Research Associates & Post-docs

Dr. Clare Marsden (Affiliated member)
cmarsden(at)ucla(dot)edu

I joined Kirk Lohmueller’s lab in September 2013 on a Computational Biosciences Institute Postdoctoral Fellowship in Bioinformatics. I am currently involved in two research projects. The first, which is being conducted in collaboration with the Wayne lab, is investigating signatures of demography and selection in the genomes of the domestic dog and their wild progenitor, the grey wolf. The second is a forensic genetics project focused on the development of new analytical approaches for low template andmixed DNA samples. In addition to these research projects, I also conduct bioinformatics training workshops for UCLA graduate students, post docsand staff. Prior to my position at UCLA I spent 3 years as a postdoc at the University of California Davis conducting research into the population genetics and genomics of two African mosquito malaria vectors; Anopheles gambiae s.s. and Anopheles arabiensis. Before this, I completed my PhD on the evolutionary and ecological genetics of the endangered African wild dog (Lycaon pictus) at the University of Glasgow. It was during my PhD on wild dogs, that I first met the Wayne lab as a visiting graduate student. [CV - Publications]


Dr. Alice Mouton (Postdoctoral Researcher)
amouton(at)ucla(dot)edu

I am an international post doc of the Wayne lab since August 2015. My research interests are mainly related to the rodent’s evolutionary history, with a particular interest for the biological and genetic diversity of animal populations in order to promote conservation. My PhD project (University of Liege, Belgium) focused on the phylogeography and the evolutionary history of a hibernating rodent strictly protected in Europe, the hazel dormouse, Muscardinus avellanarius. I was then involved as a post doc in a metabarcoding project to study the diet and identified species using NGS technologies. I am now highly interested to use genomic resources to increase the understanding of the population’s genetic structures and the mechanisms that enable their responses to environmental changes. Thanks to the Belgian American Education Foundation (BAEF), I now have the opportunity to spend one year to gain expertise in the analyses of genomics data in a conservation context. More specifically, I will focus on the bobcat (Lynx rufus) of the Santa Monica Mountain Area (CA). Using a RNA-seq approach, we will compare the gene expression between bobcats exposed and not exposed to anticoagulant rodenticides.


Dr. Meenakshi Roy (Postdoctoral Researcher)
meenakshi(at)mbi(dot)ucla(dot)edu

Dog brain transcriptome. see Collaborative Projects for more information


Graduate Students

Tiffany Armenta
tarmenta(at)ucla(dot)edu

I am a 5th year PhD candidate co-advised by Robert Wayne and Dan Blumstein with broad interests in animal personality and decision making. To better understand how free-ranging animals behave when under pressure, I am integrating next-gen sequencing, direct behavioral observations and spatial analysis on a well studied population of yellow-bellied marmots (Marmota flaviventris) at the Rocky Mountain Biological Laboratory (RMBL). Each summer our team collects genetic, hormonal, and behavioral data on these animals, resulting in a rich data set that enables us to link phenotypic and genetic traits in unique ways. A major focus of my research is comparing gene expression motifs of yearling marmots, which display extensive variation in behavioral personalities. Some yearlings are very socially gregarious, while others are relatively asocial. In addition, yearlings experience varying degrees of social pressure from conspecifics to disperse from the natal colony. By quanitfying gene expression patterns in this age group, I hope to detect a physiological response to social stress as well as how young animals physiologically prepare for dispersal events.

Learn more about RMBL marmots and my other scienTIFFic interests here


Annabel Beichman
annabelbeichman(at)ucla(dot)edu

I am particularly interested in the application of next-generation sequencing to the conservation and management of marine taxa, especially cetaceans (whales, dolphins and porpoises). I received my A.B. from Harvard University in 2012. As an undergraduate, I studied the population genetics of zebra finches, corals, and purple sea urchins. For my senior thesis, I collected right whale fecal samples in the Bay of Fundy and pyrosequenced the bacterial 16S rDNA region to characterize the microbial flora expelled from the right whale gut. After graduation, I have continued to work with my Harvard colleagues to expand our dataset so that we may characterize a wide swathof cetacean gut microbiomes and discover how they have diverged from those of terrestrial mammals. As a graduate student in the Wayne Lab, I am examining the effects of stressors,particularly persistent organic pollutants, on gene expression patterns of dolphins in the Gulf of Mexico and off the coast of California by using next-generation sequencing of RNA (RNA-Seq) to sequence full transcriptomes from skin and blubber samples.


Daniel Chavez
dechavezv(at)ucla(dot)edu

I am broadly interested in the adaptive significance of phenotypic variation among natural populations. In particular, my research focus on identifying the genetic changes responsible for color variation that affects the survival of individuals. To understand this, I use a variety of techniques (ranging from next-gen sequencing and transcriptomics to histological examination of hair follicles and skin areas) on two non-model organisms. First, the African wild dog, a species with a wide variety of color patterns including individuals with red, black, white, brown and yellow color. Second, the South American harvest mouse with melanic populations living on dark soils of the highlands of the Andes, and light-colored individuals living on light soils of inter-Andean valleys. Before entering the PhD program, I was actively studying the genetics and systematics of neotropical rodents in South America with the discovery of several species previously unknown to science. I got my bachelors degree at the Pontifical Catholic University of Ecuador, with a dissertation work focused on studying the genetic morphologic and ecological variation of harvest mice (Reitrodontomys) in the Andes of Ecuador.


