DNA barcoding and portable sequencing technology

The Molecular Lab team at the Wildlife Conservation Society works on an array of projects that employ various DNA barcoding (single gene barcoding, metabarcoding, metagenomics) techniques for conservation-related problems (particularly related to species identification to combat the illegal wildlife trade) and documenting biodiversity in remote, under-studied regions.

The illegal wildlife trade is a ~$7-23 billion industry with links to terrorism and drug and human trafficking. Species identification from processed products (e.g., fin, shark liver oil) or mixed species samples of illegally caught species is difficult and complicates law enforcement, but recent advances in portable lab equipment and bioinformatics software can help to address these challenges. I helped to develop field- and user-friendly bioinformatic analysis pipelines for species ID using the Oxford Nanopore Technologies MinION portable sequencer.

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We also used metabarcoding and whole genome shotgun sequencing to examine both the microbial and Eukaryotic communities at several high-altitude aquatic sites. Montane environments, with their extreme conditions, offer the perfect opportunity to study ecosystems experiencing climate change. The remote biological communities of the Himalayas are difficult to study and few genetic studies have been carried out to document their biodiversity across the Tree of Life.

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On the evolution and diversification of hummingbirds

At first look, the harsh physical conditions of the Andes should impose serious physiological constraints on hummingbirds, but instead, they have a wide distribution and are abundant at high altitudes. Several studies suggest highland species are well adapted to these challenging conditions. Genetic adaptation is difficult to study in non-model organisms, especially as laboratory experiments are impractical for long-lived species. However, new genomic methods have revealed specific amino acid changes, genes, and biochemical pathways that are repeatedly involved in adaptation to survival in high altitude environments.

My dissertation research investigated two questions: 1) What is the genetic basis for high-altitude adaptation in Andean hummingbirds? And 2) Are the mechanisms the same across divergent taxa and populations?

Parallel molecular evolution can occur at any of several hierarchical levels of biological organization. Collectively, my results for Andean hummingbird species and populations indicate there is predictability in the genetic mechanisms of adaptation to high altitude, although there are a variety of adaptive paths. By investigating how organisms evolved to thrive in challenging environmental conditions, we can illuminate the mechanisms of evolution and refine future study of the units on which evolution acts.

These projects were done in collaboration with the Dávalos lab, the Graham lab, Dr. Chris Witt, and Dr. Ke Bi.

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Graduate student research funding from:

  • American Genetic Association Evolutionary, Ecological, or Conservation Genomics Award
  • American Museum of Natural History Frank M. Chapman Memorial Fund
  • American Society of Naturalists Student Research Award
  • National Science Foundation Doctoral Dissertation Improvement Grant
  • Wilson Ornithological Society Research Grant
  • American Ornithologists’ Union Research Award
  • Stony Brook University Dept. of Ecology and Evolution Slobodkin Fund, Williams Fund
  • National Science Foundation Graduate Research Fellowship

Species delimitation in Otospermophilus ground squirrels

We studied species delimitation and population demography of the Otospermophilus genus of ground squirrels. Accurate species designations are vital because their diagnosis informs us about species diversity and has practical applications in conservation biology, public health, and pest management. Our team generated genetic (mtDNA, microsatellite, nuclear DNA), morphological, and ecological data to study the evolutionary history of this genus. Our results support the division of O. beecheyi into two species.

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Population connectivity and desert colonization of California voles

We conducted a statewide study of the phylogeographic distribution of California voles (Microtus californicus) to measure connectivity between populations and to discover the colonization history of voles in the deserts via ancient riparian corridors. This research also focused on measuring genetic structure amongst isolated desert populations of the Owens Valley vole (M. c. vallicola), a California Species of Special Concern, in collaboration with the California Department of Fish and Wildlife.

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Climate change and genetic diversity in Tamias chipmunks

Over the last century, there has been ~3°C increase in temperature in Yosemite National Park. Ecological surveys conducted by the Grinnell Resurvey Project at the Museum of Vertebrate Zoology found that the high-elevation Alpine chipmunk’s (Tamias alpinus) range contracted through time, while the more widespread Lodgepole chipmunk (T. speciosus) maintained a stable range. Consistent with habitat fragmentation, our genetic results showed that modern populations of T. alpinus had greater population subdivision but lower overall genetic diversity compared to historic populations. In contrast, T. speciosus showed no significant changes in genetic diversity over time. This study provides empirical evidence that climate change affects genetic diversity and demonstrates the value of museum specimens for tracking changes in population demography through time.

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