Dog and Wolf Genome Project

Dog Brain Transcriptome Project

Data from the Mammalian Genome paper by Roy et al. (2013) are available by clicking on the following links:

Canis_familiaris.BROADD2.66.bed

Dog_refseq_genes.bed

Exons.bed

Transcripts.bed

Transcript_sequences.fa.gz

Transcript_protein_seqs.txt.gz

Cerebral_Cortex.tdf

Cerebral_Cortex_splices.bed

Hypothalamus.tdf

Hypothalamus_splices.bed


Yellowstone National Park Projects

The Santa Monica Mountains Urban Carnivore Projects

The Wayne lab has a long-standing collaboration with the National Park Service (NPS) to study carnivore genetics and behavioral ecology in Santa Monica Mountains National Recreational Area (SMMNRA). SMMNRA extends from Ventura County to just a few miles from downtown Los Angeles, and comprises areas of highly protected, continuous habitat, along with areas where habitat patches are interspersed within highly fragmented, urban areas. Here, NPS biologists have a long-term bobcat and mountain lion study, and have also studied coyotes in the past.The primary goals of these projects are to understand how urbanization is influencing these carnivore populations. The projects involve the capture, radio-collaring/ear-tagging, and sample collection from mountain lions, bobcats, and coyotes. Although the Wayne lab primarily participates in these projects by contributing our genetic expertise to understanding the population dynamics of these species, we have also coauthored publications on the behavioral ecology of bobcats and coyotes in urban regions of the park. We published an important paper (Riley et al. 2006, Mol Ecol) on the role of a major freeway in the study area as a barrier to movement, gene flow, and potentially also as a social barrier increasing genetic differentiation between bobcat and coyote populations separated by the freeway. More recently, Laurel Serieys, graduate student in the lab, collaborated with NPS to increase sampling of bobcats across the entirety of SMMNRA, and found that both major freeways in the study area cause population isolation and genetic differentiation. Further, although a disease outbreak in a bobcat population caused a genetic bottleneck, balancing selection acted on a variety of immune loci to maintain genetic variation at important functional regions. Finally, as long-term collaborators to the NPS mountain lion study, we have documented a genetic bottleneck in a highly isolated urban population, first-order inbreeding events between fathers and daughters, and extremely low genetic diversity in the population. We regularly genotype mountain lions born in the population to determine paternity, and have used forensic techniques to identify individual mountain lions that have been involved in aggressive encounters with each other (the primary source of mortality for mountain lions in the population). Because of the long-term nature of these fascinating projects, there's always many more genetic questions to be answered using the samples collected over more than a 15-year period. For prospective graduate students, this is an excellent system to work with. To learn more about these projects, visit the website urbancarnivores.com and the Facebook page.

Main collaborartor: Santa Monica Mountains National Recreational Area

Californian Cetacean Project

Affiliated Researchers

Dr. Adam Boyko, Stanford University, CA

Dr. Carlos Bustamante, Stanford University, CA

Dr. David Coltman, University of Alberta

Dr. Chris Darimont

Dent Earl, University of California, Santa Cruz, CA

Dr. Marco Galaverni, University of Bologna and ISPRA, Ozzano Emilia, Italy

Dr. Eli Geffen, Tel Aviv University, Israel

Dr. Claudia Greco, Laboratory of Genetics, Institute for Environmental Protection and Research (ISPRA), Italy

Dr. Roland Kays, New York State Museum, NY

James Knowles, University of Alberta

Dr. Marco Musiani, University of Calgary

Dr. Elaine Ostrander, Dog Genome Project; NIH/NHGRI; MD

Dr. Seth Riley, Santa Monican Mountains National Recreational Area, CA

Dr. Graham Slater, University of California, Los Angeles, CA

Dr. Douglas Smith, Gray Wolf Restoration Project; Yellowstone National Park, WY

Dr. Malgorzata Pilot, Durham University