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Conservation Genetics

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

American Avocet (Recurvirostra americana) Coastal swamp forest in southeastern Louisiana. Photo credit: William H. Conner, Clemson University Horn snails Southern California Western skink Shovel-nosed snake
Birds and their Prey, Climate Change, and the Great Basin Wetlands (Haig, et al.) Coastal Freshwater Forested Wetlands (Krauss) DNA Libraries Open the Books on Trematode Parasites (Lafferty) Hotspots of Evolutionary Potential and Southern California (Vandergast) Southern Calif. Urbanization
Isolates Wildlife, Promotes

Regional Evolutionary Hotspots in the Mojave and Sonoran Deserts (Wood, Vandergast)
Predicting and Managing Climate Change:  Impacts on Semi-Arid Land Wetlands, Migratory Birds, and Their Prey
American Avocet (Recurvirostra americana)

American Avocet (Recurvirostra americana).

Anthropogenic climate change is altering aquatic ecosystems worldwide, particularly small and shallow systems such as wetlands. As a result of these abiotic changes, the terrestrial and aquatic species that depend on such wetlands are also likely to experience significant shifts in range, phenology, and population structure, particularly in arid and semi-arid regions already limited in water quantity and quality. We are developing a framework to determine and manage landscape-level impacts of climate change on wetlands and wetland-dependent species in semi-arid areas of North America’s Great Basin. We begin by determining the scope of abiotic impacts from climate change using remote sensing and ground-level monitoring to create models of the relationships between water volume, water quality, weather, and climate. We will then measure landscape-level population genetic connectivity of the aquatic invertebrates that serve as key prey species to the millions of migratory waterbirds that depend on these wetlands. We can use projections of future climate conditions to model how wetland habitat quality and species connectivity will change in the coming decades by combining estimates of landscape connectivity for these species with a model of the climate drivers of wetland patch quality. This approach will serve as a general model for understanding population- and community-level climate impacts and provide a sound basis for conservation planning and adaptive management by wetland resource managers around the world. The model will be made user-friendly for specific wetland management as well as provide regional perspectives. This novel approach integrates expertise from three USGS divisions and addresses seven of the nine broad goals and 10 more specific goals of the USGS Strategic Science Plan for the U.S. Climate Change Science Program, and will be a contribution to BLM’s Assessment, Inventory, and Monitoring (AIM), USGS Sagebrush Biome coordinated research projects, USGS’s Great Basin Integrated Landscape Monitoring (GBILM) Program, USGS SageMap program, Healthy Lands Initiative, USFWS National Shorebird Plan, North American Waterfowl Management Plan, and Western Hemisphere Shorebird Reserve Network.

Read the project summary Predicting and Managing Climate Change Impacts on Semi-Arid Land Wetlands, Migratory Birds, and Their Prey: An Integration of Remote Sensing, Molecular Genetics, Hydrology, and Environmental Modeling

For more information, contact Susan M. Haig, Forest and Rangeland Ecosystem Science Center; Mark P. Miller, Forest and Rangeland Ecosystem Science Center, Travis Schmidt, Fort Collins Science Center; and John Matthews, World Wildlife Fund (WWF).

See also Conservation Genetics - Birds >>

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Coastal Freshwater Forested Wetlands
Coastal swamp forest in southeastern Louisiana. Photo credit: William H. Conner, Clemson University

Coastal swamp forest in southeastern Louisiana.  Photo credit: William H. Conner, Clemson University

Coastal freshwater forested wetlands are under increasing stress associated with sea-level rise and salinization along the Gulf and south Atlantic Coasts.  For nearly two decades, forest ecologists at the USGS National Wetlands Research Center in Lafayette, Louisiana have studied the eco-physiological and morphological responses of genetically distinct tree populations from these areas to different salinity and flood regimes.  The goal of this research is to identify “improved” genotypes that can in turn be used for large-scale coastal swamp forest restoration efforts on marginal sites.  Research to date has targeted baldcypress (Taxodium distichum) because of its longer term survival on salt-impacted sites as well as its broad tolerance to flooding.  Studies have revealed strong intraspecific variation in tolerance to low salinity levels (approaching 4 ppt) among seedlings propagated from different coastal populations.  However, persistent exposure to higher salinities eventually results in mortality for all genotypes.  Recent research has suggested that natural selection may favor broad in lieu of narrow tolerances in baldcypress, thereby precluding strong adaptation to specific flood regimes.  The consequences of such a broadly adaptive strategy for the future of salt tolerance improvement are unknown, but will continue to be a focus of this research.

For more information, contact Ken W. Krauss, National Wetlands Research Center.


