Project Number: 2080-21000-019-035-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jan 1, 2022
End Date: Dec 31, 2024
A major goal of evolutionary genetics is to understand how changes in the genome lead to phenotypic diversity. Expanding genomic and functional genetic resources are enabling researchers to determine the ways in which genetic variation translates to phenotypic variation across a greater diversity of natural systems, thus improving our understanding of how the genome operates and making the genetic targets of evolution more predictable. The proposed research aims to determine the myriad ways in which a gene regulatory network can be altered to drive phenotypic change utilizing the bumble bee (Bombus) mimetic color radiation. We propose to identify genetic variants driving parallel acquisition of mimicry phenotypes in several bumble bee species. We will then infer how the implicated alleles change and sort across a color-diverse lineage. Although the same allele may not be targeted to make the same phenotype, alternative mutations can lead to the same downstream shifts in gene expression. To better understand the extent to which different components of these networks are altered, we will examine how gene expression patterns shift between color variants within and across species. Finally, we will develop functional genetic tools to validate effects of top candidate loci. This research builds on an established foundation of coloration genetics in a few model bumble bees towards broader discoveries in evolutionary genetics. We will accomplish our goal by pursuing these specific objectives: In Objective 1, we identify the many routes to the same phenotype by building and comparing gene networks generating convergent red-black mimetic color pattern variants in Western American bumble bees. For this we target both upstream and downstream genes using cross developmental transcriptomics and genome-wide association analysis. In Objective 2, we expand known coloration genes to include those generating yellow phenotypes in bumble bees. Previous research focused on red-black melanic variants, but yellow involves pterin pigments. We will perform transcriptomics and a GWAS to decipher the players in these transitions, to expand the set of genes driving color variation in bumble bees. In Objective 3, we will perform comparative population and phylogenomic analyses of sequence evolution in the identified genes across a bumble bee lineage. Taking advantage of newly available genomes in bumble bees, we track how each player in pigmentation, both in cis and trans, evolves, to identify important regions under selection and assess patterns of diversity, divergence, and convergence using a cross-species approach. In Objective 4, we begin to develop functional genetic approaches for examining color evolution in these bees by examining the effect of RNAi knockdown of three key genes on the phenotypes of B. melanopygus and B. vancouverensis.
For Objective 1, we will use comparative transcriptomics to examine how gene expression of red/black epidermal segments shifts across the lineage, to determine (1) which genes are changing to generate these phenotypes, (2) whether the same genes or different genes of the same gene networks are implicated in repeated phenotypes, and (3) how expression of regulatory genes shift across the clade. By tracking changes in gene expression across development and species, we can determine the relative roles of heterochrony, heterometry, and heterotypy in gene expression on phenotype, while developing an improved understanding of the relationships among genes in this network.