DOI: 10.5061/dryad.4f4qrfjjp
title: Divergent selection in low recombination regions shapes the genomic islands in two incipient shorebird species

description: Divergent selection in the face of gene flow is usually associated with a
 heterogeneous genomic landscape of divergence in nascent species pairs.
 However, multiple factors, such as divergent selection and local
 recombination rate variation, can influence the formation of these genomic
 island. This conundrum can be solved through examination of the genomic
 landscapes of species pairs that are still in the early stages of
 evolution. In this study, population genomics analyses were undertaken
 using a wide range of sampling and whole-genome resequencing data from 96
 unrelated individuals of Kentish plover (Charadrius alexandrinus) and
 white-faced plover (C. dealbatus). We suggest that the two species exhibit
 varying levels of population admixture along the Chinese coast and on
 Taiwan Island. Genome-wide analyses for introgression indicate that
 ancient introgression had occurred in Taiwan population, and recurrent
 gene flow is still ongoing in mainland coastal populations. Furthermore,
 we identified a few genomic regions with significant levels of
 interspecific differentiation and local recombination suppression, which
 contain several genes potentially associated with disease resistance,
 coloration, and regulation of plumage moulting, thus may be connected to
 the phenotypic and ecological divergence of the two nascent species.
 Overall, our findings suggest that divergent selection in low
 recombination regions may be the main force in shaping the genomic islands
 in two incipient shorebird species.
description: # Divergent selection in low recombination regions shapes the genomic
 islands in two incipient shorebird species [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.4f4qrfjjp) This dataset contains SNPs
 from whole-genome sequencing of 104 individuals, including 101 individuals
 from mainland China and Taiwan Island and 3 individuals from Azores
 Islands used as outgroup in the study. ## Data description ### Filter
 arguments The vcf has been filtered twice, first with GATK (4.1.4.1) using
 arguments "QD &lt; 2.0 || FS &gt; 60.0 || MQ &lt;40.0 || MQRankSum
 &lt; -12.5 || ReadPosRankSum &lt; -8.0 || SOR &gt; 3.0" and contains
 sites with “PASS” flag only, then with VCFtools (0.1.17) using augments
 "--minDP 3 --maf 0.05 --min-meanDP 3 --max-missing 0.5". ###
 Sampling sites and sample group | Individual | Species | Sequencing depth
 | Sampling location | Geographical group | Sex | | :--------- |
 :----------------- | :--------------- | :---------------- |
 :----------------- | :-- | | LYG-1 | Kentish Plover | 5× | Lianyungang |
 Coastal KP | M | | LYG-2 | Kentish Plover | 5× | Lianyungang | Coastal KP
 | M | | RD-1 | Kentish Plover | 5× | Rudong | Coastal KP | M | | RD-2 |
 Kentish Plover | 5× | Rudong | Coastal KP | M | | ZS-1 | Kentish Plover |
 15× | Zhoushan | Coastal KP | M | | ZS-2 | Kentish Plover | 15× | Zhoushan
