Reference genome choice compromises population genetic analyses by Maria Akopyan & Matthew Genchev & Ellie E. Armstrong & Jazlyn A. Mooney instant download

Reference genome choice compromises population genetic analyses by Maria Akopyan & Matthew Genchev & Ellie E. Armstrong & Jazlyn A. Mooney instant download

SUMMARYCharacterizing genetic variation in natural populations is vital to evolutionary biology; however, many nonmodel species lack genomic resources. Here, we demonstrate that reference bias significantly affects population genomic analyses by mapping whole-genome sequence data from gray foxes (Urocyon cinereoargenteus) to a conspecific reference and two heterospecific canid genomes (dog and Arctic fox). Mappingto the conspecific genome improved read pairing by ∼5% and detected 26%–32% more SNPs and 33%–35% more singletons. Nucleotide diversity estimates increased by over 30%, FST increased from 0.189 to0.197, and effective population size estimates were 30%–60% higher with the conspecific reference. Recombination rates varied by up to 3-fold at chromosome ends with heterospecific references. Importantly, FSToutlier detection differed markedly, with heterospecific genomes identifying twice as many unique outlierwindows. These findings highlight the impact of reference genome choice and the importance of conspecificgenomic resources for accurate evolutionary inference.