About the Blog Author
Laura Céspedes Arias (she/her) is a PhD candidate in the Committee on Evolutionary Biology at the University of Chicago and a Research Associate at the Birds collection of the Field Museum, working under the supervision of Dr. John Bates. She is interested on using genomic data from natural hybrid zones to explore genetic mechanisms that maintain species boundaries in the face of gene flow. Her dissertation research focuses on a species complex of colorful warbler (Myioborus ornatus-melanocephalus, Figure 1) that occur in the high Andes (Figure 2) and hybridize in the Colombia-Ecuador border.
Hybrid zones are geographic areas where differentiated populations or species meet and interbreed. Although reproductive isolation is by definition incomplete in hybrid zones, hybrids often exhibit lower fitness compared to parental individuals, which can effectively limit gene flow and help maintain species differentiation (Coughlan and Matute 2020; Irwin 2020). Studies of natural hybrid zones are, therefore, important to increase our understanding on how species originate and are maintained over time.
Even if hybrids are viable and fertile, other less severe forms of hybrid dysfunction can restrict gene flow. For example, behavioral and physiological studies in birds show hybrids may have reduced cognitive abilities (McQuillan et al. 2018), disrupted metabolic functions (McFarlane et al. 2016), or selection against intermediate plumage traits (Svedin et al. 2008). However, the causes of lower fitness on hybrids can be numerous, complex, or unfeasible to measure in the field or the lab. An alternative approach is to study the signatures of this selection in the genomes of hybrids.
For my dissertation research, I will be analyzing whole genomes to investigate the genetic architecture of partial reproductive isolation in a hybrid zone between two colorful Andean warblers (Myioborus ornatus and M. melanocephalus) (Figure 1), in close collaboration with Dr. Elisa Bonnacorso (Universidad San Francisco de Quito) and Dr. Andres Cuervo (Universidad Nacional de Colombia). These species have striking differences in their plumage coloration, despite showing remarkable morphological and ecological similarities. My previous research on plumage variation (Céspedes-Arias et al. 2021) shows that the two species hybridize near the border between Colombia and Ecuador. This hybrid zone extends over roughly 200 km, with hybridization occurring over multiple generations, leading to a wide diversity of intermediate plumage types. Despite the extensive hybridization, the hybrid zone is restricted to a small portion of these species’ ranges, indicating that likely some form of selection is preventing a complete collapse of the two species into one.
To study the genome-wide signatures of selection against hybrids in this hybrid zone, I will infer local ancestry in the genomes of these hybrids, which consists of identifying the origin of different “chunks” of DNA in the genomes to determine which parental species each “chunk” originates from (Schumer et al. 2020). I will employ a novel statistical approach (Groh and Coop 2024) to describe the length of these “chunks” of different ancestry and how these lengths vary across the genome. The length of these blocks in the genomes of hybrids is shaped over generations by recombination and selection, so by documenting recombination rates I can detect effects of selection (Sedghifar et al. 2016; Groh and Coop 2024). This approach allows me to both identify genomic regions likely involved in selection against hybrids and make inferences about the timing of that selection.
Thanks to the EECG award, as well as other small grants, I have completed field and lab work and will be starting data analysis soon. Together with my collaborators, past and present, I have completed the collection of Myioborus specimens and associated tissue samples across multiple localities in Colombia and Ecuador (Figure 2, Figure 3). These tissue samples include some obtained in previous collecting efforts across the hybrid zone (Céspedes-Arias et al. 2021), and some collected by myself and collaborators in the summer of 2024 (Figure 3). Using these samples, I then conducted DNA extractions and genomic library preparation at the Pritzker Lab in the Field Museum. These genomic libraries are now being sequenced. During the field collection last summer, we also preserved samples of sperm and testes of individuals in both parental populations and the hybrid zone, which I plan to use to conduct bulk gamete sequencing to infer recombination rates across the genome of these warblers (Peñalba & Wolf 2020, Dréau et al 2019) in the near future.
In total, I will be obtaining whole genome resequencing data for over 140 individuals from parental populations and the hybrid zone, which I will assemble based on a reference genome available with a collaboration with the Cadena Lab at Universidad de los Andes (Colombia). The assembled genomes will be used to conduct local ancestry inferences. This dataset of over 100 whole genomes, rare for natural hybrid zones, will allow me to study how recombination and selection have shaped the genomes of these hybrid warblers, and more broadly to contribute to an exploration of the mechanisms that maintain species boundaries in the face of gene flow across a diversity of non-model taxa.
References
Céspedes-Arias, L. N., Cuervo, A. M., Bonaccorso, E., Castro-Farias, M., Mendoza-Santacruz, A., Pérez-Emán, J. L., … & Cadena, C. D. (2021). Extensive hybridization between two Andean warbler species with shallow divergence in mtDNA. The Auk, 138(1), ukaa065.
Coughlan, J. M., & Matute, D. R. (2020). The importance of intrinsic postzygotic barriers throughout the speciation process. Philosophical Transactions of the Royal Society B, 375(1806), 20190533
Dréau, A., Venu, V., Avdievich, E., Gaspar, L., & Jones, F. C. (2019). Genome-wide recombination map construction from single individuals using linked-read sequencing. Nature Communications, 10(1), 4309.
Groh, J. S., & Coop, G. (2024). The temporal and genomic scale of selection following hybridization. Proceedings of the National Academy of Sciences, 121(12), e2309168121.
Irwin, D. E. (2020). Assortative mating in hybrid zones is remarkably ineffective in promoting speciation. The American Naturalist, 195(6), E150-E167
McFarlane, S. E., Sirkiä, P. M., Ålund, M., & Qvarnström, A. (2016). Hybrid dysfunction expressed as elevated metabolic rate in male Ficedula flycatchers. PloS one, 11(9), e0161547
McQuillan, M. A., Roth, T. C., Huynh, A. V., & Rice, A. M. (2018). Hybrid chickadees are deficient in learning and memory. Evolution, 72(5), 1155-1164.
Peñalba, J. V., & Wolf, J. B. (2020). From molecules to populations: appreciating and estimating recombination rate variation. Nature Reviews Genetics, 21(8), 476-492.
Schumer, M., Powell, D. L., & Corbett‐Detig, R. (2020). Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer. Molecular ecology resources, 20(4), 1141-1151.
Sedghifar, A., Brandvain, Y., & Ralph, P. (2016). Beyond clines: lineages and haplotype blocks in hybrid zones. Molecular ecology, 25(11), 2559-2576.
Svedin, N., Wiley, C., Veen, T., Gustafsson, L., & Qvarnström, A. (2008). Natural and sexual selection against hybrid flycatchers. Proceedings of the Royal Society B: Biological Sciences, 275(1635), 735-744.