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Conservation Genetics
Reptiles and Amphibians

Samples of genetics and genomics research from the USGS Ecosystems Mission Area about the conservation genetics of amphibians and reptiles.

Alameda whipsnake. Photo credit: U.S. Fish and Wildlife Service Bog turtle (Glyptemys muhlenbergii) Boreal toad (Bufo boreas). Photo credit: Rocky Mountain National Park Coast horned lizard. Photo credit: Chris Brown, USGS Jefferson salamander (Amybstoma jeffersonianum). Photo credit: USGS Western shovel-nosed snake. Photo credit: USGS Midget faded rattlesnake
Alameda Whipsnake (Vandergast) Bog Turtle (King) Boreal Toad (Switzer) Coast Horned Lizards
(Fisher)
Jefferson Salamanders (King) Western Shovel-Nosed Snake (Wood) Midget Faded Rattlesnake (Oyler-McCance)
Oregon spotted frog in vegetation. Photo credit: U.S. Fish and Wildlife Service Male Spotted salamander (Ambystoma maculatum) in a small forested wetland. Photo credit: USGS Wood frog (Rana sylvatica). Photo credit: USGS New turtle species (Graptemys pearlensis). Credit: Photo by Cris Hagen, University of Georgia, Savannah River Ecology Laboratory Photo: Western Pond Turtle (Actinemys marmorata). Photo credit: Chris W. Brown, USGS red-legged treefrog
Pacific Northwest Amphibians   (Haig)

Spotted Salamanders and Wood Frogs (King)

Wood Frogs (Oyler-McCance) New Turtle Species (Ennen, Lovich) Western Pond Turtle (Fisher, Markert) California red-legged frog (Fisher, Markert)

Conservation Genetics of the Endangered Alameda Whipsnake
Alameda whipsnake. Photo credit: U.S. Fish and Wildlife Service
Alameda whipsnake. Photo credit: U.S. Fish and Wildlife Service

The Alameda whipsnake (Masticophis lateralis euryxanthus) is both a federally and state listed endangered species limited to scrub and chaparral habitat within Contra Costa and Alameda Counties, CA. Loss and fragmentation of habitat due to agricultural and urban development over the last 100 years are cited as the main causes of its decline. Based on historic and current collection data, Alameda whipsnakes were grouped into 5 recovery units connected with two linkage corridors in the U.S. Fish and Wildlife Service draft recovery plan. However, the population genetic structure among and within these units has never been determined. We are developing and analyzing sensitive genetic markers (microsatellites) to determine recent patterns of population divergence among and within recovery units of this species and to determine whether designated corridors are adequate to promote dispersal and gene flow, and maintain genetic integrity across the species range.

For more information contact Amy Vandergast, Western Ecological Research Center.

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Identification of Population Structure, Metapopulation Extent, and Evolutionarily Significant Lineages in the Federally Threatened Bog Turtle: Implications for Restoration
Bog turtle (Glyptemys muhlenbergii)
Bog turtle (Glyptemys muhlenbergii)

Conceivably no species better illustrates the negative impacts of wetland loss and degradation in the United States than the bog turtle, Glyptemys muhlenbergii.  In addition, some populations are extremely localized and have been extirpated by over-collecting to supply the illegal pet trade.  As a result of these declines, the northern populations of the bog turtle were listed as threatened under the Endangered Species Act by the U.S. Fish and Wildlife Service.  Leetown Science Center (LSC) geneticists have developed a suite of species-specific microsatellite DNA markers in the bog turtle that when surveyed, resulted in unique multilocus genotypes for each individual surveyed in this study.  LSC researchers have defined the genetic population structure among multiple wetland areas throughout the species’ range, delineated management units (i.e., metapopulation extent) and evolutionarily significant lineages among geographic populations; estimated the effective population sizes of each metapopulation using intergenerational variation in allele frequencies; and provided a highly successful predictive model for assigning individual bog turtles of unknown origin to their natal geographic population (i.e., for law enforcement purposes).  To date, over 450 turtles have been collected and genotyped from throughout the species range. 

