Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using from ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis)., We extracted DNA from 40 samples of snowfinches from all eight species of the three genera (Montifringilla, Onychostruthus, and Pyrgilauda) and one further sample of the rock sparrow, Petronia petronia. All samples were either frozen blood or tissue samples preserved in ethanol or preserving buffer except two toe pad samples taken from two historical specimens of the Afghan snowfinch, P. theresae. We generated whole mitochondrial genomes for this species and representatives from the two other snowfinch genera using specific protocols for museum material. To complete a previous single-marker data set, we amplified a 1079-bp-long cytochrome-b fragment for 19 samples using the primer combination of O-L14851/ O-H16065 primers.
For inference of a genome-wide SNP data set were used for double-digest restriction site associated DNA sequencing (ddRAD seq). DdRAD seq was performed at the Deep Sequencing Facility in the Center for Molecular and Cellular Bioengineering (CMCB) Dresden. We used Qubi..., , # Data from: Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)

[https://doi.org/10.5061/dryad.m905qfv9k](https://doi.org/10.5061/dryad.m905qfv9k)

This data package includes original data from: Islam, Safiqul et al. (2024). Data from: Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, *Montifringilla* and allies). Molecular Phylogenetics and Evolution, 198, 108135. [https://doi.org/10.1016/j.ympev.2024.108135](https://doi.org/10.1016/j.ympev.2024.108135 \"Persistent link using digital object identifier\")

The package comprises sequence alignments (all in FASTA format aligned with MEGA v 10.1.8) and selected Bayesian tree files for a data set of genome-wide single-nucleotide polymorphisms (SNPs) inferred from ddRAD sequencing of 40 individuals of snowfinches (genera *Montifringilla*, *Onychostruthus* and *Pyrgilauda*), plus one sample of the rock sparrow (*Petronia petronia*). Specimen metadata are provided in supple...

博物馆馆藏的历史标本可为科学家当前难以抵达的偏远地区或冲突区域提供宝贵的研究材料。本研究依托阿富汗特有物种阿富汗雪雀（Pyrgilauda theresae）的整皮历史DNA，构建了雪雀类群的完整分类学系统发育树。为解决此前不同系统发育假说间的显著冲突，我们为选定类群生成了全新的线粒体基因组序列，并通过双酶切限制性位点关联DNA测序（double-digest restriction site associated DNA sequencing, ddRAD-seq），获取了青藏高原（Qinghai-Tibet Plateau, QTP）所有现存特有雪雀物种的全基因组单核苷酸多态性（single-nucleotide polymorphisms, SNP）数据，同时对中欧与西古北界唯一的雪雀物种——白斑翅雪雀（Montifringilla nivalis）开展了扩大的种内采样。

我们从3个属（雪雀属*Montifringilla*、地雀属*Onychostruthus*、Pyrgilauda属）的全部8个雪雀物种的40份样本，以及1份石雀（*Petronia petronia*）样本中提取了DNA。除2份取自阿富汗雪雀（*P. theresae*）历史标本的趾垫样本外，其余所有样本均为冷冻血液或经乙醇/保存缓冲液固定的组织样本。我们针对博物馆标本开发了专属实验流程，为该物种以及另外两个雪雀属的代表类群构建了完整的线粒体基因组。为完善此前的单标记数据集，我们使用O-L14851/O-H16065引物组合，为19份样本扩增得到了长度为1079bp的细胞色素b基因片段。

本研究采用双酶切限制性位点关联DNA测序（ddRAD-seq）构建全基因组SNP数据集。ddRAD测序工作在德累斯顿分子与细胞生物工程中心（Center for Molecular and Cellular Bioengineering, CMCB）的深度测序设施中完成。我们使用了Qubi……

# 数据集来源：博物馆组学助力雪雀类群（鸟纲，雀科，雪雀属及其近缘类群）的系统发育解析

[https://doi.org/10.5061/dryad.m905qfv9k]

本数据包包含的原始数据来自：Islam, Safiqul 等（2024）。数据来自：博物馆组学助力雪雀类群（鸟纲，雀科，*Montifringilla* 及其近缘类群）的系统发育解析。《分子系统发育与进化》，198卷，108135期。[https://doi.org/10.1016/j.ympev.2024.108135 "基于数字对象标识符的永久链接"]

本数据包包含序列联配文件（均为使用MEGA v10.1.8完成比对的FASTA格式），以及针对40份雪雀样本（分属*Montifringilla*、*Onychostruthus*和*Pyrgilauda*属）、外加1份石雀（*Petronia petronia*）样本的ddRAD测序推断的全基因组SNP数据集的选定贝叶斯树文件。样本元数据详见补充材料……