Affiliations: 1) University of Virginia; 2) University of Virginia; 3) University of Virginia; 4) University of Virginia
Keywords: Population history
Understanding the mechanisms that drive divergence within and between populations is key to elucidating the genetic basis of local adaptation and speciation. Investigating recently diverged species can help elucidate how disparate regions of the genome accumulate change through distinct selection regimes. Here, we investigate the evolutionary history and adaptive divergence of the Daphnia pulex clade, a group of freshwater crustaceans that experiences yearly demographic turnover across the growing season and inhabits the Holarctic. Despite the extensive use of D. pulex in ecological and evolutionary genomics, there is a fundamental knowledge gap in the distribution of genetic diversity and divergence history across the species clade. Moreover, we still don’t know the extent of genomic divergence between continental D. pulex that has led to debate regarding the current species classification. To address these issues, we have assembled a genomic panel of over 1600 North American and European samples from D. pulex, D. pulicaria, and D. obtusa from publicly available data and wild sequenced clones. Our results reveal extensive divergence across the genome of continental D. pulex consistent with highly diverged species. Additionally, we show genomic evidence for the distribution of a hybrid complex of North American D. pulex and D. pulicaria clone across European ponds, highlighting the potential of hybridized lineages to colonize a large habitat range. This work highlights over 30 million years of evolution within the D. pulex clade and reveals the putatively adaptive structural and functional gene categories that have resulted in highly disparate genetic diversity across the species range.