Genomic and geographic diversification of a “great-speciator” (Rhipidura rufifrons)

The radiation of so-called “great speciators” represents a paradox among the myriad avian radiations endemic to the southwest Pacific. In such radiations, lineages otherwise capable of dispersing across vast distances of open ocean differentiate rapidly and frequently across relatively short geographic barriers. Here, we evaluate the phylogeography of the Rufous Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no formal investigations across its range have been performed. Moreover, the delimitation of lineages within R. rufifrons, and the biogeographic implications of those relationships remain unresolved. To investigate whether R. rufifrons represents a great speciator, we identified thousands of single-nucleotide polymorphisms for 89 individuals, representing 19 described taxa. Analyses recovered seven divergent lineages and evidence of gene flow between geographically isolated populations. We also found plumage differences to be a poor proxy for evolutionary..., The following line is the only processing that has occurred for these data and was completed within the STACKS2 pipeline
process_radtags -p ./raw_manthey-data/ -b ./barcodes_key -o ./stacks_manthey/ -i gzfastq -e ndeI -c -q -r -E phred33, , # Genomic and geographic diversification of a “great-speciator” (Rhipidura rufifrons)

Dataset DOI: [10.5061/dryad.1jwstqjxx](10.5061/dryad.1jwstqjxx)

## Description of the data and file structure

#### File name: Rhip_ruf_fq-files.zip

These data were generated by the authors of the \"Genomic and geographic diversification of a great-speciator (*Rhipidura rufifrons*)\" project.

The .fq file names all include the museum accession number, and additional information for each sample can be found in Table 2 of the manuscript.

These data were generated from a single digest RAD-seq protocol (Miller et al. 2007). The raw reads have only undergone the process_radtags (demultiplexing) command within the STACKS 2 pipeline.

process_radtags -p ./input_file_location/ -b ./barcode_key_file -o ./output_directory/ -i gzfastq -e ndeI -c -q -r -E phred33

Museum Codes: KUNHM–University of Kansas Natural History Museum, AMNH-American Museum of Natural History, ANWC–Australian National Wildlife Collectio...,

所谓"快速成种类群"（great speciators）的辐射演化，在西南太平洋特有的众多鸟类辐射演化类群中构成了一个悖论。在这类辐射演化中，原本具备跨开阔大洋长距离扩散能力的支系，却会在相对较短的地理屏障之间快速且频繁地发生分化。
本研究以棕尾扇尾鹟（Rhipidura rufifrons）为研究对象，解析其系统地理学格局。尽管该物种被推测为"快速成种类群"，但此前尚未在其完整分布范围内开展过正式的系统性研究。此外，棕尾扇尾鹟种内支系的界定方案，以及这些支系关系所蕴含的生物地理学意义，至今仍未得到明确解决。
为验证棕尾扇尾鹟是否属于快速成种类群，本研究对覆盖19个已描述分类单元的89个个体进行了单核苷酸多态性（single-nucleotide polymorphisms, SNP）分型，共获得数千个有效SNP位点。分析结果共鉴定出7个分化显著的支系，并发现地理隔离种群间存在基因流的证据。同时本研究还发现，羽色差异并不能很好地作为演化进程的替代指标……
以下为该数据集唯一经过的生物信息学处理流程，已在STACKS2软件分析管道中完成：process_radtags -p ./raw_manthey-data/ -b ./barcodes_key -o ./stacks_manthey/ -i gzfastq -e ndeI -c -q -r -E phred33。# 《"快速成种类群"（棕尾扇尾鹟，Rhipidura rufifrons）的基因组与地理分化》

数据集DOI：10.5061/dryad.1jwstqjxx

## 数据与文件结构说明

### 文件名：Rhip_ruf_fq-files.zip
本数据集由《"快速成种类群"（棕尾扇尾鹟，Rhipidura rufifrons）的基因组与地理分化》研究项目的作者团队构建。所有.fq格式文件的文件名均包含标本馆藏编号，各样本的详细补充信息可参见论文的表2。
本数据集采用单酶切限制性酶切位点相关DNA测序（RAD-seq）建库方案（Miller等，2007）生成。原始测序读段仅经过STACKS2软件管道中的process_radtags命令（用于样本解复用）处理，具体命令如下：
process_radtags -p ./input_file_location/ -b ./barcode_key_file -o ./output_directory/ -i gzfastq -e ndeI -c -q -r -E phred33

馆藏机构代码：KUNHM——堪萨斯大学自然历史博物馆，AMNH——美国自然历史博物馆，ANWC——澳大利亚国家野生动物标本馆……