Evolutionary Applications最新文献

{"title":"Integrating very high resolution environmental proxies in genotype–environment association studies","authors":"Annie S. Guillaume,&nbsp;Kevin Leempoel,&nbsp;Aude Rogivue,&nbsp;Felix Gugerli,&nbsp;Christian Parisod,&nbsp;Stéphane Joost","doi":"10.1111/eva.13737","DOIUrl":"10.1111/eva.13737","url":null,"abstract":"<p>Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype–environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant <i>Arabis alpina</i> L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 7","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and epigenetic differentiation in response to genomic selection for avian lay date","authors":"Melanie Lindner,&nbsp;Irene Verhagen,&nbsp;A. Christa Mateman,&nbsp;Kees van Oers,&nbsp;Veronika N. Laine,&nbsp;Marcel E. Visser","doi":"10.1111/eva.13703","DOIUrl":"10.1111/eva.13703","url":null,"abstract":"<p>Anthropogenic climate change has led to globally increasing temperatures at an unprecedented pace and, to persist, wild species have to adapt to their changing world. We, however, often fail to derive reliable predictions of species' adaptive potential. Genomic selection represents a powerful tool to investigate the adaptive potential of a species, but constitutes a ‘blind process’ with regard to the underlying genomic architecture of the relevant phenotypes. Here, we used great tit (<i>Parus major</i>) females from a genomic selection experiment for avian lay date to zoom into this blind process. We aimed to identify the genetic variants that responded to genomic selection and epigenetic variants that accompanied this response and, this way, might reflect heritable genetic variation at the epigenetic level. We applied whole genome bisulfite sequencing to blood samples of individual great tit females from the third generation of bidirectional genomic selection lines for early and late lay date. Genomic selection resulted in differences at both the genetic and epigenetic level. Genetic variants that showed signatures of selection were located within genes mostly linked to brain development and functioning, including <i>LOC107203824</i> (<i>SOX3</i>-like). SOX3 is a transcription factor that is required for normal hypothalamo-pituitary axis development and functioning, an essential part of the reproductive axis. As for epigenetic differentiation, the early selection line showed hypomethylation relative to the late selection line. Sites with differential DNA methylation were located in genes important for various biological processes, including gonadal functioning (e.g., MSTN and PIK3CB). Overall, genomic selection for avian lay date provided insights into where within the genome the heritable genetic variation for lay date, on which selection can operate, resides and indicates that some of this variation might be reflected by epigenetic variants.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 7","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of “invasion syndrome” in invasive goldenrod is not constrained by genetic trade-offs","authors":"Laura C. Rigby,&nbsp;Matthew D. Hall,&nbsp;Keyne Monro,&nbsp;Akane Uesugi","doi":"10.1111/eva.13734","DOIUrl":"10.1111/eva.13734","url":null,"abstract":"<p>A suite of plant traits is thought to make weed populations highly invasive, including vigorous growth and reproduction, superior competitive ability, and high dispersal ability. Using a breeding design and a common garden experiment, we tested whether such an “invasion syndrome” has evolved in an invasive range of <i>Solidago altissima</i>, and whether the evolution is likely to be genetically constrained. We found an overall shift in invasive phenotypes between native North American and invasive Japanese populations. The invasive populations were taller and produced more leaves, suggesting a superior ability to exploit limited resources. The populations also produced more allelopathic compounds that can suppress competitor growth. Finally, invasive populations produced more seeds, which are smaller and are released from a greater height, indicating a potential for superior dispersal ability than the native populations. Quantitative genetics analyses found a large amount of additive genetic variation in most focal traits across native and invasive populations, with no systematic differences in its magnitude between the ranges. Genetic covariances among three traits representing invasion strategies (leaf mass, polyacetylene concentration and seed size) were small. The R metric, which measures the effect of genetic covariances on the rate of adaptation, indicated that the covariance neither constrains nor accelerates concerted evolution of these traits. The results suggest that the invasion syndrome in <i>S. altissima</i> has evolved in the novel range due to ample additive genetic variation, and relatively free from genetic trade-offs.