Divergent selection in low recombination regions shapes the genomic islands in two incipient shorebird species

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 id..., , , # 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 < 2.0 || FS > 60.0 || MQ <40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 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 |
| :--------- | :----------------- | :--------------- | :---------------- | :---------------...