Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to NRP
CONSERVATION GENETICS OF CALIFORNIA TIGER SALAMANDERS (AMBYSTOMA CALIFORNIENSE)
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0176833
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2007
Project End Date
Sep 30, 2012
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Evolution and Ecology
Non Technical Summary
Amphibian declines are occurring in many parts of the world (Alford and Richards, 1999), with some of the most severe declines in western North America . This problem is reaching near-epidemic proportions in California, where virtually all of the species of native, pond and stream-breeding amphibians are undergoing catastrophic declines (Drost and Fellers, 1996; Fisher and Shaffer, 1996). We have worked with state and federal agencies for over a decade to bring responsible management practices to agricultural and urban development that protects the habitat and genetic variation found in many Central Valley species. The California Tiger Salamander has been the primary target of our work, since its entire range is restricted to Central Valley vernal pool habitats. Our genetical and ecological work has identified divergent sets of populations requiring separate management, as well as a widespread biological invasion of non-native genes into native CTS populations. We propose to continue our work to identify highest priority areas for protection as well as the stability of the invasion front of non-native genes across central California. This project uses genetic tools to determine the most important regions of California, and the most important individual breeding sites for protection of the CTS. Identifying and securing such sites is a critical step in protection, and ultimately delisting, of this Threatened species.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
13508301080100%
Knowledge Area
135 - Aquatic and Terrestrial Wildlife;

Subject Of Investigation
0830 - Wild animals;

Field Of Science
1080 - Genetics;
Goals / Objectives
This project has four interrelated objectives, all of which seek to use molecular genetic tools to identify the most important regions and individual sites for California tiger salamander (AMBYSTOMA CALIFORNIENSE, or CTS) mitigation and recovery. The four objectives attack this problem at three spatial scales, ranging from the entire range of the species to local vernal pool breeding sites. i) At the scale of the entire species, genetically determine the fundamental management units that must be protected to ensure overall protection of the CTS? ii) Within each of these regions, use molecular data to estimate effective population sizes of individual CTS breeding sites, iii) Quantify the correlation between population size and physical and landscape characteristics for breeding sites, iv) Measure among-year changes in invasive gene frequencies in a tiger salamander hybrid swarm in central California
Project Methods
The California Tiger Salamander is a federally listed (threatened) species under the US Endangered Species Act that occurs primarily on agricultural landscapes of central California. Agricultural land uses have severely impacted the species, and have led to its listing across its range from Santa Barbara to Yolo Counties (Davidson et al., 2002b). The proposed work uses molecular genetic tools developed in our laboratory to further clarify the number and geographic extent of separate management units within the species, as well as demographic parameters critical to understanding population size, viability, and priority for protection. In conjunction with ongoing projects on landscape ecology and habitat use in our laboratory, this work will provide information that is crucial to the effective management of landscapes for agriculture and salamander conservation throughout central California. As such, it continues our long-term research on maintaining viable amphibian and reptile populations in the agricultural landscape of central California.

Progress 10/01/07 to 09/30/12

Outputs
Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? The PI relocated to UCLA in January 2012, thus there has been no information entered into the REEport system for Dr. Shaffer.

