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1,514 results for “Widespread”
Data from: Population structure of mycobionts and photobionts of the widespread lichen Cetraria aculeata
Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on DNA sequences from three loci for each symbiont we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont datasets into three groups. An AMOVA shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and co-dispersal we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of co-dispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled Cetraria aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographic range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.
Data from: Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow
The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.
Data from: Aquatic insects rich in omega-3 fatty acids drive breeding success in a widespread bird
Ecologists studying bird foraging ecology have generally focused on food quantity over quality. Emerging work suggests that food quality, in terms of highly unsaturated omega-3 fatty acids (HUFA), can have equally important effects on performance. HUFA, which are present in aquatic primary producers, are all but absent in vascular plants, and HUFA content is also correspondingly higher in aquatic insects. Here, we show that Tree Swallow (Tachycineta bicolor) chicks rapidly accumulate HUFA from food during the nestling period. Using data sampled over 24 years, we also show that Tree Swallow breeding success is positively associated with the availability of HUFA-rich aquatic insects. Variation in aquatic insect biomass during chick development was a strong predictor of fledging success, while variation in terrestrial insects had little effect on fledging success. Our results highlight the potential for nutritional mismatches between insectivores and high-quality prey to affect avian reproductive performance.
Data from: Widespread infection of Areospora rohanae in southern king crab (Lithodes santolla) populations across south Chilean Patagonia
Cottage cheese disease is caused by microsporidian parasites that infect a wide range of animal populations. Despite its potential to affect economically important activities, the spatial patterns of prevalence of this disease are still not well understood. Here, we analyze the occurrence of the microsporidian Areospora rohanae in populations of the king crab Lithodes santolla over ca. 800 km of the southeastern Pacific shore. In winter 2011, conical pots were deployed between 50 and 200 m depth to capture crabs of a wide range of sizes. The infection was widely distributed along the region, with a mean prevalence of 16 %, and no significant association between prevalence and geographic location was detected. Males, females, and ovigerous females showed similar prevalence values of 16.5 (13 – 18.9), 15 (9.2 – 15), and 16.7 % (10 – 19 %), respectively. These patterns of prevalence were consistent across crab body sizes, despite the ontogenetic and sex-dependent variations in feeding behavior and bathymetric migrations previously reported for king crabs. This study provided the first report of the geographic distribution of A. rohanae infecting southern king crabs.
Data from: Archipelagic genetics in a widespread Caribbean anole
Aim We examine the influence of fluctuating sea levels in a land-bridge archipelago on the apportioning of intraspecific genetic diversity and divergence in the widespread Puerto Rican crested anole (Anolis cristatellus). We compare three alternative scenarios for genetic diversification in an archipelagic species that contrast the relative influences of periodic isolation versus island connectedness driven by fluctuating sea levels. Our approach combines information from geography and population genetics to assess the influence of island size, island isolation, island historical geography, and population genetic processes such as drift on the contemporary distribution of genetic variation within and among islands. Location The Puerto Rico Bank in the Caribbean focusing primarily on the Spanish, British and U.S. Virgin Islands. Methods We used nuclear and mitochondrial DNA sequences and microsatellite genotypes sampled from A. cristatellus populations to investigate: 1) the broad-scale pattern of phylogeographic divergence across Puerto Rico Bank islands; and 2) diversification within the Virgin Islands archipelago. For the first component, we used sequence data to reconstruct the relationships among 542 samples from across the species' range. For the second component, we examined the relative influences of island size, isolation, and population genetic processes on the distribution of genetic diversity across the Virgin Islands. Results In the Virgin Islands, A. cristatellus is represented by a monophyletic clade except on the island of Vieques, where two divergent clades coexist. We found evidence for non-equilibrium dynamics in the Virgin Islands, suggesting spatial population expansion during intraglacial periods of low sea level. Main conclusions We found limited evidence that periods of island isolation affected patterns of genetic diversity and differentiation. Instead, we found that the patterns of genetic diversity and divergence in A. cristatellus in the Virgin Islands archipelago are likely shaped by long-term persistence in the region and periods of population spatial expansion.
Data from: Chromatin signature of widespread monoallelic expression
In mammals, numerous autosomal genes are subject to mitotically stable monoallelic expression (MAE), including genes that play critical roles in a variety of human diseases. Due to challenges posed by the clonal nature of MAE, very little is known about its regulation; in particular, no molecular features have been specifically linked to MAE. Here we report an approach that distinguishes MAE genes in human cells with great accuracy: a chromatin signature consisting of chromatin marks associated with active transcription (H3K36me3) and silencing (H3K27me3) simultaneously occurring in the gene body. The MAE signature is present in ~20% of ubiquitously expressed genes and over 30% of tissue-specific genes across cell types. Notably, it is enriched among key developmental genes that have bivalent chromatin structure in pluripotent cells. Our results open a new approach to the study of MAE that is independent of polymorphisms, and suggest that MAE is linked to cell differentiation.
