Landscape genomics of Bombus flavifrons, a widespread color-polymorphic North American bumblebee

Understanding how environmental heterogeneity and different pressures affect organism’s genome is an important goal in evolutionary biology. Landscape genomics aims to simultaneously investigate patterns of genome wide population structure and to identify loci undergoing selection in association with local environmental conditions. Bombus flavifrons is a common bumblebee species that is found throughout the western United States. This broad geographic distribution makes it likely that B. flavifrons experiences a range of environmental pressures. Additionally, B. flavifrons features multiple color patterns that correspond to some extent with geography, with westernmost populations exhibiting a black-banded color pattern and eastern populations exhibiting a red color pattern, although there is some degree of variable coloration found in intermediate populations. Taking advantage of a new chromosome-level genome assembly for B. flavifrons, we perform whole-genome resequencing of 93 samples throughout the B. flavifrons range in the western United States. We evaluate population structure, with our results indicating two major genetic clusters between the cascades mountain and the Rocky Mountains that broadly correspond to the local color pattern found in each geographic area. We employ environmental association analyses using LFMM2 to estimate patterns of local adaptation.