DOI: 10.5061/dryad.bk3j9kdjw
title: Museum genomics reveals the hybrid origin of an extinct crater lake endemic

description: 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
 lineages, similar to other prominent crater lake speciation systems, but
 this historic gene flow has not been sufficient to induce a species flock.
 Our results suggest that museum genomics approaches can be successfully
 combined with extant sampling to unravel complex speciation dynamics
 involving recently extinct species.
description: # 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 the 'gl.read.dart' function in the dartR package. This dataset was filtered and then analysed using STRUCTURE and ADMIXTOOLS following the procedure described in the method section of Tims et al. (2024). Cells marked "-" correspond to missing data. pops_list_FINAL.csv is a .csv file containing the names of all samples, the populations to which they were assigned in STRUCTURE and ADMIXTOOLS analyses, the coordinates of the sampling location, and, where applicable, the site number to which they correspond in data tables and on maps in Tims et al. (2024).  Note: there is no population code associated with samples MEEmu.1 or MEEmu.2 (cells marked NA), and precise coordinates for the outgroup population (MTBlyth) are not available (cells marked NA). fig2_plotting_code.R is a commented R script containing custom functions and an example script to aid in recreating figures similar to Figure 2.  data_for_fig2.csv is a .csv file containing population structure and lat-lon information that was used to plot Figure 2.  This is included to aid in reproducing the example code in fig2_plotting_code.R