Progress 07/01/05 to 06/30/08
Outputs
OUTPUTS: In completion of state department of Fish and Game contract PO580004, a final report outlines the findings of the project: Population genetics of California's Wild Pigs. Feral pigs (Sus scrofa), pure bred or hybrids of Eurasian wild boar and domestic pigs, have damaged California native species and environments and agriculture, and are a potential reservoir for many diseases that threaten the health of wildlife, domestic animals and humans. In order to determine key population information necessary for predicting the dynamics of wild pig populations, we developed a high-resolution panel of nuclear microsatellites DNA markers and analyzed the population genetic structure of feral pigs in California. We tested 85 microsatellite primers (probes) and developed a panel of 43 DNA markers. With the help of a number of collaborators, 1418 samples were submitted to our lab, and of those 692 were genetically typed and tested with the 43 microsatellites. The data set of 656 California pig samples and 36 domestic pig samples was pruned to include data of the final panel of 33 microsatellite markers which satisfied population genetic criteria necessary for analysis. PARTICIPANTS: PI, Holly Ernest DVM PhD; Staff Research Associates Lisa Goldberg and Tamala Gilliland worked and were trained on this project; Graduate students Elizabeth Heeg and Elizabeth Long participated and were trained in molecular genetic techniques; Collaborating biologists and field specialists from California Department of Fish and Game, USDA Wildlife Services, and County wildlife officers; TARGET AUDIENCES: state and federal wildlife managers and researchers; wildlife biologists and ecological genetics researchers; public health officials, biologists, and researchers (zoonotic diseases from wild pigs) PROJECT MODIFICATIONS: Only significant change was no-cost extension of the project to end date of December 31, 2008
Impacts
Using Bayesian genetic clustering algorithms, we found that Channel Island pigs were highly distinct from mainland and domestic pigs (an outcome of small founder population and time for evolution to occur through genetic drift). Mainland California pigs are substructured into five main genetic clusters. Pigs of the North Coast, Sutter Buttes, Sierra Nevada each assigned well into genetic clusters, while the pigs of the Central Coast were composed of primarily two clusters. Each geographic region contained a smaller number of pigs that assigned to genetic clusters other than that of the main regional cluster. These analyses indicate differing landscape level gene flow among regions. Central Coast pig DNA reflects at least two genetic clusters and containing extensive gene flow. Sutter Buttes pigs appear relatively genetically isolated from other regions - probably reflecting a few foci of breeding families. North Coast, and Sierra Nevada regions contain pigs with regionally unique genetic clusters, but also smaller numbers of contain pigs with genetic signatures from other regions - indicating that there is a small level of gene flow occurring throughout the state. This work is in preparation for peer-reviewed publication in a scientific journal. Feral pigs in California contained variable amounts of domestic pig ancestry, reflecting the likelihood of sporadic and continual domestic pig introgression (interbreeding and introduction) into feral pigs in California. Future work could address the ancestry membership of Eurasian wild boar stock in California wild pigs and periodic monitoring of population genetics for demographic modeling (predicting how many pigs there are and how well eradication efforts are working).
Publications
- No publications reported this period
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: To date we have collected and archived 369 samples from California feral pigs which include hair, tissue, and Nobuto strip blood samples. Of those samples: o 87 were supplied by Dr. Sweitzer at the University of North Dakota o 141 were submitted to us from USDA/CDFG collaborators o 36 were submitted to us Santa Clara County wildlife managers o 105 were provided by private hunters. We have currently sampled 23 counties throughout California, probably representing the core of feral pig range. We are currently working with biologists from the Channel Islands to obtain samples collected from feral pigs on Santa Cruz Island. A key focus is to increase sample size from the following counties: Humboldt, Siskiyou, Shasta, Tehama, Glenn, Lake, Mendocino, Sonoma, Napa, Madera, Fresno, and Tulare. Microsatellite Primer Development We validated and optimized 12 microsatellite primers that are polymorphic in California feral pigs, and therefore suitable tools for this study. We have
selected an additional 35 microsatellite markers adapted from the Pig Biodiversity Study (Olivier et al. 2005). Of those, we have identified 21 that were polymorphic (variable between individuals) in a preliminary screen of pig samples from 6 locations in the state. We are in the process of optimizing these markers and are in the process of screening the sample collection. Microsatellite Multiplex Development In addition to optimizing the microsatellite primer conditions, we also are developing multiplexes of the primers in order to speed processing time and efficiency. We anticipate incorporating 4-5 primers into each multiplexed reaction for a total of 25-30 DNA markers. This work will be done concurrently with the primer optimization and screening mentioned above.
