My research can be broadly split into two main themes:
Understanding the processes responsible for rapid speciation and phenotypic differentiation in an explosive radiation of South American finches in the genus Sporophila, known as the capuchino seedeaters.
Understanding the patterns of genetic differentiation among individuals and populations across landscapes, with the objective of uncovering the geological and demographic processes that contribute to genomic differentiation, primarily in Neotropical birds.
Understanding the processes responsible for rapid speciation and phenotypic differentiation in an explosive radiation of South American finches in the genus Sporophila, known as the capuchino seedeaters.
Understanding the patterns of genetic differentiation among individuals and populations across landscapes, with the objective of uncovering the geological and demographic processes that contribute to genomic differentiation, primarily in Neotropical birds.
Understanding the speciation process through the lens of the rapid capuchino radiation
Small songbirds have given rise to some of the most spectacular radiations in vertebrates, including Darwin’s finches and the Hawaiian honeycreepers. These biological systems have allowed researchers to explore the processes that govern local adaptation and speciation across ecological, behavioral, physiological, and genomic perspectives. Since the beginning of my PhD dissertation I have worked to understand a similarly explosive radiation of South American finches in the genus Sporophila, the capuchino seedeaters. Capuchino seedeaters are a group of ten species that are closely related to Darwin's finches. Both groups have comparable speciation rates, which are much higher than that of other tanagers (the avian family to which both radiations belong). Whereas Darwin's finch species differ most notably in the beak morphologies that allow them to exploit different food resources, capuchino seedeaters show extreme differences in sexually selected traits like male plumage and song, but are otherwise morphologically and genetically very similar (1-4), and they can still produce viable offspring in aviaries (5). Results from field experiments suggest male traits govern species recognition and territorial defense (6). In particular, the evolution of song—a mostly culturally inherited and thus evolutionarily liable character in these birds—could have played a key role in driving this radiation. The capuchinos are therefore a radiation in which sexual selection has likely been central in shaping diversification, in contrast to Darwin’s finches and other groups in which natural selection has sparked adaptive radiations.
For different aspects of this work I have deployed a wide variety of comparative genomic approaches, including reduced-representation methods, whole genome sequencing and assembly, and comparative whole genome re-sequencing to search for key areas of the genome that are diverged among these otherwise genetically similar, yet phenotypically variable, taxa. These studies have revealed that a small number of divergent genomic areas, located in the vicinity of pigmentation genes, are the main genetic differences among the southern capuchinos, and presumably the genes responsible for the variation in male coloration patterning (7). Capuchinos are a particularly tractable system for testing processes of genome evolution because so many species have evolved in such a short period of time, allowing for the replication to test whether the same loci are independently involved in the divergence among the different species of the group. Many of the divergent regions of the genome are involved repeatedly in pairwise comparisons of non-overlapping species pairs, and thought to contain regulatory areas which control the expression of pigmentation genes. By deploying machine learning methods and statistics derived from ancestral recombination graphs, my collaborators and I have shown that these same areas have been targets of recent, species-specific, selective sweeps (8). It is likely that the rapid phenotypic diversification in the capuchino seedeaters has been facilitated by hybridization, which has allowed the reshuffling of genetic variation and the generation of novel phenotypes (i.e., old mutations in new combinations) that are targeted by sexual selection. Assortative mating based on these traits may maintain species boundaries early in speciation while subsequent reproductive barriers accumulate (9). |
Identifying the climatic, geological and demographic processes that contribute to genomic differentiation
I have used a wide variety of genetic approaches—phylogenetics, phylogeography, population genetics/genomics, and landscape genetics/genomics—to study organisms at different degrees of divergence and sampled them using different designs (e.g., prioritizing individuals versus loci or vice versa). Most recently I've been using genomic techniques, including both reduced-representation approaches and whole genome sequencing, that allow us to detect population differentiation with spectacularly greater resolution. I am particularly interested in using computational methods to conduct demographic inferences of key population genetic parameters such as divergence times, effective population sizes and migration/hybridization rates. I often take a comparative phylogeographic approach and most (but not all) of my work has focused on Neotropical bird species.
The general motivation that links these studies is to accumulate knowledge about the drivers of population differentiation and speciation in the Neotropics, the most species-rich area of the world in terms of its avian biodiversity. My strategy with capuchino seedeaters (described above) is to study one system in depth using a variety of approaches and tools; the objective of these other studies is to make broad inferences about general processes that have (and in some cases may continue to) shape Neotropical diversity. This requires studies on various taxa spanning many different biomes to distinguish taxon-specific effects from more general processes. The studies I have conducted in these areas have highlighted the importance of river barriers, including areas of endemism in the Amazon, the role of the Andes and the glaciations (especially at high latitudes), the dynamic history of connectivity of different habitat types, and the effect of human-mediated forest fragmentation in shaping the genomes of various Neotropical taxa. I am particularly interested in evolutionary transitions which occur in island taxa, like the evolution of flightlessness in the ducks of the genus Tachyeres (10). Relevant Publications:
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