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Data from: Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies
- 负责人：
- DOI：
- doi:10.5061/dryad.r76cm3bn
- 摘要：
- Regressions of biological variables across species are rarely perfect. Usually there are residual deviations from the estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicating that they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation in regression studies. In particular, we discuss the interplay of biological deviations with deviations due to observational or measurement errors, which are also important in comparative studies based on estimated species means. We show how bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and either observational or biological error in the predictor variables. We show how all these biases can be estimated and corrected for in the presence of phylogenetic correlations. We present general formulas for incorporating measurement error in linear models with correlated data. We also show how alternative regression models, such as major-axis and reduced major-axis regression, which are often recommended when there is error in predictor variables, are strongly biased when there is biological variation in any part of the model. We argue that such methods should never be used to estimate evolutionary or allometric regression slopes.
Data from: Warming has a greater effect than elevated CO2 on predator–prey interactions in coral reef fish
- 负责人：
- DOI：
- doi:10.5061/dryad.rh27t
- 摘要：
- Ocean acidification and warming, driven by anthropogenic CO2 emissions, are considered to be among the greatest threats facing marine organisms. While each stressor in isolation has been studied extensively, there has been less focus on their combined effects, which could impact key ecological processes. We tested the independent and combined effects of short-term exposure to elevated CO2 and temperature on the predator–prey interactions of a common pair of coral reef fishes (Pomacentrus wardi and its predator, Pseudochromis fuscus). We found that predator success increased following independent exposure to high temperature and elevated CO2. Overall, high temperature had an overwhelming effect on the escape behaviour of the prey compared with the combined exposure to elevated CO2 and high temperature or the independent effect of elevated CO2. Exposure to high temperatures led to an increase in attack and predation rates. By contrast, we observed little influence of elevated CO2 on the behaviour of the predator, suggesting that the attack behaviour of P. fuscus was robust to this environmental change. This is the first study to address how the kinematics and swimming performance at the basis of predator–prey interactions may change in response to concurrent exposure to elevated CO2 and high temperatures and represents an important step to forecasting the responses of interacting species to climate change.
Data from: Origins of food crops connect countries worldwide
- 负责人：
- Khoury, Colin
- 关键词：
- food security crop diversity crop origins plant genetic resources crop domestication crop improvement
- DOI：
- doi:10.5061/dryad.s08t2
- 摘要：
- Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.
Data from: Body size, developmental instability and climate change
- 负责人：
- DOI：
- doi:10.5061/dryad.s0n86hq
- 摘要：
- Development is often temperature-dependent. We hypothesized smaller size and larger asymmetry with increasing temperatures. However, we also predicted associations with asymmetry to differ among traits that differ in their degree of functional importance (especially the functional wings in migratory birds were predicted to be more canalized), timing of development (skeletal (femur, tarsus and humerus) vs feather (wing and tail traits). We analyzed a large dataset of which we included species with at least 20 specimens resulting in 5533 asymmetry values in 1593 individuals from 66 species. There was a consistent significant decrease in size with temperature across all traits. Fluctuating asymmetry for wings and femur was on average lower, suggesting higher canalization, and it decreased with migration distance, while that was not the case for the other traits. Fluctuating asymmetry increased with increasing temperature for wings, but not for the other characters, where the different responses of different characters to temperature was significant. Since there was no significant three-way interaction between temperature, migration distance and character, the asymmetry-temperature response was similar in migratory and resident species. These findings imply that climate warming reduces size of all traits and decreases developmental instability of wings in birds.
Data from: A phylogenomic resolution of the sea urchin tree of life
- 负责人：
- Koch, Nicolás Mongiardino
- DOI：
- doi:10.5061/dryad.s11f216
- 摘要：
- Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved. Results: We performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results. Conclusions: Our investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.
Data from: Quantifying and modelling decay in forecast proficiency indicates the limits of transferability in land-cover classification
- 负责人：
- DOI：
- doi:10.5061/dryad.s156b
- 摘要：
- 1. The ability to provide reliable projections for the current and future distribution patterns of land-covers is fundamental if we wish to protect and manage our diminishing natural resources. Two inter-related revolutions made map productions feasible at unprecedented resolutions- the availability of high-resolution remotely-sensed data and the development of machine-learning algorithms. However, the ground-truth data needed for training models is in most cases spatially and temporally clustered. Therefore, map production requires extrapolation of models from one place to another and the uncertainty cost of such extrapolation is rarely explored. In other words, we focus mainly on projections, and less on quantifying how reliable they are. 2. Following the concept of ‘forecast horizon’, we suggest that the predictability of land-cover classification models should be methodologically explored with quantitative tools as a continuum against distances measured along multiple dimensions. Focusing on ten agricultural sites from England and using models specifically designed to predict multivariate decay-curves we ask: how does a model’s predictive performance decay with distance? More specifically, we explored if we could predict the proficiency (kappa statistics) of a model trained in one site when making predictions in another site based on the spatial, temporal, spectral and environmental distances between sites. 3. We found that model proficiency decays with spatial, temporal, spectral and environmental distance between sites. More importantly, we found for the first time that it is possible to predict the performance a model transferred to or from a novel site will have, based on its distances from known sites. The spatial distance variables where the most important when predicting model transferability. 4. Exploring model transferability as a continuum may have multiple usages including predicting uncertainty values in space and time, prioritization of strategies for ground-truth data collection, and optimizing model characteristics for defined tasks.
