The role of chromosomal rearrangements in reproductive isolation and introgression between species is poorly understood. In heterozygous form, rearrangements may directly interrupt meiotic progression leading to partial sterility/subfertility (underdominance) or may suppress local meiotic segregation (recombination suppression). Such unbalanced meiotic segregation may also result in reproductive isolation and play roles as a driving force of speciation. The objective of this study was to gain insight into the pattern of chromosomal rearrangements in two closely related killifish species in the genus Fundulus (F. notatus, and F. olivaceus) by constructing genetic linkage maps using high-resolution single nucleotide polymorphism (SNP) markers. Markers associated with Robertsonian (Rb) translocations in F. notatus were generated by high-throughput genotyping-by sequencing (GBS) method and intra-specific SNPs were aligned to contigs in a reference F. olivaceus genome. This SNP-based mapping approach revealed 24 linkage groups (LGs) in F. olivaceus and 20 LGs in F. notatus including four Rb fusions (corresponding to chromosomes). We also found strong homology at the LG level between our maps and a previously constructed F. heteroclitus linkage map. Finally, using these maps and GBS-SNP data, we compared patterns of hybridization and introgression between populations of F. olivaceus and F. notatus from two natural hybrid zones. We observed weak prezygotic isolation, but stronger post-zygotic isolation between karyotypically different populations, which indicated multiple chromosomal fusions in F. notatus might have influenced reproductive viability of F1 hybrids, promoting reproductive isolation between these two species --Abstract, page iii
