从全基因组序列数据推断两种衰退海鸭的种群历史和近亲繁殖情况

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
María I. Cádiz, Aja Noersgaard Buur Tengstedt, Iben Hove Sørensen, Emma Skindbjerg Pedersen, Anthony David Fox, Michael M. Hansen
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引用次数: 0

摘要

人类活动的影响已经从威胁已经稀少的物种过渡到导致曾经数量众多的生物显著减少。长尾鸭(Clangula hyemalis)和绒凫(Melanitta fusca)曾是欧洲西北部重要的采石海鸭物种,但最近的衰退导致它们在世界自然保护联盟红色名录中被重新归类为易危物种。我们对这两个物种的基因组进行了测序和组装,并对每个物种的 15 个个体进行了重新测序。通过基于位点频谱和序列马尔可夫聚合的分析,我们发现C. hyemalis表现出更大的历史人口稳定性,而M. fusca则尤其受到末次(魏希尔世)冰川期的影响。这可能反映了C. hyemalis在整个北极地区持续繁殖,冰川周期主要是将繁殖区向南或向北转移,而不会导致种群数量大幅下降,而M. fusca在南部的分布范围较为有限,在冰川时期会导致其分布范围大幅收缩。这两个物种在过去数千年中都有数量下降的迹象,这可能反映了人类活动的压力,而最近的下降则表明这一过程加速了。对同源性(ROH)的分析表明,近亲繁殖的程度很低,但并不严重,C. hyemalis 的近亲繁殖率从 0.012 到 0.063 不等,M. fusca 的近亲繁殖率从 0 到 0.047 不等。ROH的长度表明,这是由于持续的背景近亲繁殖造成的,而不是最近的衰退。总体而言,尽管在人口统计上出现了重要的下降,但这尚未导致严重的近亲繁殖和遗传侵蚀,最紧迫的保护问题可能是密度依赖(Allee)效应的风险。我们建议使用 ROH 分析法对近亲繁殖进行监测,以此作为跟踪未来发展的一种具有成本效益的方法,以支持对这些物种的有效保护。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data

Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data

Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with FROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.

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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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