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Data from: A combined mesowear analysis of Mexican Bison antiquus shows a generalist diet with geographical variation
Bison antiquus was one of the largest and most widely distributed megafaunal species during the Late Pleistocene in North America, giving rise to the modern plains bison in the middle Holocene. Despite the importance of the ancient bison, little is known about its feeding ecology. We employed a combination of extended mesowear, and mesowear III to infer the diet preference and habitat use of three Mexican samples of B. antiquus. Two northern samples from the Transmexican Volcanic Belt morphotectonic Province: La Piedad-Santa Ana and La Cinta-Portalitos, as well as one southern sample from the Sierra Madre del Sur morphotectonic province: Viko Vijin. We found that the northern Mexican samples were primarily non-strict grazers, while the southern sample displays a pattern consistent with mixer feeder habits. This suggests variability among the diets of these bison samples, caused by different paleoenvironments. This evidence complements the paleoenvironmental reconstructions in the studied localities; for the northern samples, open prairies composed of patches of woodland or shrubland and for the southern locality a fluvial floodplain with short-lived vegetation. In both scenarios, grasses (Poaceae) were non-dominant. The dietary habits of our samples of ancient bison in Mexico are the southernmost dietary inference for the species in North America and expand our knowledge of the dietary habits of Bison antiquus during the late Pleistocene.
Data from: Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus)
The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.
Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling
We estimated the effective population sizes (Ne) and tested for short-term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro-endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D-loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean Ne estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake-level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro-endemics and populations in less favourable habitats have smaller Ne, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.
Data from: Integrating genetic analysis of mixed populations with a spatially-explicit population dynamics model
Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement in an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses. Incorporation of prior information about stock abundance and movement resulted in more precise and plausible estimates of mixture compositions in time and space. Inclusion of a population dynamics model also allowed robust interpolation of expected catch composition at areas and times with no genetic observations. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.
Scripts and raw data for comparing 2D vs 3D image analysis of zebrafish embryo microscopic data
<p>Raw data and MatLab scripts used for image analysis of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a fixed zebrafish embryo, comparing a 2D vs 3D approach to segment out the Pol II Ser5P clusters. Pol II Ser5P was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer.</p>
Data from: Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers
The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.
Data from: A meta-analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long-lived seagrass Posidonia oceanica
The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short- and long-term indicators of seagrass health. Using ArcGIS maps from a recent, high-resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta-analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high-impact sites is likely a temporal artefact, reflecting the mismatch with pre-environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.
Data from: The appropriateness of language found in research consent form templates: a computational linguistic analysis
Background: To facilitate informed consent, consent forms should use language below the grade eight level. Research Ethics Boards (REBs) provide consent form templates to facilitate this goal. Templates with inappropriate language could promote consent forms that participants find difficult to understand. However, a linguistic analysis of templates is lacking. Methods: We reviewed the websites of 124 REBs for their templates. These included English language medical school REBs in Australia/New Zealand (n=23), Canada (n=14), South Africa (n=8), the United Kingdom (n=34), and a geographically-stratified sample from the United States (n=45). Template language was analyzed using Coh-Metrix linguistic software (v.3.0, Memphis, USA). We evaluated the proportion of REBs with five key linguistic outcomes at or below grade eight. Additionally, we compared quantitative readability to the REBs' own readability standards. To determine if the template's country of origin or the presence of a local REB readability standard influenced the linguistic variables, we used a MANOVA model. Results: Of the REBs who provided templates, 0/94 (0%, 95% CI=0-3.9%) provided templates with all linguistic variables at or below the grade eight level. Relaxing the standard to a grade 12 level did not increase this proportion. Further, only 2/22 (9.1%, 95% CI= 2.5-27.8) REBs met their own readability standard. The country of origin (DF= 20, 177.5, F=1.97, p=0.01), but not the presence of an REB-specific standard (DF=5, 84, F=0.73, p=0.60), influenced the linguistic variables. Conclusions: Inappropriate language in templates is an international problem. Templates use words that are long, abstract, and unfamiliar. This could undermine the validity of participant informed consent. REBs should set a policy of screening templates with linguistic software.
