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Historic DNA Phylogeography

Historical DNA Analysis

The Berkeley Museum of Vertebrate Zoology houses hundreds of thousands of specimens of vertebrates preserved as skins and crania, or as whole bodies in alcohol. For many of the species in the collection, populations have been well sampled from the same localities multiple times over the course of the last century. New forensic DNA techniques combined with genomics approaches to developing genetic markers have informed and stimulated new research among MVZ researchers. Several current and planned projects have the goal of optimizing DNA extraction and amplification methods from the preserved tissues. Successful development of new single nucleotide polymorphism (SNP) markers promise to allow relatively reliable genotyping from these degraded DNA samples. SNP development from genomic DNA libraries allows optimization of neutral, as well as non-neutral markers that are widely dispersed throughout the genome. These markers can be genotyped from very small amplicons, a feature that is likely to maximize our ability to genotype museum specimens.

One of the projects currently underway is investigating a 100-year sample set of pocket gophers (Thomomys bottae) to address long-standing questions regarding genetic change in populations over time and in response to environmental alterations. More than 11,000 museum specimens of this species have been collected in California, with sample sizes ranging from 230 to over 2800 per decade over the last 100 years. Although every specimen will not be genotyped, such a large pool of specimens will permit the design of an ideal time-series experiment. The MVZ Museum Informatics Project has georeferenced and digitized the sample data for museum specimens; with these data combined with that available in public databases, we can characterize the collection sites and their changes through time, specifically according to specimen collection records, and regional histories of land use, agricultural trends, geology, hydrology, and human population expansion. Many previous studies of the ecology, genetics, morphological variation, and systematics of this species of pocket gophers have been carried out, providing invaluable background knowledge from which to develop hypotheses for the current study. Using the museum specimens as a source of DNA for modern genetic analysis, we can actually observe the patterns of genetic change concurrent with environmental change over a century, rather than merely infer historical processes from modern observations.




Craig Moritz Research Group - Home

Museum of Vertebrate Zoology
Department of Integrative Biology
University of California, Berkeley