Biology, Stanford University

Banner image of plants and landscape from HF field work in Costa Rica

Selected Ongoing Research Projects

world map with research localities

Lagomorph population response to Quaternary environmental change in the Great Basin

North America mammal community response to climate change of past, present, and future.

Neogene paleo-environments of Central America

Extinction and diversification dynamics in insular lizard communities

Interaction of habitat change, disease, and evolution in Neotropical bats

Tiger distribution and genetic diversity in Asia

Evolutionary consequences of tropical deforestation for neotropical frogs

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

Genetics and distribution of Himalayan pika species

Evolutionary dynamics and conservation genomics of endemic insectivorous mammals

Ongoing Research Project Highlights

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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Hypoxia-tolerance in pikas (Genus Ochotona)

My research investigates the mechanisms underlying species tolerance of extreme environments, focusing on pika (genus Ochotona). There are 30 pika species, each occupying a unique elevational range between 0 - 6400 m with at least 14 species inhabiting elevations above 4000 m. Limited oxygen at high elevation stresses aerobic metabolism, and unique adaptations to this environment have been found in every high-elevation species studied to date. However, there is still much to learn about how pikas are capable of tolerating the extreme hypoxia of their high-elevation habitat. Additionally, climate change is causing many pika species to shift their ranges up in elevation. Through the utilization of museum tissue samples, extensive field work in the Indian Himalayas, and the only captive colony of pikas in the world, I have investigated hypoxia tolerance in pikas from three different angles: (1) molecular evolution in mitochondrial candidate genes; (2) variation in gene expression along an elevational gradient within a population; and (3) plasticity in gene expression within an individual in response to hypoxia.

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Evolution and conservation of the Solenodon, an endangered venomous mammal


The family Solenodontidae contains two highly enigmatic extant species, the Cuban and Hispaniolan solenodons. Molecular data suggests that solenodons diverged from all other Eulipotyphlan mammals (shrews, hedgehogs, moles) 76 million years ago. This ancient divergence combined with a low diversification rate makes this lineage highly evolutionarily distinctive. Both species are listed as Endangered by the IUCN.

I am focusing on the Hispaniolan solenodon within the broader phylogenetic context of all Eulipotyphlan mammals and the broader ecological context of the Greater Antilles. I am following in the footsteps of previous conservation-oriented radiotelemetry research done by The Last Survivors by pioneering non-invasive techniques such as genetic analyses using fecal samples to study the relatedness of solenodons sharing dens and gender-biased dispersal patterns. For a more evolutionary approach to conservation, I will integrate subfossil, historic, and modern DNA to study solenodon demographic responses through time to ancient climate change and modern patterns of deforestation. I hope to apply my phylogeographic studies to delimit subspecies and areas of high genetic diversity for conservation planning.

In addition to population-level studies of the solenodon, I am taking a candidate-gene approach to study the genetic underpinnings and gene expression patterns of solenodon venom production. I am particularly interested in patterns of molecular evolution of venom-related genes within all Eulipotyphlan mammals.

Undergraduate Research: I currently have two undergraduate research assistants. Honors student Laura Cussen is using geometric morphometric techniques combined with ancient DNA and isotopes to study the only other Eulipotyphlan mammals of the Caribbean, the now extinct family Nesophontidae. Alan Propp is developing a morphological dataset to help understand the co-evolution of venom genes and morphological envenomation apparatuses in Eulipotyphlan mammals.

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Hadly Lab, Department of Biology, Stanford University, Stanford, CA 94305-5020
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