DOI: 10.6076/d1bp4f
title: Data from: Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence

description: All mitochondrial-encoded proteins and RNAs function through interactions
 with nuclear-encoded proteins, which are critical for mitochondrial
 performance and eukaryotic fitness. Coevolution maintains inter-genomic
 (i.e., mitonuclear) compatibility within a taxon, but hybridization can
 disrupt coevolved interactions, resulting in hybrid breakdown. Thus,
 mitonuclear incompatibilities may be important mechanisms underlying
 reproductive isolation and, potentially, speciation. Here we utilize
 Pool-seq to assess the effects of mitochondrial genotype on nuclear allele
 frequencies in fast- and slow-developing reciprocal inter-population F2
 hybrids between relatively low-divergence populations of the intertidal
 copepod Tigriopus californicus. We show that mitonuclear interactions lead
 to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on
 two chromosomes in crosses between populations with 1.5% or 9.6% fixed
 differences in mitochondrial DNA nucleotide sequence. However, we also
 find evidence of excess mismatched (i.e., non-coevolved) alleles on three
 or four chromosomes per cross, respectively, and of allele frequency
 differences consistent with effects involving only nuclear loci (i.e.,
 unaffected by mitochondrial genotype). Thus, our results for
 low-divergence crosses suggest an underlying role for mitonuclear
 interactions in variation in hybrid developmental rate, but despite
 substantial effects of mitonuclear coevolution on individual chromosomes,
 no clear bias favouring coevolved interactions overall.
description: Pool-seq count data - collected by isolating DNA from pools of
 fast- or slow-developing <em>Tigriopus
 californicus </em>copepodids from reciprocal hybrids lines; DNA was
 sequenced by whole-genome sequencing on a NovaSeq 6000; reads were mapped
 to a hybrid reference genome and counted using <em>bwa</em>;
 allele-specific read counts were determined with
 <em>Samtools</em> and
 <em>popoolation.</em> Population-specific
 reference genomes - re-sequenced genome sequences for individual
 <em>Tigriopus californicus</em> populations; obtained by
 mapping whole-genome sequencing reads to the previously published San
 Diego, California reference sequence; population-specific consensus
 sequences were determined
 with <em>bwa</em>, <em>Samtools</em>
 and <em>popoolation</em>. PE mtDNA sequence
 - consensus sequence from WGS reads from the Pescadero Beach, California
 <em>Tigriopus californicus</em> population; reads were mapped
 to a previously published mtDNA sequence for a population from Santa Cruz,
 California with <em>CLC Genomics Workbench</em> which was also
 used to determine the consensus PE sequence. Hybrid
 reference genomes - assembled from previously published sequences and the
 PE mtDNA sequence using <em>R</em>. Fixed
 SNP lists - list of single-nucleotide polymorphisms displaying fixed
 differences between pairs of <em>Tigriopus californicus</em>
 populations; determined by reciprocal whole-genome sequencing read mapping
 and processing
 with <em>bwa</em>, <em>Samtools</em>
 and <em>popoolation</em>.
description: All files can be opened in text editors, spreadsheet programs or
 the statistical software R.