Data from: Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host–symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.
Data from: Development of genomic tools in a widespread tropical tree, Symphonia globulifera L.f.: a new low-coverage draft genome, SNP and SSR markers
Population genetic studies in tropical plants are often challenging because of limited information on taxonomy, phylogenetic relationships and distribution ranges, scarce genomic information and logistic challenges in sampling. We describe a strategy to develop robust and widely applicable genetic markers based on a modest development of genomic resources in the ancient tropical tree species Symphonia globulifera L.f. (Clusiaceae), a keystone species in African and Neotropical rainforests. We provide the first low-coverage (11X) fragmented draft genome sequenced on an individual from Cameroon, covering 1.027 Gbp or 67.5% of the estimated genome size. Annotation of 565 scaffolds (7.57 Mbp) resulted in the prediction of 1046 putative genes (231 of them containing a complete open reading frame) and 1523 exact simple sequence repeats (SSRs, microsatellites). Aligning a published transcriptome of a French Guiana population against this draft genome produced 923 high-quality single nucleotide polymorphisms. We also preselected genic SSRs in silico that were conserved and polymorphic across a wide geographical range, thus reducing marker development tests on rare DNA samples. Of 23 SSRs tested, 19 amplified and 18 were successfully genotyped in four S. globulifera populations from South America (Brazil and French Guiana) and Africa (Cameroon and São Tomé island, FST = 0.34). Most loci showed only population-specific deviations from Hardy–Weinberg proportions, pointing to local population effects (e.g. null alleles). The described genomic resources are valuable for evolutionary studies in Symphonia and for comparative studies in plants. The methods are especially interesting for widespread tropical or endangered taxa with limited DNA availability.
Data from: Widespread introgression of mountain hare genes into Fennoscandian brown hare populations
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the lower levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
Data from: Temperature- and latitude-specific individual growth rates shape the vulnerability of damselfly larvae to a widespread pesticide
1. Freshwater ecosystems are especially vulnerable to climate change and pollution. One key challenge for aquatic toxicology is to determine and manage the combined effects of temperature increase and contaminants across species' ranges. 2. We tested how thermal adaptation and life-history evolution along a natural temperature gradient influence the vulnerability of an aquatic insect to a pesticide under global warming. We applied a space-for-time substitution approach to study the effect of warming on the vulnerability of Ischnura elegans damselfly larvae to the pesticide chlorpyrifos in a common garden warming experiment (20 and 24 °C) with replicated populations from three latitudes spanning >1500 km in Europe. 3. Chlorpyrifos was more toxic to damselfly larvae at the higher temperature: mortality only occurred at 24 °C and the reductions in growth rate were stronger at 24 °C. This could partly be explained by parallel reductions in food intake but not by the activities of two widespread enzymatic biomarkers, glutathione S-transferase (GST) and acetylcholinesterase (AChE). 4. There was some evidence that the increased toxicity of the high chlorpyrifos concentration at 24 °C was stronger in terms of growth reduction in the faster-growing larvae from the low-latitude populations. This is consistent with energy allocation trade-offs between growth rate and pesticide tolerance, but suggests that local thermal adaptation does not play a role in coping with pesticide stress. 5. Synthesis and applications. Damselfly larvae from populations in lower latitudes were more vulnerable to a common pesticide at higher temperatures and pesticide concentrations, whereas evidence for the influence of local thermal adaptation on the vulnerability of larvae was weak. These results emphasize the need for spatially explicit bioassessment and conservation tools. Management practices aimed at mitigating pesticide run-off into aquatic ecosystems are particularly important in agricultural areas at low latitudes.
