| Summary: | Identifying genomic regions associated with morphological and ecological differences can help understand the processes of evolution and speciation. Single nucleotide polymorphisms (SNPs) from genomic data can be analyzed, using a large sample size per group, to help find regions that differ between groups. In Lake Þingvallavatn, four closely related ecomorphs of Arctic charr (Salvelinus alpinus), two benthic, the small benthivorous (SB), and the large benthivorous (LB), as well as two limnetic, planktivorous (PL) and piscivorous (PI). They diverged into these forms in the last 10,000 years. This study aimed to study the genetic differences between these four morphs, to find regions of separation and identify which linkage group the sex-determining gene was on. A morph specific analysis using one-to-all comparisons showed that most significant SNPs were associated with SB-, PL- and LB-charr, with the fewest linked with PI-charr. The significant SNPs were found on almost all linkage groups, and in some cases, they could pinpoint certain genomic regions. Pairwise comparisons between all the morphs showed that the highest number of SNPs was between the SB and the limnetic morphs, while only a few significant SNPs were between PL and PI. Although, most of the significant SNPs were shared between four comparisons, confirming early split among the benthic-limnetic morphs in the Lake. In continuation, a limnetic-benthic comparison provided a high number of significant SNPs, most of them grouped on few LGs. A male-female comparison was done both on the entire dataset and within each morph. The morph specific analyses showed a high number of significant SNPs on known sex-related LGs in the PL- and PI-charr. This may reflect technical differences or biological. In the future, the RADseq data will be aligned to WGS data to observe if significant regions in the two datasets intersect, which preliminary data suggest they do in some cases. This project provides insights into the genetic components related to morphological and ...
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