Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes

Extreme environments serve as natural laboratories for studying evolutionary processes, with caves offering replicated instances of independent colonisations. The timing, mode, and genetic underpinnings underlying cave-obligate organismal evolution remain enigmatic. We integrate phylogenomics, fossils, paleoclimatic modeling, and newly sequenced genomes to elucidate the evolutionary history and adaptive processes of cave colonisation in the study group, the North American Amblyopsidae fishes. Amblyopsid fishes present a unique system for investigating cave evolution, encompassing surface, facultative cave-dwelling, and cave-obligate (troglomorphic) species. Using 1,105 exon markers and total-evidence dating, we reconstructed a robust phylogeny that supports the nested position of eyed, facultative cave-dwelling species within blind cavefishes. We identified three independent cave colonisations, dated to the Early Miocene (18.5 Mya), Late Miocene (10.0 Mya), and Pliocene (3.0 Mya). Evolu..., We performed short-read shotgun genome sequencing on Percopsiformes fishes, then harvested exons using Hughes et al. (2018) FishLifeExonHarvesting pipeline. Exon markers were used to create a phylogeny, then extinct fossil taxa were added as tips in the phylogeny to time-calibrate the tree. , , # Ancient climate changes drive mode and tempo of cave colonization in North American cavefishes

[https://doi.org/10.5061/dryad.3bk3j9ktx](https://doi.org/10.5061/dryad.3bk3j9ktx)

## Description of the data and file structure

The dataset contains the aligned exons (fasta format) harvested from whole genome resequencing data for the dataset in Hart et al. (in review). Also included is the coding scheme for the morphological matrix used to incorporate fossil Percopsiformes taxa into the total-evidence divergence analyses.

### Folders, Files, and variables

#### File: Percopsiformes\_exons\_NT\_Concatenated\_alignments.fasta

**Description:** All exons harvested from whole genome resequencing data for all specimens aligned.

#### File: Percopsiformes\_fossil\_coding.csv

**Description:** Coding of fossil taxa into the morphological matrix from Armbruster et al. (2016).

##### Variables

* Fossil_Taxa
* Order
* Family
* Morphological characters from Armbruster et al. (2016)

#### File: ...,