Publications


    Progress 01/01/10 to 12/31/10

    Outputs
    OUTPUTS: My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. The focus of this work has increasingly been on the California Tiger Salamander (CTS), a federally listed species under the US Endangered Species Act (ESA) that exists entirely within the agricultural land-use matrix of Central California. During the review period, we continued working on projects that characterize genetic variation within the species, and how to use that genetic data to learn about population history, population movement patterns, and species boundaries. Key outputs from the last year include several landscape genetic studies of CTS in different parts of their Central Valley range based on microsatellite markers developed in our lab and expanding our EST (Expressed Sequence Tag) library to study both the population differentiation of CTS across their range and the hybridization dynamics of CTS with a non-native, introduced congener in the Salinas Valley. We have also continued to work on upland habitat use by the California Tiger Salamander (work supported by the Agricultural Experiment Station initially, leading to new funding from the US Bureau of Reclamation and the Department of Defense), and have applied those results to better understand and manage salamander populations in agricultural landscapes. We have also used these results to develop Ecological Niche Models to predict the occurrence of California Tiger Salamanders in agricultural landscapes at both narrow (Solano County, California) and broad (across the range of the species) geographic scales. Results supported in part by the Agricultural Experiment Station were used as preliminary results for a new US Fish and Wildlife Service grant on landscape genetics of the California Tiger Salamander, to motivate an Interagency Agreement between the California Department of Fish and Game and UC Davis, a Cooperative Agreement with Travis Air Force base, and for a new NSF grant (submitted in January 2011). This work has resulted in several papers, several talks at major universities and national meetings, and continued collaborative work between agency biologists and our lab group. We also ran a day-long meeting with California Department of Fish and Game to inform their biologists on the status, consequences, and possible solutions to remove hybrid salamanders from the California landscape. These are areas of great interest to the agricultural community, given the impact that agriculture has on this federally endangered species. PARTICIPANTS: Individuals who worked on this project include: Jarrett Johnson: Postdoctoral research associate Ian Wang: Ph. D. candidate (completed) Maureen Ryan: Ph. D. candidate (completed) Adam Clause: Undergraduate technician Cathy Newman: MA technician Ben Johnson: Undergraduate technician Partner organizations: US Fish and Wildlife Service/Bureau of Reclaimation California Department of Fish and Game Department of Defense (Travis Air Force Base) Training and Development: Full day workshop with 35 CDFG and 5 USFWS personnel, led by Shaffer, to develop strategies for hybrid salamander management and CTS protection. Training for DoD personnel at Travis Air Force Base Training for approximately 10 agency and private consultants on CTS field work for certification. TARGET AUDIENCES: Our primary target audience (aside from the broad scientific community) has been and continues to be the agencies that manage lands and endangered species within the Great Central Valley ecosystem of California. These include the California Department of Fish and Game, the US Fish and Wildlife Service, the US Geological Survey, CalTrans and Travis Air Force Base. We are also developing new relationships with Fort Hunter Liggett personnel. We also reach out to more local agencies, including Solano County land trust and the Jepson Prairie docents. Shaffer has taken over as the director of the Jepson Prairie Advisory team for UC Davis to increase outreach through the Natural Reserve System. Our outreach to these audiences have been very successful. PROJECT MODIFICATIONS: As reported last year, our major change to this project has been to expand its boundaries to include management and research on other species of amphibians and reptiles besides just the California tiger salamander. The major species added is the Western Pond Turtle (EMYS MARMORATA), with additional work on a wide range of species under the auspices of the Amphibian and Reptile Species of Special Concern project discussed earlier.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS), species boundaries, and landscape connectivity for amphibians and reptiles. Because we apply these results to agricultural landscapes in California, we help to define the biological units of protection for these species. Our results are essential for the effective coexistence of agriculture and sensitive species on the same landscapes, and have been increasingly recognized by the California Department of Fish and Game and the US Fish and Wildlife service as such. As we continue to develop increasingly sophisticated molecular markers for this important work, my achievements in this system were recognized by my election as president of the American Genetic Association, and the international symposium I hosed on Conservation Genomics in July, 2010. My presidential address focused exclusively on work conducted under the AES. We provided the US Fish and Wildlife Service with critical data on landscape genetics of the endangered CTS to help guide management, and our newest work (in press in Conservation Genetics, submitted to PNAS) highlight how CTS utilize both agricultural and natural landscapes. Several papers from our group have focused on hybrid salamanders in the Salinas Valley region, including both genetic and ecological impacts of this critical biological invasion. As we continue to collaborate with both state and federal agencies, we have submitted proposals to both agencies to help continue to fund the work made possible by the AES, including two Section 6 ESA proposals and ones targeted to the Department of Defense. We are rewriting the CDFG Species of Special Concern document for amphibians and reptiles, a project with wide-ranging consequences for California agriculture. This project is nearly complete, and we are negotiating with US Press to publish it as a book. Given the sometimes conflicting goals of agriculture, development and species protection, our work strives to help identify the critical areas where species should be protected, while still keeping the maximal options for alternative land uses open across a species' range.

    Publications

    • Johnson, J. R., B. B. Johnson and H. B. Shaffer. 2010 Genotype and temperature affect locomotor performance in a tiger salamander hybrid swarm. Functional Ecology 24:1073-1080. Johnson, J. R., B. M. Fitzpatrick and H. Bradley Shaffer. 2010 Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders. BMC Evolutionary Biology 2010, 10:147.
    • Fitzpatrick, B. M., J. R. Johnson, D. K. Kump, J. J. Smith, S. R. Voss, and H. B. Shaffer. 2010 Rapid spread of invasive genes into a threatened native species. Proceedings of the National Academy of Sciences, USA, 107:3606-3610.
    • Lind, A. J., P. Q. Spinks, G. M. Fellers and H. B. Shaffer. 2011 Rangewide phylogeography and landscape genetics of the western U. S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers. Conservation Genetics 12:269-284.
    • Savage, W., A. Fremier, and H. B. Shaffer. 2010 Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time. Molecular Ecology 19:3301-3314.
    • Barley, A. J., P. Q. Spinks, R. C. Thomson and H. Bradley Shaffer. 2010 Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Molecular Phylogenetics and Evolution 55:1189-1194.
    • Thomson, R. C. and H. B. Shaffer. 2010 Rapid progress on the vertebrate tree of life. BMC Biology 2010, 8:19.


