Rachel’s contact info:

rlm (at) colostate.edu

Mercedita Madison-Villar

Becky’s contact info:

becky.chong (at) colostate.edu

  Mersee joined the lab from U.T. Arlington as an NSF postdoctoral fellow. Her research is focused on small RNA-mediated TE silencing in salamander genomes.

    I came to Colorado State in 2007 after completing a postdoctoral fellowship at The University of Chicago, graduate studies at U.C. Berkeley and the D.O.E. Joint Genome Institute, and several years as a research associate at U.C. San Francisco. My primary research interests are in genome evolution and phylogenetics, but my research remains grounded in organismal biology and natural history.  Plethodontid salamanders have been the main focus of my research because they have not one but two unusual genomes — both their nuclear and their mitochondrial DNA is remarkable and illustrative of some fundamental processes governing genome evolution.

    I teach Herpetology (every Spring), Life 102 - Introductory Biology (alternate Fall semesters), and Molecular Evolution (alternate Spring semesters), as well as seminars in evolutionary biology and bioinformatics.

    I am generally interested in molecular evolution and phylogenetics. Specifically, I am interested in examining how the interaction between mutation and population structure affect genome size and content variation, which may ultimately lead to extreme genome expansion. Within the diverse salamander family Plethodontidae, the 6-species genus Aneides exhibits both nuclear and mitochondrial genome size variation, providing a tractable system in which to explore genome evolution in detail. 

    I joined the lab in August 2008.  Prior to coming to CSU, I was a researcher with Dr. Jim McGuire at the Museum of Vertebrate Zoology where I studied the phylogeography of Bent-toed geckos (Genus Cyrtodactylus) on the island of Sulawesi, Indonesia.        

Nick Jones, Undergraduate Researcher

    Nick’s research addressed nuclear genome size evolution in plethodontids. He generated a uniform molecular dataset for branch length estimation necessary for modeling the history of genome size evolution across the plethodontid phylogeny.

Rachel’s CV

José’s contact info

jlopez6 (at) colostate.edu

Carrie Foster, Undergraduate Researcher

    Carrie’s research addressed molecular evolution in a duplicated region of the mitochondrial genome in the plethodontid salamander species Hydromantes brunus and Hydromantes platycephalus.

Jessica Borden, Senior Honors Thesis Student

    Jessica’s thesis addressed molecular evolution in a duplicated region of the mitochondrial genome in the plethodontid salamander species Batrachoseps attenuatus.

Dr. Don Shepard, Postdoc

    Don’s research used 454 shotgun sequence data to characterize the repeat element content in several plethodontid genomes.

Cheng’s contact info:

transposable.element (at) gmail.com

     Transposable elements (TEs) are pieces of DNA that can jump from one locus to another, and they are the main components of most eukaryotic genomes.  I am interested in TEs and their contribution to genome evolution. Generally, I want to know (1) how TEs can serve as powerful agents for generating genomic plasticity, (2) how they promote genome expansion, and (3) how they can generate novel genic sequences or cis-elements that can be co-opted to serve essential roles for the host.     

     I joined the lab in March 2011, and currently, my goal is to understand how TEs contribute to genome expansion in salamanders, which possess the largest genomes among vertebrates.

Becky’s Website

    I joined the Mueller lab in Fall of 2010 after graduating from the University of California, Merced. While at Merced I worked with Dr. Andres Aguilar as an undergraduate researcher on the phylogenetics of the Branchinecta coloradensis species group.

    My current research interest is in the genomic factors that can facilitate speciation.  Specifically, I am exploring if and how intraspecific differences in cytosine methylation, transposable elements, and genome size can lead to speciation.

    When studying a process, it is ideal to observe it from beginning to end; however, speciation takes place over large time scales and is therefore difficult to study. To alleviate this problem, I use as my system the salamander Ensatina eschscholtzii, as it is one of the few well- characterized species where whole speciation process can be observed in space rather than time. Furthermore, salamander genomes are very dynamic, containing vast numbers of transposable elements and showing large variation in size.

Dr. Rachel Schwartz,  NSF postdoctoral fellow in bioinformatics

   Rachel’s research used simulations and empirical data to examine the phylogenetic performance of molecular markers, with particular emphasis on branch length estimation and divergence dating.

    Melissa is a senior at CSU majoring in Zoology and Biological Sciences. Melissa’s work is focused on mitochondrial genome evolution in two genera of plethodontid salamanders: Aneides and Plethodon.

   Matthew is a junior at CSU majoring in Biology with a minor in Computer Science. Matthew is estimating rates of DNA loss through ectopic recombination in salamanders and other vertebrates with more typical genome sizes.

Melissa Plakke

Matthew Frahry