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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.