DOI: 10.5061/dryad.kwh70rzdn
title: Data from: Homoploid hybrid speciation in a marine pelagic fish

description: Homoploid hybrid speciation (HHS) is an enigmatic evolutionary process
 where new species arise through hybridization of divergent lineages
 without changes in chromosome number. Although increasingly documented in
 various taxa and ecosystems, convincing cases of HHS in marine fishes have
 been lacking. This study presents a possible case of HHS in a pelagic
 marine fish based on comprehensive genomic, morphological, and ecological
 analyses. Population genomics, species tree estimation, and tests of
 introgression and admixture identified three sympatric clusters in
 Megalaspis cordyla in the western Pacific and the admixed nature of one
 cluster between the others. Moreover, model-based demographic inference
 favored a hybrid speciation scenario over introgression for the origin of
 the admixed cluster. While contemporary gene flow suggested partial
 reproductive isolation, examination of occurrence data and ecologically
 relevant morphological characters suggested ecological differences between
 the clusters, potentially contributing to the reproductive isolation and
 niche partitioning in sympatry. The clusters are also morphologically
 distinguishable and thus can be taxonomically recognized as separate
 species. The hybrid cluster is restricted to the coasts of Taiwan and
 Japan, where all three clusters coexist. The parental clusters are
 additionally found in lower latitudes, where they display non-overlapping
 distributions. Given the geographical distributions, estimated times of
 the species formation, and patterns of historical demographic changes, we
 propose that the Pleistocene glacial cycles were the primary driver of HHS
 in this system. We also develop an ecogeographic model of HHS in marine
 coastal ecosystems, including a novel hypothesis to explain the initial
 stages of HHS.
description: We analyzed a total of 160 specimens of <em>M.
 cordyla</em> collected from various localities in the western
 Pacific.  We obtained partial sequences of the
 mitochondrial cytochrome b gene (CYTB: 873 bp) from all specimens.
 Additionally, we obtained partial sequences of the following seven loci
 from a subset of the specimens: cytochrome c oxidase subunits 1 (COI: 612
 bp) and 2 (COII: 657 bp), NADH dehydrogenase subunits 1 (ND1: 828 bp), 2
 (ND2: 531 bp), 4 (ND4: 828 bp), and 5 (ND5: 801 bp), and the control
 region (CR: 760 bp). These sequences were used for divergent time
 estimation, haplotype network construction, and Neighbor-Joining tree
 estimation. We genotyped 115 specimens using MIG-seq, a
 reduced representation sequencing method targeting SNPs in the
 inter-simple sequence repeat region. We processed the raw MIG-seq reads by
 the single-end mode of fastp v0.20.1, merging the processed reads 1 and 2
 into a single FASTQ file, and mapped them to the <em>Caranx
 ignobilis</em> reference genome (GenBank JAFHLA000000000.1) using
 BWA-mem v0.7.17 with default settings. Unmapped or low-quality reads were
 removed using Samtools v1.12. The resulting BAM files were processed using
 Stacks v2.5.4, bcftools v1.8, VCFtools v0.1.16, and R package ‘SNPfiltR’
 v1.0.0 to perpare suitable datasets for downstream analyses.
 We examined 37 linear measurements and 17 countable characters in
 37 specimens.  The ecological data is based on the
 catch data of <em>M. cordyla</em> in Taiwan during 2000–2001,
 originally reported in Su et al. (2020:Scientific Reports 10:
 16829). More details of data collection, processing,
 and analyses are described in the Supplementary Material
 (Supplement_text.docx).
