María I. Cádiz, Aja Noersgaard Buur Tengstedt, Iben Hove Sørensen, Emma Skindbjerg Pedersen, Anthony David Fox, Michael M. Hansen
{"title":"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","authors":"María I. Cádiz, Aja Noersgaard Buur Tengstedt, Iben Hove Sørensen, Emma Skindbjerg Pedersen, Anthony David Fox, Michael M. Hansen","doi":"10.1111/eva.70008","DOIUrl":null,"url":null,"abstract":"<p>Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (<i>Clangula hyemalis</i>) and velvet scoter (<i>Melanitta fusca</i>) 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 <i>C</i>. <i>hyemalis</i> to show more historical demographic stability, whereas <i>M. fusca</i> was affected particularly by the Last (Weichselian) Glaciation. This likely reflects <i>C</i>. <i>hyemalis</i> 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 <i>M. fusca</i> 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 <i>F</i><sub>ROH</sub> from 0.012 to 0.063 in <i>C</i>. <i>hyemalis</i> and ranging from 0 to 0.047 in <i>M. fusca</i>. 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.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70008","citationCount":"0","resultStr":"{\"title\":\"Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data\",\"authors\":\"María I. Cádiz, Aja Noersgaard Buur Tengstedt, Iben Hove Sørensen, Emma Skindbjerg Pedersen, Anthony David Fox, Michael M. Hansen\",\"doi\":\"10.1111/eva.70008\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (<i>Clangula hyemalis</i>) and velvet scoter (<i>Melanitta fusca</i>) 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 <i>C</i>. <i>hyemalis</i> to show more historical demographic stability, whereas <i>M. fusca</i> was affected particularly by the Last (Weichselian) Glaciation. This likely reflects <i>C</i>. <i>hyemalis</i> 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 <i>M. fusca</i> 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 <i>F</i><sub>ROH</sub> from 0.012 to 0.063 in <i>C</i>. <i>hyemalis</i> and ranging from 0 to 0.047 in <i>M. fusca</i>. 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.</p>\",\"PeriodicalId\":168,\"journal\":{\"name\":\"Evolutionary Applications\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70008\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Evolutionary Applications\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1111/eva.70008\",\"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.70008","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
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.
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.