James R. Walters' Lab
Assistant Professor of Evolutionary Genomics
Ecology & Evolutionary Biology
University of Kansas, Lawrence
(Jamie)
Research Overview
Major themes of research in our lab include evolutionary genetics, molecular evolution, and sexual selection. Particularly appealing are projects where these three areas intersect. Methodologically, we concentrate on genomic approaches such as next-generation sequencing and shotgun proteomics. However, our work with these genome-wide data-sets is motivated by fundamental observations about organismal biology. Current research tends to focus on insects, with an emphasis on moths and butterflies. Details regarding some of our recent and ongoing projects follow below.
Distribution of Male:Female expression ratios for autosomal (black) and Z-linked (red) genes in silkworm (Bombyx mori).
Sex chromosome dosage compensation
In species with differentiated sex chromosomes (e.g. with XY males or ZW females), the heterogametic sex has half the gene dose relative to the homogametic sex. For instance in mammals, males have one X chromosome while females have two. Yet both sexes have two copies of each autosome, creating the potential for negative effects of unbalanced gene dosage between the X and autosomes in males. Theory predicts that epigenetic mechanisms should evolve to equilbrate gene expression on the X or Z chromosome between sexes. Yet empirical results show that this theory is not well-supported and a variety of patterns actually exist in various taxa. Work in our lab has examined this prediction in Lepidoptera, showing that the Z chromosome is balanced between sexes, but apparently through down-regulation in diploid males, a result contradicting theory. We are currently working to further assess this pattern in more species and also to uncover the molecular mechanisms underlying this pattern. At the same time, we are developing novel bioinformatic software to improve and standardize relevant analytical approaches.
Mating system, sexual selection, and the molecular evolution of reproductive proteins
Reproductive proteins tend to diverge unusually rapidly between species. This pattern is frequently attributed to post-mating sexual selection. However, despite many well-characterized examples of rapidly evolving reproductive proteins, relatively little data exist which directly address this widely invoked hypothesis. Research in our lab aims to test the relationship between rates of molecular evolution and mating system using Lepidoptera. Many species have good estimates of female mating rates based on counts of spermatophores from wild-caught individuals. Building on our proteomic identification of sperm and seminal fluid proteins, we are employing comparative and population genomic methods to infer pattern and process in the molecular evolution of reprodcutive proteins. Our early work in this regard focused on The Heliconius genus of butterflies by contrasting patterns of reproductive protein evolution between clades with divergent mating systems: adult-mating and pupal-mating. With few exceptions, pupal-mating females mate only once, which severely limits the opportunity for post-mating sexual selection to act. In contrast, adult-mating females mate repeatedly throughout life, providing ample opportunity for post-mating sexual selection to drive the adaptive evolution of reproductive proteins. More recently we have expanded this work in Danaus butterflies and Manduca moths.
A pupal-mating H. sara male inserts it’s abdomen into the chrysalis of a female to mate with her just before she closes.
Resequencing coverage of males versus females delineates sex-linked from autosomal scaffolds in Heliconius genome assembly.
Lepidopteran genome projects
Molecular evolution of sex-biased and sex-linked genes
The theories of fast-X, faster-male, and sexual antagonism predict distinct evolutionary dynamics for genes differentially affiliated with males versus females – either via sex linkage or sex-specific function (often assayed by sex-biased gene expression). We are pursuing an integrated genomic analysis of these phenomena in Heliconius and other Lepidoptera. This entails combining genomic-scale data sets concerning chromosomal linkage, gene expression, and comparative sequence analysis to examine the molecular evolutionary effects of sex-linkage and sex-biased gene expression. Combining these data sets provides the necessary components to evaluate several related theoretical predictions by testing for differences in: 1) evolutionary rates between sex chromosomes and autosomes (fast-X), 2) evolutionary rates between male-, female-, and unbiased genes (faster-male), and 3) the abundance of sex-biased genes across the chromosomes (sexual antagonism).
Our lab has played a leading role or made major contributions in genome proejcts for several different species, including Heliconius melpomene (postman butterfly) Manduca sexta (Tabacco Hornworm moth), Cydia pomonella (Coddling moth) and Danaus plexippus (monarch butterfly). Supporting the development of new and improved genomic resources for Lepidoptera and other insects is an important part of our research efforts.
Excerpt from BLAT/Artemis and MUMmer alignments between BAC sequence and a genomic scaffold.
Bundles of eupyrene sperm and the ‘loose’ apyrene sperm, dissected from the reproductive tract of a Hornworm moth (Manduca sexta).
Proteomics of dimorphic sperm in Lepidoptera
Why would males make sperm – lots of them – that have no nucleus and can’t fertilize an egg? This is the question motivating our effort to characterize the lepidopteran sperm proteome. Nearly all species of moths and butterflies produce two types of sperm. Eupyrene sperm are ‘normal’ in that they have nuclei and fertilize eggs. In contrast, apyrene sperm lack nuclei, do not carry a haploid complement of the genome, and cannot directly fertilize eggs. Nonetheless, a substantial fraction of sperm transferred to females is apyrene, as much as 99% of sperm in some species. In collaboration with Steve Dorus at Syracuse University, I am using mass-specrometry proteomic techniques to characterize the molecular differences between apyrene and eupyrene sperm. Our hope is to then apply molecular evolutionary methods to assess differences in selective pressures acting on the the different sperm components.