    Progress 01/01/09 to 12/31/09

    Outputs
    OUTPUTS: My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. The focus of this work has increasingly been on the California Tiger Salamander (CTS), a federally listed species under the US Endangered Species Act (ESA) that exists entirely within the agricultural land-use matrix of Central California. During the review period, we continued working on projects that characterize genetic variation within the species, and how to use that genetic data to learn about population history, population movement patterns, and species boundaries. One of the most exciting directions that we have been working on is to use large DNA databases to study landscape genetics across species. We have primarily used an EST (Expressed Sequence Tag) library to study two aspects of CTS biology and management. We have developed two panels of about ~120 single nucleotide polymorphism (SNP) markers that are variable 1) across native CTS to study population differentiation and 2) that differentiate native from non-native genes, allowing us to study how non-native genes are invading populations of native CTS, particularly in the Salinas Valley. Finally, we have refined a set of microsatellite markers to study historical demography of California Tiger Salamanders in isolated, sets of populations in Monterey County (at old Fort Ord) and Santa Barbara county. We have also continued to work on upland habitat use by the California Tiger Salamander (work supported by the Agricultural Experiment Station initially, leading to funding from CalTrans and the US Bureau of Reclamation), and have applied those results to better understand and manage salamander populations in agricultural landscapes. We have also used these results to develop Ecological Niche Models to predict the occurrence of California Tiger Salamanders in agricultural landscapes at both narrow (Solano County, California) and broad (across the range of the species) geographic scales. Results supported in part by the Agricultural Experiment Station were used as preliminary results for a new US Fish and Wildlife Service grant on landscape genetics of the California Tiger Salamander, to motivate an Interagency Agreement between the California Department of Fish and Game and UC Davis, and for a new NSF grant (submitted in January 2010). This work has resulted in several papers, several talks at major universities and national meetings, and continued collaborative work between agency biologists and our lab group. All of these are areas of great interest to the agricultural community, given the impact that agriculture has on this federally endangered species. PARTICIPANTS: Individuals who worked on this project include: Jarrett Johnson: Postdoctoral research associate Ian Wang: Ph. D. candidate Wesley Savage: Ph. D. candidate (completed) Maureen Ryan: Ph. D. candidate Steven Michaletti: Undergraduate technician Levi Gray: Undergraduate technician Ben Johnson: Undergraduate student, technician Partner organizations: US Fish and Wildlife Service/Bureau of Reclaimation California Department of Fish and Game Department of Defense (Travis Air Force Base) Training and Development: California Department of Fish and Game, Interagency Agreement "Collaborative research on management-relevant Threatened and Endangered Species" 2007 - 2011 ($1,342,000) Department of Defense, "Conservation of California tiger salamanders (Ambystoma californiense) at Travis Air Force Base, Solano County, California. 2009-2010, $95,000. TARGET AUDIENCES: Our primary target audience (aside from the broad scientific community) has been and continues to be the agencies that manage lands and endangered species within the Great Central Valley ecosystem of California. These include the California Department of Fish and Game, the US Fish and Wildlife Service, the US Geological Survey, CalTrans and Travis Air Force Base. We also reach out to more local agencies, including Solano County land trust. Our outreach to these audiences have been very successful. PROJECT MODIFICATIONS: As reported last year, our major change to this project has been to expand its boundaries to include management and research on other species of amphibians and reptiles besides just the California tiger salamander. The major species added is the Western Pond Turtle (EMYS MARMORATA), with additional work on a wide range of species under the auspices of the Amphibian and Reptile Species of Special Concern project discussed earlier.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS), species boundaries, and landscape connectivity for amphibians and reptiles. Because we apply these results to agricultural landscapes in California, we help to define the biological units of protection for these species. Our results are essential for the effective coexistence of agriculture and sensitive species on the same landscapes. Our work exploring the use of Single Nucleotide Polymorphisms (SNPs) to define species originally was highlighted in an international symposium (Society for Systematic Biology in 2006) and our current work is being actively used to determine cryptic species boundaries in CTS that are critical for management. We provided the US Fish and Wildlife Service with critical data on landscape genetics of the endangered CTS to help guide management, and our landscape genetics of CTS at the Ft. Ord site in Monterey County at the northern end of the Salinas Valley was a critical breakthrough in how salamanders utilize habitat. Several papers from our group have focused on hybrid salamanders in the Salinas Valley region, including both genetic and ecological impacts of this critical biological invasion. We continue to work closely with agencies on issues ranging from acreage in need of protection to the consequences of invasive genes. We recently entered into a collaborative agreement with the California Department of Fish and Game to fund 18 independent proposals that cover a wide range of species and their management. These range from CTS to native Red Fox, Western Pond Turtles, and a variety of other taxa, many of which are of direct relevance to agricultural land management in California. As a part of that larger objective (which brought over 1.4 million dollars to UC Davis), we are rewriting the CDFG Species of Special Concern document for amphibians and reptiles, a project with wide-ranging consequences for California agriculture. This project is moving along nicely, and we anticipate its completion in the 09-10 academic year. Given the sometimes conflicting goals of agriculture, development and species protection, our work strives to help identify the critical areas where species should be protected, while still keeping the maximal options for alternative land uses open across a species' range.

    Publications

    • Spinks, P. Q. and H. B. Shaffer. 2009. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) Species Complex, and what they tell us about biogeography and hybridization. Systematic Biology 58:1-20.
    • Spinks, P. Q., R. C. Thomson, G. A. Lovely and H. B. Shaffer. 2009. Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. BMC Evolutionary Biology 2009 9:56 (pages 1-17).
    • Genome 10K Community of Scientists (66 coauthors). 2009. Genome 10K: A proposal to obtain whole-genome sequence for 10,000 vertebrate species. Journal of Heredity 100:659-674.
    • Fitzpatrick, B. M., J. R. Johnson, D. K. Kump, H. B. Shaffer, J. J. Smith and S. R. Voss. 2009. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. BMC Evolutionary Biology 9:176.
    • Wang, I. J., W. K. Savage and H. B. Shaffer. 2009. Landscape genetics and least cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense). Molecular Ecology 18:1365-1374.
    • Other papers that are directly relevant to our conservation genetics in the central valley include: (2009-2010)
    • Spinks, P. Q., R. C. Thomson, and H. B. Shaffer. 2010. Nuclear gene phylogeography reveals the historical legacy of an ancient inland sea on lineages of the western pond turtle, Emys marmorata in California. Molecular Ecology 19:542-556.
    • Thomson, R. C. and H. B. Shaffer. 2010. Sparse supermatrices for phylogenetic inference: Taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Systematic Biology 59:42-58 (Cover Article).