 | Coastal KP | M | | ZS-3 | Kentish Plover | 15× | Zhoushan | Coastal KP |
 F | | ZS-4 | Kentish Plover | 30× | Zhoushan | Coastal KP | M | | ZS-5 |
 Kentish Plover | 15× | Zhoushan | Coastal KP | M | | ZS-6 | Kentish Plover
 | 15× | Zhoushan | Coastal KP | F | | ZS-7 | Kentish Plover | 30× |
 Zhoushan | Coastal KP | F | | TS-1 | Kentish Plover | 5× | Tangshan |
 Coastal KP | M | | TS-2 | Kentish Plover | 5× | Tangshan | Coastal KP | M
 | | QH-1 | Kentish Plover | 5× | Qinghai | Inland KP | M | | QH-2 |
 Kentish Plover | 5× | Qinghai | Inland KP | M | | QH-3 | Kentish Plover |
 5× | Qinghai | Inland KP | M | | QH-4 | Kentish Plover | 5× | Qinghai |
 Inland KP | M | | QH-5 | Kentish Plover | 5× | Qinghai | Inland KP | M | |
 QH-6 | Kentish Plover | 15× | Qinghai | Inland KP | F | | QH-7 | Kentish
 Plover | 15× | Qinghai | Inland KP | M | | QH-8 | Kentish Plover | 15× |
 Qinghai | Inland KP | F | | QH-9 | Kentish Plover | 15× | Qinghai | Inland
 KP | F | | QH-10 | Kentish Plover | 15× | Qinghai | Inland KP | M | |
 QH-11 | Kentish Plover | 15× | Qinghai | Inland KP | F | | QH-12 | Kentish
 Plover | 30× | Qinghai | Inland KP | F | | TW-1 | Kentish Plover | 5× |
 Taiwan | Taiwan KP | M | | TW-2 | Kentish Plover | 5× | Taiwan | Taiwan KP
 | M | | TW-3 | Kentish Plover | 5× | Taiwan | Taiwan KP | M | | TW-4 |
 Kentish Plover | 5× | Taiwan | Taiwan KP | F | | TW-5 | Kentish Plover |
 5× | Taiwan | Taiwan KP | M | | TW-6 | Kentish Plover | 15× | Taiwan |
 Taiwan KP | M | | TW-7 | Kentish Plover | 15× | Taiwan | Taiwan KP | F | |
 TW-8 | Kentish Plover | 15× | Taiwan | Taiwan KP | M | | TW-9 | Kentish
 Plover | 15× | Taiwan | Taiwan KP | M | | TW-10 | Kentish Plover | 15× |
 Taiwan | Taiwan KP | F | | TW-11 | Kentish Plover | 15× | Taiwan | Taiwan
 KP | F | | TW-12 | Kentish Plover | 15× | Taiwan | Taiwan KP | F | | TW-13
 | Kentish Plover | 15× | Taiwan | Taiwan KP | F | | TW-14 | Kentish Plover
 | 15× | Taiwan | Taiwan KP | F | | XJ-1 | Kentish Plover | 5× | Xinjiang |
 Inland KP | M | | XJ-2 | Kentish Plover | 5× | Xinjiang | Inland KP | F |
 | XJ-3 | Kentish Plover | 5× | Xinjiang | Inland KP | M | | XJ-4 | Kentish
 Plover | 5× | Xinjiang | Inland KP | M | | XJ-5 | Kentish Plover | 5× |
 Xinjiang | Inland KP | F | | XJ-6 | Kentish Plover | 5× | Xinjiang |
 Inland KP | M | | XJ-7 | Kentish Plover | 15× | Xinjiang | Inland KP | F |
 | XJ-8 | Kentish Plover | 15× | Xinjiang | Inland KP | F | | XJ-9 |
 Kentish Plover | 15× | Xinjiang | Inland KP | M | | CZ-1 | Kentish Plover
 | 15× | Cangzhou | Coastal KP | M | | CZ-2 | Kentish Plover | 15× |
 Cangzhou | Coastal KP | M | | CZ-3 | Kentish Plover | 15× | Cangzhou |
 Coastal KP | M | | CZ-4 | Kentish Plover | 15× | Cangzhou | Coastal KP | F
 | | CZ-5 | Kentish Plover | 15× | Cangzhou | Coastal KP | M | | CZ-6 |
 Kentish Plover | 15× | Cangzhou | Coastal KP | F | | CZ-7 | Kentish Plover
 | 15× | Cangzhou | Coastal KP | F | | CZ-8 | Kentish Plover | 15× |
 Cangzhou | Coastal KP | F | | CZ-9 | Kentish Plover | 15× | Cangzhou |