Data from: Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species
BACKGROUND: In the mid 20th Century, Ernst Mayr and Theodosius Dobzhansky championed the significance of circular overlaps or ring species as the perfect demonstration of speciation, yet in over 50 years since only a handful of such taxa are known. We developed a topographic model to evaluate whether the geographic barriers that favor processes leading to ring species are common or rare, and to predict where other candidate ring barriers might be found. RESULTS: Of the 952,147 geographic barriers identified on the planet, only about 1% are topographically similar to barriers associated with known ring taxa, with most of the likely candidates occurring in under-studied parts of the world (e.g., marine environments, tropical latitudes). Predicted barriers separate into two distinct categories: (i) single cohesive barriers (<50,000 km2), associated with taxa that differentiate at smaller spatial scales (salamander: Ensatina eschscholtzii; tree: Acacia karroo); and (ii) composite barriers – formed by groups of barriers (each 184,000 to 1.7 million km2) in close geographic proximity (totaling 1.9 to 2.3 million km2) – associated with taxa that differentiate at larger spatial scales (birds: Phylloscopus trochiloides and Larus [sp. argentatus and fuscus]). When evaluated globally, we find a large number of cohesive barriers that are topographically similar to those associated with known ring taxa. Yet, compared to cohesive barriers, an order of magnitude fewer composite barriers are similar to those that favor ring divergence in species with higher dispersal. CONCLUSIONS: While these findings confirm that the topographic conditions that favor evolutionary processes leading to ring speciation are in fact rare, they also suggest that many understudied natural systems could provide valuable demonstrations of continuous divergence towards the formation of new species. Distinct advantages of the model are that it (i) requires no a priori information on the relative importance of features that define barriers, (ii) can be replicated using any kind of continuously distributed environmental variable, and (iii) generates spatially explicit hypotheses of geographic species formation. The methods developed here – combined with study of the geographical ecology and genetics of taxa in their environments – should enable recognition of ring species phenomena throughout the world.
Data from: Geometric morphometric analysis applied to theropod tracks from the lower Cretaceous (Berriasian) of Spain
Geometric morphometric methods applied to theropod tracks from the Huérteles Formation (Berriasian, Spain) are here shown to be invaluable for drawing comparisons between theropod tracks with different preservation modes (true tracks, shallow undertracks and natural casts) or differing in the preservation of anatomical features (e.g. digital pads). Principal components analysis and thin-plate spline methods can quantitatively distinguish between the broad groups of tracks in a sample and establish the main differences between them. These methods offer a promising approach for estimating ichnodiversity, achieved by evaluating just the morphology of the tracks independent of other factors such as size. The theropod tracks of the Huérteles Formation can be classified into two broad groups: minute-to-medium-sized gracile theropod tracks (Kalohipus bretunensis) and medium-to-large-sized robust theropod tracks (Iberosauripus). The presence of a third group of more gracile medium-to-large-sized theropod tracks (Megalosauripus) cannot be proven with certainty on the basis of the current data. These results indicate that the theropod ichnodiversity of the Huérteles Formation is probably lower than that estimated by means of conventional methods alone (e.g. qualitative description of the tracks) and that many of the described theropod morphotypes may represent extramorphological or ontogenetic variations of other morphotypes.
Data from: An analysis of the impacts of Cretaceous Oceanic Anoxic Events on global molluscan diversity dynamics
Oceanic Anoxic Events (OAEs) are contemporaneous with 11 of the 18 largest Phanerozoic extinction events, but the magnitude and selectivity of their paleoecological impact remains disputed. OAEs are associated with abrupt, rapid warming and increased CO2 flux to the atmosphere, thus insights from this study may clarify the impact of current anthropogenic climate change on the biosphere. We investigated the influence of the Late Cretaceous Bonarelli Event (OAE2; Cenomanian – Turonian stage boundary; ~ 94 Ma) on generic- and species-level molluscan diversity, extinction rates, and ecological turnover. Cenomanian – Turonian results were compared with changes across all Cretaceous stage boundaries, some of which are coincident with less severe OAEs. We found increased generic turnover, but not species-level turnover, associated with several Cretaceous OAEs. The absence of a species-level pattern may reflect species occurrence data that are too temporally coarse to robustly detect patterns. Five hypotheses of ecological selectivity relating anoxia to survivorship were tested across stage boundaries with respect to faunality, mobility and diet using generalized linear models. Increasingly benthic taxa were consistently selected against throughout the Cretaceous regardless of the presence or absence of OAEs. These results suggest that: (1) the Cenomanian – Turonian boundary (OAE2) was associated with a decline in mollusk diversity, and increase in extinction rate, that was significantly more severe than Cretaceous background levels; and (2) no differential ecological selectivity was associated with OAE-related diversity declines among the variables tested here.