    Progress 01/01/08 to 12/31/08

    Outputs
    OUTPUTS: My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. The focus of this work has increasingly been on the California Tiger Salamander (CTS), a federally listed species under the US Endangered Species Act (ESA) that exists entirely within the agricultural land-use matrix of Central California. During the review period, we continued working on projects that characterize genetic variation within species, and how to use that genetic data to learn about population history, population movement patterns, and species boundaries. One of the most exciting directions that we have been working on is to use large DNA databases to study landscape genetics across species. We have primarily used an EST (Expressed Sequence Tag) library to study two aspects of CTS biology and management. First, we have developed a panel of about 80 markers that are variable across native CTS to study population differentiation and speciation in this endangered species. Second, we have developed a panel of 96 markers to study hybrid California Tiger Salamander populations from the Salinas Valley, allowing us to study how non-native genes are invading populations of native CTS. Finally, we have refined a set of microsatellite markers to study historical demography of California Tiger Salamanders in isolated, but currently genetically pure populations in Monterey County (at old Fort Ord) and Santa Barbara county. We have also continued to work on upland habitat use by the California Tiger Salamander (work supported by the Agricultural Experiment Station initially, leading to funding from CalTrans and the US Bureau of Reclamation), and have applied those results to mitigation ratio analyses to better manage salamander populations in agricultural landscapes. We have also used these results to develop Ecological Niche Models to predict the occurrence of California Tiger Salamanders in agricultural landscapes at both narrow (Solano County, California) and broad (across the range of the species) geographic scales. Results supported in part by the Agricultural Experiment Station were used as preliminary results for a new US Fish and Wildlife Service grant on landscape genetics of the California Tiger Salamander, and to motivate an Interagency Agreement between the California Department of Fish and Game and UC Davis. This work has resulted in several papers, several talks at major universities and national meetings, and continued collaborative work between agency biologists and our lab group. I organized a workshop in March, 2008 that produced a white paper for the US Fish and Wildlife Service on Best Scientific Practices for relocation of captured CTS specimens, and continue to work with state and federal agencies to determine how to preserve CTS in the Central Valley and Salinas Valley ecosystems. Both of these are areas of great interest to the agricultural community. PARTICIPANTS: Individuals who worked on this project include: Jarrett Johnson: Postdoctoral research associate Ian Wang: Ph. D. candidate Wesley Savage: Ph. D. candidate Maureen Ryan: Ph. D. candidate Steven Michaletti: Undergraduate technician Levi Gray: Undergraduate technician Partner organizations: US Fish and Wildlife Service California Department of Fish and Game Training and Development: Workshop on Relocation of Endangered California Tiger Salamanders (organized by Shaffer, in collaboration with USFWS & CDFG) 21 March 2008. California Department of Fish and Game, Interagency Agreement "Collaborative research on management-relevant Threatened and Endangered Species" 2007 - 2009, 987,500 dollars. TARGET AUDIENCES: Our primary target audience (aside from the broad scientific community) has been and continues to be the agencies that manage lands and endangered species within the Great Central Valley ecosystem of California. These include the California Department of Fish and Game, the US Fish and Wildlife Service, the US Geological Survey, CalTrans and most recently Travis Air Force Base. We also reach out to more local agencies, including Solano County land trust. Our outreach to these audiences have been very successful. PROJECT MODIFICATIONS: Our major change to this project has been to expand its boundaries to include management and research on other species of amphibians and reptiles besides just the California tiger salamander. The major species added is the Western Pond Turtle (EMYS MARMORATA), with additional work on a wide range of species under the auspices of the Amphibian and Reptile Species of Special Concern project discussed earlier.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS), species boundaries, and landscape connectivity for amphibians and reptiles. Because we apply these results to agricultural landscapes in California, we help to define the biological units of protection for these species. Our results are essential for the effective coexistence of agriculture and sensitive species on the same landscapes. Our work exploring the use of Single Nucleotide Polymorphisms (SNPs) to define species originally was highlighted in an international symposium (Society for Systematic Biology in 2006) and our current work is being actively used to determine cryptic species boundaries in CTS that are critical for management. We provided the US Fish and Wildlife Service with critical data on landscape genetics of the endangered CTS to help guide management, and have a paper in press that presents new data on landscape genetics of CTS at the Ft. Ord site in Monterey County at the northern end of the Salinas Valley. We continue to work closely with agencies on issues ranging from acreage in need of protection to the genetic consequences of invasive genes. We recently entered into a collaborative agreement with the California Department of Fish and Game to fund 18 independent proposals that cover a wide range of species and their management. These range from CTS to native Red Fox, Western Pond Turtles, and a variety of other taxa, many of which are of direct relevance to agricultural land management in California. As a part of that larger objective (which brought nearly 1,000,000 dollars to UC Davis), we are rewriting the CDFG Species of Special Concern document for amphibians and reptiles, a project with wide-ranging consequences for California agriculture. This project is moving along nicely, and we anticipate its completion in the 09-10 academic year. Given the sometimes conflicting goals of agriculture, development and species protection, our work strives to help identify the critical areas where species should be protected, while still keeping the maximal options for alternative land uses open across a species' range.

