DOI: 10.5061/dryad.9w0vt4bdm
title: Pervasive mitonuclear coadaptation underlies fast development in interpopulation hybrids of a marine crustacean

description: Cellular energy production requires coordinated interactions between
 genetic components from the nuclear and mitochondrial genomes. This
 coordination results in coadaptation of interacting elements within
 populations. Interbreeding between divergent gene pools can disrupt
 coadapted loci and result in hybrid fitness breakdown. While specific
 incompatible loci have been detected in mutiple eukaryotic taxa, the
 extent of the nuclear genome that is influenced by mitonuclear
 coadaptation is not clear in any species. Here, we used
 F2 hybrids between two divergent populations of the
 copepod Tigriopus californicus to examine mitonuclear
 coadaptation across the nuclear genome. Using developmental rate as a
 measure of fitness, we fount that fast-developing copepods had higher ATP
 synthesis capacity than slow developers, suggesting variation in
 developmental rates is at least partly associated with mitochondrial
 dysfunction. Using Pool-seq, we detected strong biases for maternal
 alleles across 7 (of 12) chomosomes in both reciprocal crosses in
 high-fitness hybrids, while low-fitness hybrids showed shifts towards the
 paternal population. Comparison with previous results on a different
 hybrid cross revealed largely different patterns of strong mitonuclear
 coadaptation associated with developmental rate. Our findings suggest that
 functional coadaptation between interacting nuclear and mitochondrial
 components is reflected in strong polygenic effects on this life-history
 phenotype, and reveal that molecular coadaptation follows independent
 evolutionary trajectories among isolated populations.
description: <b>SDxSH_FAST_read_counts.txt:</b> Mapped read counts for fast-developing F2 hybrids from the cross SD-female x SH-male. Counts for each allele are the average across mappings to each reciprocal genome reference. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SDxSH_SLOW_final_counts.txt:</b> Mapped read counts for slow-developing F2 hybrids from the cross SD-female x SH-male. Counts for each allele are the average across mappings to each reciprocal genome reference. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SHxSD_FAST_read_counts.txt:</b> Mapped read counts for fast-developing F2 hybrids from the cross SH-female x SD-male. Counts for each allele are the average across mappings to each reciprocal genome reference. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SHxSD_SLOW_final_counts.txt:</b> Mapped read counts for slow-developing F2 hybrids from the cross SH-female x SD-male. Counts for each allele are the average across mappings to each reciprocal genome reference. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SDxSH_FAST_AF.txt: </b>Allele frequencies for fast-developing F2 hybrids from the cross SD-female x SH-male. Only SNP loci that were successfully genotyped in the four sampled pools are shown in the table. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SDxSH_SLOW_AF.txt: </b>Allele frequencies for slow-developing F2 hybrids from the cross SD-female x SH-male. Only SNP loci that were successfully genotyped in the four sampled pools are shown in the table. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SHxSD_FAST_AF.txt: </b>Allele frequencies for fast-developing F2 hybrids from the cross SH-female x SD-male. Only SNP loci that were successfully genotyped in the four sampled pools are shown in the table. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SHxSD_SLOW_AF.txt: </b>Allele frequencies for slow-developing F2 hybrids from the cross SH-female x SD-male. Only SNP loci that were successfully genotyped in the four sampled pools are shown in the table. SD: San Diego, California; SH: Strawberry Hill, Oregon. <b>SDxSH_FAST_200kb_win.txt:</b> Window-average allele frequencies of the respective "AF" files. <b>SDxSH_SLOW_200kb_win.txt: </b>Window-average allele frequencies of the respective "AF" files. <b>SHxSD_FAST_200kb_win.txt:</b> Window-average allele frequencies of the respective "AF" files. <b>SHxSD_SLOW_200kb_win.txt:</b> Window-average allele frequencies of the respective "AF" files.