{"title":"塔普蓝星(Amsonia tharpii)的保护基因组学评估,并与广布(A. longilora)和狭义特有(A. fugatei)同系物进行比较。","authors":"Dylan H. Cohen, Jeremie B. Fant, Krissa A. Skogen","doi":"10.1111/eva.13736","DOIUrl":null,"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":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11186748/pdf/","citationCount":"0","resultStr":"{\"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, Jeremie B. Fant, Krissa A. Skogen\",\"doi\":\"10.1111/eva.13736\",\"DOIUrl\":null,\"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\":null,\"pages\":null},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-06-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11186748/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Evolutionary Applications\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/eva.13736\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Evolutionary Applications","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/eva.13736","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
土地使用的变化和栖息地的破碎化是对生物多样性的威胁。可用栖息地的减少、隔离的增加以及种群内部的交配会导致近亲繁殖增加、遗传多样性降低和适应性变差。在这里,我们研究了两个稀有和濒危植物物种 Amsonia tharpii 和 A. fugatei 的遗传学,并将它们与广泛分布的同种 A. longiflora 进行了比较。我们还首次报告了杏属(Apocynaceae)的系统发育研究,包括 17 个类群中的 10 个类群和多个取样地点,以了解物种关系。我们使用双消化限制性位点相关 DNA 测序(ddRADseq)方法研究了每个物种的遗传多样性和基因流,并建立了最大似然系统发生。ddRADseq 数据被映射到参考基因组上,以分离出叶绿体和核标记,用于种群遗传分析。结果表明,所有三个物种的遗传多样性和近交率都很低。A.tharpii的叶绿体和核数据集高度结构化,而A. fugatei的叶绿体和核数据集没有结构化,A. longiflora的核数据缺乏结构化,但叶绿体数据没有结构化。系统发育结果表明,A. tharpii 与 A. fugatei 是不同的姐妹物种,它们与 A. longiflora 的亲缘关系较远。我们的研究结果表明,进化历史和当代生态过程在很大程度上影响了Amsonia的遗传多样性。有趣的是,我们发现在A. tharpii中,尽管授粉者是体型庞大的鹰蛾,它们能够远距离携带花粉,但A. tharpii中的遗传多样性结构仍然很明显,这表明在A. tharpii种群中观察到的遗传多样性结构是由其他因素造成的。由于 A. fugatei 的分布范围有限,因此需要为其制定保护计划。
Conservation genomics assessment of Tharp's bluestar (Amsonia tharpii) with comparisons to widespread (A. longilora) and narrowly endemic (A. fugatei) congeners
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, Amsonia tharpii and A. fugatei, and we compare them to a widespread congener A. longiflora. We also report the first phylogenetic study of the genus Amsonia (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 A. tharpii were highly structured, whereas they showed no structure for A. fugatei, while A. longiflora lacked structure for nuclear data but not chloroplast. Phylogenetic results revealed that A. tharpii is distinct and sister to A. fugatei, and together they are distantly related to A. longiflora. Our results demonstrated that evolutionary history and contemporary ecological processes largely influences genetic diversity within Amsonia. Interestingly, we show that in A. tharpii 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 A. tharpii populations. Conservation efforts should focus on protecting all of the A. tharpii populations, as they contain unique genetic diversity, and a protection plan for A. fugatei needs to be established due to its limited distribution.
期刊介绍:
Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.