    Publications

    • Wang, I. J. and H. B. Shaffer. 2008. Coloration is a highly labile trait in an aposematic species: A phylogenetic analysis of color evolution in the strikingly polymorphic strawberry poison-dart frog. Evolution 62:2742-2759.
    • Thomson, R. C., A. M. Shedlock, S. V. Edwards, and H. B. Shaffer. 2008. Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Molecular Phylogenetics and Evolution 49:514-525.


    Progress 01/01/07 to 12/31/07

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. The focus of this work has increasingly been on the California Tiger Salamander, a federally listed species under the US Endangered Species Act (ESA) that exists entirely within the agricultural land-use matrix of Central California. During the review period, we continued working on projects that characterize genetic variation within species, focusing a great deal of attention on how to use single nucleotide polymorphisms (SNPs) to learn about population history and species boundaries. One of the most exciting directions that we have been working on is to use large DNA databases, either from EST libraries, BAC end-sequence libraries, or whole genome sequences, to study landscape genetics across species. We have now completed such a project, using an existing BAC end-sequence library from one species (the Painted Turtle) to create markers for other turtles, including the threatened Western Pond Turtle that exists in Central Valley agricultural landscapes. We have also used an EST (Expressed Sequence Tag) library to study hybrid California Tiger Salamander populations from the Salinas Valley, and microsatellite markers to study historical demography of California Tiger Salamanders in the isolated, but currently genetically pure populations in Monterey County (at old Fort Ord) and Santa Barbara county. We have continued to work on upland habitat use by the California Tiger Salamander (work supported by the Agricultural Experiment Station initially, leading to new funding from CalTrans), and have applied those results to mitigation ratio analyses to better manage salamander populations. We have also used these results to develop Ecological Niche Models to predict the occurrence of California Tiger Salamanders in agricultural landscapes at both narrow (Solano County, California) and broad (across the range of the species) geographic scales. Results supported in part by the Agricultural Experiment Station were used as preliminary results for a new US Fish and Wildlife Service grant on landscape genetics of the California Tiger Salamander, and to motivate an Interagency Agreement between the California Department of Fish and Game and UC Davis. This work has resulted in several papers, several talks at major universities and national meetings, and continued collaborative work between agency biologists and our lab group. I organized a meeting with the USFWS to discuss mitigation of California tiger salamanders, and have a workshop planned for early 2008 to create a white paper for the Service on Best Scientific Practices for relocation of captured specimens. Both of these are areas of great interest to the agricultural community.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS), species boundaries, and landscape connectivity for amphibians and reptiles. Because we apply these results to agricultural landscapes in California, we help to define the biological units of protection for these species. Our results are essential for the effective coexistance of agriculture and sensitive species on the same landscapes. Our work exploring the use of SNPs to define species was highlighted in an international symposium (Society for Systematic Biology) and meetings/ presentations with both agency and consultants continued to help refine ideas about how sensitive species can coexist within agricultural landscapes. We provided the US Fish and Wildlife Service with critical data on landscape genetics of the endangered CTS to help guide management, and we continue to work closely with agencies on issues ranging from acreage in need of protection to the genetic consequences of invasive genes. Most recently, we have entered into a collaborative agreement with the California Department of Fish and Game to rewrite their Species of Special Concern document for amphibians and reptiles, a project with wide-ranging consequences for California agriculture. Given the sometimes conflicting goals of agriculture, development and species protection, our work strives to help identify the critical areas where species should be protected, while still keeping the maximal options for alternative land uses open across a species' range.

    Publications

    • Shaffer, H.B. and R.C. Thomson. 2007. Delimiting species in recent radiations. Systematic Biology 56:896-906. Fitzpatrick, B.M. and H.B. Shaffer. 2007. Hybrid vigor between native and introduced salamanders raises new challenges for conservation. Proceedings of the National Academy of Sciences, USA 104:15793-15798.
    • Spinks, P.Q. and H.B. Shaffer. 2007. Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, nuts, and inferences from multiple nuclear loci. Conservation Genetics 8:641-657.
    • Pauly, G.B., O. Piskurek and H.B. Shaffer. 2007. Phylogeographic concordance in the southeastern United States: the flatwoods salamander, AMBYSTOMA CINGULATUM, as a test case. Molecular Ecology 16:415-429.
    • Gamble, T., P.B. Berendzen, H.B, Shaffer, D.E. Starkey and A.M. Simons. 2008. Species limits and phylogeography of North American cricket frogs (Acris: Hylidae). Molecular Phylogenetics and Evolution (in press).
    • Searcy, C.A. and H.B. Shaffer. 2008. Calculating biologically accurate mitigation credits: insights from the California tiger salamander. Conservation Biology (in press).


