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The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evol...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200822/ https://www.ncbi.nlm.nih.gov/pubmed/30356056 http://dx.doi.org/10.1038/s41598-018-33646-x |
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author | Liu, Yang Liu, Simin Yeh, Chia-Fen Zhang, Nan Chen, Guoling Que, Pinjia Dong, Lu Li, Shou-hsien |
author_facet | Liu, Yang Liu, Simin Yeh, Chia-Fen Zhang, Nan Chen, Guoling Que, Pinjia Dong, Lu Li, Shou-hsien |
author_sort | Liu, Yang |
collection | PubMed |
description | Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics. |
format | Online Article Text |
id | pubmed-6200822 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-62008222018-10-26 The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies Liu, Yang Liu, Simin Yeh, Chia-Fen Zhang, Nan Chen, Guoling Que, Pinjia Dong, Lu Li, Shou-hsien Sci Rep Article Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics. Nature Publishing Group UK 2018-10-24 /pmc/articles/PMC6200822/ /pubmed/30356056 http://dx.doi.org/10.1038/s41598-018-33646-x Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Liu, Yang Liu, Simin Yeh, Chia-Fen Zhang, Nan Chen, Guoling Que, Pinjia Dong, Lu Li, Shou-hsien The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
title | The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
title_full | The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
title_fullStr | The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
title_full_unstemmed | The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
title_short | The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
title_sort | first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200822/ https://www.ncbi.nlm.nih.gov/pubmed/30356056 http://dx.doi.org/10.1038/s41598-018-33646-x |
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