Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utilit...
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ftdoajarticles:oai:doaj.org/article:32ee9b1740ea4f07944976d57fa68056 2023-10-01T03:59:02+02:00 Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event Kevin Winker Travis C. Glenn Brant C. Faircloth 2018-10-01T00:00:00Z https://doi.org/10.7717/peerj.5735 https://doaj.org/article/32ee9b1740ea4f07944976d57fa68056 EN eng PeerJ Inc. https://peerj.com/articles/5735.pdf https://peerj.com/articles/5735/ https://doaj.org/toc/2167-8359 doi:10.7717/peerj.5735 2167-8359 https://doaj.org/article/32ee9b1740ea4f07944976d57fa68056 PeerJ, Vol 6, p e5735 (2018) Conserved loci Genome sampling Speciation Passeriformes Plectrophenax Medicine R article 2018 ftdoajarticles https://doi.org/10.7717/peerj.5735 2023-09-03T00:45:45Z Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths. Article in Journal/Newspaper Plectrophenax nivalis Directory of Open Access Journals: DOAJ Articles Kya ENVELOPE(8.308,8.308,63.772,63.772) PeerJ 6 e5735 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Conserved loci Genome sampling Speciation Passeriformes Plectrophenax Medicine R |
spellingShingle |
Conserved loci Genome sampling Speciation Passeriformes Plectrophenax Medicine R Kevin Winker Travis C. Glenn Brant C. Faircloth Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event |
topic_facet |
Conserved loci Genome sampling Speciation Passeriformes Plectrophenax Medicine R |
description |
Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths. |
format |
Article in Journal/Newspaper |
author |
Kevin Winker Travis C. Glenn Brant C. Faircloth |
author_facet |
Kevin Winker Travis C. Glenn Brant C. Faircloth |
author_sort |
Kevin Winker |
title |
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event |
title_short |
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event |
title_full |
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event |
title_fullStr |
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event |
title_full_unstemmed |
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event |
title_sort |
ultraconserved elements (uces) illuminate the population genomics of a recent, high-latitude avian speciation event |
publisher |
PeerJ Inc. |
publishDate |
2018 |
url |
https://doi.org/10.7717/peerj.5735 https://doaj.org/article/32ee9b1740ea4f07944976d57fa68056 |
long_lat |
ENVELOPE(8.308,8.308,63.772,63.772) |
geographic |
Kya |
geographic_facet |
Kya |
genre |
Plectrophenax nivalis |
genre_facet |
Plectrophenax nivalis |
op_source |
PeerJ, Vol 6, p e5735 (2018) |
op_relation |
https://peerj.com/articles/5735.pdf https://peerj.com/articles/5735/ https://doaj.org/toc/2167-8359 doi:10.7717/peerj.5735 2167-8359 https://doaj.org/article/32ee9b1740ea4f07944976d57fa68056 |
op_doi |
https://doi.org/10.7717/peerj.5735 |
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PeerJ |
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6 |
container_start_page |
e5735 |
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1778532464161980416 |