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403 results for “Landscape Genomics”
Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis
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The genomic landscapes of desert birds form over multiple time scales
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Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity
<p>Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (<i>Lucania goodei</i>) and rainwater killifish (<i>L. parva</i>) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioral, extrinsic, and intrinsic postzygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between <i>L. parva </i>and <i>L. goodei</i> to explore the genetic architecture of salinity tolerance, behavioral isolation, and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in <i>L. parva</i> (relative to <i>L. goodei</i>). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome, and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioral or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between <i>Lucania</i> species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioral and intrinsic isolation as a byproduct. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioral isolation instead, possibly facilitated by linkage between behavioral isolation and intrinsic isolation loci on the fused chromosome.</p>
Data from: The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.
Data from: Long-term in situ persistence of biodiversity in tropical sky-islands revealed by landscape genomics
Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (1) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation, and; (2) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky-islands (the Transmexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains, and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow.
Data from: Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa
The adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought-sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through landscape genomic approaches. Genotyping-By-Sequencing was used to identify SNPs across the genome, resulting in 1990 SNPs. Although a relatively low percentage of putative adaptive SNPs was detected (2.86% outlier SNPs), we observed clear associations among outlier allele frequencies, temperature, and plant traits. In line with the typical drought avoiding nature of A. glutinosa, leaf size varied according to a temperature gradient and significant associations with multiple outlier loci were observed, corroborating the ecological relevance of the observed outlier SNPs. Moreover, the lack of isolation-by-distance, the very low genetic differentiation among populations and the high intra-population genetic variation all support the notion that high gene exchange combined with strong environmental selection promotes adaptation to environmental cues.
Common barriers, but temporal dissonance: genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community
<p>Assessments of spatial and temporal congruency across taxa from genetic data provide insights into the extent to which similar processes structure communities. However, for coastal regions that are affected continuously by cyclical sea-level changes over the Pleistocene, congruent interspecific response will not only depend upon co-distributions, but also on similar dispersal histories among taxa. Here, we use SNPs to test for concordant genetic structure among four co-distributed taxa of freshwater fishes (Teleostei: Characidae) along the Brazilian Atlantic coastal drainages. Based on population relationships and hierarchical genetic structure analyses, we identify all taxa share the same geographic structure suggesting the fish utilized common passages in the past to move between river basins. In contrast to this strong spatial concordance, model-based estimates of divergence times indicate that despite common routes for dispersal, these passages were traversed by each of the taxa at different times resulting in varying degrees of genetic differentiation across barriers with most divergences dating to the Upper Pleistocene, even when accounting for divergence with gene flow. Interestingly, when this temporal dissonance is viewed through the lens of the species-specific ecologies, it suggests that an ecological sieve influenced whether species dispersed readily, with an ecological generalist showing the highest propensity for historical dispersal among the isolated rivers of the Brazilian coast (i.e., the most recent divergence times and frequent gene flow estimated for barriers). We discuss how our findings, and in particular what the temporal dissonance, despite common geographic passages, suggest about past dispersal structuring coastal communities as a function of ecological and paleo-landscape sieves.</p>
Data for: The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats
<p>A species tree is a central concept in evolutionary biology whereby a single-branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) – a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that proximate chromosomal regions tended to have more similar phylogenetic histories. While we found no clear relationship between local tree similarity and recombination rates in house mice, we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.</p>
Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape
<p><em>Phrynosoma mcallii</em> (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analyzed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and Salton Sea. We recommend additional lands in the U.S. and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy (RMS). We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change and other long-term impacts.</p>
Projection of high-dimensional genome-wide expression on SOM transcriptome landscapes: supplementary datasets
<p>This is a supplementary dataset with raw data, scripts, and complete analysis results for the paper "Supervised projection of high-dimensional genome-wide expression on SOM transcriptome landscapes". </p> <p>The archive contains three folders:</p> <p>1. "Simdata" folder contains data, scripts, and results of performance evaluation of extension SOM and supervised SOM with simulated data. </p> <p>2. "IBD" - folder contains data, scripts, and results of analysis of Inflammatory bowel disease datasets.</p> <p>3. "BC" - folder contains data, scripts, and results of analysis of breast cancer datasets.</p>
Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome
<p>Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.</p>
Highland forest's environmental complexity drives landscape genomics and connectivity of the rodent Peromyscus melanotis
