Austin C. Koontz, Emily K. Schumacher, Emma S. Spence, Sean M. Hoban
{"title":"Ex situ conservation of two rare oak species using microsatellite and SNP markers","authors":"Austin C. Koontz, Emily K. Schumacher, Emma S. Spence, Sean M. Hoban","doi":"10.1111/eva.13650","DOIUrl":null,"url":null,"abstract":"<p>Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For <i>Quercus acerifolia</i>, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for <i>Q. boyntonii</i>. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13650","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Evolutionary Applications","FirstCategoryId":"99","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/eva.13650","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
Abstract
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
植物园和树木园收藏的植物是异地保护的重要组成部分。保持这些收藏的遗传多样性,可使它们成为补充野生种群的资源。然而,大多数为实现足够的异地遗传多样性而推荐的最小样本量都是基于微卫星标记,而这些样本量在最近开发的下一代测序(NGS)方法中是否仍然有效仍是未知数。为了填补这一知识空白,我们研究了两种濒危橡树物种的园林样本和野生样本中的微卫星和单核苷酸多态性(SNPs)得出的原生境保护状况和采样建议有何不同。与微卫星相比,SNPs 对野生等位基因多样性的原位代表性较低,最小样本量估计值也略低,而对 Q. boyntonii 而言,每种标记的结果基本相似。应用缺失数据过滤器往往会提高原位代表性,而不同 SNP 调用方法的影响则取决于所分析的物种。不同标记物对物种内种群分化的测量结果大致相似,但更多的 SNP 位点可提高种群结构的分辨率,并更清晰地将异地个体分配到野生源种群中。我们的研究结果为今后利用 SNP 数据进行异地保护评估提供了指导,例如缺失数据过滤器的应用和参考基因组的使用,并说明微卫星和 SNP 仍是植物园和树木园确保其收藏品遗传多样性的可行选择。
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.