description: # Data from: Homoploid hybrid speciation in a marine pelagic fish
 [https://doi.org/10.5061/dryad.kwh70rzdn](https://doi.org/10.5061/dryad.kwh70rzdn) ## Description of the data and file structure This dataset consists of genetic, morphological, and ecological data and associated codes to reproduce the results (Data_from_Muto_etal.zip) and supplementary materials (Supplement_Figs.pdf; Supplement_Tables.xlsx; Supplement_text.docx). Data and associated codes for each alaysis are provided in separate directories, which are compressed in a single zip file. The data was obtained as outlined in Methods. Softwares and packages required are described in the codes. ## Contents of each directory #### PCA This directory contains the files required to reproduce the the result of the Principal Components Analysis based on the genome-wide SNPs data. data1.vcf.gz: a gzipped vcf file of 2926 SNPs across 105 samples (1st dataset as referred to in the manuscript). pca.R: An R script for performing PCA using the adegenet package. #### admixtools This directory contains the files required to reproduce D-statistics and f3 statistics using ADMIXTOOLS based on the genome-wide SNPs data. data2.geno/ind/ped/snp: input files for ADMIXTOOLS/admixr based on 6789 SNPs across 24 samples of M. cordyla with C. ignobilis as an outgroup (2nd dataset as referred to in the manuscript). admixtools.R: An R script to run ADMIXTOOLS via amixr, a wrapper R package for ADMIXTOOLS. #### arlequin This directory contains the files required to reproduce the genome-wied Fst value using Arlequin v3.5.2.2. To get the result, put the two files listed below in the directory where the console version of Arlequin (arlecore) is installed, and execute LaunchArlecore.sh. data1_pure.arp: SNPs data to be fed to Arlequin. 2962 SNPs across 102 samples (i.e., 1st dataset as referred to in the manuscript minus 3 individulas of putative early-generation hybrids). data1_pure.ars: setting file for Arlequin. #### bayesass This directory contains the files required to reproduce the the result of Bayesass. data1.vcf.gz: a gzipped vcf file of 2926 SNPs across 105 samples (1st dataset as referred to in the manuscript). popmap.tsv: population information for the samples. bayesass.sh: procedure to reproduce the result. rep_summary.sh: script to summarize the result (used in bayesass.sh) rep_summary.R: script to summarize the result (used in bayesass.sh) ugnix: contains ugnix scripts (used in bayesass.sh). see [https://github.com/brannala/ugnix](https://github.com/brannala/ugnix) rep*: contains the input files preapred by the author. bayesass.sh explains both how to run Bayesass using these files and how to prepare these files by subsampling data1.vcf.gz #### BPP This directory contains the files required to reproduce the the result of BPP. BPP.sh: procedure to reproduce the result. filtered.fa.gz: A fasta file filtered as described in Materials and Methods, containing 1197 loci of 24 samples. Imap.txt: population information for the samples to be used in BPP run. msci_mC_A.ctl, msci_mC_BEast.ctl, msci_mC_BWest.ctl, msci_mC_C.ctl: control files for BPP. popmap: population information for the samples to be used for data conversion. #### easySFS This directory contains the files required to reproduce SFS based on the genome-wide SNPs data. easySFS developed by Isaac Overcast ([https://github.com/isaacovercast/easySFS](https://github.com/isaacovercast/easySFS)) is used. data4.vcf.gz: A gzipepd vcf file of 6,341 SNPs across 24 samples, polarized by two outgroups C. ignobilis and C. melampygus, used for creating the SFS for demographic model selection (4th dataset as referred to in the manuscript). data5.vcf.gz: A gzipepd vcf file of 22,326 SNPs plus 920,184 invariant sites across 24 samples, polarized by two outgroups C. ignobilis and C. melampygus, used for creating the SFS for demographic parameter estimation and Stairway Plot analysis (5th dataset as referred to in the manuscript). pop.tsv: population information for the samples. easySFS.sh: procedure to reproduce SFS. #### ecology This directory contains the files required to reproduce the result of the Random Forest classification, hierarchical clustering, and Factor Analysis of Mixed Data of the ecology data. ecology_data.csv: a comma-separated file of ecology data for M. cordyla in Taiwan, reproduced from Su et al. (2020). ecology.R: An R script for performing the analyses. #### fastsimcoal This directory contains scripts and other files required to reproduce the results of demographic model selection and parameter esitmation using fastsimcoal2. Results of the fastsimcoal runs are also provided since they are computationllly intensive tasks and take a lot of time to reproduce. The files related to demographic model selection and parameter esitmation are provided in separate directories ("modelselectoin/" and "param/"). For more details, pleaes see readme files in these directories. #### fst_locus_by_locus This directory contains the files required to reproduce lpucs-by-locus Fst between genetic clusters using populations implemented in Stacks based on the genome-wide SNPs data. data1_pure.arp: SNPs data to be fed to populations. 2962 SNPs across 102 samples (i.e., 1st dataset as referred to in the manuscript minus 3 individulas of putative early-generation hybrids). popmap.tsv: population information for the samples. fst_locus_by_locus.sh: procedure to reproduce the result. #### hiest This directory contains the files required to reproduce the results of the HIest analysis based on the genome-wide SNPs data. The files with a prefix "2pop" are for the analysis assuming the East and West clusters to be potential parents, where as those with "3pop" are for the one assuming the three clusters to be potential parents. 