  • Krauss, K.W., T.W. Doyle, and R.J. Howard. 2009. Is there evidence of adaptation to tidal flooding in saplings of baldcypress subjected to different salinity regimes? Environmental and Experimental Botany 67: 118-126.
  • Krauss, K.W., J.L. Chambers, and D. Creech. 2007. Selection for salt tolerance in tidal freshwater swamp species: advances using baldcypress as a model for restoration. Pages 385-410 in W.H. Conner, T.W. Doyle, K.W. Krauss (eds.), Ecology of Tidal Freshwater Forested Wetlands of the Southeastern United States. Springer. 505 p.
  • Krauss, K.W., J.L. Chambers, J.A. Allen, D.M. Soileau, Jr., and A.S. DeBosier. 2000. Growth and nutrition of baldcypress families planted under varying salinity regimes in Louisiana, USA. Journal of Coastal Research 16: 153-163.
  • Krauss, K.W., J.L. Chambers, J.A. Allen, B. Luse, and A.S. DeBosier. 1999. Root and shoot responses of Taxodium distichum seedlings subjected to saline flooding. Environmental and Experimental Botany 41: 15-23.
  • Krauss, K.W., J.L. Chambers, and J.A. Allen. 1998. Salinity effects and differential germination of several half-sib families of baldcypress from different seed sources. New Forests 15: 53-68.
  • Allen, J.A., W.H. Conner, R.A. Goyer, J.L. Chambers, and K.W. Krauss. 1998. Chapter 4: Freshwater forested wetlands and global climate change. Pages 33-44 in G.R. Guntenspergen and B.A Vairin (eds.), Vulnerability of coastal wetlands in the Southeastern United States: climate change research results, 1992-97. U.S. Geological Survey, Biological Resources Division Biological Science Report USGS/BRD/BSR-1998-0002. 101 p.
  • Allen, J.A., J.L. Chambers, and S.R. Pezeshki. 1997. Effects of salinity on baldcypress seedlings: physiological responses and their relation to salinity tolerance. Wetlands 17: 310-320.
  • Allen JA, S.R. Pezeshki, and J.L. Chambers. 1996. Interaction of flooding and salinity stress on baldcypress (Taxodium distichum). Tree Physiology 16: 307-313
  • Allen, J.A., J.L. Chambers, and M. Stine. 1994. Prospects for increasing the salt tolerance of forest trees: a review. Tree Physiology 14: 843-853
  • Allen, J.A., J.L. Chambers, and D. McKinney. 1994. Intraspecific variation in the response of Taxodium distichum seedlings to salinity. Forest Ecology and Management 70: 203-214

See also Conservation Genetics - Plants >>

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DNA Libraries Open the Books on Trematode Parasites
Horn snails in a salt marsh at Morro Bay, California. Photo credit: Kevin D. Lafferty, USGS
Larger view
Like “mobile data recorders,” these horn snails in a salt marsh at Morro Bay, California, reflect in their complement of trematode parasites the predator-prey relationships occurring in the salt marsh during their lifetime. Photo credit: Kevin D. Lafferty, USGS

Scientists at the USGS Western Ecological Research Center and the University of California, Santa Barbara, are developing libraries of the mitochondrial cytochrome oxidase I (COI) gene from easy-to-identify trematode cercariae to help in the identification of more difficult trematode stages by extracting DNA, Polymerase Chain Reaction (PCR) amplification and comparison with sequences from the libraries. By surveying the trematode parasite population in resident horn snails, a hub for more than 20 trematode species, whose lifestyle requires multiple sequential hosts, the scientists strive to develop trematodes as indicators of ecosystem health in estuaries along the Pacific Coast.

Read more about the parasite studies:

For more information contact Kevin D. Lafferty, Western Ecological Research Center.

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GIS-Based Approach to Identify Hotspots of Evolutionary Potential Applied to Southern California
Southern California. Photo credit: NASA/Goddard Space Flight Center, The SeaWiFS Project and ORBIMAGE, Scientific Visualization Studio
Southern California. Photo credit: NASA/Goddard Space Flight Center, The SeaWiFS Project and ORBIMAGE, Scientific Visualization Studio

Protected areas most often encompass rare habitats, or “typical” exemplars of ecoregions and geomorphic provinces.  This approach focuses on current biodiversity, and typically ignores the evolutionary processes that control the gain and loss of biodiversity at other levels (e.g., genetic, ecological). 

In order to include evolutionary process in conservation planning efforts, its spatial components must first be identified and mapped.  We have developed a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a “Multi-species Genetic Landscape”, or MGL).  Using this approach, we analyzed 21 mitochondrial DNA datasets from vertebrate and invertebrate species in Southern California to identify areas with common phylogeographic breaks and high intralineage diversity. The result is an evolutionary framework for southern California within which genetic biodiversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design.

More information can be viewed at Finding Evolutionary Hotspots in Southern California for Conservation Planning. For more information, contact Amy Vandergast, Western Ecological Research Center.

