If you would like to view my complete publication list, please visit my google scholar profile.
Here I have included a more detailed breakdown of the main foci of my research program:
Biodiversity genomics
My main research interest is understanding how and why biodiversity evolves. To understand how >1 million described species have accumulated on earth, I seek to reconstruct and understand the dynamics of this process at its simplest level: the splitting of a single ancestral lineage into reproductively isolated daughter populations. Identifying groups of organisms where this speciation process can be reconstructed and studied in detail fundamentally requires knowledge about how many lineages exist and where they are distributed within a given group. For this reason, my research program relies on accurate natural history information based on detailed study of phylogeographic patterns of relatedness.
One of these focal groups I am interested in is the scrub-jays. These birds are known for their complex patterns of relatedness and unclear species limits, and for providing a textbook example of ecological adaptation. With the goal of eventually studying the scrub-jays as a window into the speciation process, I began by sequencing thousands of genomic loci from all known scrub-jay populations, to ask how many discrete lineages of scrub-jays exist, and where do these lineages occur? Resulting paper below:
- Devon A DeRaad, John E McCormack, Nancy Chen, A Townsend Peterson, Robert G Moyle, Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays, Systematic Biology, Volume 71, Issue 6, November 2022, Pages 1453–1470, https://doi.org/10.1093/sysbio/syac034. PDF available here.
- Please see media coverage of this paper from KU, The Wildlife Society, and Science Daily.
This paper is the first chapter of my dissertation, and it details the systematics and species limits of the scrub-jay species complex with range-wide sampling. I am quite proud of the comprehensive nature of the genomic sampling, made possible by the exhaustive fieldwork performed by co-author Town Peterson during his dissertation work at University of Chicago. We found consistent statistical support for five scrub-jay species, indicating that the current taxonomy is failing to recognize the population in southern Mexico as a distinct species.
This graphical abstract illustrates the main result of our paper, that scrub-jays from southern Mexico (sampling sites 24 & 25) diverged deep in the evolutionary past from all other scrub-jay populations, with little evidence for ongoing gene flow. Meanwhile the populations in green, pink, and purple can be differentiated genetically, but are likely closely related enough to share alleles regularly via gene flow. Based on this updated understanding that there are actually seven genomically identifiable lineages of scrub-jays (and probably five species), not just the four described species, I am generating whole genome data for each lineage to investigate how different regions of the genome track the divergence process across the entire scrub-jay species complex.
Additional papers on the topic of biodiversity genomics:
Venkatraman, M. X., Deraad, D. A., Tsai, W. L., Zarza, E., Zellmer, A. J., Maley, J. M., & Mccormack, J. E. (2019). Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird. Biological Journal of the Linnean Society, 126(1), 1-15. https://doi.org/10.1093/biolinnean/bly156.
How do characteristics of the genome affect patterns of relatedness at the DNA sequence level?
The genome is composed of individual segments of DNA known as chromosomes, which can be broken up and recombined during meiosis to form novel combinations in resulting offspring. Because of this process, different regions of the genome can actually have distinct evolutionary histories, and are expected to show varying patterns of relatedness among organisms based on both stochastic (e.g., the coalescent process) and deterministic (e.g., introgression) processes. Understanding how the heterogeneous composition of the genome (e.g., organellar genomes, sex chromosomes, inversions, coding vs. non-coding, etc.) affects these patterns of relatedness, and whether these effects are predictable across taxa, is a major goal in the current landscape of evolutionary biology.
I am hoping to use multiple comparisons between the lineages of scrub-jays we identified in the previously mentioned paper in Systematic Biology to test whether the frequencies of patterns of relatedness across the genome are consistent across comparisons, which would indicate that genome architecture influences the coalescent process in predictable ways. This project is ongoing.
Current papers on understanding patterns of relatedness across the genome:
DeRaad, D. A., McCullough, J.M., DeCicco, L.H., Hime, P.M., Joseph, L., Andersen, M.J., & Moyle, R. G. Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers. Molecular Ecology (in review).
Hybrid zones as windows into the speciation process
Another fascinating feature of recombination is its ability to break up associated gene combinations when organisms hybridize. For example, in the scrub-jays, all California Scrub-Jays have deep, hooked bills adapted for prying open the shells of acorns. Meanwhile, all Woodhouse’s Scrub-Jays have long, thin bills adapted for pulling pinyon seeds out of pinecones. Sequencing the genomes of these birds won’t allow us to determine which genes are involved in this divergent ecological adaptation because all Woodhouse’s and California scrub-jays differ at thousands of regions across the genome owing to their millions of years evolving in isolation. But, thanks to recombination between California and Woodhouse’s scrub-jay genomes in hybrid offspring, we should be able to test statistically for an association between each variable site in the genome and the phentoype we are interested in (bill morphology). This project is ongoing but I hope to have some cool results soon.
Current papers investigating hybrid zones as windows into the speciation process
DeRaad, D. A., Applewhite, E. E., Tsai, W. L., Terrill, R. S., Kingston, S. E., Braun, M. J., & McCormack, J. E. (2023). Hybrid zone or hybrid lineage: a genomic reevaluation of Sibley’s classic species conundrum in Pipilo towhees. Evolution. 77(3), 852-869.