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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00919

Demographic histories and genome-wide patterns of divergence in incipient species of shorebirds

Xuejing Wang1,  Kathryn H. Maher2, Nan Zhang1,  Pinjia Que3,  Chenqing Zheng1, Simin Liu1,  Biao Wang4, Qin Huang5, De Chen3, Xu Yang6, Zhengwang Zhang3,  Tamas Szekely2, Araxi Urrutia2* and  Yang Liu1*
  • 1Sun Yat-sen University, China
  • 2University of Bath, United Kingdom
  • 3Beijing Normal University, China
  • 4Shenzhen University, China
  • 5Sun Yat-Sen Memorial Hospital, China
  • 6Shenzhen Realomics Biological Technology Ltd., China

Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behaviour, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.

Keywords: speciation, Population Genomics, shorebirds, Gene Flow, natural selection

Received: 24 Feb 2019; Accepted: 30 Aug 2019.

Copyright: © 2019 Wang, Maher, Zhang, Que, Zheng, Liu, Wang, Huang, Chen, Yang, Zhang, Szekely, Urrutia and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Araxi Urrutia, University of Bath, Bath, BA2 7AY, South West England, United Kingdom, au207@bath.ac.uk
Dr. Yang Liu, Sun Yat-sen University, Guangzhou, 510275, Guangdong Province, China, yangliubnu@gmail.com