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Southern Calif. Urbanization Isolates Wildlife, Promotes Inbreeding
Western skink
Photo: The Western skink (Plestiodon skiltonianus) is a relatively common and widespread lizard in Southern California. Credit: Chris Brown/USGS Western Ecological Research Center
Wrentit genetic isolation map, Thousand Oaks, Calif.
Photo: This map of the Thousand Oaks, Calif. area visualizes the degree of genetic isolation being experienced by the wrentit (Chamaea fasciata), a small songbird. This graphic was originally published in the journal PLoS ONE. Credit: USGS/NPS/PLoS ONE. Larger view
Photo: The wrentit (Chamaea fasciata) is a small, monagamous songbird found in California's coastal scrublands. Credit: Tom Grey/Stanford University

Urban development can isolate wildlife populations and promote inbreeding. Researchers from National Park Service and USGS studied three commonly found species of lizards and a small songbird, the wrentit, comparing the DNA of animals collected throughout the now-isolated scrubland patches and parks surrounding Thousand Oaks and State Route 23 — an area that was a single, mostly contiguous wilderness only 50 years ago. Animals in these "habitat islands" have unique genetic profiles, so that individuals even in closely neighboring patches are unlikely to be related. Additionally, animals within the smaller or more isolated habitat patches are closely related to one another. Both of these trends appear to be correlated to whether roadways are nearby and how long ago a patch became isolated. The data showed that the populations of lizards and wrentits have become disconnected and isolated as their natural habitats became divided and fragmented by roadways and housing. As the animals are unable to cross these urban barriers, they begin to inbreed and lose their genetic diversity. Decreased genetic diversity may increase a species' chance of extinction. The study is among the first concrete evidence of significant population genetic changes caused by habitat fragmentation, especially within a small region and over a short time period. Researchers chose these lizard and bird species because they represent different ecological niches and range of mobility within the scrubland ecosystem. For example, Western skinks tend to be secretive debris dwellers, while Western fence lizards are fast-running, more mobile animals. Researchers found the same pattern of genetic isolation in all four animals, even a flying species like the wrentit. The assumption would be that birds could fly across urban barriers and remain a continuous population, but this was not the case, at least with a smaller sedentary bird like the wrentit.

For more information, contact Katy Delaney (NPS) , Seth Riley (NPS) and Robert N. Fisher (USGS),,


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Regional Evolutionary Hotspots in the Mojave and Sonoran Deserts
Shovel-nosed snake

Researchers analyzed 12 desert species, including small burrowing species like the shovel-nosed snake (Chionactis occiptalis), to map out the evolutionary hotspots. Photo credit: Zachary Cava, USGS

In light of increased questions on wildlife conservation and energy developments in the U.S. Southwest, USGS has been conducting landscape genetics research in the desert southwest to identify regions of conservation importance. A study in Diversity and Distributions by USGS researchers profiles the use of genetic data and GIS to identify hotspots of genetic divergence and diversity — areas that may ensure evolutionary resilience of animal populations — and to assess whether protected lands overlapped with these evolutionary hotspots. Researchers analyzed genetic data for 12 species of reptiles, amphibians, small mammals and spiders found across the Mojave and Sonoran Deserts. Distinct lineages were identified and dated within species, and researchers also tested for a signature of population expansion within lineages and dated expansion. For all species assessed, six hotspots of high genetic divergence and diversity were concentrated along the Colorado River and across the Mojave and the Sonoran Desert ecotone. At least some proportion of the land within each recovered hotspot was categorized as protected, yet four of the six also overlapped with major areas of human development. Lineage dating suggests that many species diversified prior to the “Last Glacial Maximum” — suggesting that many species have persisted despite long-term environmental change. In addition, distinctive Mojave and Sonoran lineages were recovered in most species studied, suggesting that protection throughout both of these ecoregions is warranted.

Background information:

Wood, D.A., Vandergast, A.G., Barr, K.R., Inman, R.D., Esque, T.C., Nussear, K.E., and R.N. Fisher. 2012. Comparative phylogeography reveals deep lineages and regional evolutionary hotspots in the Mojave and Sonoran Deserts. Diversity and Distributions, Early View, 16p.

Read the project summary Mapping Habitat and Genetic Diversity in the Desert Southwest. For more information, contact Dustin A. Wood or Amy G. Vandergast, Western Ecological Research Center.

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Featured Publication

A recent article from the National Wetlands Research Center examines how plant populations may adapt to environmental conditions over time by developing genetically based morphological or physiological characteristics. Using baldcypress (Taxodium distichum (L.) L.C. Rich) from the southeastern United States, findings suggest that adaptations of coastal baldcypress to broad (rather than narrow) environmental conditions may promote ecophysiological and growth enhancements under a range of global-change-induced stressors, perhaps reflecting a natural resilience to environmental change while precluding adaptations for specific flood regimes.

See the related research summary Coastal Freshwater Forested Wetlands.

For more information contact Ken W. Krauss, National Wetlands Research Center.

Krauss, K.W., Doyle, T.W., and Howard, R.J. Is there evidence of adaptation to tidal flooding in saplings of baldcypress subjected to different salinity regimes? Environmental and Experimental Botany, Volume 67, Issue 1, November 2009, Pages 118-126. doi:10.1016/j.envexpbot.2009.05.005 
Online abstract >>

This research was funded by the Global Change Science of the Terrestrial, Freshwater, and Marine Ecosystems Program.

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