基因组多样性作为一项关键的保护标准:哺乳动物全基因组重测序数据的概念验证

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
Jong Yoon Jeon, Andrew N. Black, Erangi J. Heenkenda, Andrew J. Mularo, Gina F. Lamka, Safia Janjua, Anna Brüniche-Olsen, John W. Bickham, Janna R. Willoughby, J. Andrew DeWoody
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引用次数: 0

摘要

许多国际、国家、州和地方组织都会对受威胁和濒危物种进行优先排序,以帮助指导保护工作。例如,世界自然保护联盟(IUCN)评估了物种的绿色状态,并发布了具有影响力的濒危物种红色名录。遗憾的是,这些保护标准并没有明确考虑遗传或基因组多样性(GD),尽管GD与当代进化适应性、个体生存能力和未来进化潜力呈正相关。为了检验基因组序列群是否有助于改进保护评估,我们从 82 个公开的哺乳动物数据集中估算了 GD 指标,并考察了它们与保护相关属性的统计学关联。我们还考虑了可能影响 GD 的内在生物因素,包括营养水平和体重,并量化了它们的相对影响。我们的研究结果确定了反映和预测世界自然保护联盟保护类别的关键种群广东十一选五指标。具体来说,我们的分析表明,沃特森θ(种群突变率)和自交系(近亲繁殖的产物)与当前的红色名录分类相关,这可能是因为导致 "列入 "决定的人口减少也降低了常存遗传变异的水平。我们认为,由于这种关系,世界自然保护联盟等保护组织可以利用新出现的基因组序列数据来帮助划分红色名录的威胁等级(尤其是数据不足的物种)和/或加强绿色状态评估,为未来的种群监测建立基线。因此,我们的论文(1)概述了基于绿色状态的新评估标准的理论和实证依据;(2)提供了一个生物信息学管道,用于从种群基因组数据中估算绿色状态;(3)提出了一个分析框架,可用于测量基线绿色状态,同时提供量化的绿色状态背景,供保护机构考虑。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Genomic Diversity as a Key Conservation Criterion: Proof-of-Concept From Mammalian Whole-Genome Resequencing Data

Genomic Diversity as a Key Conservation Criterion: Proof-of-Concept From Mammalian Whole-Genome Resequencing Data

Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to “listing” decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.

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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
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.
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