Molecular Ecology最新文献

{"title":"Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch","authors":"María-Eugenia López,&nbsp;Mikhail Ozerov,&nbsp;Lilian Pukk,&nbsp;Kristina Noreikiene,&nbsp;Riho Gross,&nbsp;Anti Vasemägi","doi":"10.1111/mec.17659","DOIUrl":"10.1111/mec.17659","url":null,"abstract":"<p>How genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free-living species still lack a comprehensive understanding of the primary molecular mechanisms of adaptation. Here, we characterised the targets of selection associated with drastically different aquatic environments—humic and clear water—in the common freshwater fish, Eurasian perch (<i>Perca fluviatilis</i>). By using whole-genome sequencing (WGS) on a large population dataset (<i>n</i> = 42 populations) and analysing 873,788 SNPs, our primary aim was to uncover novel and confirm known footprints of selection. We compared individual and pooled WGS, and developed a novel approach, termed dynamic outlier slicing, to assess how the choice of outlier-calling stringency influences functional and Gene Ontology (GO) enrichment. By integrating genome-environment association (GEA) analysis with allele frequency-based approaches, we estimated composite selection signals (CSS) and identified 2679 outlier SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic outlier slicing identified robust enrichment signals in five annotation categories (upstream, downstream, synonymous, 5′UTR and 3′UTR) highlighting the crucial role of regulatory elements in adaptive evolution. Furthermore, GO analyses revealed strong enrichment of molecular functions associated with gated channel activity, transmembrane transporter activity and ion channel activity, emphasising the importance of osmoregulation and ion balance maintenance. Our findings demonstrate that despite substantial random drift and divergence, WGS of high number of population pools enabled the identification of strong selection signals associated with adaptation to both humic and clear water environments, providing robust evidence of widespread adaptation. We anticipate that the dynamic outlier slicing method we developed will enable a more thorough exploration of adaptive divergence across a diverse range of species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17659","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Swatting Flies: Biting Insects as Non-Invasive Samplers for Mammalian Population Genomics.","authors":"Anubhab Khan, Ryan Carter, Chengetai D Mpamhanga, Daniel Masiga, Manun Channumsin, Marc Ciosi, Oliva Manangwa, Furaha Mramba, Umer Zeeshan Ijaz, Harriet Auty, Barbara K Mable","doi":"10.1111/mec.17661","DOIUrl":"https://doi.org/10.1111/mec.17661","url":null,"abstract":"<p><p>Advances in next-generation sequencing have allowed the use of DNA obtained from unusual sources for wildlife studies. However, these samples have been used predominantly to sequence mitochondrial DNA for species identification while population genetics analyses have been rare. Since next-generation sequencing allows indiscriminate detection of all DNA fragments in a sample, technically it should be possible to sequence whole genomes of animals from environmental samples. Here we used a blood-feeding insect, tsetse fly, to target whole genome sequences of wild animals. Using pools of flies, we compared the ability to recover genomic data from hosts using the short-read sequencing (Illumina) and adaptive sampling of long-read data generated using Oxford nanopore technology (ONT). We found that most of the short-read data (85%-99%) was dominated by tsetse fly DNA and that adaptive sampling on the ONT platform did not substantially reduce this proportion. However, once tsetse reads were removed, the remaining data for both platforms tended to belong to the dominant host expected in the tsetse fly blood meal. Reads mapping to elephants, warthogs and giraffes were recovered more reliably than for buffalo, and there was high variance in the contribution of DNA by individual flies to the pools, suggesting that there are host specific biases. For elephants, using short-read sequencing we were able to identify over 300,000 unfiltered SNPs, which we used to estimate the allele frequencies and expected heterozygosity for the population. Overall, our results show that at least for certain wild mammals, it is possible to recover genome-wide host data from blood-feeding insects.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17661"},"PeriodicalIF":4.5,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circumpolar Population Structure, Diversity and Recent Evolutionary History of the Bearded Seal in Relation to Past and Present Icescapes","authors":"Morgan L. McCarthy,&nbsp;Alba Refoyo Martínez,&nbsp;Steven H. Ferguson,&nbsp;Aqqalu Rosing-Asvid,&nbsp;Rune Dietz,&nbsp;Binia De Cahsan,&nbsp;Lennart Schreiber,&nbsp;Eline D. Lorenzen,&nbsp;Rikke Guldborg Hansen,&nbsp;Raphaela Stimmelmayr,&nbsp;Anna Bryan,&nbsp;Lori Quakenbush,&nbsp;Christian Lydersen,&nbsp;Kit M. Kovacs,&nbsp;Morten Tange Olsen","doi":"10.1111/mec.17643","DOIUrl":"10.1111/mec.17643","url":null,"abstract":"<p>The Arctic environment plays a critical role in the global climate system and marine biodiversity. The region's ice-covered expanses provide essential breeding and feeding grounds for a diverse assemblage of marine species, who have adapted to thrive in these harsh conditions and consequently are under threat from global warming. The bearded seal (<i>Erignathus barbatus</i>), including two subspecies (<i>E. barbatus nauticus—</i>Pacific and <i>E. barbatus