DOI: 10.5061/dryad.s4mw6m9bb
title: Data from: Patterns of genomic heterogeneity in a classic field cricket mosaic hybrid zone

description: Barriers to gene exchange can be semi-permeable; some genes are expected
 to freely flow across species boundaries whereas others, under divergent
 selection or responsible for reproductive isolation, might not. Genome
 scans in recently diverged species have identified divergent genomic
 regions, a pattern that has often been interpreted as islands of
 restricted introgression in a background of relatively free gene exchange
 (“genomic islands of speciation”).  Areas of high
 differentiation, most located in the X chromosome (females XX, males X0),
 have been identified in the hybridizing field crickets Gryllus firmus and
 Gryllus pennsylvanicus.  These species were assumed to follow an
 islands of speciation model, with highly differentiated areas interpreted
 as areas of reduced introgression.  We sequenced the G. firmus
 genome to localize previously studied SNPs and sample a larger area around
 them in 8 allopatric populations (4 of each species). We use this data to
 test expectations for the islands model, in which non-introgressing areas
 should have both high absolute and relative differentiation.  We
 find that in the allopatric populations, the areas with high relative
 differentiation (mostly X-linked), previously interpreted as
 non-introgressing, do not have high absolute differentiation as would be
 expected under the “islands model.”. We also show that the estimated
 divergence time based on nuclear DNA is about 4× older than that estimated
 based on mtDNA (800K vs 200K years ago).  We discuss the
 implications of our results for introgression into allopatric populations.
description: Word, Excel, R, gff file needs to be opened with genomic programs
 such as Geneious or other genomic browsers
description: # Patterns of genomic heterogeneity in a classic Gryllus mosaic hybrid
 zone --- This dataset contains all the loci used in the study, the R code,
 the data used in the R code, supplementary tables and figures, and the
 annotated draft genome for Gryllus firmus. ## Description of the data and
 file structure There are five supplementary tables and one supplementary
 figure (on Zenodo as Supplemental Information): Table 1: IMa information
 for each locus including mutation rate and length of reads Table 2:
 Assemblage details from Supernova Table 3: Gene annotation for genes that
 fall inside sequenced loci Table 4: Autosomal non-introgressing genes with
 low Tajima’s D, all located in chromosome LG14 Table 5: Primers used for
 longPCR of the 48 loci Figure 1: Flow-chart for the Gryllus genome
 annotation We also included the IMa3 input file (cricket_IMa_input), and
 output (results, IMa_output_final_run) as "data" Fasta_files:
 These are the sequenced loci (~5K basepairs) for 4 populations of Gryllus
 firmus and 4 population of G. pennsylvanicus. See paper for more
 information. The population sequences for each of the 47 loci are in DNAsp
 Fasta Format - see Read_me_Fasta for more information All of these data is
 uploaded on Genbank - see paper for accession numbers We also included one
 file of the concatenated loci used to build the tree - 79 individuals, 34
 loci (concat_file.fasta). The annotated draft genome is the .gff dataset.
 Genome file with annotation for scaffolds that contain the loci studied:
 GryllusFragmentsAnnotated.gff putative gene functions for annotated genes:
 PutativeGeneFunctions.txt The complete draft genome:
 complete_draft_genome_gryllus.gff Additional files related to genome
 annotations: allstats.txt, alldb.blatp, final_no_seq.gff Fasta files for
 annotated proteins and transcripts are in: final.all.maker.proteins and
 final.all.maker.transcripts ## Sharing/Access information Data was derived
 from the following sources: Whole genome sequence -&gt;primer design for
 long PCR based on existing previously described SNPs-&gt; long sequencing
 of 48 individuals for each species (96 total). ## Code/Software (uploaded
 as "data") The R code used in the analyses for Dxy and Fst as
 well as the dataset itself data:
 Complete_data_species_Dxy_Fis_Pi_9_26_24_new.cvs - this data set contains
 all of the studied loci ("gene") - values were calculated with
 DnaSP ([http://www.ub.edu/dnasp/](http://www.ub.edu/dnasp/)). The labels
 refer to: information on introgressing status ("Intro", yes or
 no), if loci are X linked or not ("sex"). Chromosome location of
 each locus ("Chromosome"). The total number of sequenced
 nucleotides ("N_sites_no_gaps"). Number of G. pennsylvanicus
 sequenced individuals ("Pnumber"). Number of G. fimrus sequenced
 individuals ("Fnumber"). Total number of individuals
 ("Ntot"). Number of G. pennsylvanicus populations and G. firmus
 populations sampled ("Ppops" and "Fpops"
 respectively). The number of haploypes observed in G. firmus and G.
 pennsylvanicus ("F_hap_N" and "P_hap_N"). The total
 number of variable sites in G. firmus and G. pennsylvanicus
 ("F_S" and "P_S"). The total number of mutations
 "eta" for G. firmus and G. pennsylvanicus ("F_eta" and
 "P_eta"). The nucleotide diversity, pi, for G. firmus and G.
 pennsylvanicus ("F_Pi" and "P_Pi"). And several
 measures of population diversity calculated with the command &gt;gene flow
 and genetic differentiation - including relative differentiation
 ("Fst" and absolute diferentaition "Dxy"). R code
 used: Rcode_gryllus_DxyFst.R