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Shaffer Lab applies new genomic tools to the conservation of understudied organisms

Brad Shaffer and Evan McCartney-Melstad are featured in the August 2018 podcast from the journal Heredity, which broadcasts interviews with the people behind the journal, the science and a digest of breaking news.

The focus of the podcast is the application of new genomic methods to understudied organisms, including a recent study published by Shaffer and McCartney-Melstad on an endangered species of western US frog (Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog).

Click here to listen to Brad and Evan discuss their application of genomics tools when revisiting the population genetics of the declining foothill yellow-legged frog and how their work may help the US Fish and Wildlife Service determination of whether or not it should be listed under the Endangered Species Act. Their interview begins about 10 minutes into the podcast.

CalTrans awards grant to Shaffer Lab

Landscape Genomics Study for California Tiger Salamander

The California Tiger Salamander (CTS) is state and federally listed species. As a result, Caltrans is required to consult with regulatory agencies about impacts of transportation projects. A major conservation issue for CTS is the ongoing hybridization with the introduced non‐native Barred Tiger Salamander (BTS). Thus, CTS recovery, in part, depends on preventing the geographical spread of such introgression.

This project will provide measurable effects of roads on the movement of pure CTS genes where undercrossings will be useful to promote movement of native genes and areas where such crossings should not be installed to inhibit the spread of non‐native BTS genes.

The main tasks that will be completed in this research are:

  • running simulations to determine how many animals per pond to sequence;
  • identifying tissue samples to examine from existing database;
  • identifying and collecting new samples from georeferenced sampling locations; and
  • collecting molecular data from all samples


NRS video highlights Shaffer Lab

UC Natural Reserve System research has laid the foundation for conserving species across the state. A prime example: UCLA professor Brad Shaffer’s work on California tiger salamanders was instrumental in protecting the upland habitats this endangered amphibian needs to survive.

Welcome visiting professor Ugur Kaya

Professor Ugur Kaya is a Turkish ecologist and herpetologist, and a Full Professor at Ege University, one of the top rated academic institutions in the country. Professor Kaya’s research centers on the ecology, population demography, and conservation of Turkish amphibians, which he has studied since his PhD. He currently is the primary collaborator on an NSF research grant with the Shaffer lab, working on species boundaries in the endangered Turkish salamander genus Lyciasalamandra. These unique animals are geographically restricted to coastal Turkey and several adjacent islands in Greece, and they have been placed in up to 10 very narrowly distributed species on the Lycian coast. In collaboration with UCLA postdoctoral researcher Peter Scott, we are collecting RADseq data on over 150 field-collected samples to redefine species in the group, and use those newly defined taxa as the basic units of conservation in Lyciasalamandra. Ugur is visiting UCLA for two months to complete this project and work with Shaffer and Scott to analyze and write up the resulting data. We welcome Ugur to Los Angeles, the lab, and UCLA.