barbatus</i>—Atlantic), is an ice-obligate Arctic species using sea ice for many aspects of its life history, rendering it particularly vulnerable to sea ice loss. It is one of the least studied and hence enigmatic of the Arctic marine mammals, with little knowledge regarding genetic structure, diversity, adaptations, and demographic history, consequently hampering management and conservation efforts. Here, we sequenced 70 whole nuclear genomes from across most of the species' circumpolar range, finding significant genetic structure between the Pacific and the Atlantic subspecies, which diverged during the Penultimate Glacial Period (~200 KYA). Remarkably, we found fine-scale genetic structure within both subspecies, with at least two distinct populations in the Pacific and three in the Atlantic. We hypothesise sea-ice dynamics and bathymetry had a prominent role in shaping bearded seal genetic structure and diversity. Our analyses of highly differentiated genomic regions can be used to complement the health, physiological, and behavioural research needed to conserve this species. In addition, we provide recommendations for management units that can be used to more specifically assess climatic and anthropogenic impacts on bearded seal populations.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.17643","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population Genomics Reveals Local Adaptation Related to Temperature Variation in Two Stream Frog Species: Implications for Vulnerability to Climate Warming.","authors":"Brenna R Forester, Amanda S Cicchino, Alisha A Shah, Austin B Mudd, Eric C Anderson, Jessen V Bredeson, Andrew J Crawford, Jason B Dunham, Cameron K Ghalambor, Erin L Landguth, Brent W Murray, Daniel Rokhsar, W Chris Funk","doi":"10.1111/mec.17651","DOIUrl":"10.1111/mec.17651","url":null,"abstract":"<p><p>Identifying populations at highest risk from climate change is a critical component of conservation efforts. However, vulnerability assessments are usually applied at the species level, even though intraspecific variation in exposure, sensitivity and adaptive capacity play a crucial role in determining vulnerability. Genomic data can inform intraspecific vulnerability by identifying signatures of local adaptation that reflect population-level variation in sensitivity and adaptive capacity. Here, we address the question of local adaptation to temperature and the genetic basis of thermal tolerance in two stream frogs (Ascaphus truei and A. montanus). Building on previous physiological and temperature data, we used whole-genome resequencing of tadpoles from four sites spanning temperature gradients in each species to test for signatures of local adaptation. To support these analyses, we developed the first annotated reference genome for A. truei. We then expanded the geographic scope of our analysis using targeted capture at an additional 11 sites per species. We found evidence of local adaptation to temperature based on physiological and genomic data in A. montanus and genomic data in A. truei, suggesting similar levels of sensitivity (i.e., susceptibility) among populations regardless of stream temperature. However, invariant thermal tolerances across temperatures in A. truei suggest that populations occupying warmer streams may be most sensitive. We identified high levels of evolutionary potential in both species based on genomic and physiological data. While further integration of these data is needed to comprehensively evaluate spatial variation in vulnerability, this work illustrates the value of genomics in identifying spatial patterns of climate change vulnerability.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17651"},"PeriodicalIF":4.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host Specificity and Geographic Dispersion Shape Virome Diversity in Rhinolophus Bats","authors":"Daxi Wang,&nbsp;Linmiao Li,&nbsp;Zirui Ren,&nbsp;Yepin Yu,&nbsp;Zhipeng Zhang,&nbsp;Jiabin Zhou,&nbsp;Hailong Zhao,&nbsp;Zhiwen Zhao,&nbsp;Peibo Shi,&nbsp;Xinrui Mi,&nbsp;Xin Jin,&nbsp;Ziqing Deng,&nbsp;Junhua Li,&nbsp;Jinping Chen","doi":"10.1111/mec.17645","DOIUrl":"10.1111/mec.17645","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Rhinolophus</i> bats have been identified as natural reservoirs for viruses with global health implications, including severe acute respiratory syndrome–related coronaviruses (SARSr-CoV) and swine acute diarrhoea syndrome-related coronavirus (SADSr-CoV). In this study, we characterised the individual viromes of 603 bats to systematically investigate the diversity, abundance and geographic distribution of viral communities within <i>R. affinis</i>, <i>R. sinicus</i> and 11 other bat species. The massive metatranscriptomic data revealed substantial viral genome resources of 133 vertebrate-infecting viral clusters, which contain occasional cross-species transmission across mammalian orders and especially across bat families. Notably, those viruses included nine clusters closely related to human and/or livestock pathogens, such as SARS-CoVs and SADS-CoVs. The investigation also highlighted distinct features of viral diversity between and within bat colonies, which appear to be influenced by the distinct host population genetics of <i>R. affinis</i> and <i>R. sinicus</i> species. The comparison of SARSr-CoVs further showed varied impact of host specificity along genome-wide diversification and modular viral evolution among <i>Rhinolophus</i> species. Overall, the findings point to a complex interaction between host genetic diversity, and the way viruses spread and structure within natural populations, calling for continued surveillance efforts to understand factors driving viral transmission and emergence in human populations. These results present the underestimated spillover risk of bat viruses, highlighting the importance of enhancing preparedness and surveillance for emerging zoonotic viruses.