Data from: Social network analysis of psychological morbidity in an urban slum of Bangladesh: a cross-sectional study based on a community census
Background Social ties are believed to play important roles in mitigating depression and anxiety, as well as fostering mental health in the population. We test this association for young urban men in Bangladesh. Methods Using a locally adapted GHQ-12 instrument, we enumerate self-reported mental health outcomes for 824 post-adolescent young men between the ages of 18 and 29 in a low-income urban community in Dhaka, Bangladesh. We further measure the social network for all our subjects and estimate the association of social network of the respondents with self-reported mental health outcomes controlling for possible confounders. Results We find there are considerable variations in both the mental health outcomes and social network across respondents. The GHQ scores (mean = 9.2, SD = 4.9) suggest significant psychological morbidity among the respondents. However, our findings imply better social ties and connections can potentially mitigate negative mental health outcomes (0.05-0.65 lower standardized GHQ score). Among other factors, being married and a recent migrant are also associated with better mental health status (0.17-0.20 and 0.16-0.17 lower standardized GHQ scores respectively). Conclusion Our results underscore the importance of social connection in providing buffer against stress and anxiety through psychosocial support from one's peer in a resource constraint urban setting. Our findings also suggest incorporating social network and ties in designing mental health policies and interventions.
Data from: A multi-genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World
This study investigated the population genetics, demographic history and pathway of invasion of the Russian wheat aphid (RWA) from its native range in Central Asia, the Middle East and Europe to South Africa and the Americas. We screened microsatellite markers, mitochondrial DNA, and endosymbiont genes in 504 RWA clones from nineteen populations worldwide. Following pathway analyses of microsatellite and endosymbiont data, we postulate that Turkey and Syria were the most likely sources of invasion to Kenya and South Africa, respectively. Furthermore, we found that one clone transferred between South Africa and the Americas was most likely responsible for the New World invasion. Finally, endosymbiont DNA was found to be a high resolution population genetic marker, extremely useful for studies of invasion over a relatively short evolutionary history timeframe. This study has provided valuable insights into the factors that may have facilitated the recent global invasion by this damaging pest.
Data from: Angiosperm fleshy fruits and seed dispersers: a comparative analysis of adaptation and constraints in plant-animal interactions
Variation in phenotypic traits of angiosperm fleshy fruits has been explained as the result of adaptations to their mutualistic seed dispersers. By analyzing the information available on fleshy fruit characteristics of 910 angiosperm species, I assess the hypothesis of evolutionary association between fruit phenotypic traits and type of seed disperser (birds, mammals, and mixed dispersers) and address explicitly and quantitatively alternative null hypotheses about phylogenetic effects. Phylogenetic affinity among plant taxa is accounted for by comparative methods including nested ANOVA, phylogenetic autocorrelation, and independent contrasts. Averaging over the 16 fruit traits examined, phylogenetic effects down to genus level explain 61% of total variance. Phylogenetic autocorrelations are strong among close relatives, reaching significance for 11 of the 16 fruit traits examined. When assessed by independent contrast methods, correlated evolution between type of disperser and fruit traits is confined to fruit diameter. Differences among dispersal syndromes in other traits vanish after accounting for phylogenetic effects. These analyses reveal that seed dispersal syndromes are not entirely interpretable as current adaptations to seed dispersers. Their status as exaptations can be assessed by combining experimental studies of natural selection on fruit size and rigorous comparative and cladistic tests of adaptational hypotheses.
Data from: Forest loss in protected areas and intact forest landscapes: a global analysis
In spite of the high importance of forests, global forest loss has remained alarmingly high during the last decades. Forest loss at a global scale has been unveiled with increasingly finer spatial resolution, but the forest extent and loss in protected areas (PAs) and in large intact forest landscapes (IFLs) have not so far been systematically assessed. Moreover, the impact of protection on preserving the IFLs is not well understood. In this study we conducted a consistent assessment of the global forest loss in PAs and IFLs over the period 2000–2012. We used recently published global remote sensing based spatial forest cover change data, being a uniform and consistent dataset over space and time, together with global datasets on PAs' and IFLs' locations. Our analyses revealed that on a global scale 3% of the protected forest, 2.5% of the intact forest, and 1.5% of the protected intact forest were lost during the study period. These forest loss rates are relatively high compared to global total forest loss of 5% for the same time period. The variation in forest losses and in protection effect was large among geographical regions and countries. In some regions the loss in protected forests exceeded 5% (e.g. in Australia and Oceania, and North America) and the relative forest loss was higher inside protected areas than outside those areas (e.g. in Mongolia and parts of Africa, Central Asia, and Europe). At the same time, protection was found to prevent forest loss in several countries (e.g. in South America and Southeast Asia). Globally, high area-weighted forest loss rates of protected and intact forests were associated with high gross domestic product and in the case of protected forests also with high proportions of agricultural land. Our findings reinforce the need for improved understanding of the reasons for the high forest losses in PAs and IFLs and strategies to prevent further losses.
