Evolutionary consequences of tropical deforestation for neotropical frogs

This research project revolves around two major themes. First, mechanistically, how does local deforestation determine which species can survive after habitat conversion? Second, how has deforestation combined with ancient evolutionary patterns to influence the recent evolution trajectory of species in human-dominated landscapes? To address these questions I'm focused on a pair of closely related neotropical leaf litter frogs in the genus Craugastor that show alternative habitat affinities in our mid-elevation study site in southern Costa Rica; Craugastor crassidigitus is restricted to forest habitat, while Craugastor fitzingeri is found exclusively in open pastures, coffee plantations, urban areas, and very young secondary forest. I've honed in on temperature differences between these habitats as the primary driver explain the difference in habitat affiliation between these species. By comparing how temperature structures occupancy and performance ability at multiple spatial scales, from the regional to the individual I demonstrate how novel human interventions in a landscape (i.e. deforestation) interact with large scale patterns along regional and elevational gradients in temperature. Going forward I intend to assess how both neutral and adaptive genetic variation in these species has been shaped by recent human impacts in the system, and to gain an appreciation of the roles of both contemporary evolution, and preadaptation, in determining the ability of species to survive and thrive in a human dominated world.

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Extinction and diversification dynamics in insular lizard communities

I am broadly interested in how environmental perturbations (such as climate change, sea level rise, and volcanism) impact biodiversity through time and space. My research focuses on the dynamics of extinction and diversification in the Caribbean lizard fauna. The Caribbean is a model system for insular studies, as it has over 7,000 islands, cays, and islets of varying size, geological substrate, and age. A geologically complex region, its biodiversity has been shaped by volcanism, plate tectonics, and sea-level fluctuations. The region is a biodiversity hotspot, hosting numerous endemic flora and fauna in addition to widespread species (some of which were introduced into the archipelago by humans). The lizards of the Caribbean are morphologically and genetically diverse. The iconic lizard genus Anolis has over 150 species in the Caribbean, and countless new species in this genus (and other genera that have been poorly studied to date) are still being described. Despite the high biodiversity that we encounter today, little is known about how this biodiversity accumulated, and to what extent it has been eroded.

This is a persistent problem in evolutionary biology that I aim to address. My approach is to use the Quaternary fossil record to examine extinction bias, changes in genetic diversity, and body size evolution in the Caribbean lizard fauna. Despite the humid, warm climate, there are significant subfossil deposits in the Caribbean, found on each Greater Antillean island and many Lesser Antillean localities as well. I have successfully amplified ancient DNA from Caribbean lizard subfossils and will use these data to reconstruct the genetic diversity of lizard species, and see how biotic and abiotic perturbations influence population sizes and population connectivity.

I am currently in the process of synthesizing data on all fossil occurrences of lizards in the Caribbean to understand regional patterns in species turnover and put extinction events in the context of island area change and human colonization. My hope is to elucidate how species have responded to perturbations in the past, and use this information to inform not only their current status, but also how they might respond to future stressors.

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Tracing the impact of environmental stressors on the population genetics of tuco-tucos over time

I am studying the impact of volcanism on the genetics and genomics of the tuco-tuco, a rodent genus endemic to South America. More specifically, in collaboration with the Lacey lab at the University of California-Berkeley, I am focusing on the social tuco-tuco (Ctenomys sociabilis), a species that is listed as critically endangered by the IUCN. My research will tie together population genetics, genomics, demography, and theoretical modeling to better elucidate the genetic responses of C. sociabilis after a catastrophic event.

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Genetics and distribution of Himalayan pika species

What are the genetic and genomics adaptations that underlie Himalayan pikas' ability to survive in severely hypoxic conditions? Himalayan pikas are being forced to higher elevations due to climate change but some of these species may not have the genetic adaptions necessary to survive the hypoxia of their new higher elevation habitat. Through a candidate gene approach, looking at mitochondrial genes and hemoglobin genes, as well as a less targeted genomics approach we are hoping to identify genetic adaptations to hypoxia in different Himalayan pika species. By looking at how adaptations are distributed across the pika phylogeny we also hope to gain new insight into the mechanisms driving evolution at high altitudes.

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Evolutionary dynamics and conservation genomics of endemic insectivorous mammals

Phylogenetic Reconstructions -- Molecules and Morphology

It is has been established by molecular markers that Solenodons are a basal lineage of Eulipotyphlan mammals that diverged ~76 million years ago during the separation of the proto-Antilles from North America. However, little is known regarding possible relatives of ancestral Solenodons in North America.

Recent mass extinctions in the Caribbean have further obscured our knowledge of the biogeographic and evolutionary history of Caribbean Eulipotyphlans. There have existed up to 4 species of Solenodon with 2 recently extinct (S. marcanoi and S. arrendondo) and 9 species within the extinct genus Nesophontes (island-shrews). Nesophontes sp. may be closely related to Solenodons or instead related to true shrews (Soricidae).

I will use geometric morphometrics and ancient DNA to elucidate the species-level relationships within Nesophontes existing on different islands, and the Nesophontes genus as a whole to other Eulipotyphlan mammals. I will also investigate the validity of species distinctions for extinct Solenodons and determine their patterns of speciation based on phylogenetic reconstructions.

Macroecology and Body Size Evolution

The Greater Antilles, prior to Holocene extinctions, was home to myriad endemic sloths, primates, rodents, and Solenodons/Nesophontes. Using existing data on body size and morphology from fossil mammals and geometric morphometric data I have collected on Solenodons/Nesophontes, I will reconstruct the mammalian paleocommunity of the Greater Antilles to assess trends in island biogeography and selectivity of extinction.

I will use geometric morphometric data overlaid on phylogenetic reconstructions to assess patterns in the distribution of body size for Nesophontes and Solenodons, as they relate to speciation and extinction dynamics. I will place Caribbean Eulipotyphlans in the larger context of global Eulipotyphlan body size distributions.

Conservation Genetics/Genomics and Paleobiology

Both extant species of Solenodons (S. cubanus of Cuba and S. paradoxus of Hispaniola) are listed as endangered by the IUCN due to habitat loss associated with deforestation and predation by invasive predators (feral dogs and cats, mongooses).

Solenodons are also listed by the EDGE of Existence program (Zoological Society of London) as highly evolutionarily distinct species whose loss would disproportionately erase living evolutionary history. I am working with conservationists associated with non-governmental organizations, The Last Survivors and Grupo Jaragua, to facilitate genetic sampling of the Hispaniolan solenodon for ddRADseq, mitochondrial, and nuclear DNA analyses of population structuring for conservation priorities. I also plan to sample Cuban individuals in the future.

If you are interested in supporting conservation efforts for solenodons, please see the EDGE of Existence webpage.

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