 Coastal KP | F | | CZ-10 | Kentish Plover | 15× | Cangzhou | Coastal KP |
 F | | BH-1 | White-faced Plover | 5× | Beihai | WFP | M | | BH-2 |
 White-faced Plover | 5× | Beihai | WFP | M | | SW-1 | White-faced Plover |
 5× | Shanwei | Contact zone WFP | M | | SW-2 | White-faced Plover | 5× |
 Shanwei | Contact zone WFP | M | | XM-1 | White-faced Plover | 5× | Xiamen
 | Contact zone WFP | M | | XM-2 | White-faced Plover | 15× | Xiamen |
 Contact zone WFP | F | | XM-3 | White-faced Plover | 30× | Xiamen |
 Contact zone WFP | F | | XM-4 | White-faced Plover | 15× | Xiamen |
 Contact zone WFP | F | | XM-5 | White-faced Plover | 15× | Xiamen |
 Contact zone WFP | M | | XM-6 | White-faced Plover | 15× | Xiamen |
 Contact zone WFP | F | | XM-7 | White-faced Plover | 15× | Xiamen |
 Contact zone WFP | F | | FZ-1 | White-faced Plover | 15× | Fuzhou |
 Contact zone WFP | M | | FZ-2 | White-faced Plover | 15× | Fuzhou |
 Contact zone WFP | M | | FZ-3 | White-faced Plover | 15× | Fuzhou |
 Contact zone WFP | F | | FZ-4 | White-faced Plover | 30× | Fuzhou |
 Contact zone WFP | F | | ZJ-1 | White-faced Plover | 5× | Zhanjiang | WFP
 | M | | ZJ-2 | White-faced Plover | 5× | Zhanjiang | WFP | M | | ZJ-3 |
 White-faced Plover | 15× | Zhanjiang | WFP | F | | ZJ-4 | White-faced
 Plover | 15× | Zhanjiang | WFP | M | | ZJ-5 | White-faced Plover | 15× |
 Zhanjiang | WFP | M | | ZJ-6 | White-faced Plover | 15× | Zhanjiang | WFP
 | M | | ZJ-7 | White-faced Plover | 15× | Zhanjiang | WFP | M | | ZJ-8 |
 White-faced Plover | 15× | Zhanjiang | WFP | F | | ZJ-9 | White-faced
 Plover | 15× | Zhanjiang | WFP | M | | ZJ-10 | White-faced Plover | 15× |
 Zhanjiang | WFP | F | | ZJ-11 | White-faced Plover | 30× | Zhanjiang | WFP
 | F | | ZJ-12 | White-faced Plover | 15× | Zhanjiang | WFP | F | | ZJ-13 |
 White-faced Plover | 15× | Zhanjiang | WFP | F | | HN-1 | White-faced
 Plover | 5× | Hainan | WFP | M | | HN-2 | White-faced Plover | 15× |
 Hainan | WFP | M | | HN-3 | White-faced Plover | 15× | Hainan | WFP | F |
 | HN-4 | White-faced Plover | 15× | Hainan | WFP | M | | HN-5 |
 White-faced Plover | 15× | Hainan | WFP | M | | HN-6 | White-faced Plover
 | 15× | Hainan | WFP | F | | HN-7 | White-faced Plover | 15× | Hainan |
 WFP | M | | HN-8 | White-faced Plover | 15× | Hainan | WFP | F | | HN-9 |
 White-faced Plover | 15× | Hainan | WFP | M | | HN-10 | White-faced Plover
 | 15× | Hainan | WFP | F | | HN-11 | White-faced Plover | 15× | Hainan |
 WFP | F | | HN-12 | White-faced Plover | 15× | Hainan | WFP | F | | HN-13
 | White-faced Plover | 15× | Hainan | WFP | M | | HN-14 | White-faced
 Plover | 15× | Hainan | WFP | F | | HN-15 | White-faced Plover | 15× |
 Hainan | WFP | F | ## Sharing/Access information This dataset contains
 samples that have been used in previous study: [Wang X, Maher K H, Zhang
 N, et al. Demographic histories and genome-wide patterns of divergence in
 incipient species of shorebirds\[J\]. Frontiers in Genetics, 2019, 10:
 919.](https://doi.org/10.3389/fgene.2019.00919)