Data from: A critical analysis of the potential for EU Common Agricultural Policy measures to support wild pollinators on farmland
<p>1. Agricultural intensification and associated loss of high-quality habitats are key drivers of insect pollinator declines. With the aim of decreasing the environmental impact of agriculture, the 2014 EU Common Agricultural Policy (CAP) defined a set of habitat and landscape features (Ecological Focus Areas: EFAs) farmers could select from as a requirement to receive basic farm payments. To inform the post-2020 CAP, we performed a European-scale evaluation to determine how different EFA options vary in their potential to support insect pollinators under standard and pollinator-friendly management, as well as the extent of farmer uptake.</p> <p> 2. A structured Delphi elicitation process engaged 22 experts from 18 European countries to evaluate EFAs options. By considering life cycle requirements of key pollinating <i>taxa</i> (i.e. bumble bees, solitary bees and hoverflies), each option was evaluated for its potential to provide forage, bee nesting sites and hoverfly larval resources.</p> <p>3. EFA options varied substantially in the resources they were perceived to provide and their effectiveness varied geographically and temporally. For example, field margins provide relatively good forage throughout the season in Southern and Eastern Europe but lacked early-season forage in Northern and Western Europe. Under standard management, no single EFA option achieved high scores across resource categories and a scarcity of late season forage was perceived.</p> <p>4. Experts identified substantial opportunities to improve habitat quality by adopting pollinator-friendly management. Improving management alone was, however, unlikely to ensure that all pollinator resource requirements were met. Our analyses suggest that a combination of poor management, differences in the inherent pollinator habitat quality and uptake bias towards catch crops and nitrogen-fixing crops severely limit the potential of EFAs to support pollinators in European agricultural landscapes.</p> <p>5. <i>Policy Implications.</i> To conserve pollinators and help protect pollination services, our study highlights the need to create a variety of interconnected, well-managed habitats that complement each other in the resources they offer<i>. </i>To achieve this the CAP post-2020 should take a holistic view to implementation that integrates the different delivery vehicles aimed at protecting biodiversity (e.g. enhanced conditionality, eco-schemes and Agri-Environment and Climate Measures). To improve habitat quality we recommend an effective monitoring framework with target-orientated indicators and to facilitate the spatial targeting of options collaboration between land managers should be incentivised.</p>
Data from: Social network analysis shows direct evidence for social transmission of tool use in wild chimpanzees.
Claims of culture in animals have been stimulated by studies on a wide range of taxa revealing group-specific behavior patterns that remain stable through generations, consistent with different behavioral innovations spreading within groups by social transmission in a manner similar to human culture. In chimpanzees, 39 behaviors have been identified as 'cultural', because alternative genetic and environmental explanations for the observed regional variation appear less plausible. This interpretation is supported by experimental data from captive chimpanzee groups. However, there is no experimental evidence for social learning in the wild, nor has there been direct observation of social diffusion of spontaneously occurring behavioral innovations. Here, we document the spread of two novel tool-use variants, 'moss-sponging' and 'leaf-sponge re-use', in the Sonso chimpanzee community of Budongo Forest, Uganda. We use traditional network-based diffusion analysis (NBDA) to test whether these novel behaviors spread by social learning, as well as a newly developed dynamic version of NBDA, capable of capturing temporal aspects of acquisition, i.e. how each successive personal observations impact the subsequent acquisition of behavior. Both models provide strong evidence that diffusion patterns of moss-sponging, but not leaf-sponge re-use, are significantly better explained by social than asocial learning, therefore showing that wild chimpanzees socially learned moss-sponging from each other. The most conservative estimate of social transmission accounts for 85% of observed events with an estimated 11-fold increase in learning rate for each time a novice observed an informed individual performing moss-sponging. We conclude that group-specific behavioral variants in chimpanzees can be socially learned, suggesting this prerequisite for culture originated in a common ancestor of great apes and humans, long before the advent of modern humans.
