DOI: 10.5061/dryad.d51c5b0gj
title: Data from: Geographic breaks and seascape features shape diversification in cryptobenthic reef fishes

description: 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 connectivity. In
 contrast, the GC exhibited more variable structure shaped by dynamic
 currents and a semi-enclosed geography with a mosaic of islands, with the
 strongest breaks across the Eastern Caribbean, Bahamas, and Gulf of
 Mexico. Seascape genomic analyses identified depth, temperature, and
 chlorophyll-α as key environmental drivers. Depth played a major role in
 TEP speciation, separating tide pool– and reef-associated clades.
 Phylogenomic analyses uncovered an early divergence (~23 Ma) linked to
 Isthmus uplift, followed by asynchronous transisthmian speciation in two
 clades (~5.2–7.6 Ma). Our results highlight the spatially
 variable roles of marine barriers and environmental features in the
 diversification of cryptobenthic reef fishes and marine organisms more
 broadly.
description: # 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). --- ##
 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 plot the summary of
 the estimated effective migration surfaces (EEMS) for all species. ## 2.
 Macroevolution The **Macroevolution.zip** directory contains vcf files and
 scripts used to investigate broad-scale evolutionary patterns across the
 genus *Malacoctenus*. This includes: * **ecoevolity**\ Configuration and
 data files used to test synchronic cladogenetic events with *ecoevolity*.
 * **PhylogeneticTrees**\ Estimated phylogenetic trees for *Malacoctenus*,
 representing macroevolutionary relationships among species. These include
 mtDNA and SNP data trees. * **TimeCalibration**\ Files and constrains used
 to time-calibrate a phylogenetic tree using 279 SNPs. --- --- ### 3.
 GeoMorpho_Malacoctenus.R * Script used to conduct geometric morphometric
 analyses, including error rate quantification. ## 3. SeascapeGenomics The
 **SeascapeGenomicsMalacoctenus.zip** directory contains files and datasets
 used to perform seascape genomic analyses at both **microevolutionary**
 and **macroevolutionary** scales. These analyses integrate genomic data
 with environmental and oceanographic variables across the: * **Tropical
 Eastern Pacific**, and * **Greater Caribbean**. This folder includes
 materials supporting statistical and spatial analyses aimed at
 understanding how environmental heterogeneity and seascape features shape
 genetic variation across populations and how it might have influence
 speciation across the genus. --- ## Contact For questions regarding data
 structure, file organization, or analysis workflows, please contact
 [cpedrazamarron@ucmerced.edu](mailto:cpedrazamarron@ucmerced.edu)