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.

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.

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.

Jefferson salamander (Amybstoma jeffersonianum). Photo credit: Jim Julian, USGS Leetown Science Center

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.

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 (1–25) 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, Rocky Mountain Center for Conservation Genetics and Systematics.

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 http://fresc.usgs.gov/research/StudyDetail.asp?Study_ID=47 and contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center.

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.

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 http://www.werc.usgs.gov/sandiego/shovel_page.html and contact Dustin A. Wood, Western Ecological Research Center.

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 8–14 microsatellite loci for each individual.

For more information view http://www.fort.usgs.gov/Research/research_tasks.asp?TaskID=2227 and contact Sara J. Oyler-McCance, Rocky Mountain Center for Conservation Genetics and Systematics.