Data from: Variation of xylem vessel diameters across a climate gradient: insight from a reciprocal transplant experiment with a widespread boreal tree
Xylem vessel diameters represent an important plant hydraulic trait to ensure sufficient water supply from the roots to the leaves. The ability to adjust the hydraulic pathway to environmental cues is key in order to satisfy transpirational demands and maximize growth and survival. We evaluated the variability of vessel diameters in trembling aspen in a reciprocal transplant experiment. We tested six provenances from three ecological regions of North America planted at four test sites in western Canada. All test sites were established at the same time with the same provenances arranged in a randomized complete block design. Vessel diameter showed a strong interaction of population and test site suggesting a high degree of phenotypic plasticity in this trait. Gaussian kernel density estimates support plastic as well as genetic contributions in vessel diameter control trending from bimodal distributions at the most northern test site towards unimodal distributions at the warmest and mildest test site. Furthermore, we used test site-specific climate data in form of a 2-year, 5-year and 10-year average of 21 directly and derived climatic variables and found that average site-specific vessel diameters correlated strongly with summer moisture availability. A previously found negative relationship with vessel diameter and tree height in central Alberta was also found at two other boreal test sites but reversed at a wetter and milder sub-boreal test site. In summary, vessel diameters were highly plastic in response to different environments and varied with summer moisture availability. The variability of vessel diameter and tree height correlations suggests that vessel diameter alone cannot serve as a reliable proxy for long-term growth performance beyond boreal environments. Instead, selecting aspen populations with a high degree of plasticity in this trait appears to be the safest option for assisted migration and seed transfer programmes under climate change.
Data from: Widespread chemical detoxification of alkaloid venom by formicine ants
The ability to detoxify defensive compounds of competitors provides key ecological advantages that can influence community-level processes. Although common in plants and bacteria, this type of detoxification interaction is extremely rare in animals. Here, using laboratory behavioral assays and analyses of videotaped interactions in South America, we report widespread venom detoxification among ants in the subfamily Formicinae. Across both data sets, nine formicine species, representing all major clades, used a stereotyped grooming behavior to self-apply formic acid (acidopore grooming) in response to fire ant (Solenopsis invicta and S. saevissima) venom exposure. In laboratory assays, this behavior increased the survivorship of species following exposure to S. invicta venom. Species expressed the behavior when exposed to additional alkaloid venoms, including both compositionally similar piperidine venom of an additional fire ant species and the pyrrolidine/pyrroline alkaloid venom of a Monomorium species. In addition, species expressed the behavior following exposure to the uncharacterized venom of a Crematogaster species. However, species did not express acidopore grooming when confronted with protein-based ant venoms or when exposed to monoterpenoid-based venom. This pattern, combined with the specific chemistry of the reaction of formic acid with venom alkaloids, indicates that alkaloid venoms are targets of detoxification grooming. Solenopsis thief ants, and Monomorium species stand out as brood-predators of formicine ants that produce piperidine, pyrrolidine, and pyrroline venom, providing an important ecological context for the use of detoxification behavior. Detoxification behavior also represents a mechanism that can influence the order of assemblage dominance hierarchies surrounding food competition. Thus, this behavior likely influences ant-assemblages through a variety of ecological pathways.
Data from: Lean-season primary productivity and heat dissipation as key drivers of geographic body-size variation in a widespread marsupial
Geographic body-size variation characterises many mammal species. Hypotheses centring around heat conservation, heat dissipation, primary productivity and seasonality have been advanced to explain geographic body-size patterns. However, identification of the primary body-size drivers has often been hampered by a paucity of data for broadly distributed species and the application of regression models that have not explicitly accounted for the spatial clustering inherent in such datasets. We used Australia's most widespread marsupial, the common brushtail possum Trichosurus vulpecula, as a model species with which to test five proposed drivers of geographic body-size variation. Using geo-referenced skull measurements from 588 specimens and a suite of putative environmental covariates, we employed spatial simultaneous autoregressive models, together with information criteria, to evaluate these different hypotheses. Our analysis identified a strong, positive relationship between possum body size and primary productivity during the least productive season, whereas the relationship with mean annual productivity received less support. Consistent with the heat-dissipation hypothesis, T. vulpecula body size also decreased with increasing mean summer maximum temperature. Spatial autoregression coefficients estimated from the simultaneous autoregressive models were always high, suggesting that additional abiotic or biotic factors might contribute to the spatial patterns observed. We argue that the analysis of geographic body-size variation should consider multi-causal possibilities rather than treating the numerous hypotheses as competing, mutually exclusive alternatives.
Data from: Genome-wide scans detect adaptation to aridity in a widespread forest tree species.
Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation.
Data from: Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance
Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed "hemiplasy"—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and to introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.
