All data items for "Museomics sheds light on evolutionary diversity in a critically endangered cockatoo species from Wallacea"

Data items:VCF files containing the SNPs for 2 datasets: 1) <i>C. sulphurea </i>plus <i>C. galerita,</i> 2) <i>C. sulphurea, C. galerita</i> plus <i>C. sanguinea</i> (and corresponding namelists that indicates which sample the codes pertain to). Fasta files of alignments for mtDNA genes CytB, COI, ND2 for <i>C. sulphurea</i> subspecies and <i>C. galerita.</i>SFS files for <i>C. sulphurea</i> subspecies and other Cacatua species used to calculate <i>Da</i>Abstract:Accurate identification of evolutionarily significant units of rare and threatened organisms provides a foundation for effective management and conservation. Up to seven subspecies of the critically endangered Yellow-crested Cockatoo (Cacatua sulphurea) have been described, four of which were commonly recognised pre-2014. In the absence of genotypic data, C. sulphurea subspecies delimitation has been based on morphology, behaviour and biogeography. To clarify genetic relationships and shed light on the diversification of this parrot radiation, whole genomes were sequenced for 16 museum specimens, covering the geographic range of the proposed seven subspecies as well as one C. galerita galerita. Combined with four museum-derived wild Cacatua sequences from NCBI, the results indicate there are three distinct C. sulphurea subspecies clusters centred in different biogeographic subregions of Wallacea (Timor; Sumba; as well as the Sulawesi Region and the main Lesser Sunda chain), separated by shallow genetic distances (da&lt;0.148%). The results raise questions about the recent species-level elevation of the phenotypically most distinct subspecies, C. s. citrinocristata, and about the origins of C. s. abbotti, the only subspecies west of Wallace’s Line. Our analyses suggest C. s. abbotti is unlikely to be embedded within C. sulphurea, suggesting its origin on the remote Masalembu islands may be due to human translocation via historical trade routes. These genomic results inform the prioritisation and streamlining of conservation measures for the critically endangered C. sulphurea by identifying and delimiting likely conservation units.

数据内容：包含两个数据集单核苷酸多态性（Single Nucleotide Polymorphism, SNP）信息的VCF（Variant Call Format）文件：1）黄冠凤头鹦鹉（Cacatua sulphurea）与葵花凤头鹦鹉（Cacatua galerita）；2）黄冠凤头鹦鹉、葵花凤头鹦鹉以及红肛凤头鹦鹉（Cacatua sanguinea），附带对应的样本名称列表，用于指明编码对应的具体样本。针对黄冠凤头鹦鹉亚种与葵花凤头鹦鹉的线粒体DNA（mitochondrial DNA, mtDNA）基因CytB、COI、ND2的比对FASTA格式文件。用于计算遗传距离Da的黄冠凤头鹦鹉亚种及其他凤头鹦鹉属（Cacatua）物种的站点频率谱（Site Frequency Spectrum, SFS）文件。

摘要：精准识别珍稀濒危物种的进化显著单元（evolutionarily significant unit），可为有效开展管理与保护工作奠定基础。极危物种黄冠凤头鹦鹉（Cacatua sulphurea）曾被描述有多达7个亚种，其中4个亚种在2014年前被广泛认可。在缺乏基因型数据的情况下，黄冠凤头鹦鹉的亚种划分曾基于形态学、行为学与生物地理学特征。为阐明该鹦鹉类群的遗传关系并揭示其辐射分化历程，研究人员对覆盖已提出的全部7个亚种分布范围的16件博物馆标本以及1件葵花凤头鹦鹉指名亚种（Cacatua galerita galerita）样本开展了全基因组测序。结合从NCBI（National Center for Biotechnology Information）获取的4条博物馆馆藏野生凤头鹦鹉属物种序列，分析结果显示，黄冠凤头鹦鹉存在3个独立的亚种支系，分别以华莱士区的不同亚区域为分布核心：帝汶岛、松巴岛，以及苏拉威西区域与小巽他群岛主链，支系间的遗传分化程度极低（Da<0.148%）。该研究结果对近期将表型特征最显著的亚种C. s. citrinocristata提升为物种级分类单元的观点，以及仅分布于华莱士线以西的C. s. abbotti的起源问题提出了质疑。本研究分析表明，C. s. abbotti并不隶属于黄冠凤头鹦鹉，其起源于偏远的马萨伦布群岛，大概率是通过历史贸易路线经人类活动引入的。这些基因组学研究结果通过识别并界定潜在的保护单元，可为极危物种黄冠凤头鹦鹉的保护措施优先级制定与流程优化提供科学支撑。