Museum genomics reveals the hybrid origin of an extinct crater lake endemic

Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine li..., , , # Museum genomics reveals the hybrid origin of an extinct crater lake endemic

[https://doi.org/10.5061/dryad.bk3j9kdjw](https://doi.org/10.5061/dryad.bk3j9kdjw)

This dataset contains the DArT and silicoDArT files used in the analyses described in Tims et al. (2024), as well as a file allocating each specimen to a population and sampling location. The .pdf document containing supplementary figures, tables and discussion is also available here

## Description of the data and file structure

astral_silicodarts_FINAL.csv and FDA_silicodarts_FINAL.csv are silicoDArT files, which can be read into R using the 'gl.read.silicodart' function in the dartR package. astral_silicodarts_FINAL.csv contains the silicodart data used to construct input trees for ASTRAL. FDA_silicodarts_FINAL.csv is the filtered dataset used to identify unique variants within different populations. Cells marked \"-\" correspond to missing data.

unfiltered_snp_data_FINAL.csv is a DArT file, which can be read into R using t...

火山口湖鱼类是常见的演化模型系统，近期研究表明基因流在推动快速适应与物种形成过程中发挥关键作用。然而，针对这些年轻火山口湖的研究常会因人类活动介导的物种灭绝而变得复杂。因此，整合近期灭绝物种遗传数据的博物馆基因组学方法，对于解析这些脆弱生态系统的复杂演化历史至关重要。本研究聚焦一种已灭绝的南半球火山口湖特有物种——彩虹鱼（Melanotaenia eachamensis）的演化历史。我们对澳大利亚阿瑟顿台地现存的彩虹鱼种群进行了全面采样，并结合历史博物馆馆藏标本，旨在探明该灭绝火山口湖种群的演化起源，以及整个生态区内的基因流动态。该灭绝火山口湖物种因两个邻近河流类群间的历史基因渐渗，在遗传上与所有其他邻近种群均存在显著分化……
# 博物馆基因组学揭示已灭绝火山口湖特有物种的杂交起源
https://doi.org/10.5061/dryad.bk3j9kdjw

本数据集包含Tims等人（2024）研究中分析所用的DArT与silicoDArT文件，以及一份将每个标本分配至对应种群与采样位点的文件。包含补充图表、表格与讨论内容的PDF文档也可在此处获取。

## 数据与文件结构说明
astral_silicodarts_FINAL.csv与FDA_silicodarts_FINAL.csv为silicoDArT文件，可通过dartR包中的`gl.read.silicodart`函数读取至R环境中。astral_silicodarts_FINAL.csv包含用于构建ASTRAL分析输入树的silicoDArT数据。FDA_silicodarts_FINAL.csv为经过过滤的数据集，用于鉴定不同种群内的特有变异位点。标记为"-"的单元格代表缺失数据。

unfiltered_snp_data_FINAL.csv是DArT文件，可通过[...]读取至R环境中