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 7","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11211922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine","authors":"Emily L. Cavill,&nbsp;Hernán E. Morales,&nbsp;Xin Sun,&nbsp;Michael V. Westbury,&nbsp;Cock van Oosterhout,&nbsp;Wilna Accouche,&nbsp;Anna Zora,&nbsp;Melissa J. Schulze,&nbsp;Nirmal Shah,&nbsp;Pierre-André Adam,&nbsp;M. de L. Brooke,&nbsp;Paul Sweet,&nbsp;Shyam Gopalakrishnan,&nbsp;M. Thomas P. Gilbert","doi":"10.1111/eva.13739","DOIUrl":"10.1111/eva.13739","url":null,"abstract":"<p>The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 7","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141464649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dominance of African racial ancestry in honey bee colonies of Mexico 30 years after the migration of hybrids from South America","authors":"María de Jesús Aguilar-Aguilar,&nbsp;Jorge Lobo,&nbsp;E. Jacob Cristóbal-Pérez,&nbsp;Francisco J. Balvino-Olvera,&nbsp;Gloria Ruiz-Guzmán,&nbsp;José Javier G. Quezada-Euán,&nbsp;Mauricio Quesada","doi":"10.1111/eva.13738","DOIUrl":"10.1111/eva.13738","url":null,"abstract":"<p>The Africanized honey bee, a hybrid of <i>Apis mellifera scutellata</i> from Africa with European subspecies, has been considered an invasive species and a problem for beekeeping. Africanized bees arrived in Mexico in 1986, 30 years after their accidental release in Brazil. Although government programs were implemented for its eradication, Africanized populations persist in Mexico, but precise information on the patterns of genetic introgression and racial ancestry is scarce. We determined maternal and parental racial ancestry of managed and feral honey bees across the five beekeeping regions of Mexico, using mitochondrial (mtDNA, COI-COII intergenic region) and nuclear markers (94 ancestrally informative SNPs), to assess the relationship between beekeeping management, beekeeping region, altitude, and latitude with the distribution of maternal and parental racial ancestry. Results revealed a predominantly African ancestry in the Mexican honey bees, but the proportion varied according to management, beekeeping regions, and latitude. The Mexican honey bees showed 31 haplotypes of four evolutionary lineages (<i>A</i>, <i>M</i>, <i>C</i>, and <i>O</i>). Managed honey bees had mitochondrial and nuclear higher proportions of European ancestry than feral honey bees, which had a higher proportion of African ancestry. Beekeeping regions of lower latitudes had higher proportions of African nuclear ancestry. Managed and feral honey bees showed differences in the proportion of maternal and nuclear racial ancestry. Managed honey bees from the Yucatan Peninsula and feral honey bees had a higher mtDNA than nuclear proportions of African ancestry. Managed honey bees, except those on the Yucatan Peninsula, had a higher nuclear than mtDNA proportion of African ancestry. Our study demonstrates that Africanized honey bee populations are genetically diverse and well established in Mexico, which highlights the limitations of management and government programs to contain the Africanization process and demands the incorporation of this lineage in any breeding program for sustainable beekeeping.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11196837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141449160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple introductions of divergent lineages and admixture conferred the high invasiveness in a widespread weed (Hypochaeris radicata)","authors":"Soo-Rang Lee,&nbsp;Tae-Young Choi,&nbsp;Dong-Chan Son","doi":"10.1111/eva.13740","DOIUrl":"https://doi.org/10.1111/eva.13740","url":null,"abstract":"<p>Biological invasion consists of spatially and temporally varying stages, accompanied by ecological and evolutionary changes. Understanding the genomics underlying invasion dynamics provides critical insights into the geographic sources and genetic diversity, contributing to successful invasions across space and time. Here, we used genomic data and model-based approaches to characterize the invasion dynamics of <i>Hypochaeris radicata</i> L., a noxious weed in Korea. Genetic diversity and assignment patterns were investigated using 3563 SNPs of 283 individuals sampled from 22 populations. We employed a coalescent-based simulation method to estimate demographic changes for each population and inferred colonization history using both phylogenetic and population genetic model-based approaches. Our data suggest that <i>H. radicata</i> has been repeatedly been introduced to Korea from multiple genetic sources within the last 50 years, experiencing weak population bottlenecks followed by subsequent population expansions. These findings highlight the potential for further range expansion, particularly in the presence of human-mediated dispersal. Our study represents the first population-level genomic research documenting the invasion dynamics of the successful worldwide invader, <i>H. radicata</i>, outside of Europe.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13740","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish","authors":"Katie M. Kobayashi,&nbsp;Rosealea M. Bond,&nbsp;Kerry Reid,&nbsp;J. Carlos Garza,&nbsp;Joseph D. Kiernan,&nbsp;Eric P. Palkovacs","doi":"10.1111/eva.13712","DOIUrl":"https://doi.org/10.1111/eva.13712","url":null,"abstract":"<p>Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here, we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead and resident rainbow trout (<i>Oncorhynchus mykiss</i>). