Speciation typically occurs when two populations split and begin to accumulate genetic differences. My group studies the process of how these genetic differences accumulate in a variety of organisms ranging from Drosophila to human pathogens. The ultimate aim of my lab is to understand the genetic basis of speciation and disentangle what factors lead to biological diversity. As a group, we tackled bold questions and are not constrained by biological systems; we will follow the data wherever it takes us. We use a range approaches that include classical genetics, field biology, genomics and phylogenetic reconstruction.
Speciation in pathogens
There are a number of endemic fungal diseases that affect Latin America particularly severely that I studied as a microbiology student in Colombia. Because these diseases are endemic to the tropics, they are under-studied by scientists in North America and Europe despite their relatively large disease burden and their likely march north with climate change. I generated the largest population genetics sample for the genus Paracoccidioides and described the existence of three previously unreported species. I also applied population genetics to develop diagnostic tools to aid the identification of genetic groups within this pathogenic fungus. My findings revealed unknown diversity among these pathogens, explored their evolutionary histories, and developed molecular methods for diagnosing them from clinical samples. Examples of lab publications:
Mavengere, H., Mattox, K., Teixeira, M.M., Sepulveda, V., Gomez, O., Hernandez, O., McEwen-Ochoa, J.G. and Matute, D.R., 2020. Paracoccidioides genomes reflect high levels of species divergence and little interspecific gene flow. mBio. 2020 Dec 22;11(6):e01999-20
b.Matute DR, Sepúlveda VE. Fungal species boundaries in the genomics era. Fungal Genetics and Biology. 2019 Jul 4:103249. [Indexed for MEDLINE] c.Matute DR, Sepúlveda VE. Fungal species boundaries in the genomics era. Fungal Genetics and Biology. 2019 Jul 4:103249.Maxwell C.S., Sepulveda V.E., Turissini D. A., Goldman W.E., and Matute D.R. Recent admixture between species of the fungal pathogen Histoplasma. Evolution Letters, 2018. 2: 210-220. doi:10.1002/evl3.59 d.Sepúlveda VE, Márquez R, Turissini DA, Goldman WE, Matute DR. Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum. MBio. 2017 Dec 5;8(6). pii: e01339-17. doi: 10.1128/mBio.0133PMC5717386
Hybrid zones
When two closely related species overlap in their range and have the chance to interbreed, the completeness of speciation completeness of speciation is put to the test. If hybrids are formed, the two species could collapse back into a single interbreeding group, or the hybrids could suffer enough of a fitness deficit or be formed rarely enough that the species stay distinct. This process had been described more by evolutionary theory than observed by naturalists in the field, and the predictions of theory sorely needed testing in empirical settings. My graduate and postdoctoral fieldwork identified five hybrid zones in four different, increasing the number of known Drosophilahybrid zones to six. I assessed the species and hybrids found in these regions genetically as well as for traits related to ecological and behavioral speciation, to learn how interactions between organisms and their environment contribute to the stability of species. This line of research has led to the development of probabilistic frameworks to identify shared ancestry in hybridizing species.
Examples of lab publications:
Cooper BS, Sedghifar A, Nash WT, Comeault AA, Matute DR. A Maladaptive Combination of Traits Contributes to the Maintenance of a Drosophila Hybrid Zone. Curr Biol. 2018 Aug 11. pii: S0960-9822(18)30904-7. doi: 10.1016/j.cub.2018.07.005. PMCID: PMC6402799
Turissini DA, Matute DR. Fine scale mapping of genomic introgressions within the Drosophila yakuba clade. PLoS Genet. 2017 Sep 5;13(9):e1006971. doi: 10.1371/journal.pgen.1006971. PMCID: PMC5600410
Schrider DR, Ayroles J, Matute DR, Kern AD. Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. PLoS Genet. 2018 Apr 23;14(4):e1007341. PMCID: PMC5933812
Cooper BS, Ginsberg PS, Turelli M, Matute DR. Wolbachia in the Drosophila yakuba Complex: Pervasive Frequency Variation and Weak Cytoplasmic Incompatibility, but No Apparent Effect on Reproductive Isolation. Genetics. 2017 Jan;205(1):333-351. doi: 10.1534/genetics.116.196238. Epub 2016 Nov 7. PMCID:PMC5223512
Hybrid inviability One way to study the evolution of reproductive isolation is to identify alleles involved in inviability of hybrids. However, hybrid inviability signals more than just the evolution of reproductive isolation: it signals functional divergence in developmental pathways beyond what could be predicted from sequence divergence because it screens for genetic function. Our goal is to understand how function changes as divergence unfolds. We focus on species pairs that are highly diverged (10-15 mya) but still can interbreed and produce viable offspring. Our lab studies multiple hybrid crosses to not only dissect what genes cause inviability but also to reveal precisely how they do it and what are the evolutionary processes that have led to their divergence.
Examples of lab publications: Turissini DA, McGirr JA, Patel SS, David JR, Matute DR. The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila. Mol Biol Evol. 2018 Feb 1;35(2):312-334. doi: 10.1093/molbev/msx271. PMC5850467 Matute DR, Gavin-Smyth J, Liu G. Variable post-zygotic isolation in Drosophila melanogaster/D. simulanshybrids. J Evol Biol. 2014 Aug;27(8):1691-705. [Indexed for MEDLINE] Matute DR, Gavin-Smyth J. Fine mapping of dominant X-linked incompatibility alleles in Drosophila hybrids. PLoS Genet. 2014 Apr 17;10(4):e1004270. P PMCID: PMC3990725. Matute DR, Butler IA, Turissini DA, Coyne JA. A test of the snowball theory for the rate of evolution of hybrid incompatibilities. Science. 2010 Sep 17;329(5998):1518-21.
Experimental speciation
Evolutionary biologists often study events that happened in the ancient past, or events that have unfolded of thousands if not millions of years. Studying evolution in an experimental setting has largely been limited to microbes as focal organisms because of their fast generation time, fast mutation rate, and the ease of keeping them in massive population sizes necessary to see chance mutations arise and take hold. I discovered that the trait of reinforcement that I documented in wild populations of D. yakuba on the island of São Tomé evolves rapidly under artificial selection in the lab. I used this finding to conduct experiments on various factors that might affect the speed or efficacy of selection, to empirically test theoretical limits to the evolution of reinforcement.
Examples of lab publications:
Matute DR. Noisy neighbors can hamper the evolution of reproductive isolation by reinforcing selection. Am Nat. 2015 Feb;185(2):253-69.
Matute DR. The role of founder effects on the evolution of reproductive isolation. J Evol Biol. 2013 Nov;26(11):2299-311.
Matute DR. Reinforcement can overcome gene flow during speciation in Drosophila. Curr Biol. 2010 Dec 21;20(24):2229-33. PMCID: PMC3019097.
Comeault AA, Matute DR. Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation. Proc Natl Acad Sci U S A. 2018 Sep 12. pii: 201809685. doi: 10.1073/pnas.1809685115. PMCID: PMC6166845