engleski

Haplotype richness drop: a new method for mapping selection signatures

Under the pressure of natural and artificial selection, the pattern of genomic landscape of domestic animals is constantly changing, leaving visible signs of selection. Here, we propose a new approach called haplotype richness drop (HRiD), which is able to identify selection signals from genomic information contained in male haplotypes. This applies to males genotyped on the X- chromosome, although extension to diploid genotypes that are accurately phased is also possible. HRiD is based on the assumption that genomic regions subject to positive selection exhibit a sudden decrease (drop) in haplotype richness. Thus, the main task of HRiD is to identify outlying genomic regions that exhibit a sudden drop in haplotype richness. Using empirical datasets, we have shown that HRiD complements other within-population approaches, such as extreme Runs of Homozygosity islands, integration Haplotype Scores, and the number of Segregating Sites by Length. In addition, we demonstrated that HRiD results can be readily combined with phylogenetic analyses of selection signals (haplotypes). This study was supported by the Croatian Science Foundation under the project ANAGRAMS, IP-2018-01-8708, and by the Operational Programme for Competitiveness and Cohesion from 2014 to 2020 under the project SirjeIN, KK.01.1.1.04.0058, while the participation of Luboš Vostry was supported by the Ministry of Agriculture of the Czech Republic (project no. QK1910156).

selection signals; new approach; male haplotypes; X-chromosome

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