For more information contact Timothy L. King at the Leetown Science Center.

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Boreal toad (Bufo boreas boreas)
Boreal toad (Bufo boreas). Photo credit: Rocky Mountain National Park
Boreal toad (Bufo boreas). Photo credit: Rocky Mountain National Park

The boreal toad (Bufo boreas boreas) is distributed across much of the western U.S. and Canada.  It is locally common, but rapid losses and declines of many populations have caused concern.  The Southern Rocky Mountain (SRM) populations of B. boreas ranges from south central Wyoming, throughout the mountains of Colorado, and into northern New Mexico. The SRM population of B. boreas was recently withdrawn as a candidate for protection under the Endangered Species Act because it did not constitute a distinct population segment as defined by the ESA.  In order to further test the genetic differentiation of the SRM population relative to other populations of B. boreas, and species of the B. boreas group, a phylogeographic analysis was conducted.  For this study, mitochondrial DNA sequence data from the control region, as well as microsatellite genotype data, were generated for over 800 from throughout the range of B. boreas, as well as samples of B. canorus, B. exsul and B. nelsoni.

For more information contact John F. Switzer, Leetown Science Center.

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Coast Horned Lizards Integrating Genetic, Morphological, and Ecological Data to Identify Species
Coast horned lizard. Photo credit: Chris Brown, USGS
Coast horned lizards from northern Baja to northern California, like this one from Torrey Pines State Park, are distinctly different from populations in central and southern Baja California, and now are designated a new species, Phrynosoma blainvillii. Photo by Chris Brown, USGS

Coast horned lizard populations are in decline from southern Baja California to Northern California due to several factors, including loss of lowland habitat from agriculture and urbanization and the introduction of Argentine ants, which displace the more nutritious native ants. The coast horned lizard is on the International Union for Conservation of Nature's Red List of Threatened Species. In California coast horned lizard is a Species of Special Concern. A new study not only identifies three species of coast horned lizards, but also provides clarity to useful conservation units within the declining horned lizards in coastal California. In the study, published during the week of July 20, 2009 in the early online edition of the journal Proceedings of the National Academy of Sciences, researchers from the University of California, Berkeley, and the U.S. Geological Survey integrated genetic, anatomical and ecological information and showed that when the coast horned lizard moved north from Baja California and spread to northern California, it diverged into at least two new species. The oldest and original species, P. coronatum, is found only in southern Baja California. The researchers identified a second species, P. cerroense, in central Baja and a third, P. blainvillii, whose range extends from northern Baja to Northern California. Additionally, the researchers found enough genetic and ecological differences to suggest there are at least three distinct populations of P. blainvillii, each requiring separate management and protection.

Newsroom: Read the Press Release at UC Berkely News

Background about coast horned lizards:

Fisher, R.N., Suarez, A.V. and T.J. Case. 2002. Spatial patterns in the abundance of the coastal horned lizard. Conservation Biology 16:205-215. [online article, PDF 2.45 MB Acrobat]

For more information contact Robert N. Fisher, Western Ecological Research Center.

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Identification of the Basic Unit of Management Unit Among Jefferson Salamanders Inhabiting Delaware Water Gap National Recreational Area (DEWA)
Jefferson salamander (Amybstoma jeffersonianum). Photo credit: USGS
Jefferson salamander (Amybstoma jeffersonianum). Photo credit: Jim Julian, USGS Leetown Science Center
Jefferson salamander eggs. Photo credit: USGS
Jefferson salamander eggs. Photo credit: Craig Snyder, USGS Leetown Science Center

Few natural ecosystems illustrate the patchwork characteristics of the landscape mosaic like the sharply defined habitats created by vernal pools.  Although it is generally held that vernal pool-breeding amphibians exist as spatially delimited local populations coupled by some degree of migration (i.e., resemble theoretical metapopulations), few studies have documented population structure within these species or independently determined the existence or extent of metapopulation structure.  Patterns in microsatellite DNA variation have allowed delineation of the genetic structure within and among populations of the Jefferson salamander (Ambystoma jeffersonianum) and provided an effective method for identification of hybrid individuals directly from embryos.  The findings of this research indicate that each distinct pond is the fundamental unit of management for this species.  The conservation implications are that while population independence may be expected at more wide-ranging spatial scales, assumptions about population connectivity within this species will overestimate actual patterns of gene flow at finer spatial scales.