Devaughn Fraser
devaughn(at)ucla(dot)edu

Broadly, I am interested in how wildlife is affected by anthropogenic stressors in the environment, with the aim of identifying solutions for best practices to mitigate these threats and to make human-need practices more sustainable. My current research focuses on characterizing the health and dietary responses of bats to pest management strategies in agricultural systems in California. My research synthesizes field-based methods with ecological modeling and advanced molecular sequencing to determine if there are immunological and dietary differences among bat populations across a gradient of insecticide-use. I will apply my findings toward developing a better framework for pest management that considers the important role that bats play. For more information on my research, visit my reasearch page at www.agribats.com.


Audra A. Huffmeyer
ahuffmeyer(at)ucla(dot)edu

I am a first year in the Wayne Lab. I completed my M.S. in EEB at the University of Michigan- Ann Arbor, where I completed my thesis work at Smithsonian Conservation Biology Institute. I studied, and continue to study, the molecular evolution of Apolipoprotein-B in Eutherian mammals. Broadly, I am interested in applying next-generation sequencing techniques to better understand sperm morphology in carnivores. My research explores the consequences of inbreeding on differential gene expression and gene regulation in abnormal sperm, in carnivores. The mechanisms behind abnormal sperm production in wildlife are largely unexplored and are of key concern in conservation breeding to maintain endangered species.


Rachel Johnston
racheljo(at)ucla(dot)edu

A broad objective in biology is to connect complex phenotypes to their genetic bases. I aim to apply several methods to identify genotype-phenotype associations in two non-model species for my PhD thesis. First, I am investigating the molecular mechanisms underlying avian migration, a complex behavioral phenotype shared by a vast number of species across a broad array of lineages. Specifically, I am investigating the genetics of migration in the obligate migratory Swainson’s thrush, Catharus ustulatus, by using RNA-Seq to identify genes up- or down-regulated during migration in captive individuals. I am also examining whether migration-related genes identified in the Swainson’s thrush are conserved at the expression or sequence level in other migratory species. This comparative approach across species will provide insight into the extent to which the same genes and gene mutations underlie a convergently evolved behavior. Finally, I will take an experimental approach to investigate the phenotypes associated with a pleiotropic gene that has been shown to underlie coat color in canids and believed to be involved in mammalian innate immunity. For this study, I’m investigating the allele-specific functions of the canine beta-defensin 103 gene by performing gene expression network analyses on RNA-Seq data from primary cell culture of the gray wolf, Canis lupus. This study will develop a valuable approach for identifying and experimentally testing gene function in non-model species.


Sergio Nigenda-Morales
snigenda(at)ucla(dot)edu

I earned my bachelor degree in Marine Biology in 2005 at the Autonomous University of South Baja California (UABCS) in Mexico. During my tenure in UABCS I worked on research projects to determine the genetic structure of various marine mammal species in the Gulf of California and Mexican Pacific. Currently my PhD research is focused on ecological genomics of mammals, in particular studying the genetic mechanisms underlying recent adaptive variation across different environments and in response to environmental changes. I am also interested in studying the population genetics and phylogeography of different vertebrate species distributed from North to Central America. For more information,please visit my website.


Gabriela M Pinho
gabrielapinho(at)ucla(dot)edu

I am a biologist from Brazil, sponsored by the Science without Borders initiative. I started my PhD studies in September 2014 and will be working on the yellow-bellied marmot population at the Rocky Mountain Biological Laboratory (RMBL), being co-advised by Professors Robert Wayne and Daniel Blumstein. I am interested in the relationship between genes and animal behavior, and will be conducting an annotation of the marmot genome, as well as genomic comparisons among mammal species to gather insights into the genetic basis for behavioral traits. In my Master's studies at the National Institute for Amazonian Research (INPA), I investigated lowland tapir social behavior by estimating relatedness between individuals based on non invasive sampling. Since this project I have been collaborating in the Lowland Tapir Conservation Initiative.


Jacqueline Robinson
jarobinson(at)ucla(dot)edu

My graduate research is focused on the evolution of small populations in isolation. The motivation for this research is to gain understanding of how strong genetic drift due to inbreeding and isolation impacts the genome, often leading to population extinction, but occasionally leading to speciation. This phenomenon is of critical importance in understanding the evolution of island species and in conserving endangered species that have dropped to low population sizes. The species I am focusing on is the Channel Island fox (Urocyon littoralis) - a dwarfed descendant of the gray fox (Urocyon cinereoargenteus) - which inhabits six of the Channel Islands off the coast of California. My methods include sequencing the whole genomes and transcriptomes of island foxes from each of the six island subpopulations and of mainland gray foxes to characterize genomic diversity in individual genomes, subpopulations, and the island fox species as a whole. My past projects include genetic research of other canid species, such as coyotes, red wolves, gray wolves, and golden jackals. I received my Bachelor of Science degree in Biological Sciences from the University of Southern California in 2008.


