Genomic data for Australian, Little and Forest Ravens

Genomic data supporting the publication: \nAnna M. Kearns, Alex Drew, Lynn P. Pedler, Maya Penck, Stephen Donnellan and Leo Joseph. Unexpected hybridization and limited population structure uncovers perplexing taxonomic issues in the Australian, Little, and Forest Ravens. in prep.\n\nAbstract:\nHybridization is common across the tree of life, and signals of introgression can be found in the genomes of birds world-wide. However, it is not always easy to differentiate between alternative evolutionary histories from genomic data. Here we use reduced representation sequencing to test hypotheses concerning the taxonomy and evolutionary history of a recently diverged lineage of ravens endemic to Australia. We find clear support for current species boundaries separating the Australian Corvus coronoides, Little C. mellori and Forest C. tasmanicus Ravens. Unexpectedly, however, we find genomic evidence for hybridization between C. mellori and C. coronoides in south-eastern Australia. Our data reject the hypothesis based on similar flocking behaviour, morphometrics, plumage and vocalisations that suggest the western subspecies of the Australian Raven C. c. perplexus may be sister to C. mellori. Instead, we find that C. c. perplexus is nested among other populations of C. coronoides, which themselves show little population structuring across the near continent-wide range of the species. Our genomic data reject the hypothesis that C. c. perplexus and C. c. coronoides are distinct species. Whether subspecies are warranted within C. coronoides depends on resolution of the significance of two critical sampling gaps and whether isolation-by-distance or historical allopatry and secondary contact best explain population structure. Our study highlights the diversity of biogeographic signals for widespread birds in Australia, the identification challenges existing among phenotypically similar species that also hybridise and the critical evolutionary insights that can be gained from historical museum specimens.\nLineage: Tissues of Australian (Corvus coronoides), Little (C. mellori) and Forest (C. tasmanicus) Ravens from ANWC, SAMA and MV were submitted to DArT for reduced representation sequencing using the DArTseq pipeline. Raw data were aligned by DArT to the Corvus moneduloides reference genome (GCF_009650955.1; bCorMon1) and genotyped using their bioinformatics pipeline. Raw data were also aligned by AMK to the Corvus coronoides reference mitogenome (NC_035877.1) to obtain bycatch mtDNA reads. \n\nThis collection contains:\n1. Raw fastq sequences for all samples\n2. Genotyped datasets from DArT\n3. MtDNA alignments

支持本出版物的基因组数据：
Anna M. Kearns、Alex Drew、Lynn P. Pedler、Maya Penck、Stephen Donnellan及Leo Joseph。《澳大利亚渡鸦、小渡鸦与森林渡鸦中意外的杂交现象及有限的种群结构揭示了令人困惑的分类学问题》（待发表）

摘要：
杂交现象在整个生命树中普遍存在，且全球鸟类基因组中均能检测到基因渗入（introgression）的信号。然而，从基因组数据中区分不同的进化历史并非总是易事。本研究采用简化基因组测序（reduced representation sequencing）技术，对澳大利亚特有的一个近期分化的渡鸦谱系（lineage）的分类学（taxonomy）及进化历史相关假说进行验证。研究结果明确支持当前划分澳大利亚渡鸦（Corvus coronoides）、小渡鸦（C. mellori）与森林渡鸦（C. tasmanicus）的物种界限（species boundaries）。但意外的是，我们在澳大利亚东南部发现了C. mellori与C. coronoides之间杂交的基因组证据。基于相似的集群行为（flocking behaviour）、形态测量学（morphometrics）特征、羽色（plumage）及鸣声（vocalisations）提出的假说认为，澳大利亚渡鸦的西部亚种C. c. perplexus可能是C. mellori的姊妹类群，而本研究数据不支持这一假说。相反，我们发现C. c. perplexus嵌套（nested）于C. coronoides的其他种群中，而C. coronoides自身在其近乎覆盖整个大陆的分布范围内几乎无种群结构（population structuring）。我们的基因组数据驳斥了C. c. perplexus与C. c. coronoides为不同物种的假说。C. coronoides内部是否应划分亚种，取决于两个关键采样缺口的意义是否明确，以及距离隔离（isolation-by-distance）或历史异域分布（historical allopatry）与二次接触（secondary contact）哪种模式能更好地解释其种群结构。本研究凸显了澳大利亚广布鸟类生物地理信号（biogeographic signals）的多样性、表型相似且存在杂交的物种间的鉴定挑战，以及从历史博物馆标本中可获取的重要进化洞见。
谱系：
来自ANWC、SAMA和MV的澳大利亚渡鸦（Corvus coronoides）、小渡鸦（C. mellori）与森林渡鸦（C. tasmanicus）组织样本被提交至DArT，采用DArTseq流程进行简化基因组测序。DArT将原始数据比对至新喀里多尼亚渡鸦（Corvus moneduloides）参考基因组（GCF_009650955.1；bCorMon1），并利用其生物信息学流程进行基因分型。AMK还将原始数据比对至澳大利亚渡鸦参考线粒体基因组（NC_035877.1），以获取附带捕获的线粒体DNA reads。

本数据集包含：
1. 所有样本的原始fastq序列
2. DArT提供的基因分型数据集
3. 线粒体DNA比对结果