PARTICIPANTS: Holly Ernest DVM PhD Jay Well SRA II Undergraduate student interns Past graduate students, Elizabeth Heeg and Elizabeth Long Tamala Gilliland SRA Partner organizations: California Dept of Fish and Game USDA Wildlife Resources UC Davis Veterinary Genetics Laboratory Service Unit
TARGET AUDIENCES: California Dept of Fish and Game USDA Wildlife Resources
Impacts
Investigations into the effect of spatial pattern on invasion are necessary to determine the prospects of land management programs to control invasive species. This is especially important since the structure of the landscape affects the spread of invasion in multiple ways. Feral pigs are an invasive species of concern worldwide. They are particularly damaging to agriculture and native environments through their feeding and rooting behaviors, and they are a potential reservoir for many diseases. Feral pigs have previously been found to cluster around water sources in arid environments in Australia and Texas, a behavior that is reflected in their genetic structure. We seek to determine whether pigs were genetically clustered in California, and if that clustering was due to the effects of geographic barriers.
Publications
- No publications reported this period
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Progress 01/01/06 to 12/31/06
Outputs
Investigations into the effect of spatial pattern on invasion are necessary to determine the prospects of land management programs to control invasive species. This is especially important since the structure of the landscape affects the spread of invasion in multiple ways. Feral pigs are an invasive species of concern worldwide. They are particularly damaging to agriculture and native environments through their feeding and rooting behaviors, and they are a potential reservoir for many diseases. Feral pigs have previously been found to cluster around water sources in arid environments in Australia and Texas, a behavior that is reflected in their genetic structure. Through samples collected from the USDA Wildlife Services, the California Department of Fish and Game, county agencies, hunters, and trappers, we are examining the genetic diversity and population structure of wild pigs throughout California. In a preliminary study, we analyzed the population genetic
structure of feral pigs in the Central Coast region of California using 142 unrelated individuals and a panel of 12 DNA markers (microsatellites). Using a clustering analysis of the genetic data (program STRUCTURE) we determined that there are two to four clusters present and are grouped mostly to the north or south. Next we examined the local area for natural and human-caused barriers (mountains, roads, waterways, land use patterns, etc.) that might contribute to the genetic pattern we observed. Previously reports indicated that channelized streams can be a barrier to pig movement. We examined the local water ways as a potential barrier and found that the split in the genetic clustering roughly corresponded to the San Benito River. The individuals on either side of the river displayed low to moderate genetic differences, which might be expected with low summertime flows of and the lack of channelization throughout much of the river's course. In conclusion, this preliminary study
indicates that feral pigs in the California Central Coast region exhibit a small level of genetic structure, and do not show any genetic signs of recent bottlenecks or outbreeding events. Over the next two years, we will add more microsatellite loci to increase statistical power and more samples from regions throughout pig range in California to complete the genetic analysis, and submit a final report to CDFG, and write a manuscript for peer-review journal submission.
Impacts
This study will contribute to knowledge of feral pig ecology and population biology in California. Through knowledge of population structure and migration patterns, state and federal wildlife biologists and administrators can better manage this invasive introduced species to benefit California's natural resources, included coast range habitat degraded by pig activities.
Publications
- No publications reported this period
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