For more information contact Timothy L. King at the Leetown Science Center.

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Population Structure and Dynamics of the Midget Faded Rattlesnake
Midget faded rattlesnake
Midget faded rattlesnake

Very little is known about the ecology of Midget Faded Rattlesnakes (Crotalus viridis concolor), considered rare throughout their range. Midget Faded Rattlesnakes exist in very small, isolated groups centered around den sites with few (125) individuals, and seasonal movements may be only a few hundred meters. Such natural history traits make these rattlesnakes a sensitive species vulnerable to various human impacts. In addition, the construction of Flaming Gorge Reservoir over 50 years ago divided the population in half and forced them to higher ground. This virtually prevents gene flow between the two sides of the reservoir, with possible genetic consequences. This study is investigating the population structure and dynamics of these snakes, using genetic analyses of microsatellite DNA markers in the lab and radio telemetry in the field. USGS scientists are analyzing the genetic structure of the population as a whole, as well as localized characteristics of subpopulations around the reservoir. Results will provide the information needed to properly manage this sensitive species.

For more information contact Sara J. Oyler-McCance, Molecular Ecology Lab (MEL).

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Conservation Genetics of Threatened Pacific Northwest Amphibians
Oregon spotted frog in vegetation. Photo credit: U.S. Fish and Wildlife Service
Oregon spotted frog in vegetation. Photo credit: U.S. Fish and Wildlife Service

Amphibians may be disproportionately affected by habitat fragmentation due to their sensitivity to temperature, short dispersal ranges, and extreme site fidelity. These physical and habitat limitations may affect a population’s genetic structure and status. The USGS has used molecular genetic methods to assess population characteristics for a number of frogs and salamanders considered species of concern in the Pacific Northwest: the spotted frog, Oregon slender salamander, Larch Mountain salamander, southern torrent salamander, Cascade torrent salamander, Columbia torrent salamander, and Olympic torrent salamanders. This research provides critical information about these populations plus tests the utility of molecular techniques in resolving various aspects of amphibian evolution, population change, behavior, and conservation status.

For more information view the study description Conservation Genetics of Threatened Pacific Northwest Salamanders and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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Identification of Population Structure, Metapopulation Extent, and Evolutionarily Significant Lineages of the Spotted Salamanders and Wood Frogs Inhabiting Vernal Pools in Six National Parks
Male Spotted salamander (Ambystoma maculatum) in a small forested wetland. Photo credit: USGS
Male Spotted salamander (Ambystoma maculatum). Photo taken March 2003 in a small forested wetland in the Delaware Water Gap National Recreation Area, Pike county, PA. Photo credit: Michael Eackles, Leetown Science Center with lab camera

If vernal pool amphibian species are managed as metapopulations but intraspecific genetic patterns suggest otherwise, extinctions may occur because habitat connectivity to source populations no longer exists, thus recolonization does not supervene.  Therefore, pool-breeding amphibians present a management conundrum due to uncertainty in defining the basic demographic unit of management.  For pool-breeding amphibians this fundament unit of management could be the individual pond, a local pond cluster, a group of pond clusters, or some larger scale that is ultimately determined primarily by a combination of dispersal and colonization ability and the degree of habitat fragmentation. To develop management strategies for maintaining evolutionarily significant lineages in obligate vernal pool species that will ensure long-term population persistence, it is essential that resource stewards first identify this minimal demographic unit.  Accordingly, established patterns of genetic variation offer the only true estimate of effective migration and recolonization rates (i.e., gene flow) among local vernal pools and other intraspecific sub-structuring.