    Progress 01/01/06 to 12/31/06

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. During the review period, we continued working on projects on genetic variation in the Western Spadefoot toad, the foothill yellow-legged frog, the California tiger salamander, and we are either preparing or revising manuscripts on all three systems. We also completed a related project on the impact of mosquitofish on the endangered California tiger salamander (CTS). Finally, we have continued to work on upland habitat use by the CTS (work supported by the Experiment Station initially, leading to new funding from CalTrans), and have applied those results to mitigation ratio analyses to better manage salamander populations. Results supported in part by the Agricultural Experiment Station were used as preliminary results for a new National Science Foundation grant on invasive tiger salamander interactions with native CTS. This work has resulted in several papers, and several talks at major universities and meetings were also given.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS), species boundaries, and lanscape connectivity for several sensitive species of amphibians and reptiles in California. Because we work in agricultural landscapes, helping to define the biological units of protection and how species utilize those landscapes is essential for the effective management of both agriculture and sensitive species on the same landscapes. We provided the US Fish and Wildlife Service with critical data on landscape genetics of the endangered CTS to help guide management, and we continue to work closely with agencies on issues ranging from acreage in need of protection to the genetic consequences of invasive genes. We also work closely with the California Department of Fish and Game, and have been active in their work to list the CTS as a state endangered species. Our spatial ecology work has provided critical data on management and regulation of CTS, and our work on hybrids provides important information on threats. Given the sometimes conflicting goals of agriculture, development and species protection, our work strives to help identify the critical areas where species should be protected, while still keeping the maximal options for alternative land uses open across a species' range.

    Publications

    • Fitzpatrick, B.M. and H.B. Shaffer. 2007. Managing invasive hybrids: Introduction history and habitat heterogeneity explain the landscape genetics of hybrid tiger salamanders. Ecological Applications. IN PRESS.
    • Davidson, C., M.F. Benard, H.B. Shaffer, J. Parker, C. O'Leary, J.M. Conlon and L.A. Rollins-Smith. 2007. Effects of chytrid and carbaryl exposure on survival, growth and skin peptide defenses in foothill yellow-legged frogs. Environmental Science and Technology. IN PRESS.


    Progress 01/01/05 to 12/31/05

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. During the review period, we completed projects on genetic variation in the Western Spadefoot toad and the foothill yellow-legged frog, and prepared a manuscript on the latter species. We also completed a related project on the impact of mosquitofish on the endangered California tiger salamander (CTS). Finally, we finished collecting data on an exhaustive, 10-gene analysis of variation across the range of the CTS, and are preparing a manuscript on that material. Results supported in part by the Agricultural experiment station were used as preliminary results for a new National Science Foundation grant on invasive tiger salamander interactions with native CTS. In addition, our lab has entered into a new relationship with CalTrans to examine the landscape ecology of CTS in the Central Valley and how both agriculture and roads impact this endangered species. Several talks at major universities and meetings were also given.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS) and species boundaries of several sensitive species of amphibians and reptiles in California. Because we work in agricultural landscapes, helping to define the biological units of protection, be they species or DPSs, is essential for the effective management of both agriculture and sensitive species on the same landscapes. We provided the US Fish and Wildlife Service with critical data on DPS of the endangered CTS to help guide management; this work led to the listing of the CTS under the US Endangered Species Act during the last review period, and we continue to work closely with agencies on issues ranging from acreage in need of protection to the genetic consequences of invasive genes. Our spatial ecology work has provided critical data on management and regulation of CTS, and our work on hybrids provides important information on threats. Given the sometimes conflicting goals of agriculture, development and species protection, our work helps to identify the critical areas where species must be protected, while still keeping the maximal options for alternative land uses open across a species range.

    Publications

    • Trenham, P.C. and H. B. Shaffer. 2005. Amphibian upland habitat use and its consequences for population viability. Ecological Applications 15:1158-1168.


    Progress 01/01/04 to 12/31/04

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. During the review period, we completed two projects on the landscape genetics of an endangered salamander (the California tiger salamander, CTS) and an endangered frog (the California red-legged frog), both of which demonstrate that existing conservation protection needs to be reconsidered. We also completed a project documenting that the hybridization dynamics of a non-native and native species of salamanders are extensive and ubiquitous, calling into question how to manage the federally endangered CTS. Finally, we have completed and published a spatial ecology project on upland habitat use in the endangered California tiger salamander. We have continued to collect material for genetic analyses of additional species of threatened amphibians and reptiles in the Central Valley, including the foothill yellow-legged frog, California tiger salamander (CTS), western Spadefoot and western pond turtle. Relevant publications that were accepted, submitted, or published during this review period are listed below. Several talks at major universities were also given.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS) and species boundaries of several sensitive species of amphibians and reptiles in California. Because we work in agricultural landscapes, helping to define the biological units of protection, be they species or DPSs, is essential for the effective management of both agriculture and sensitive species on the same landscapes. We provided the US Fish and Wildlife Service with critical data on DPS of the endangered CTS to help guide management; this work led to the listing of the CTS under the US Endangered Species Act during this review period. Our spatial ecology work has provided critical data on management and regulation of CTS, and our work on hybrids provides important information on threats. Given the sometimes conflicting goals of agriculture, development and species protection, our work helps to identify the critical areas where species must be protected, while still keeping the maximal options for alternative land uses open across a species' range.

    Publications

    • Shaffer, H. B. and P. C. Trenham. 2005. AMBYSTOMA CALIFORNIENSE. Pp. 1093-1102. In Lannoo, M.J. (Ed.), Status and Conservation of U.S. Amphibians. Volume 2: Species Accounts. University of California Press, Berkeley, California. In Press.
    • Shaffer, H. B. 2005. AMBYSTOMA GRACILE. Pp. 1113-1120. In Lannoo, M.J. (Ed.), Status and Conservation of U.S. Amphibians. Volume 2: Species Accounts. University of California Press, Berkeley, California. In Press.
    • Trenham, P.C. and H. B. Shaffer. 2005. Upland spatial distribution and habitat use in a declining amphibian. Ecological Applications. In Press.
    • Shaffer, H. B., G. B. Pauly, J. C. Oliver and P. C. Trenham. 2004. The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, AMBYSTOMA CALIFORNIENSE. Molecular Ecology 13:3033-3049.
    • Fitzpatrick, B. J. and H. B. Shaffer. 2004. Environment-dependent admixture dynamics in a tiger salamander hybrid zone. Evolution 58(6):1282-1293.