Shaelynn Sleater-Squires
sasleater(at)ucla(dot)edu

Broadly speaking, I am interested in the evolution of behavior. I am particularly curious about how genetic variation and gene regulation shape behavioral traits and how behavioral variation in individuals generates evolutionary change in populations at the molecular level. For my graduate research, I am exploring how the genetic architecture of nonapeptide-related gene pathways contributes to social behavioral variation across canid species and also among individual wild gray wolves (Canis lupus) in Yellowstone National Park. Additionally, I am exploring differential gene expression associated with environmentally-induced stressors, especially pollutants, in wild dolphin (Delphinus and Tursiops spp.) populations using high-throughput sequencing of RNA (RNA-seq) from blubber and skin samples in collaboration with Annabel Beichman and Sergio Nigenda-Morales. Prior to joining the Wayne Lab, I worked as a Research Associate on the Shark Bay Dolphin Project with Dr. Janet Mann. As part of my continued association with this project, I am currently investigating the use of behavioral data in estimating the length of gestation in our Shark Bay study population of Indo-Pacific bottlenose dolphins (Tursiops sp.). I obtained my B.S. in biology and psychology from Georgetown University in 2009 where I conducted my undergraduate thesis research on the genetic basis of photoperiodic diapause in the Asian tiger mosquito, Aedes albopictus, with Dr. Peter Armbruster.



Distinguished Alumni


Dr. John Pollinger

As the Director of the UCLA Conservation Genetics Resource Center and as Associate Director of the Center forTropical Research, I lead and support the development, refinement and application of characterization analysis methods for conservation genetics and their application to key conservation issues for animals and plants. In addition, my interests include finding solutions to identification and protection of key ecosystems and reserves critical to preserving current animal and plant diversity and future evolutionary potential; and identifying sustained support mechanisms to assure their stable existence and preservation.

Please also see the Conservation Genetics Resource Center and my webpage on the CTR/IOES website for more details.


Dr. Bridgett vonHoldt (Assistant Professor, Princeton University)

Since July 2013, Dr. Bridgett vonHoldt is Assistant Professor at Princeton University. She continues to explore the genomics of the Yellowstone wolf population in collaboration with Wayne Lab and the Yellowstone Wolf Project (National Park Service). Using applied population genomic techniques, this research continues to explore genomic consequences of inbreeding, selection, and disease on this recovering population and conduct pedigree-based studies.

Other Ph.D. and Post-docs alumni

Dr. Andy Aguilar; University of California, Merced, CA

Dr. Kerry Deere; Human Genetics Dept, Univeristy of California, Los Angeles, CA

Dr. Adam Freedman; Dept Organismic and Evolutionary Biology at Harvard University and Boston University, Boston, MA

Dr. Marco Galaverni Laboratory of Genetics, Italian Istitute for Environmental Protection and Research (ISPRA) and University of Bologna, Department of Evolutionary Biology, Bologna, Italy

Dr. Derek Girman Sonoma State University, CA

Dr. Melissa Gray; University of Wisconsin, Madison, WI

Dr. Yi-Bo Hu; Institute of Zoology, Chinese Academy of Sciences, Beijing, China

Dr. Klaus-Peter Koepfli; Dobzhansky Center for Genome Bioinformatics, St. Petersburg, Russia

Dr. Michael Kohn; Rice University, TX

>Dr. Brenda Larison; Adjunct Professor, UCLA Center for Tropical Research & EEB

Dr. Niles Lehman; Portland State University, OR

Dr. Jennifer Leonard; Estacion Biologica de Donana, Sevilla, Spain

Dr. Jesus Maldonado; Smithsonian National Museum of Natural History, Genetics Lab

Dr. Borja Mila; Museo Nacional de Ciencias Naturales, Madrid, Spain

Dr. Imelda Nava; University of California, Los Angeles, CA

Dr. Katherine Pease; University of California, Los Angeles, CA

Dr. Debra Pires; University of California, Los Angeles, CA

Dr. Shauna Price; George Washington University, Washington, D.C.

Dr. Gary Roemer; New Mexico State University, NM

Dr. Rena Schweizer; NSF Postdoctoral Fellow, Cheviron Lab, University of Montana, Missoula, MT

Dr. Katy Semple Delaney; National Park Service Ecologist, California

Dr. Gary Shin; California State University, Long Beach, CA

Dr. Daniel Stahler; Project Biologist, Yellowstone Gray Wolf Recovery Project, National Park Service, Yellowstone Center for Resources, Yellowstone National Park, WY

Dr. Olaf Thalmann (email: olatha at utu dot fi)

Dr. Lisa Torres; California State University, Los Angeles, CA

Dr. Carles Vila; Estacion Biologica de Donana, Sevilla, Spain

Previous Research Support Staff

Daniel Greenfield, LA Police Department (Forensics), CA

Sarah Hendricks; Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho

Amanda Lea

Doreen Schwochow