<p>We evaluate how the environmental complexity of La Malinche volcano influences patterns of genomic variation in <em>Peromyscus melanotis</em>, across two mountain slopes and global and regional geographic scales.Using reduced representation genomic sequencing we estimated population genetic diversity, subdivisions and migration rates. Remote sensing data and drone image processing were used to characterize landscape variables. We evaluated their effect on connectivity, based on a landscape analyses framework, using resistance surfaces, circuit theory and omnidirectional connectivity. Our findings showed how the forest environmental complexity across different geographic scales drives dispersal, genomic structure and connectivity patterns in this rodent, where dirt roads and disturbed areas limit its connectivity, while exhibiting higher connectivity at the highest elevations where the forest is less disturbed. Notably, that our 3D variable of tree height was significant demonstrates the utility in incorporating 3D vegetation structure variables into landscape genetic analyses.</p>
Data for isolation-by-environment and its consequences for range shifts with global change: Landscape genomics of the invasive common tansy
<p>Invasive species are a growing global economic and ecological problem. However, it is not well understood how environmental factors mediate invasive range expansion. In this study, we investigated the recent and rapid range expansion of common tansy across environmental gradients in Minnesota, U.S.A. We densely sampled individuals across the expanding range and performed reduced representation sequencing to generate a dataset of 3071 polymorphic loci for 176 individuals. The dataset includes additional samples from the native range in Finland that were not used in the downstream analysis but are contributed for completeness. The dataset includes the genotype calls for all individuals sampled and sequenced. The genotype file was generated by stacks2.59 running the denovo pipeline and then using the populations function where we kept loci that were in 70% of populations and had a minor allele frequency of at least 1%. We used non-spatial and spatially-explicit analyses to determine the relative influences of geographic distance and environmental variation on patterns of genomic variation. We found no evidence for isolation-by-distance (IBD) but strong evidence for isolation-by-environment (IBE), indicating that environmental factors may have modulated patterns of range expansion.</p>
Data from: Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic 'landscape' of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.
Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite Toad (Anaxyrus canorus)
<p>An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future "Geminate Evolutionary Units" (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo-genomic simulations. Using this process, we delineated conservation units for the Yosemite toad (<em>Anaxyrus</em> <em>canorus</em>), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome-wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection (R<sup>2</sup> ranging from 0.09–0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF-North (high winter snowpack with moderate summer rainfall), YF-East (low to moderate snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF-East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non-model species with genomic data alone and has wide applicability to other declining species.</p>
Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age
<p><span>The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We used resequenced whole genomes to</span><span> i</span><span>nvestigate </span><span>how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpeckers, species co-distributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (1) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (2) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.</span></p>
Data from: Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle
<p>Organisms living in mountains contend with extreme climatic conditions, including short growing seasons and long winters with extensive snow cover. Anthropogenic climate change is driving unprecedented, rapid warming of montane regions across the globe, resulting in reduced winter snowpack. Loss of snow as a thermal buffer may have serious consequences for animals overwintering in soil, yet little is known about how variability in snowpack acts as a selective agent in montane ecosystems. Here we examine genomic variation in California populations of the leaf beetle <em>Chrysomela aeneicollis</em>, an emerging natural model system for understanding how organisms respond to climate change. We used a genotype-environment association approach to identify genomic signatures of local adaptation to microclimate in populations from three montane regions with variable snowpack and a coastal region with no snow. We found that both winter-associated environmental variation and geographic distance contribute to overall genomic variation across the landscape. We identified non-synonymous variation in novel candidate loci associated with cytoskeletal function, ion transport and membrane stability, cellular processes associated with cold tolerance in other insects. These findings provide intriguing evidence that variation in snowpack imposes selective gradients in montane ecosystems.</p>
BriTROC-1 study: genomic landscape of recurrent ovarian high grade serous carcinoma - pre processed data
<p>Dataset containing pre-processed data files required to replicate analysis performed in the publication "<strong>The genomic landscape of recurrent ovarian high grade serous carcinoma: the BriTROC-1 study</strong>" (<a href="https://doi.org/10.1038/s41467-023-39867-7">Smith & Bradley et al. 2023</a>).</p>
Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant
<p><span>Crop wild relatives possess desirable traits that confer resilience to various environmental stresses. We applied landscape genomics, that associates environment with genomic variation to understand the genetic basis of their adaptation. <br></span></p> <p> </p> <p><span>In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hotspot of these wild relatives. Further, we explored the correlation between the genetic variations and the bio-climatic and soil conditions at their collection sites.</span></p> <p> </p> <p><span><span>Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected also candidate SNPs associated with ten environmental factors. Some of these SNPs signal genes involved in pathways that help with adaptation to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. </span><br></span></p>
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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.