    Progress 01/01/03 to 12/31/03

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. During the review period, we completed several projects, and made substantial progress on others. Major completed projects now include: 1) a spatial ecology project on upland habitat use in the endangered California tiger salamander, 2) completion of a systematic study of the endangered California red-legged frogs, 3) completion of a second study examining the detailed genetic interactions of native and introduced tiger salamanders in the Salinas Valley, and 4) discovery of a new nuclear gene that is useful in molecular analyses of our target turtle species. We have continued to collect material for genetic analyses of four species of threatened amphibians and reptiles in the Central Valley, including the foothill yellow-legged frog, California tiger salamander (CTS), western Spadefoot and western pond turtle. Relevant publications that were accepted, submitted, or published during this review period are listed below. Several talks at major universities were also given.

    Impacts
    Our work on population genetics continues to define Distinct Population Segments (DPS) of several sensitive species of amphibians. We provided the US Fish and Wildlife Service critical data on DPS of the endangered CTS to help guide management. Our spatial ecology work has provided critical data on management and regulation of CTS, and our work on hybrids provides important information on threats.

    Publications

    • Shaffer, H. B. 2003. Mole salamanders (Ambystomatidae), p. 355-361. IN Hutchins, M., Duellman, W. E., and Schlager, N. (Editors), GRZIMEK'S ANIMAL LIFE ENCYCLOPEDIA, Second edition, Volume 6: Amphibians. Gale Group, Farmington Hills, MI.
    • Fujita, M.K., T.N. Engstrom, D.E. Starkey and H.B. Shaffer. 2004. Turtle phylogeny: Insights from a novel nuclear intron. Molecular Phylogenetics and Evolution. In Press.
    • Shaffer, H. B. and P. C. Trenham. 2004. Ambystoma californiense, p. 1093-1102. IN Lannoo, M.J. (Ed.), STATUS AND CONSERVATION OF U.S. AMPHIBIANS, Volume 2: Species Accounts. University of California Press, Berkeley, California. In Press.
    • Shaffer, H. B. 2004. Ambystoma gracile, p. 1113-1120. IN Lannoo, M.J. (Ed.), STATUS AND CONSERVATION OF U.S. AMPHIBIANS, Volume 2: Species Accounts. University of California Press, Berkeley, California. In Press.
    • Shaffer, H. B., G. M. Fellers, S. R. Voss, J. C. Oliver and G. B. Pauly. 2004. Species boundaries, phylogeography, and conservation genetics of the red-legged frog (RANA AURORA/DRAYTONII) complex. Molecular Ecology. In Press.


    Progress 01/01/02 to 12/31/02

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians and reptiles, particularly in the Great Central Valley. During the review period, we completed three projects, and made substantial progress on others. Major projects which are now complete include: 1) completion of a project on the effects of agrochemicals on 8 sensitive species of amphibians in the state and 2) completion of a long-term study on threats and recovery strategies for native pond turtles in an urban, Central Valley location, and 3) completion of a study of the effects of exotic species introductions on a native salamander in the Salinas Valley. We have continued to collect material for genetic analyses of four species of threatened amphibians and reptiles in the Central Valley, including the foothill yellow-legged frog, California tiger salamander (CTS), western Spadefoot and western pond turtle. Our work on the CTS is now complete, and demonstrates that at least three, and possibly six very differentiated lineages exist within the Central Valley and require separate protection. Our completed work also demonstrates that windborne agrochemicals and habitat loss are the two major factors driving amphibian declines in California, and that introduced exotic salamanders from the fish bait industry are a major threat to native CTS. Four relevant publications were accepted during this review period, several talks at major universities were given, and four major grants were funded/continued based on this work.

    Impacts
    Our work on population genetics defines Distinct Population Segments (DPS) of several sensitive species of amphibians. We provided US Fish and Wildlife Service critical data on DPS of the endangered CTS to help guide management. We demonstrated that agrochemicals can profoundly influence some amphibian species while others are primarily effected by habitat loss due to agriculture and urbanization.

    Publications

    • Davidson, C., H.B. Shaffer and M.R. Jennings. 2003. Spatial tests of the pesticide drift, habitat destruction, UV-B and climate change hypotheses for California amphibian declines. Conservation Biology. In Press.
    • Riley, S.P.D., H.B. Shaffer, S.R. Voss and B.M. Fitzpatrick. 2003. Hybridization between a rare, native tiger salamander (AMBYSTOMA CALIFORNIENSE) and its introduced congener. Ecological Applications. In Press.
    • Shaffer, H.B. 2003. Mole salamanders (Ambystomatidae). In: GRZIMEK'S ANIMAL LIFE ENCYCLOPEDIA. In Press.
    • Spinks, P.Q., G.B. Pauly, J.J. Crayon and H.B. Shaffer. 2003. Survival of the western pond turtle (EMYS MARMORATA) in an urban environment. Biological Conservation. In Press.


