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Front Genet. 2019 Nov 8;10:919. doi: 10.3389/fgene.2019.00919. eCollection 2019.

Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds.

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State Key Laboratory of Biocontrol, Department of Ecology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.
Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China.
Department of Bioinformatics, Shenzhen Realomics Biological Technology Ltd, Shenzhen, China.
School of Biosciences, University of Melbourne, Parkville, VIC, Australia.
Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.


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 behavior, 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.


gene flow; natural selection; population genomics; shorebirds; speciation

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