Geographic breaks and seascape features shape diversification in cryptobenthic reef fishes

Because ocean environments often lack clear barriers to dispersal, the limited mobility and strong habitat fidelity of cryptobenthic reef fishes make them ideal for uncovering spatial patterns of evolutionary divergence in the marine realm. We conducted a comparative phylogeographic study of 23 of the 25 known species in the cryptobenthic fish genus Malacoctenus, integrating genome-wide SNPs from over 500 individuals, geometric morphometrics, and seascape data to assess the effectiveness of historical and contemporary marine barriers in the Tropical Eastern Pacific (TEP) and Greater Caribbean (GC). Population-level analyses across 14 species revealed generally well-structured populations with limited admixture, reinforcing the value of our study system for evaluating the efficacy and permeability of marine barriers. In the TEP, linear coastlines and broad sandy gaps, including the Sinaloan and Central American breaks and the open-ocean Galápagos break, consistently constrained connectiv..., , # Geographic breaks and seascape features shape diversification in cryptobenthic reef fishes

#### author: \"Carmen Pedraza\"

#### date: \"2025-08-12\"

# Repository Overview

This repository contains the SNP matrices and scripts used to conduct geometric morphometric, population genomic, seascape genomic, and phylogenetic analyses at the micro and macroevolutionary level.

demultiplexed PE ddRADseq data is available at NCBI [https://www.ncbi.nlm.nih.gov/](https://www.ncbi.nlm.nih.gov/) under the BioProject PRJNA1371759 (SRA accessions SAMN53515416-SAMN53515915).

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## 1. Microevolution

The **Microevolution.zip** directory includes datasets related to within-species evolutionary analyses.

### PopulationGenomics

* A folder containing one subdirectory per species that were sampled across various geographic locations.
* Each species subdirectory includes:
* **VCF files and population maps** used in downstream population genomic analyses.
-EESM-summary.R script used to calculate and pl...,