DOI: 10.5061/dryad.nk98sf85h
title: Data from: Population genomics, local adaptation, and cryptic speciation in a temperate reef fish, the black surfperch, <em>Embiotoca jacksoni</em>, using genome-wide resequencing

description: The black surfperch, Embiotoca jacksoni, an apelagic reef fish with
 limited dispersal due to its lack of a pelagic larval stage, offers a
 unique model for studying local adaptation and potential cryptic
 speciation in marine species. This study employs medium-coverage whole
 genome resequencing to explore population structure, local adaptation, and
 genetic divergence across a latitudinal gradient from central California
 to Baja California, Mexico, including offshore islands. We identify strong
 genetic differentiation between five four distinct groups, a coastal group
 and four three island groups (Santa Catalina Island, San Clemente Island,
 and Isla Guadalupe, and Isla San Jerónimo), from Principal Components
 Analysis (PCA), Fst estimation, and ancestry (sNMF) admixture and
 phylogenetic analyses. For coastal populations, genetic structure
 correlates with geographic distance, and isolation-by-distance (IBD)
 patterns are evident. Further, we identify numerous outlier loci
 associated with adaptive traits, particularly genes linked to reproductive
 isolation, such as Spermine oxidase, Izumo sperm-egg fusion protein 1, and
 SPAG1, which are involved in fertilization success. These loci suggest
 that reproductive barriers are contributing to divergence among genetic
 groups. The presence of signatures of both genetic drift and selective
 pressures, particularly in genes governing fertilization, indicates that
 these distinct populations may represent incipient or cryptic species. Our
 findings highlight the role of low dispersal in fostering local adaptation
 and speciation in marine systems and underscore the potential for rapid
 evolutionary responses to environmental gradients. This research provides
 insights into the complex processes of speciation in marine vertebrates,
 particularly those with limited gene flow, and offers a baseline for
 monitoring genetic shifts in response to climate change.
description: # Data from: Population genomics, local adaptation, and cryptic speciation
 in a temperate reef fish, the black surfperch, *Embiotoca jacksoni*, using
 genome-wide resequencing Dataset DOI:
 [10.5061/dryad.nk98sf85h](10.5061/dryad.nk98sf85h) ## Description of the
 data and file structure The main file of this analysis is
 EJA_GenPop_data/data/8-Embiotoca_filtered.vcf.gz and all steps leading to
 these data are in main article's Material&Methods sections
 *Sampling*, *DNA extraction – Library preparation.* and *Mapping and
 Variant calling.* ### Files and variables #### EJA_GenPop_data.zip ```
 EJA_GenPop_data.zip/ └─ EJA_GenPop_data/ ├─ BayeScan2.1/
 (https://cmpg.unibe.ch/software/BayeScan/). See
 https://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.0_manual.pdf for
 more details │ ├─ EJA_Bayescan.sel ------------------------------------
 Text file, table - Output from the MCMC algorithm, each line provides the
 trace of the parameters estimated by the mode (LogLikelihood and the 15
 populations Fst values) for one run. │ └─ EJA_Bayescan_fst.txt
 -------------------------------- Text file, table - Results of the
 BayeScan analysis, for each line representing a loci and will display the
 folowing information: The index of the locus corresponding to the index in
 the input file; The posterior probability for the model including
 selection; The logarithm of Posterior Odds to base 10 for the model
 including selection. Note that this value is arbitrarily fixed to 1000
 when the posterior probability is 1 (should be infinity); The estimated
 alpha coefficient indicating the strength and direction of selection. A
 positive value of alpha suggests diversifying selection, whereas negative
 values suggest balancing or purifying selection; The FST coefficient
 averaged over populations. In each population FST is calculated as the
 posterior mean using model averaging. ├─ data/ │ ├─
 8-Embiotoca_filtered.vcf.gz ------------------------- Compressed variant
 call format - genomic data from 144 *Embiotoca jacksoni* individuals
 collected along the Californian (US and Baja) coast. │ ├─
 individuals_coordinates.csv ------------------------- Comma-separated
 values - Metadata for the 144 indivuals collected (sample ID,
 localisation, longitude, latitude, population) │ ├─
 Individuals_plot_order.txt -------------------------- Text file - Help
 file for plotting purpose │ └─ population_map_bsc.txt
 ------------------------------ Text file - Population map for data
 conversion from .vcf to .geste (BayeScan), each line matches a sample ID
 to its population. └─ output/ ├─ admixture/ │ ├─
 8-Embiotoca_filtered_r8.8.Q ---------------------- Text file, table -
 Lines represent individuals and columns the proportion of ancestry of each
 inferred ancestral population. 8th run of sNMF using K = 8 parameter
 (amount of column), all ancestry percentages for the 144 individudals
 sampled (amount of lines) │ ├─ 8-Embiotoca_filtered_r16.5.Q
 --------------------- Text file, table - Lines represent individuals and
 columns the proportion of ancestry of each inferred ancestral population.
 16th run of sNMF using K = 5 parameter (amount of column), all ancestry
 percentages for the 144 individudals sampled (amount of lines) │ ├─
 8-Embiotoca_filtered_r16.6.Q --------------------- Text file, table -
 Lines represent individuals and columns the proportion of ancestry of each
 inferred ancestral population. 16th run of sNMF using K = 6 parameter
 (amount of column), all ancestry percentages for the 144 individudals
 sampled (amount of lines) │ └─ 8-Embiotoca_filtered_r46.7.Q
 --------------------- Text file, table - Lines represent individuals and
 columns the proportion of ancestry of each inferred ancestral population.
 46th run of sNMF using K = 7 parameter (amount of column), all ancestry
 percentages for the 144 individudals sampled (amount of lines) ├─
 EJA_allele_frequencies_tb.rds ----------------------- R data file, data
 frame - Results from running the makefreq() function of the adegenet
 2.1.11 R package formated as a data frame. Each pair of line are the two
 alleles of each SNPs, they are identified by the first 3 columns of the
 table (CHROM, POs and ALLELE) and the subsequent column represent the
 allele frequencies in each of the 15 studied populations. └─
 EJA_lcwgs_Edward_distance.rds ----------------------- R data file, dist R
 object - Raw results from running the dist.genpop() function of the
 adegenet 2.1.11 R package. Pairwise distance matrix from the 15
 populations. Use as.matrix() to see the actual distance matrix
 (symmetrical with null coefficient on the diagonal). ``` ####
 EJA_ML_tree.zip ``` EJA_ML_tree.zip/ ├─
 8-Embiotoca.pruned.min4.fasta.varsites.phy.contree -------- Text file -
 Consensus tree with assigned branch supports where branch lengths are
 optimized on the original alignment from running the [IQ-TREE software
 version 2](https://github.com/iqtree/iqtree2) ├─
 8-Embiotoca.pruned.min4.fasta.varsites.phy.iqtree --------- Text file -
 Full result of the run, this is the main report file from running the
 [IQ-TREE software version 2](https://github.com/iqtree/iqtree2) (All the
 estimated model parameters for each tree and the tree weights are shown in
 this file) └─ Create_ML_tree_with_IQ-TREE_EJA.md ------------------------
 Text file - Full code for the phylogenetic analysis, can also be find at
 [jtoy7/EJA_lcwgs](https://github.com/jtoy7/EJA_lcwgs) ``` ## Code/software
 All codes and scripts used for the analyses can be found at
 [https://doi.org/10.5281/zenodo.17076840](https://doi.org/10.5281/zenodo.17076840) and [https://github.com/jtoy7/EJA_lcwgs](https://github.com/jtoy7/EJA_lcwgs).