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Title Date Issued Date Released Description
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.