    Progress 01/01/01 to 12/31/01

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians, particularly in the Central Valley. Major projects which are now complete include: 1) a large study of population genetic variation in the California Tiger Salamander, AMBYSTOMA CALIFORNIENSE, 2) completion of a phylogenetic analysis of the red-legged frog, RANA AURORA, demonstrating that a previously undescribed cryptic species exists in this taxon, 3) completion of a project on the metapopulation dynamics of the threatened California Tiger Salamander, 4) completion of a project on the effects of agrochemicals on 8 species of sensitive species of amphibians in the state. Our major results demonstrate that 1) amphibian populations are very differentiated, even in the relatively homogeneous Central Valley, and 2) that windborne agrochemicals may be having a major detrimental impact on amphibians. Two relevant publications were accepted during this review period, several talks at major universities were given, and two major grants were funded based on this work.

    Impacts
    Our work on population genetics continues to help define management units of several sensitive species of amphibians, guiding resource agencies on conservation prioritization decisions. Our work with pesticides on amphibian populations demonstrates that agrochemicals can profoundly influence amphibian populations, and should help determine policy on adverse agrochemical effects on wildlife.

    Publications

    • Shaffer, H. B. and Trenham, P. C. 2001. AMBYSTOMA CALIFORNIENSE, p. 1093-1102. IN Lannoo, M.J. (Ed.), STATUS AND CONSERVATION OF U.S. AMPHIBIANS. VOLUME 2: SPECIES ACCOUNTS. University of California Press, Berkeley, California.
    • Shaffer, H. B. 2001. AMBYSTOMA GRACILE, p. 1113-1120. IN Lannoo, M.J. (Ed.), STATUS AND CONSERVATION OF U.S. AMPHIBIANS. VOLUME 2: SPECIES ACCOUNTS. University of California Press, Berkeley, California.


    Progress 01/01/00 to 12/31/00

    Outputs
    My work in California examines the influence of agriculture and urban land use on native amphibians, particularly in the Central Valley. Major projects which are now complete include: 1) a large study of population genetic variation in the California Tiger Salamander, AMBYSTOMA CALIFORNIENSE, 2) completion of a phylogenetic analysis of the red-legged frog, RANA AURORA, demonstrating that a previously undescribed cryptic species exists in this taxon, 3) completion of a project on the metapopulation dynamics of the threatened California Tiger Salamander, and 4) completion of a project on the effects of agrochemicals on the endangered Red-legged frog, RANA AURORA DRAYTONI. Our major results demonstrate that 1) amphibian populations are very differentiated, even in the relatively homogeneous Central Valley, and 2) that windborne agrochemicals may be having a major detrimental impact on amphibians. Two publications were accepted during this review period. Results from several of these studies were presented at four invited lectures at meetings or universities.

    Impacts
    Our work on population genetics should help define management units of several sensitive species of amphibians, guiding resource agencies on conservation prioritization decisions. Our work with pesticides on amphibian populations demonstrates that agrochemicals can profoundly influence amphibian populations, and should help determine policy on adverse agrochemical effects on wildlife.

    Publications

    • Davidson, C., Shaffer, H.B. and Jennings, M.R. 2001. Declines of the California red-legged frog: climate, UV-B, habitat, and pesticides hypotheses. Ecological Applications. In press.
    • Trenham, P.C., Koenig, W.D. and Shaffer, H.B. 2001. Spatially autocorrelated demography and interpond dispersal in the pond breeding salamander AMBYSTOMA CALIFORNIENSE. Ecology. In press.


    Progress 01/01/99 to 12/31/99

    Outputs
    We have completed several projects, and made significant progress on several others during the past year of work. Major projects which are now complete include: 1) completion of a large study of genetic variation in the Yosemite toad, BUFO CANORUS, across its range in Yosemite and Sequoia national parks, 2) completion of a phylogenetic analysis of the red-legged frog, RANA AURORA, demonstrating that a previously undescribed cryptic species exists in this taxon, 3) completion of two projects on the population biology and demography of the threatened California tiger salamander, AMBYSTOMA CALIFORNIENSE, and 4) completion of a project on the effects of agrochemicals on the endangered Red-legged frog, RANA AURORA DRAYTONI. In addition, we have added a substantial new data set to our work on the genetics of A. CALIFORNIENSE, and will complete this work during the coming year. Results from several of these studies were presented at Colorado State University and an invited symposium of the Geological Society of America.

    Impacts
    In investigating the effect of California agricultural practices on declining amphibians, the most striking result is the profound effect of agrochemicals on the endangered red-legged frog and the importance of on-site management in the genetic fragmentation of many amphibian species. We work with California Fish and Game to help manage these species in light of California agricultural practices.

    Publications

    • Trenham, P. C., Shaffer, H.B., Koenig, W.D. and Stromberg, M.R. 2000. Long-term demographic variation in the California Tiger Salamander (AMBYSTOMA CALIFORNIENSE). Copeia. In Press.
    • Shaffer, H. B., Fellers, G.M., Magee, A. and Voss. S.R. 2000. The genetics of amphibian declines: Population substructure and molecular differentiation in the Yosemite Toad, BUFO CANORUS (Anura, Bufonidae) based on SSCP and mtDNA sequence data. Molecular Ecology. In Press.