RESEARCH
My research broadly focuses on leveraging the biological information contained in the genomes to understand the evolutionary processes that generate and maintain variation (both genetic and phenotypic) across organisms.
Epigenetics of flexible homeostasis in mammals
All organisms have evolved mechanisms to cope with environmental variation. The ability to adapt to diverse and often challenging conditions stands as a cornerstone of life on our planet. However, the degree of resilience to various stressors varies among species. My research delves deeply into understanding how cells of diverse species of mammals have evolved strategies to thrive in the face of extreme environmental conditions. Fruit bats experience high levels of blood glucose when feeding, camels and squirrels’ body temperatures fluctuate widely in hot and cold environments, and deep-diving mammals, such as whales and seals, deplete blood oxygen during submergence. Remarkably, these species maintain homeostasis even under such atypical abiotic conditions. The cellular and epigenetic mechanisms underlying this remarkable robustness remain largely unknown.
To investigate how cellular epigenotypes respond to these environmental perturbations, I am employing an innovative “common-garden” experiment culturing dermal fibroblasts from several species of mammals across a range of temperature, glucose, and oxygen conditions and measuring their differences in response. I am implementing a multi-omics approach, collecting data on cell physiology, cell morphology, gene expression (RNA-seq), chromatin accessibility (ATAC-seq) and applying statistical modeling to infer gene-regulator interactions and uncover key driver genes.
This ongoing research holds great promise for elucidating epigenetic mechanisms that promote cellular robustness and environmental adaptation and offers promising avenues for developing therapies against diseases of compromised homeostasis.
Comparative genomics of local adaptation
One question of particular interest in evolutionary biology is the relative role of determinism and stochasticity in evolution. If independent lineages are subjected to the same selective forces, how often will they adapt via the same genetic mechanisms? In the past decades an increasing body of empirical studies have suggested that genetic parallelism is more common than previously thought. Such repeated use of the same loci during independent episodes of adaptation indicate particular constraints on the number of evolutionary pathways available for evolution, as some genes might contribute more often to adaptation than others. Under such circumstances, closely related taxa diverging along a similar environmental gradient, such as North America’s latitudinal cline, tend to exhibit substantial genetic parallelism, as natural selection will operate on a similar genetic background.
I study the genetic basis of adaptation in two largely sympatric and ecologically similar species of woodpeckers that occur across North American climatic gradient, the Hairy (Dryobates villosus) and Downy (Dryobates pubescens) woodpeckers. These two species are sympatric and syntopic over most of their distribution and exhibit remarkably parallel patterns of geographic variation in plumage and body size. Phenotypic variation, however, is mostly clinal and seems to be strongly correlated with climate (e.g., temperature and precipitation), suggesting a potential effect of natural selection in shaping phenotypes.
Considering the ecological similarities between the Downy and Hairy woodpeckers and the variety of biotic and abiotic selective pressures they have shared throughout their evolutionary history, one question that arises is whether the genes that have been targeted by natural selection are the same in both species. In other words, did evolution operate on the same genetic mechanisms to promote local adaptation in the Downy and Hairy Woodpeckers? I am currently using several methods to look for signatures of selection that might shed lights on the genetic mechanisms promoting local adaptation in these two species.
Factors shaping the genomic landscape of diversity
Levels of genetic diversity vary widely along the genome, as a results of both extrinsic (e.g. demography, natural selection) and intrinsic factors (e.g. mutation rate, recombination rate, base composition). Despite this variation, the genomic landscape of diversity is often highly correlated among closely-related species.
In order to elucidate the factors underlying this correlation, I explore the role of shared demographic history, natural selection, and recombination rate variation in patterns of genetic diversity along the genome of the Hairy and Downy woodpecker. These two sympatric species share common selective pressures, a conserved recombination landscape, and have been severely affected by the climatic fluctuations of the Quaternary, which makes them a good system to understand the contribution of these different predictors.
Landscape genomics and biogeography of Neotropical birds
Spatial patterns of intraspecific variation can be driven by geographic distance among populations (isolation-by-distance), historical changes in gene flow (isolation-by-history), and environmental heterogeneity (isolation-by-environment). Although these processes are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation.
I combine genomic, phenotypic, and environmental information to explore the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits marked geographic variation in body size across its range.