2pop_G_2pop.tsv: genotype matrix of 108 loci whose allele frequencies were differentiated by &gt; 0.5 between the East and West clusters. First row is locus name. A, T, G, C are coded as 1, 2, 3, 4.\ 2pop_G_rownames.txt: a list of sample IDs to be combined with the genotype matrix. 2pop_P.tsv: allele frequency matrix of the 108 loci. 3pop_G_2pop.tsv: genotype matrix of 130 loci whose allele frequencies differed by more than &gt; 0.5 between at least one pair of clusters. First row is locus name. A, T, G, C are coded as 1, 2, 3, 4. 3pop_G_rownames.txt: : a list of sample IDs to be combined with the genotype matrix. 3pop_P.tsv: allele frequency matrix of the 130 loci. hiest.R: R script to perform HIest analysis. #### hyde This directory contains the files required to reproduce the results of HyDe analysis based on the genome-wide SNPs data. data2.phylip: a phylip format data of 6,789 SNPs across 24 samples of M. cordyla plus C. ignobilis as an outgroup (2nd dataset as referred to in the manuscript). data2.map: population information of the samples. data2.trio: a file to specify triples to be tested. hyde.sh: procedure to reproduce the results. #### morphology This directory contains the files required to reproduce the result of the Principal Components Analysis of morphological characters. morphology.txt: a tab-separated file of raw morphology data for 37 samples. 54 characters including 37 linear measurements and 17 countable characters are listed, of which 24 are used for the PCA. All linear measurements are in mm. pca.R: An R script for performing the PCA. #### mtDNA_alignment This directory contains the following mitochondrial DNA sequence alignments: CR.fas: 760 bp alignment of control region sequences of 70 samples. Cytb.fas: 873 bp alignment of Cytb sequences of 161 samples. coding.fas: 5124 bp alignment of 7 protein-coding genes of 20 samples. Partial sequences of the following genes are concatenated in this order: COI (606 bp); COII (657 bp); Cytb (873 bp); ND1 (828 bp); ND2 (531 bp); ND4 (828 bp); ND5 (801 bp). all.fas: 5884 bp alignment (including gaps) of the 7 protein-coding genes (identical as above) plus control region sequences of 20 samples. all_ignobilis.fas: 5919 bp alignment (including gaps) of the 7 protein-coding genes (identical as above) plus control region sequences Caranx ignobilis as an outgroup and 11 samples of M. cordyla. The difference in the alignment length between "all.fas" and "all_ignobilis.fas" is due to gaps inserted in the control region sequence of the latter. Sequence titles consist of voucher number, assigment to genetic cluster (east, west, north, or their hybrid), country and region of collection. "all_ignobilis.fas" was used for divergence time estimation, whereas others were used for haplotype network construction. #### mtDNA_divergencetime This directory contains the files required to reproduce the result of divergence time estimation based on mtDNA sequences. mtDNA_alignment.nex: a nexus file containing the aligned mtDNA sequences. run1/, run2/: directories containing .xml files to be used in BEAST runs. mtDNA_divergence.sh: procedure to reproduce the result. #### nQuire This directory contains the files required to reproduce the the result of nQuire. popmap.tsv: population information for the samples. nQuire.sh: procedure to reproduce the result. bis: contains the input files (filtered, denoised, and converterted to "BIN" format required by nQuire) preapred by the author. nQuire.sh explains both how to run nQuire using these files and how to prepare these files from BAM files. #### snapp This directory contains the files required to reproduce the result of divergence time estimation based on the genome-wide SNPs data using SNAPP. data3.vcf: a vcf file of 3179 SNPs across 9 M. cordyla samples plus a C. ignobilis as an outgroup (3rd dataset as referred to in the manuscript). samples.txt: population information for the samples. constraints.txt: a file specifying age constraints. snapp.sh: procedure to reproduce the result. #### splitstree This directory contains the file required to reproduce neighbor-net network using splitstree v5.3.0. splitstree.nex: a nexus file of 2926 SNPs across 105 samples (1st dataset as referred to in the manuscript). #### stairwayplot This directory contains the files required to reproduce the result of historical population size estimations using Stairway Plot 2 based on the genome-wide SNPs data. 0_west / 1_north / 2_east_DAFpop0.obs: SFS for each cluster calculated using easyfSFS based on 22,326 SNPs plus 920,184 invariant sites across 24 samples (8 per cluster), polarized by two outgroups C. ignobilis and C. melampygus (5th dataset as referred to in the manuscript). west / east / north.blueprint: input file for Stairway Plot 2 containing the SFS for each cluster and other settings, manually prepared following [https://github.com/xiaoming-liu/stairway-plot-v2/blob/master/READMEv2.1.pdf](https://github.com/xiaoming-liu/stairway-plot-v2/blob/master/READMEv2.1.pdf) stairwayplot.sh: procedure to reproduce the results. #### structure This directory contains the files required to reproduce the result of STRUCTURE analysis based on the genome-wide SNPs data. data1.str: 2926 SNPs across 105 samples (1st dataset as referred to in the manuscript) formatted for STRUCTURE. structure.sh: procedure to reproduce the results.