Inferences regarding the migration, colonization, and extinction of vernal pool inhabitants, such as coexisting indicator species the spotted salamander (Ambystoma maculatum) and the wood frog (Rana sylvatica), are necessary for the effective conservation of these species.  Geneticists at the Leetown Science Center have teamed with the National Park Service and Dr. James Petranka (UNC-Asheville), Dr. Charles Smith (High Point University), and Dr. Floyd Scott (Austin Peay State University, Clarksville, TN), to collected spotted salamander and wood frog eggs from the same clusters of ponds sampled from six national parks (Great Smokey Mountains National Park (GRSM), Blue Ridge Parkway (BLRI), Cumberland Gap National Historical Park (CUGA), Mammoth Cave National Park (MACA), Delaware Water Gap National Recreation Area (DEWA), and Acadia National Park (ACAD).  Over 1,700 spotted salamanders and 1,200 wood frogs have been genotyped at 13 and 11 microsatellite DNA markers, respectively.  Preliminary results suggest that the local cluster of ponds serves as the basic unit of management for the spotted salamander and the more vigil wood frogs should be managed at the region (or park level). 

For more information contact Timothy L. King at the Leetown Science Center.

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Unraveling the Morphological and Genetic Diversity in the Western Shovel-Nosed Snake
Western shovel-nosed snake. Photo credit: USGS
Western shovel-nosed snake. Photo credit: Chris Brown, USGS

Uncovering patterns of genetic diversity within species can aid in conservation decisions when listing and management efforts first require that distinct population segments or evolutionary significant units (ESUs) are defined. An ESU is a population ssegment with a distinct long-term evolutionary history that is separate from other populations. Subspecies designations, based on morphological variation have often served as surrogates for ESUs. However, in some cases, subspecies designations may not reflect the evolutionary units supported by genetic evidence. USGS scientists have examined genetic and morphological diversity in the western shovel-nosed snake. Neither genetic data nor morphological characters support the current subspecies designations within the Western shovel-nosed snake that were originally defined based mainly on banding patterns.

For more information view the project overview Assessing Population Structure and Genetic Diversity in the Western Shovel-nosed Snake (Chionactis occipitalis) across Arizona, with Special Emphasis on the Validity of the Tuscon Shovel-nosed Snake (Chionactis occipitalis klauberi) and contact Dustin A. Wood, Western Ecological Research Center.

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Population Genetics of Wood Frogs in Rocky Mountain National Park
Wood frog (Rana sylvatica). Photo credit: USGS
Wood frog (Rana sylvatica). Photo credit: ARMI National Atlas for Amphibian Distributions, USGS Patuxent Wildlife Research Center

Wood frogs (Rana sylvatica) are considered to be a species of conservation concern and have been listed as an endangered species in the State of Colorado. Population sizes have been declining, likely due to habitat loss associated with hydrological changes, disease, and other environmental factors. A pilot study conducted by USGS scientists on wood frogs in this region showed that there were some significant differences between ponds (contrary to published work on wood frogs in other states). This suggests that there may be reduced levels of gene flow within Rocky Mountain National Park due to changes in hydrology. For this study, investigators are collecting a much more rigorous and complete sample of wood frogs in Rocky Mountain National Park. A new sampling regime is being employed to circumvent previous problems associated with sampling closely related individuals. In this study, investigators are extracting DNA from eggs and amplifying 814 microsatellite loci for each individual.

For more information view the summary Population Genetics of Wood Frogs in Rocky Mountain National Park and contact Sara J. Oyler-McCance, Molecular Ecology Lab (MEL).

