The impact of adaptor selection on genotyping in 2b-RAD studies

Population genomic studies have increased in the last decade, showing great potential to understand evolutionary patterns a variety of organisms, mostly relying on RAD sequencing techniques obtain reduced representations genomes. Among them, 2b-RAD can provide further secondary reduction adjust experimental costs by using base-selective adaptors, although its impact genotyping is unknown. Here we empirical comparisons and genetic differentiation when fully degenerate or adaptors assess missing data. We built libraries with two types for same individuals generated independent combined datasets different missingness filters (presence 100%, 75% 50% libraries). Our approach, exploring locus-by-locus, found 92% identical genotypes between individual loci shared among 100% libraries, which decreased 35% working present at least them. show that data major source differentiation. The discordant were low frequency (7.67%) all filtered files. Only 0.96% them directly attributable reducing heterozygosity. An underestimation heterozygosity 6.44% was degenerated ca. 70% had <10 reads per locus indicating sufficient read depth should be ensured correct genotyping. Base-selective reduce number loci, increase their coverage, reliable no lower cost. demonstrate concern identification differentiation, not neglected studies. Thus, conclude are robust tool use population genomics regardless target species genome size, promoting future