Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?

When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot’s pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot’s pipit populations, between subspecies across archipelag..., Whole genome data from six populations of Berthelot's pipit across the three archipelagos of their range in the North Atlantic. Resequencing data was generated by mapping Illumina HiSeq reads to a reference genome and calling variants using GATK HaplotypeCaller. 
Genomic landscapes of divergence where assessed using pairwise FST across different population comparisons across the geographic range of the species'. Peaks of divergence were then charaterised using a range of population genomic statistics to elucidate the evolutionary drivers of divergence in these regions. 
Individual-based simulations of genomic divergence, under neutral and selective processes, were then used to further understand the patterns detected in the empirical genomic datasets. , , # Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?

Claudia A. Martin, Eleanor C. Sheppard, Hisham Ali, Juan Carlos Illera, Alexander Suh, Lewis G. Spurgin and David S. Richardson
[https://doi.org/10.5061/dryad.1g1jwsv4b](https://doi.org/10.5061/dryad.1g1jwsv4b)

For any further queries please contact [[e-mail]](mailto:[e-mail]) /[e-mail]

## Data

#### Data obtained from published datasets

Original RAW reads for the Berthelot's pipit draft genome are not supplied here as they are already available through previously published data by Armstrong et al. 2018 under [https://doi.org/10.5061/dryad.9642b](https://doi.org/10.5061/dryad.9642b)

These files include \"Anthus_berthelotii_PS_816_genome.zip\"

This zip file contains a BLAST database of the draft Berthelot's pipit genome as described in the Supplementary Methods of Armstrong et al. 2018. This genome was sequenced from sample 816 from ...

当种群定居新环境时，它们可能面临新的选择压力（selection pressure），但也会因奠基者效应（founder effect）、种群规模小及种群间基因流（interpopulation gene flow）有限而遭受显著遗传漂变（genetic drift）。基因组学方法（genomic approach）使我们能够研究这些因素如何驱动分化（divergence），并区分中性效应（neutral effect）与特定基因座（specific locus）因选择产生的差异。

本研究利用全基因组重测序（whole-genome resequencing）（>22X覆盖度（coverage）），对贝氏鹨（Anthus berthelotii）——一种特有于北大西洋三大群岛的雀形目鸟类（passerine）、特有种（endemic）——的遗传多样性（genetic diversity）与分化模式展开调查。

该物种分布范围内的种群存在显著环境梯度（environmental gradients）（包括病原体压力（pathogen pressure）差异），使其成为研究适应（adaptation）及/或初始物种形成（incipient speciation）关键性状的理想系统。

首先，我们量化基因组分化（genomic divergence）在物种形成连续体（speciation continuum）中的累积模式，即贝氏鹨种群间、跨群岛亚种间的分化模式……本研究使用北大西洋三大群岛范围内六个贝氏鹨种群的全基因组数据（whole-genome data）。重测序数据通过将Illumina HiSeq测序读段（Illumina HiSeq reads）比对至参考基因组（reference genome），并利用GATK HaplotypeCaller进行变异检测（variant calling）获得。

通过对物种地理分布范围内不同种群进行成对FST分析（pairwise FST analysis），评估分化的基因组景观（genomic landscape of divergence）。随后利用一系列种群基因组统计量（population genomic statistics）表征分化峰值，以阐明这些区域分化的进化驱动因素（evolutionary drivers of divergence）。

随后，我们利用中性与选择过程（neutral and selective processes）下的基因组分化个体模拟（individual-based simulation of genomic divergence），进一步理解实证基因组数据集（empirical genomic datasets）中检测到的模式。

# 岛屿鸟类种群间分化的基因组景观：平行适应的证据，但位于不同基因座？

Claudia A. Martin, Eleanor C. Sheppard, Hisham Ali, Juan Carlos Illera, Alexander Suh, Lewis G. Spurgin and David S. Richardson
[https://doi.org/10.5061/dryad.1g1jwsv4b](https://doi.org/10.5061/dryad.1g1jwsv4b)

如有进一步疑问，请联系[[e-mail]](mailto:[e-mail]) /[e-mail]

## Data

#### 来自已发表数据集的数据（data obtained from published datasets）

贝氏鹨基因组草图的原始RAW读段（original RAW reads）未在此处提供，因其已通过Armstrong等人2018年发表的数据公开获取，链接为[https://doi.org/10.5061/dryad.9642b](https://doi.org/10.5061/dryad.9642b)

这些文件包括"Anthus_berthelotii_PS_816_genome.zip"

该压缩包包含贝氏鹨基因组草图的BLAST数据库（BLAST database），如Armstrong等人2018年的补充方法（Supplementary Methods）所述。该基因组由样本816测序获得，样本来自……