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...