Data from: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

  • Simin Liu (Contributor)
  • Shou-Hsien Li (Contributor)
  • Pinjia Que (Contributor)
  • Simin Liu (Contributor)
  • Nan Zhang (Contributor)
  • Lu Dong (Contributor)
  • Yang Liu (Contributor)
  • Yang Liu (Contributor)
  • Pinjia Que (Contributor)
  • Nan Zhang (Contributor)
  • Guoling Chen (Contributor)
  • Lu Dong (Contributor)
  • Chia Fen Yeh (Contributor)
  • Guoling Chen (Contributor)

Dataset

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.,alignments of universal nuclear protein-coding loci and Perl script for BLAST1. Alignment of 48species at 65genes; 2. Alignment of the four populations of Kentish Plover at 19 genes; 3. Partition of 48species at 65 genes; 4. Partition of the four populations of Kentish Plover at 19 genes; 5.Perl Script for BLASTDRYAD_NPCL_Data.zip,
Date made available2018 Dec 1
PublisherUnknown Publisher

Cite this