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seascape Genomics of Red Abalone: Limited Range-Wide Population Structure and Evidence for Local Adaptation","authors":"Joanna S. Griffiths,&nbsp;Kendall Smith,&nbsp;Andrew Whitehead","doi":"10.1111/mec.17650","DOIUrl":"10.1111/mec.17650","url":null,"abstract":"<div>\u0000 \u0000 <p>Characterising patterns of genetic diversity including evidence of local adaptation is relevant for predicting and managing species recovering from overexploitation in the face of climate change. Red abalone (<i>Haliotis rufescens</i>) is a species of conservation concern due to recent declines from overharvesting, disease and climate change, resulting in the closure of commercial and recreational fisheries. Using whole-genome resequencing data from 23 populations spanning their entire range (southern Oregon, USA, to Baja California, MEX) we investigated patterns of population connectivity and genotype-environment associations that would reveal local adaptation across the mosaic of coastal environments that define the California Current System (CCS). We discovered high genetic diversity that is shared within and among populations, suggesting high historical range-wide gene flow. We found little evidence for large selective sweeps between populations that occupy local habitats that vary by pH, strength of upwelling, chlorophyll, salinity and sea surface temperature. This is consistent with a broad range of species with similar life histories that show limited neutral or adaptive genetic variation across the same region and the same environments, suggesting that the mosaic of environmental variation across the CCS is insufficient to drive local adaptation in the face of high gene flow for some broad-cast spawning species. Given the high genetic connectivity across their range, state-mandated regulatory actions would be most effective if aligned across jurisdictional boundaries (i.e., Mexico, California and Oregon).</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-Larva RNA Sequencing Reveals That Red Sea Urchin Larvae Are Vulnerable to Co-Occurring Ocean Acidification and Hypoxia","authors":"Tina Nguyen,&nbsp;Greg Pelletier,&nbsp;Nina Bednaršek,&nbsp;Andrew Gracey","doi":"10.1111/mec.17658","DOIUrl":"10.1111/mec.17658","url":null,"abstract":"<div>\u0000 \u0000 <p>Anthropogenic carbon dioxide emissions have been increasing rapidly in recent years, driving pH and oxygen levels to record low concentrations in the oceans. Eastern boundary upwelling systems such as the California Current System (CCS) experience exacerbated ocean acidification and hypoxia (OAH) due to the physical and chemical properties of the transported deeper waters. Research efforts have significantly increased in recent years to investigate the deleterious effects of climate change on marine species, but have not focused on the impacts of simultaneous OAH stressor exposure. Additionally, few studies have explored the physiological impacts of these environmental stressors on the earliest life stages, which are more vulnerable and represent natural population bottlenecks in organismal life cycles. The physiological response of the ecologically and commercially important red sea urchin (<i>Mesocentrotus franciscanus</i>) was assessed by exposing larvae to a variety of OAH conditions, mimicking the range of ecologically relevant conditions encountered currently and in the near future along the CCS. Skeleton dissolution, larval development, and gene expression show a response with clearly delineated thresholds that were related to OAH severity. Skeletal dissolution and the induction of <i>Acid-sensing Ion Channel 1A</i> at pH 7.94/5.70 DO mg/L provide particularly sensitive markers of OAH, with dramatic shifts in larval morphology and gene expression detected at the pH/DO transition of 7.71/3.71–7.27/2.72 mg/L. Experimental simulations that describe physiological thresholds and establish molecular markers of OAH exposure will provide fishery management with the tools to predict patterns of larval recruitment and forecast population dynamics.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Locally Specific Genome-Wide Signatures of Adaptation to Environmental Variation at High Resolution in an Alpine Plant","authors":"Aude Rogivue,&nbsp;Kevin Leempoel,&nbsp;Annie S. Guillaume,&nbsp;Rimjhim Roy Choudhury,&nbsp;François Felber,&nbsp;Michel Kasser,&nbsp;Stéphane Joost,&nbsp;Christian Parisod,&nbsp;Felix Gugerli","doi":"10.1111/mec.17646","DOIUrl":"10.1111/mec.17646","url":null,"abstract":"<div>\u0000 \u0000 <p>Microevolutionary processes shape adaptive responses to heterogeneous environments, where these effects vary both among and within species. However, it remains largely unknown to which degree signatures of adaptation to environmental drivers can be detected based on the choice of spatial scale and genomic marker. We studied signatures of local adaptation across two levels of spatial extents, investigating complementary types of genomic variants—single-nucleotide polymorphisms (SNPs) and polymorphic transposable elements (TEs)—in populations of the alpine model plant species <i>Arabis alpina</i> . We coupled environmental factors, derived from remote