Data from: Comparative analysis indicates historical persistence and contrasting contemporary structure in sympatric woody perennials of semi-arid south-west Western Australia
We used a comparative approach to assess congruence of phylogeographic and genetic structure and diversity, demographic signals, and ratios of pollen to seed dispersal, in the context of species-specific life-history traits, for two widespread sympatric perennial plant species. We sampled Grevillea paradoxa and Melaleuca nematophylla across the species' ranges throughout the Transitional Rainfall Zone and extending slightly into the Arid Zone of south-west Western Australia. Both species exhibited range-wide phylogeographic and contemporary genetic structure. Moderate haplotype diversity centred in populations on Banded Ironstone Formation (BIF) outcrops and within the Murchison River gorge supports a hypothesis of historical persistence and evolution in these mesic refugia. These features are likely to play important roles in evolutionary persistence with ongoing climate change. There was little evidence of particularly complex demographic histories for the region. More limited haplotype diversity, as well as more limited nuclear genetic diversity and connectivity, in G. paradoxa was consistent with predictions from life-history traits of shorter lifespan, lower fecundity, more limited seed dispersal, and shorter plants, but inconsistent with a prediction of greater pollen dispersal by bird pollinators. Low pollen to seed dispersal ratios suggest seed dispersal plays a greater than expected role in maintaining connectivity in this semi-arid landscape. The study highlights a need for research that integrates aspects of seed ecology and seed and pollen dispersal as well as phylogeographic and genetic patterns in Gondwanan shrublands and other semi-arid landscapes globally.
Data from: Grains of connectivity: analysis at multiple spatial scales in landscape genetics
Landscape genetic analyses are typically conducted at one spatial scale. Considering multiple scales may be essential for identifying landscape features influencing gene flow. We examined landscape connectivity for woodland caribou (Rangifer tarandus caribou) at multiple spatial scales using a new approach based on landscape graphs that creates a Voronoi tessellation of the landscape. To illustrate the potential of the method, we generated five resistance surfaces to explain how landscape pattern may influence gene flow across the range of this population. We tested each resistance surface using a raster at the spatial grain of available landscape data (200 m grid squares). We then used our method to produce up to 127 additional grains for each resistance surface. We applied a causal modelling framework with partial Mantel tests, where evidence of landscape resistance is tested against an alternative hypothesis of isolation-by-distance, and found statistically significant support for landscape resistance to gene flow in 89 of the 507 spatial grains examined. We found evidence that major roads as well as the cumulative effects of natural and anthropogenic disturbance may be contributing to the genetic structure. Using only the original grid surface yielded no evidence for landscape resistance to gene flow. Our results show that using multiple spatial grains can reveal landscape influences on genetic structure that may be overlooked with a single grain, and suggest that coarsening the grain of landcover data may be appropriate for highly-mobile species. We discuss how grains of connectivity and related analyses have potential landscape genetic applications in a broad range of systems.
Data from: Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)
Insights into the genetic characteristics of a species provide important information for wildlife conservation programs. Here, we used the OvineSNP50 BeadChip developed for domestic sheep to examine population structure and evaluate genetic diversity of snow sheep (Ovis nivicola) inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1121 polymorphic SNPs were used to test 80 specimens representing five populations, including four populations of the Verkhoyansk Mountain chain: Kharaulakh Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n = 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations were genetically structured according to a geographical pattern. Pairwise FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2 as the most likely number of ancestral populations. A Neighbor-Net tree showed that TIK was an isolated group related to the main network through ORU. TreeMix analysis revealed that TIK and MOM originated from two different ancestral populations and detected gene flow from MOM to ORU. This was supported by the f3 statistic, which showed that ORU is an admixed population with TIK and MOM/SKH heritage. Genetic diversity in the studied groups was increasing southward. Minimum values of observed (Ho) and expected (He) heterozygosity and allelic richness (Ar) were observed in the most northern population–TIK, and maximum values were observed in the most southern population–SKH. Thus, our results revealed clear genetic structure in the studied populations of snow sheep and showed that TIK has a different origin from MOM, SKH and VER even though they are conventionally considered a single subspecies known as Yakut snow sheep (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during the late Pleistocene glaciations of Verkhoyansk Range.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.