Data from: Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs
Secondary contact between closely related taxa routinely occurs during postglacial migrations. After initial contact, the location of hybrid zones may shift geographically or remain spatially stable over time in response to various selective pressures or neutral processes. Studying the extent and direction of introgression using markers having contrasted levels of gene flow can help unravel the historical dynamics of hybrid zones. Thanks to their contrasted maternal and paternal inheritance, resulting in different levels of gene flow for mitochondrial and chloroplast DNA (mtDNA and cpDNA), the Pinaceae stand out as a relevant biological model for this purpose. The objective of the study was to assess whether the hybrid zone between Abies balsamea and Abies lasiocarpa (two largely distributed Pinaceae) has moved or remained stable over time by analysing the distribution of cytoplasmic DNA variation as well as published palaeobotanical data. Interspecific gene flow was higher for cpDNA than mtDNA markers; hence, the geographic distribution of mitotypes was more congruent with species distributions than chlorotypes. This genetic signature was contrary to expectations under a moving hybrid zone scenario, as well as empirical observations in other conifers. Genetic evidence for this rare instance of stable hybrid zone was corroborated by the colonization chronology derived from published fossil data, indicating that the two fir species initially came into contact in the area corresponding to the current sympatric zone 11 kyr ago. While an explanatory analysis suggested the putative influence of various environmental factors on the relative abundance of cytoplasmic genome combinations, further research appears necessary to assess the role of both demographic history and selective factors in driving the dynamics of hybrid zones.
Data from: Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae)
Habitat fragmentation and changed land use have seriously reduced population size in many tropical forest tree species. Formerly widespread species with limited gene flow may be particularly vulnerable to the negative genetic effects of forest fragmentation and small population size. Vateriopsis seychellarum (Dipterocarpaceae) is a formerly widespread canopy tree of the Seychelles, but is now reduced to 132 adult individuals distributed in eleven sites. Using ten microsatellite loci, a genetic inventory of all adult trees and a sample of 317 progeny, we demonstrate that despite its restricted range, overall genetic diversity was relatively high (HE: 0.56). The juvenile cohort, however, had significantly lower allelic richness (adults RS: 3.91; juveniles RS: 2.83) and observed heterozygosity than adult trees (adults HO: 0.62; juveniles HO: 0.48). Rare alleles were fewer and kinship between individuals was stronger in juveniles. Significant fine-scale spatial genetic structure was observed in remnant adults, and parentage analysis indicated that more than 90% of sampled progeny disperse <25 m and pollen dispersed <50 m. The molecular data confirmed that two populations were derived entirely from self-fertilized offspring from a single surviving mother tree. These populations produce viable offspring. Despite this extreme genetic bottleneck, self-compatibility may provide V. seychellarum with some resistance to the genetic consequences of habitat fragmentation, at least in the short term. We discuss our findings in the context of other rare and threatened dipterocarp species which are vulnerable to mis-management of genetic resources and population fragmentation.
Data from: Density-dependent effects of a widespread invasive herbivore on tree survival and biomass during reforestation
Reforestation has been widely adopted as a solution to multiple global change issues. However, the role of herbivory by invasive species in the restoration of grassland to forest has received little attention. We conducted a field experiment to investigate the impacts of a widespread invasive mammalian herbivore, the European rabbit (Oryctolagus cuniculus), on trees planted in a landscape-scale reforestation program in south-eastern Australia. Three native tree species were planted inside and outside rabbit-proof exclosures within 10 experimental units, and a random half of the units were subjected to intensive and sustained rabbit control for the remainder of the experiment. Quarterly survival of trees, and total aboveground biomass at the conclusion of the experiment, were estimated using hierarchical Bayesian models. Control substantially reduced rabbit densities on the five treatment units relative to the five non-treatment units. Survival of trees planted outside exclosures was highest at lowest rabbit density and declined non-linearly with increasing rabbit density for all three tree species, but even very low rabbit densities had strong negative effects on the survival of trees outside exclosures. There was a three-way interaction between tree height, being outside an exclosure, and rabbit density. Smaller trees planted outside exclosures always had substantially lower overall survival than trees of the same height planted inside exclosures, and the magnitude of the difference increased with increasing rabbit density. Increasing rabbit densities reduced the overall survival of increasingly taller trees of all three species planted outside exclosures. The aboveground biomass of trees surviving outside exclosures was significantly greater in treatment units compared with non-treatment units for all three species. The combined effects of differential survival and accumulation of aboveground biomass led to higher biomasses inside exclosures relative to outside exclosures just 21 months after planting. The aboveground biomass of trees planted outside exclosures declined with increasing rabbit density, and was effectively zero when rabbit densities exceeded 100 active warren entrances/ha. These results demonstrate that invasive herbivores can rapidly arrest the conversion of grassland to forest. Invasive herbivores such as the European rabbit may need to be completely excluded in order to maximize the benefits of reforestation.
Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography
Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure, and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analyzed 10 microsatellite loci from over 1,900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation, and management.
Data from: Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)
The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia, which formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the Phylogenetic Species Concept, the existence of mutual haplotypic exclusivity and non-admixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation, and thus, two species following the Biological Species Concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.
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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.