sensed digital elevation models (DEMs) at very high resolution (0.5 m), with whole-genome sequencing data of 304 individuals across four populations. By comparing putatively adaptive loci detected between each local population versus a regional assessment including all populations simultaneously, we demonstrate that responses of <i>A. alpina</i> to similar amounts of abiotic variation are largely governed by local evolutionary processes. Furthermore, we find minimally overlapping signatures of local adaptation between SNPs and polymorphic TEs. Notably, functional annotations of candidate genes for adaptation revealed several symbiosis-related genes associated with the abiotic factors studied, which could represent selective pressures from biotic agents. Our results highlight the importance of considering different spatial extents and types of genomic polymorphisms when searching for signatures of adaptation to environmental variation. Such insights provide key information on microevolutionary processes and could guide management decisions to mitigate negative impacts of climate change on alpine plant populations.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 4","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142996914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Domestication During Restoration: Unintentional Selection During Eight Generations of Wild Seed Propagation Reduces Herkogamy, Dichogamy and Heterozygosity in Clarkia pulchella.","authors":"Julie R Etterson, Paige Fliehr, Riley Pizza, Briana L Gross","doi":"10.1111/mec.17655","DOIUrl":"https://doi.org/10.1111/mec.17655","url":null,"abstract":"<p><p>Seed production on native seed farms has increased to meet the rising demand for plant material for restoration. Although these propagation efforts are necessary for restoration, cultivating wild populations may also result in unintentional selection and elicit evolutionary changes that mimic crop domestication, essentially turning these efforts into artificial domestication experiments. Here, we investigated whether phenotypic and genomic changes associated with domestication occurred in the wildflower Clarkia pulchella Pursh (Onagraceae) by comparing the wild source populations to the farmed population after eight generations of cultivation. At the phenotypic level, the farmed population shifted towards a floral morphology associated with self-pollination, with a significant decrease in both dichogamy and herkogamy. At the genomic level, > 6500 SNPs revealed that mean expected heterozygosity of the farmed population was significantly lower than the wild populations, despite the fact that the farmed population originated from a pool of multiple wild populations. Both the shift towards a selfing phenotype and the loss of diversity are expected consequences of domestication, although the phenotypic shifts in particular occurred much more rapidly than has been observed for other domestication traits. We discuss these results in the context of plant domestication and the implications for retaining the genetic integrity of wild populations during the process of seed production for restoration.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17655"},"PeriodicalIF":4.5,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental Variation Influences Genome Evolution in Hispaniolan Trunk Anoles (Anolis distichus)","authors":"Tanner C. Myers,&nbsp;Pietro L. H. de Mello,&nbsp;Paul M. Hime,&nbsp;Richard E. Glor","doi":"10.1111/mec.17622","DOIUrl":"10.1111/mec.17622","url":null,"abstract":"<div>\u0000 \u0000 <p>Environmental variation often drives evolutionary processes like population differentiation, local adaptation and speciation. We used genome-scale data to investigate the contribution of environmental variation to evolution of the North Caribbean bark anole (<i>Anolis distichus</i>), a widespread common lizard that exhibits impressive phenotypic variation across varying habitats on the island of Hispaniola. We obtained new double-digest restriction-associated DNA sequence data (ddRADseq) from nearly 200 individuals and used 53 GIS data layers representing a range of environmental variables. We first asked how environmental variation has contributed to genome-wide differentiation across Hispaniola. We found that Hispaniola's three major mountain ranges contribute to deep genome-wide divergence and patterns of migration, that some deeply genomically divergent populations occupy significantly different environments, and that environmental variation is broadly capable of explaining more range-wide genomic differentiation than geographic distance alone. We then asked whether specific loci exhibit evidence of local adaptation to environmental variation using genotype-environment association (GEA) methods. We initially identified hundreds of loci broadly distributed across the genome that are significantly correlated with one or more environmental variables, but ultimately found that fewer than 100 of these candidate loci are shared across different GEA methods applied to our entire dataset, and that only 10 candidate loci are shared by independent analyses of two regional subsets of our dataset, suggesting parallel evolution is infrequent. Our study shows that abiotic environmental variation has played a critical role in explaining the evolution and diversity of a widespread and phenotypically diverse Caribbean anole species.</p>\u0000 </div>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":"34 3","pages":""},"PeriodicalIF":4.5,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}