatial distribution of neutral genetic diversity within and among populations of Alaskan coho salmon. Genetic analysis yielded four results that provide insight into forces influencing genetic diversity in Alaskan coho salmon and have important conservation implications: 1) significant population differentiation was found within each region; 2) the degree of differentiation (FST = 0.099) among populations was as large or larger than that reported for other Pacific salmon species in Alaska; 3) phenetic clustering of populations showed weak geographic concordance; 4) strong genetic isolation by distance was only apparent at the finest geographic scale (within a drainage). These results suggest that coho salmon populations are small relative to populations of other Pacific salmon, and the genetic diversity within and among coho salmon populations is influenced primarily by genetic drift, and not gene flow. Resource management and conservation actions affecting coho salmon in Alaska must recognize that the populations are generally small, isolated, and probably exhibit local adaptation to different spawning and freshwater rearing habitats. These factors justify managing and conserving Alaskan coho salmon at a fine geographic scale.
Data from: Effects of inversions on within- and between-species recombination and divergence
08-09-2011 05-31-2017
Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and D. persimilis, we detected one double-recombinant among 9739 progeny from F1 hybrids screened, consistent with published double crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species vs. within species. Moreover, we observed strong ‘interchromosomal effect’ (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within vs. between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible effects of inversions on interspecies gene exchange that had not been considered previously.
Data from: Using striated tooth marks on bone to predict body size in theropod dinosaurs: a model based on feeding observations of Varanus komodoensis, the Komodo monitor
01-05-2012 08-20-2015
Mesozoic tooth marks on bone surfaces directly link consumers to fossil assemblage formation. Striated tooth marks are believed to form by theropod denticle contact, and attempts have been made to identify theropod consumers by comparing these striations with denticle widths of contemporaneous taxa. The purpose of this study is to test whether ziphodont theropod consumer characteristics may be accurately identified from striated tooth marks on fossil surfaces. There are three major objectives; 1) experimentally produce striated tooth marks and explain how they form; 2) determine whether body size characteristics are reflected in denticle widths; 3) determine whether denticle characters are accurately transcribed onto bone surfaces in the form of striated tooth marks. Controlled feeding trials were conducted with the dental analogue Varanus komodoensis (the Komodo monitor). Goat (Capra hircus) carcasses were introduced to captive, isolated individuals. Striated tooth marks were then identified, and striation width, number, and degree of divergence were recorded for each. Denticle widths and tooth/body size characters were taken from photographs and published accounts of both theropod and V. komodoensis skeletal material, and regressions were compared among and between the two groups. Striated marks tend to be regularly striated with a variable degree of branching, and may co-occur with scores. Striation morphology directly reflects contact between the mesial carina and bone surfaces during the rostral reorientation when defleshing. Denticle width is primarily influenced by tooth size, and correlates well with body size displaying negative allometry in both groups regardless of taxon or position. When compared, striation widths fall within or below the range of denticle widths extrapolated for similar sized V. komodoensis individuals. Striation width is directly influenced by the orientation of the carina during feeding, and may underestimate but cannot overestimate denticle width. Although body size may theoretically be estimated solely by a striated tooth mark under ideal circumstances, many caveats should be considered. These include the influence of negative allometry across taxa and throughout ontogeny, the existence of theropods with extreme denticle widths, and the potential for striations to underestimate denticle widths. This method may be useful under specific circumstances, especially for establishing a lower limit body size for potential consumers.
Data from: The risk and intensity of sperm ejection in female birds
07-19-2011 05-31-2017
The way females utilise the gametes of different males has important consequences for sexual selection, sexual conflict and intersexual coevolution in natural populations. However, patterns of sperm utilisation by females are difficult to demonstrate, and their functional significance remains unclear. Here, we experimentally study sperm ejection in the fowl, Gallus gallus domesticus, where females eject preferentially the sperm of socially subordinate males. We study two measures of sperm ejection: (i) the probability that an ejaculate is ejected ('risk'), and (ii) the proportion of semen ejected ('intensity'), and show that both measures are strongly non-random with respect to characteristics of the ejaculate, the male and the female. Sperm ejection neutralised on average 80% of an ejaculate, and while larger ejaculates suffered a higher ejection risk, smaller ejaculates suffered more intense ejection. After controlling for ejaculate volume, socially subdominant males suffered higher ejection intensity. After controlling for male and ejaculate effects, ejection risk increased and intensity declined as females mated with successive males. Collectively, these results reveal that sperm ejection risk and intensity are at least partly actively caused by female behaviour, and generate independent selective pressures on male and ejaculate phenotypes.
Data from: A new species of marsupial frog (Anura: Hemiphractidae: Gastrotheca) from the Andes of southern Peru
11-10-2011 10-29-2012
Gastrotheca nebulanastes sp. nov. from cloud forests in the upper Kosñipata Valley, Manu National Park, in the Andes of southern Peru is similar to G. excubitor, which inhabits grasslands in higher elevations than the cloud forests. The two species differ in relative lengths of the fingers, skin texture, coloration, and advertisement call. Although the new species has an elevational range of 2000–3300 m, it is most abundant at 2400–2800 m. A phylogenetic analysis of a previously defined clade of Gastrotheca based on a fragment of 16S mitochondrial gene provides strong support that the sister taxon to the new species is G. atympana, a species from farther north in the Cordillera Oriental in Peru.