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident <i>O. mykiss</i> populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep","authors":"Fuping Zhao,&nbsp;Rui Xie,&nbsp;Lingzhao Fang,&nbsp;Ruidong Xiang,&nbsp;Zehu Yuan,&nbsp;Yang Liu,&nbsp;Lixian Wang","doi":"10.1111/eva.13697","DOIUrl":"https://doi.org/10.1111/eva.13697","url":null,"abstract":"<p>As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed-specific traits subject to selection. Here, we conducted whole-genome resequencing on 206 Hu sheep individuals, each with an approximate 6-fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: <i>BMPR1B</i> and <i>GNRH2</i>, both of which have documented associations with fertility, and a HOXA gene cluster (<i>HOXA1</i>-<i>5</i>, <i>HOXA9</i>, <i>HOXA10</i>, <i>HOXA11</i> and <i>HOXA13</i>) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (<i>LAMTOR3</i>, <i>EEF1A2</i>), ear size (<i>HOXA1</i>, <i>KCNQ2</i>), fat tail formation (<i>HOXA10</i>, <i>HOXA11</i>), growth and development (<i>FAF1</i>, <i>CCNDBP1</i>, <i>GJB2</i>, <i>GJA3</i>), fat deposition (<i>ACOXL</i>, <i>JAZF1</i>, <i>HOXA3</i>, <i>HOXA4</i>, <i>HOXA5</i>, <i>EBF4</i>), immune (<i>UBR1</i>, <i>FASTKD5</i>) and feed intake (<i>DAPP1</i>, <i>RNF17</i>, <i>NPBWR2</i>). Our results offer novel insights into the genetic mechanisms underlying the selection of breed-specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13697","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What does effective population size tell us about loss of allelic variation?","authors":"Fred W. Allendorf,&nbsp;Ola Hössjer,&nbsp;Nils Ryman","doi":"10.1111/eva.13733","DOIUrl":"https://doi.org/10.1111/eva.13733","url":null,"abstract":"<p>There are two primary measures of the amount of genetic variation in a population at a locus: heterozygosity and the number of alleles. Effective population size (<i>N</i>_e) provides both an expectation of the amount of heterozygosity in a population at drift-mutation equilibrium and the rate of loss of heterozygosity because of genetic drift. In contrast, the number of alleles in a population at drift-mutation equilibrium is a function of both <i>N</i>_e and census size (<i>N</i>_C). In addition, populations with the same <i>N</i>_e can lose allelic variation at very different rates. Allelic variation is generally much more sensitive to bottlenecks than heterozygosity. Expressions used to adjust for the effects of violations of the ideal population on <i>N</i>_e do not provide good predictions of the loss of allelic variation. These effects are much greater for loci with many alleles, which are often important for adaptation. We show that there is a linear relationship between the reduction of <i>N</i>_C and the corresponding reduction of the expected number of alleles at drift-mutation equilibrium. This makes it possible to predict the expected effect of a bottleneck on allelic variation. Heterozygosity provides good estimates of the rate of adaptive change in the short-term, but allelic variation provides important information about long-term adaptive change. The guideline of long-term <i>N</i>_e being greater than 500 is often used as a primary genetic metric for evaluating conservation status. We recommend that this guideline be expanded to take into account allelic variation as well as heterozygosity.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13733","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conservation genomics assessment of Tharp's bluestar (Amsonia tharpii) with comparisons to widespread (A. longilora) and narrowly endemic (A. fugatei) congeners","authors":"Dylan H. Cohen,&nbsp;Jeremie B. Fant,&nbsp;Krissa A. Skogen","doi":"10.1111/eva.13736","DOIUrl":"10.1111/eva.13736","url":null,"abstract":"<p>Land-use change and habitat fragmentation are threats to biodiversity. The decrease in available habitat, increase in isolation, and mating within populations can lead to elevated inbreeding, lower genetic diversity, and poor fitness. Here we investigate the genetics of two rare and threatened plant species, <i>Amsonia tharpii</i> and <i>A. fugatei</i>, and we compare them to a widespread congener <i>A. longiflora</i>. We also report the first phylogenetic study of the genus <i>Amsonia</i> (Apocynaceae), including 10 of the 17 taxa and multiple sampling locations, to understand species relationships. We used a double digest restriction-site associated DNA sequencing (ddRADseq) approach to investigate the genetic diversity and gene flow of each species and to create a maximum likelihood phylogeny. The ddRADseq data was mapped to a reference genome to separate out the chloroplast and nuclear markers for population genetic analysis. Our results show that genetic diversity and inbreeding were low across all three species. The chloroplast and nuclear dataset in <i>A. tharpii</i> were highly structured, whereas they showed no structure for <i>A. fugatei</i>, while <i>A. longiflora</i> lacked structure for nuclear data but not chloroplast. Phylogenetic results revealed that <i>A. tharpii</i> is distinct and sister to <i>A. fugatei</i>, and together they are distantly related to <i>A. longiflora</i>. Our results demonstrated that evolutionary history and contemporary ecological processes largely influences genetic diversity within <i>Amsonia</i>. Interestingly, we show that in <i>A. tharpii</i> there was significant structure despite being pollinated by large, bodied hawkmoths that are known to be able to carry pollen long distances, suggesting that other factors are contributing to the structure observed among <i>A. tharpii</i> populations. Conservation efforts should focus on protecting all of the <i>A. tharpii</i> populations, as they contain unique genetic diversity, and a protection plan for <i>A. fugatei</i> needs to be established due to its limited distribution.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 6","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11186748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141430921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}