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.
Genotypes for individual F2 hybrids
Genotypes 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.xlsx
Allele frequency per SNP for F2 hybrids
Allele 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.txt
Allele frequency for F2 hybrids after sliding window averaging of 500 SNP
Allele 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.txt
Allele frequency for F2 hybrids after sliding window averaging of 1000 SNP
Allele 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.txt
Allele frequency for F2 hybrids after sliding window averaging of 2000 SNP
Allele 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.txt
Allele frequency for F2 hybrids after sliding window averaging of 3000 SNP
Allele 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