RT Journal Article SR Electronic T1 Identifying evolutionary divergence in gene expression across species and organs: a case-study using Hawaiian Drosophila JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.11.30.470652 DO 10.1101/2021.11.30.470652 A1 Church, Samuel H. A1 Munro, Catriona A1 Dunn, Casey W. A1 Extavour, Cassandra G. YR 2022 UL http://biorxiv.org/content/early/2022/04/14/2021.11.30.470652.abstract AB With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know when differences in gene expression across species are significant, we first need to know how much evolutionary variation in gene expression we expect to observe. Here we provide an answer by analyzing RNAseq data across twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that over evolutionary time, there exists a cohort of ovary specific genes that is stable and that largely corresponds to described expression patterns from laboratory model Drosophila species. However, our results provide a demonstration of the prediction that, as phylogenetic distance increases, variation between species overwhelms variation between tissue types. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression, and use this to identify gains and losses of ovary expression across these twelve species. We then use this distribution to calculate the evolutionary correlation in expression changes between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that share evolutionary trajectories, and we present these results as a dataset of new testable hypotheses about genetic roles and interactions in the Drosophila ovary.Competing Interest StatementThe authors have declared no competing interest.