Leache Lab

Research

Old school preparation of a genomic library for next-generation sequencing. Nowadays we use a pippin prep. Photo by Duncan Reid.

Washington Reptiles

Pygmy short-horned lizard from Central Washington. Photo: Jared Grummer

Washington Amphibians

Western red-backed salamander from West Seattle. Photo: Matt McElroy

Fieldwork

A look inside our work tent on a recent collecting trip to West Africa. Photo: Duncan Reid.

Herp Collection

Students prepare a 15 foot python at the Burke Museum.

Lab Members

Graduate Student Matt McElroy petting a wolverine at the Burke Museum.

Publications

Species delimitation using genome-wide SNP data. Systematic Biology.

SEQloporus

SEQloporus: we're using next-generation sequence data to build a phylogenomic tree for Sceloporus

Molecular Evolution: A Statistical Approach

Posted on April 4, 2014 by Adam

Ziheng Yang’s new book with Charles Linkem’s cover photo.

Ziheng Yang’s new book, “Molecular Evolution: A Statistical Approach” is on sale at Amazon. The cover photo, a western fence lizard (Sceloporus occidentalis), was taken by Charles Linkem during our collecting trip to Oregon last summer. Some people think that the lizard is beautiful, while others (Ziheng included) think that it looks terrifying. The book covers the statistical and computational foundations of molecular evolution, phylogenetics and phylogeography. It provides explanations and examples using real data analysis. The data and computer programs are available on the web, and course materials are provided at the end of each chapter. This will make it easy to use the book for teaching, perhaps in a graduate seminar course.

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Bayesian Phylogenetics Workshop

Posted on April 1, 2014 by Adam

A new workshop on Bayesian phylogenetic analysis using the program RevBayes is happening August 25-31, 2014 at the National Evolutionary Synthesis Center (NESCent) in Durham, NC. The course will cover a lot of useful material, including probability theory, divergence dating, species trees, biogeography, phylodynamics, comparative methods, and fully integrative Bayesian inference of phylogenetic parameters. The course instructors are awesome too:
Bastien Boussau, LBBE, Lyon, France
Tracy Heath, UC Berkeley & U Kansas
Sebastian Höhna, UC Davis & UC Berkeley
John Huelsenbeck, UC Berkeley
Michael Landis, UC Berkeley
Nicolas Lartillot, LBBE, Lyon, France
Brian Moore, UC Davis
Fredrik Ronquist, NRM Stockholm
Tanja Stadler, ETH Zürich

They expect a lot of competition for space, so get your application in early.

Also, dress will be very casual, with a good chance of thunderstorms.

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New Postdoc. Andreas Chavez Joins the Lab!

Posted on March 13, 2014 by Adam

A new postdoctoral researcher recently joined the lab. Dr. Andreas Chavez is a recent graduate from UW Biology. He is a mammalogist who specializes in phylogenetics, phylogeography, and hybrid zones. Andreas will only be with us until Summer, and then he’s moving to UC Berkeley to start work on a new postdoctoral research position at the Museum of Vertebrate Zoology. While he’s still here, Andreas is going to learn how to work with next-generation sequence data, including library preparation for RADseq and sequence capture approaches, data management, bioinformatics, and also phylogenetic analysis. Welcome to the lab!

Dr. Andreas Chavez

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Anaconda Boxcavation

Posted on February 15, 2014 by Adam

Last week at the annual Burke Museum Behind the Scenes Night we excavated the skeleton of a yellow anaconda. We acquired the anaconda from the Woodland Park Zoo, and we skinned the snake at the 2013 Behind the Scenes Night.

Anaconda boxcavation. Photo by Mike Etnier.

Mike Etnier from Boxcavations helped with the logistics, which involved burying the snake in a box of sand and storing it for the last year. You can watch the entire excavation process on youtube

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In the long run, herpetologist Tyrone Hayes beats big industry

Posted on February 5, 2014 by Adam

A new article in the New Yorker tells the incredible story of UC Berkeley professor Tyrone Hayes, and his long fight against industry giant Syngenta’s herbicide (and frogicide) atrazine. To put the story in Star Wars terms, Syngenta is the “Evil Empire”, and the Tyrone Hayes lab is the “Rebel Alliance.” The Empire seems to have unlimited resources at their disposal for lobbying and pushing their agenda. Meanwhile, scientific studies continue to paint a dismal picture for the impacts of atrizine on the environment.

Hayes has devoted the past fifteen years to studying atrazine, a widely used herbicide made by Syngenta. The company’s notes reveal that it struggled to make sense of him, and plotted ways to discredit him. Photograph by Dan Winters.

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