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

By Yang Liu, Simin Liu, Chia-Fen Yeh, Nan Zhang, Guoling Chen, Pinjia Que, Lu Dong, Shou-hsien Li

Posted 27 Feb 2018
bioRxiv DOI: 10.1101/272732 (published DOI: 10.1038/s41598-018-33646-x)

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 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 (polymerase chain reaction) 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 using touch-down PCR (TD-PCR). The sixty-two 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 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 could be consistently amplified in the Kentish plover and 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.

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