Data from: Data sharing by scientists: practices and perceptions
06-29-2011 05-31-2017
Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers –data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings: A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions of the barriers and enablers of data sharing. Scientists do not make their data electronically available to others for various reasons, including insufficient time and lack of funding. Most respondents are satisfied with their current processes for the initial and short-term parts of the data or research lifecycle (collecting their research data; searching for, describing or cataloging, analyzing, and short-term storage of their data) but are not satisfied with long-term data preservation. Many organizations do not provide support to their researchers for data management both in the short- and long-term. If certain conditions are met (such as formal citation and sharing reprints) respondents agree they are willing to share their data. There are also significant differences and approaches in data management practices based on primary funding agency, subject discipline, age, work focus, and world region. Conclusions/Significance: Barriers to effective data sharing and preservation are deeply rooted in the practices and culture of the research process as well as the researchers themselves. New mandates for data management plans from NSF and other federal agencies and world-wide attention to the need to share and preserve data could lead to changes. Large scale programs, such as the NSF-sponsored DataNET (including projects like DataONE) will both bring attention and resources to the issue and make it easier for scientists to apply sound data management principles.
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Data from: Reverse evolution: selection against costly resistance in disease-free microcosm populations of Paramecium caudatum
06-16-2011 12-15-2011
Evolutionary costs of parasite resistance arise if genes conferring resistance reduce fitness in the absence of parasites. Thus, parasite-mediated selection may lead to increased resistance and a correlated decrease in fitness, whereas relaxed parasite-mediated selection may lead to reverse evolution of increased fitness and a correlated decrease in resistance. We tested this idea in experimental populations of the protozoan Paramecium caudatum and the parasitic bacterium Holospora undulata. After 8 years, resistance to infection and asexual reproduction were compared among paramecia from (i) infected populations, (ii) uninfected naive populations and (iii) previously infected, parasite-free (recovered) populations. Paramecia from infected populations were more resistant (+12%), but had lower reproduction (-15%) than naive paramecia, indicating an evolutionary trade-off between resistance and fitness. Recovered populations showed similar reproduction to naive populations; however, resistance of recently (<3 years) recovered populations was similar to paramecia from infected populations, while longer (>3 years) recovered populations were as susceptible as naive populations. This suggests a weak, convex trade-off between resistance and fitness, allowing recovery of fitness, without complete loss of resistance, favouring the maintenance of a generalist strategy of intermediate fitness and resistance. Our results indicate that (co)evolution with parasites can leave a genetic signature in disease-free populations.
Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.
06-16-2011 12-15-2011
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of measurements that define corallite architecture, and could partition additive and non-additive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h² estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h² were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.
Data from: Genetic and phenotypic variation across a hybrid zone between ecologically divergent tree squirrels (Tamiasciurus)
07-19-2011 05-31-2017
A hybrid zone along an environmental gradient should contain a clinal pattern of genetic and phenotypic variation. This occurs because divergent selection in the two parental habitats is typically strong enough to overcome the homogenizing effects of gene flow across the environmental transition. We studied hybridization between two parapatric tree squirrels (Tamiasciurus spp.) across a forest gradient over which the two species vary in coloration, cranial morphology, and body size. We sampled 397 individuals at 29 locations across a 600-km transect to seek genetic evidence for hybridization; upon confirming hybridization, we examined levels of genetic admixture in relation to maintenance of phenotypic divergence despite potentially homogenizing gene flow. Applying population assignment analyses to microsatellite data, we found that T. douglasii and T. hudsonicus form two distinct genetic clusters but also hybridize, mostly within transitional forest habitat. Overall, based on this nuclear analysis, 48% of the specimens were characterized as T. douglasii, 9% as hybrids, and 43% as T. hudsonicus. Hybrids appeared to be reproductively viable, as evidenced by the presence of later-generation hybrid genotypes. Observed clines in ecologically important phenotypic traits—fur coloration and cranial morphology—were sharper than the cline of putatively neutral mtDNA, which suggests that divergent selection may maintain phenotypic distinctiveness. The relatively recent divergence of these two species (probably late Pleistocene), apparent lack of pre-zygotic isolating mechanisms, and geographic coincidence of cline centers for both genetic and phenotypic variation suggest that environmental factors play a large role in maintaining the distinctiveness of these two species across the hybrid zone.
Data from: A century of genetic change and metapopulation dynamics in the Galápagos warbler finches (Certhidea)
06-16-2011 11-17-2011
Populations that are connected by immigrants play an important role in evolutionary and conservation biology, yet we have little direct evidence of how such metapopulations change genetically over evolutionary time. We compared historic (1895-1905) to modern (1988-2006) genetic variation in 11 populations of warbler finches at 14 microsatellite loci. Although several lines of evidence suggest that Darwin’s finches may be in decline, we found that the genetic diversity of warbler finches has not generally declined, and broad scale patterns of variation remained similar over time. Contrary to expectations, inferred population sizes have generally increased over time (6-8%) as have immigration rates (8-16%), which may reflect a recent increase in the frequency and intensity of El Niño events. Individual island populations showed significant declines (18-19%) and also substantial gains (18-20%) in allelic richness over time. Changes in genetic diversity were correlated with changes in immigration rates, but did not correspond to population size or human disturbance. These results reflect the expected stabilizing properties of whole metapopulations over time. However, the dramatic and unpredictable changes observed in individual populations during this short time interval suggests that care should be taken when monitoring individual population fragments with snapshots of genetic variation.