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New Turtle Species Discovered
New turtle species (Graptemys pearlensis). Credit: Photo by Cris Hagen, University of Georgia, Savannah River Ecology Laboratory
New turtle species (Graptemys pearlensis). Credit: Photo by Cris Hagen, University of Georgia, Savannah River Ecology Laboratory

A new species of turtle no bigger than a small dinner plate has been discovered, bringing the number of native turtle species in the U.S. to 57. The Pearl River map turtle is found only in the Pearl River in Louisiana and Mississippi. It is a relic of sea-level fluctuations between glacial and interglacial periods, which isolated map turtles in different rivers along the Gulf Coast. Eventually, the turtles evolved into unique species confined to a single river system. USGS scientists Jeff Lovich and Josh Ennen, (who first suspected the Pearl River map turtles were a new species while conducting doctoral research at University of Southern Mississippi),said the turtle, whose new scientific name is Graptemys pearlensis, had previously been confused with another turtle species in a nearby river, the Pascagoula map turtle. The Pearl River map turtle is a native freshwater reptile that lives in large rivers to medium-sized streams. Females are much larger than males, measuring between 6 and 11 inches as adults, and use large crushing surfaces on their jaws to open clams. Males, meanwhile, grow to a comparatively small 4 to 6 inches and eat some mollusks, but mostly insects and fish.Altogether, the data was enough to make it plain: the Pearl River map turtle and the Pascagoula River map turtle are definitely two different species. The genetic data was clear on this, though the visual differences are more subtle -- one of the most obvious is the Pearl River map turtle sports a continuous black stripe down its back whereas the Pascagoula map turtle has a broken black stripe.
Chelonian Conservation and Biology International Journal of Turtle and Tortoise Research. For more information, contact Josh Ennen and Jeff Lovich, USGS Southwest Biological Science Center.

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Population Genetic Diversity Among Western Pond Turtles (Actinemys marmorata)
Photo: Western Pond Turtle (Actinemys marmorata). Photo credit: Chris W. Brown, USGS

Western Pond Turtle (Actinemys marmorata). Photo credit: Chris W. Brown, USGS

USGS researchers are using state of the art genetic and analytical methods to measure both the extent of population connectivity and the levels of within population genetic diversity among western pond turtles (Actinemys marmorata) in southern California.  Collaborators include Jeffrey Markert, Robert Fisher, the California Department of Fish and Game and Shaffer Lab at the University of California, Davis.

For more information, visit http://www.werc.usgs.gov/Project.aspx?ProjectID=212 , and contact Jeffrey Markert, Robert Fisher, Western Ecological Research Center.

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Genetic Determination of Source Populations of the California Red-legged Frog (Rana draytonii) for Reestablishment Efforts in Southern California
http://www.fhwa.dot.gov/environment/wildlifeprotection/images/CA_redlgd_frog(USGS).jpg

California Red-legged Frog (Rana draytonii).

The once common California red-legged frog (Rana draytonii) has been extirpated from most of its historical range in southern California.  The California red-legged frog was listed as a threatened species under the Endangered Species Act in 1996 and final critical habitat was designated in 2006. Because there are so few populations, recovery of the species is dependent on stabilizing the existing populations and reestablishing additional populations to watersheds with suitable habitat.  The recovery plan for this species identifies the reestablishment of historic populations as a criterion to consider for delisting. The plan also calls for augmentation of existing populations and reestablishment of extirpated populations as priority recovery actions in southern California.

For more information, visit http://www.werc.usgs.gov/Project.aspx?ProjectID=213 , and contact Jeffrey Markert, Robert Fisher, Western Ecological Research Center.

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Featured Publication

Coast horned lizard. Photo credit: Chris Brown, USGSGenetics Identifies Three Species of Coast Horned Lizards
A new study not only identifies three species of coast horned lizards, but also provides clarity to useful conservation units within the declining horned lizards in coastal California. In the study, published during the week of July 20, 2009 in the early online edition of the journal Proceedings of the National Academy of Sciences, researchers from the University of California, Berkeley, and the U.S. Geological Survey integrated genetic, anatomical and ecological information and showed that when the coast horned lizard moved north from Baja California and spread to northern California, it diverged into at least two new species.

For more information, see the research summary Coast Horned Lizards and the following publication:

Adam D. Leach, Michelle S. Koo, Carol L. Spencer, Theodore J. Papenfuss, Robert N. Fisher, and Jimmy A. McGuire. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma). [online article from PNAS]

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