Deep genome‐wide phylogeographic structure indicates cryptic diversity in the Middle Spotted Woodpecker (Dendrocoptes medius)

Deep phylogeographic structure in mitochondrial DNA not reflected in morphological variation has been uncovered in a number of species over the past few decades. However, inferred phylogeographic structure based solely on mitochondrial DNA can be misleading and might not reflect the true history of evolutionary lineages. Consequently, such cases should be further investigated based on genome‐wide data. One of these examples is provided by the Middle Spotted Woodpecker Dendrocoptes medius, a non‐migratory habitat specialist associated with old deciduous forests of the Western Palaearctic. It displays strong genetic divergence in mitochondrial DNA between Asian and European populations despite there being only slight variation in morphology between them. Here, we found a clear genomic divergence between Asian and European populations that is consistent with mitochondrial divergence patterns. As revealed by isolation by distance analyses, this differentiation in two lineages was not merely..., , , # Deep genome-wide phylogeographic structure indicates cryptic diversity in the middle spotted woodpecker Dendrocoptes medius

[https://doi.org/10.5061/dryad.m905qfv2z](https://doi.org/10.5061/dryad.m905qfv2z)

## Description of the data and file structure

Beagle format file of filtered SNPs

The file Woodpecker57_Maf0.01_GL2.beagle.gz contains the filtered SNPs from the GBS dataset of 57 middle spotted woodpecker individuals. SNPs were called and genotyped using angsd with filetering parameters: a maximum p-value of 10−3 for being variable, a minimum mapping quality of 20, a minimum base quality score of 20, a minimum total read depth of 120, a minimum individual read depth of 5 and a minimum minor allele frequency of 0.01 (-SNP_pval 1e-3 -minQ 20 -minMapQ 20 -setMinDepth 120 -geno_minDepth 5 -minMaf 0.01).

近数十年来，学界已在多个物种中发现，线粒体DNA（mitochondrial DNA）所呈现的深层系统发育结构（phylogeographic structure），并未在形态变异中得到体现。然而，仅基于线粒体DNA推断的系统发育结构可能存在误导性，无法反映演化支系（evolutionary lineages）的真实历史。因此，此类案例应借助全基因组数据（genome-wide data）开展进一步研究。其中一个典型案例即为中斑啄木鸟（Middle Spotted Woodpecker，学名*Dendrocoptes medius*）——这是一种非迁徙性的生境特化物种，依赖西古北界的老旧落叶林生存。该物种的亚洲与欧洲种群在线粒体DNA上存在显著遗传分化，但二者间的形态差异却十分微弱。本研究中，我们发现亚洲与欧洲种群间存在清晰的基因组分化，这与线粒体分化模式相一致。通过距离隔离分析（isolation by distance analyses）可知，这两个支系的分化并非仅仅……

# 全基因组系统发育结构揭示中斑啄木鸟（*Dendrocoptes medius*）的隐存多样性

[https://doi.org/10.5061/dryad.m905qfv2z](https://doi.org/10.5061/dryad.m905qfv2z)

## 数据与文件结构说明
本数据集包含经过滤的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的Beagle格式（Beagle format）文件。
文件`Woodpecker57_Maf0.01_GL2.beagle.gz`包含了57只中斑啄木鸟个体的基因组简化测序（Genotyping-by-Sequencing, GBS）数据集所筛选出的SNP。SNP的识别与基因型分型通过angsd软件完成，筛选参数如下：变异检测的最大P值为10⁻³，最低比对质量值为20，最低碱基质量值为20，总测序深度下限为120，单个体测序深度下限为5，最小次要等位基因频率为0.01（对应参数：-SNP_pval 1e-3 -minQ 20 -minMapQ 20 -setMinDepth 120 -geno_minDepth 5 -minMaf 0.01）。