DOI: 10.5061/dryad.r3v52
title: Data from: Using Pool-seq to search for genomic regions affected by hybrid inviability in the copepod T. californicus

description: The formation of reproductive barriers between allopatric populations
 involves the accumulation of incompatibilities that lead to intrinsic
 postzygotic isolation. The evolution of these incompatibilities is usually
 explained by the Dobzhansky-Muller model, where epistatic interactions
 that arise within the diverging populations, lead to deleterious
 interactions when they come together in a hybrid genome. These
 incompatibilities can lead to hybrid inviability, killing individuals with
 certain genotypic combinations, and causing the population’s allele
 frequency to deviate from Mendelian expectations. Traditionally, hybrid
 inviability loci have been detected by genotyping individuals at different
 loci across the genome. However, this method becomes time consuming and
 expensive as the number of markers or individuals increases. Here we test
 if a Pool-seq method can be used to scan the genome of F2 hybrids to
 detect genomic regions that are affected by hybrid inviability. We survey
 the genome of hybrids between two populations of the copepod Tigriopus
 californicus, and show that this method has enough power to detect even
 small changes in allele frequency caused by hybrid inviability. We show
 that allele frequency estimates in Pool-seq can be affected by the
 sampling of alleles from the pool of DNA during the library preparation
 and sequencing steps, and that special considerations must be taken when
 aligning hybrid reads to a reference when the populations/species are
 divergent.
description: Genotypes for individual
 F2 hybridsGenotypes for F2 hybrids
 from crosses between the San Diego (SD) and Abalone Cove (AB) populations
 of the copepod Tigriopus californicus. Individuals were genotyped at 14
 PCR based markers across the 12 chromosomes. AB refers to the AB
 homozygous genotype, SD is homozygous SD and H refers to
 heterozygotes.Genotypes.xlsxAllele frequency per SNP for F2 hybridsAllele frequencies per SNP from Pool-seq data of F2 hybrids between the San Diego (SD) and Abalone cove (AB) populations of the copepod Tigriopus californicus. Allele frequencies are in reference to the AB population. Nauplii_AF refers to the allele frequency for the nauplii dataset; Adult_AF refers to the allele frequency for the adults dataset.DAN_DAA_all_chrm_AF.txtAllele frequency for F2 hybrids after sliding window averaging of 500 SNPAllele frequencies from Pool-seq data of F2 hybrids between the San Diego (SD) and Abalone cove (AB) populations of the copepod Tigriopus californicus. Allele frequencies are the average allele frequency of 500 consecutive SNP. Allele frequencies are in reference to the AB population. Position is the SNP position for the last SNP in the averaged window. Nauplii_AF refers to the allele frequency for the nauplii dataset; Adult_AF refers to the allele frequency for the adults dataset.DAN_DAA_slwin500.txtAllele frequency for F2 hybrids after sliding window averaging of 1000 SNPAllele frequencies per SNP from Pool-seq data of F2 hybrids between the San Diego (SD) and Abalone cove (AB) populations of the copepod Tigriopus californicus. Allele frequencies are the average allele frequency of 1000 consecutive SNP. Allele frequencies are in reference to the AB population. Position is the SNP position for the last SNP in the averaged window. Nauplii_AF refers to the allele frequency for the nauplii dataset; Adult_AF refers to the allele frequency for the adults dataset.DAN_DAA_slwin1000.txtAllele frequency for F2 hybrids after sliding window averaging of 2000 SNPAllele frequencies per SNP from Pool-seq data of F2 hybrids between the San Diego (SD) and Abalone cove (AB) populations of the copepod Tigriopus californicus. Allele frequencies are the average allele frequency of 2000 consecutive SNP. Allele frequencies are in reference to the AB population. Position is the SNP position for the last SNP in the averaged window. Nauplii_AF refers to the allele frequency for the nauplii dataset; Adult_AF refers to the allele frequency for the adults dataset.DAN_DAA_slwin2000.txtAllele frequency for F2 hybrids after sliding window averaging of 3000 SNPAllele frequencies per SNP from Pool-seq data of F2 hybrids between the San Diego (SD) and Abalone cove (AB) populations of the copepod Tigriopus californicus. Allele frequencies are the average allele frequency of 3000 consecutive SNP. Allele frequencies are in reference to the AB population. Position is the SNP position for the last SNP in the averaged window. Nauplii_AF refers to the allele frequency for the nauplii dataset; Adult_AF refers to the allele frequency for the adults dataset.DAN_DAA_slwin3000.txt