Data from: Optimal taxonomic groups for biodiversity assessment: a meta-analytic approach
- 负责人：
- DOI：
- doi:10.5061/dryad.s1660
- 摘要：
- A fundamental decision in biodiversity assessment is the selection of one or more study taxa, a choice that is often made using qualitative criteria such as historical precedent, ease of detection, or available technical or taxonomic expertise. A more robust approach would involve selecting taxa based on the a priori expectation that they will provide the best possible information on unmeasured groups, but data to inform such hypotheses are often lacking. Using a global meta-analysis, we quantified the proportion of variability that each of 12 taxonomic groups (at the Order level or above) explained in the richness or composition of other taxa. We then applied optimization to matrices of pairwise congruency to identify the best set of complementary surrogate groups. We found that no single taxon was an optimal surrogate for both the richness and composition of unmeasured taxa if we used simple methods to aggregate congruence data between studies. In contrast, statistical methods that accounted for well-known drivers of cross-taxon congruence (spatial extent, grain size, and latitude) lead to the prioritization of similar surrogates for both species richness and composition. Advanced statistical methods were also more effective at describing known ecological relationships between taxa than simple methods, and show that congruence is typically highest between taxonomically and functionally dissimilar taxa. Birds and vascular plants were most frequently selected by our algorithm as surrogates for other taxonomic groups, but the extent to which any one taxon was the ‘optimal’ choice of surrogate for other biodiversity was highly context-dependent. In the absence of other information – such as in data-poor areas of the globe, and under limited budgets for monitoring or assessment – ecologists can use our results to assess which taxa are most likely to reflect the distribution of the richness or composition of ‘total’ biodiversity.
Data from: Quality and quantity of genetic relatedness data affect the analysis of social structure
- 负责人：
- DOI：
- doi:10.5061/dryad.rq2dg6m
- 摘要：
- Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species’ or population’s mating system and pattern of dispersal, and empirical data from longitudinal studies are crucial to validate these methods. We use data from a long-term behavioral study of a polygynandrous, bisexually philopatric marine mammal to measure accuracy and precision of parentage and genetic relatedness estimation against a known partial pedigree. We show that with moderate but obtainable sample sizes of approximately 4235 SNPs and 272 individuals, highly accurate parentage assignments and genetic relatedness coefficients can be obtained. Additionally, we subsample our data to quantify how data availability affects relatedness estimation and kinship assignment. Lastly, we conduct a social network analysis to investigate the extent to which accuracy and precision of relatedness estimation improve statistical power to detect an effect of relatedness on social structure. Our results provide practical guidance for minimum sample sizes and sequencing depth for future studies, as well as thresholds for post hoc interpretation of previous analyses.
Data from: Impaired hippocampal place cell dynamics in a mouse model of the 22q11.2 deletion
- 负责人：
- Zaremba, Jeff
- 关键词：
- hippocampus calcium imaging in vivo imaging two-photon imaging schizophrenia 22q11.2 deletion syndrome place cells place cell stability spatial learning reward learning
- DOI：
- doi:10.5061/dryad.rq560
- 摘要：
- Hippocampal place cells represent the cellular substrate of episodic memory. Place cell ensembles reorganize to support learning but must also maintain stable representations to facilitate memory recall. Despite extensive research, the learning-related role of place cell dynamics in health and disease remains elusive. Using chronic two-photon Ca2+ imaging in hippocampal area CA1 of wild-type and Df(16)A+/? mice, an animal model of 22q11.2 deletion syndrome, one of the most common genetic risk factors for cognitive dysfunction and schizophrenia, we found that goal-oriented learning in wild-type mice was supported by stable spatial maps and robust remapping of place fields toward the goal location. Df(16)A+/? mice showed a significant learning deficit accompanied by reduced spatial map stability and the absence of goal-directed place cell reorganization. These results expand our understanding of the hippocampal ensemble dynamics supporting cognitive flexibility and demonstrate their importance in a model of 22q11.2-associated cognitive dysfunction.
Data from: Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data
- 负责人：
- DOI：
- doi:10.5061/dryad.p7g5p
- 摘要：
- Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, only few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean 1?4 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.
