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Ecosystems - Genetics and Genomics

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Conservation Genetics
Insects and Invertebrates

Samples of genetics and genomics research from the USGS Ecosystems Mission Area about the conservation genetics of insects, chelicerates, and crustaceans.

Ptilothrix bombiformis specimen. Photo credit: Graham Snodgrass, used with permission Endangered fairy shrimp, Branchinecta sandiegonensis. Photo credit: D. Parsick, University of San Diego Horseshoe crabs on Florida shore. Photo credit: Thomas A. Hermann/NBII.Gov Mahogany Jerusalem Cricket. Photo credit: David Weissman, California Academy of Sciences Madison cave isopod. Photo credit: Courtesy Virginia DCR Natural Heritage Program
Bee Conservation (Droege, Brady) Fairy Shrimps (Vandergast) Horseshoe Crabs (King) Jerusalem Crickets (Vandergast) Madison Cave Isopods (King)
Riverside Fairy Shrimp photo credit Chris W. Brown, USGS        
Riverside fairy shrimp (Vandergast)        


Bee Conservation
Ptilothrix bombiformis specimen. Photo credit: Graham Snodgrass, used with permission

Ptilothrix bombiformis specimen. Photo credit: Graham Snodgrass, used with permission

Four thousand bee species are thought to be native to the United States. Bees inhabit tundra to desert biomes with diversity hotspots in the Southwest deserts and areas of deep sand. There is a long history of taxonomic struggles to separate out species among these groups. Males and females often look quite different, nests are hard to find, and many species are detected only occasionally. Further impediments to the renewed interest in the ecological and biological aspects of this group is the dwindling supply of taxonomic experts. Such is the dearth that of the 4000 species, 500 are estimated to have been collected but lack any published name. In collaboration with the Packer Lab at York University in Toronto, Canada and Sean Brady at the Smithsonian we have been supplying thousands of specimens for their investigations of species boundaries, male/female associations, and phylogenetic work. Of personal interest to our lab (USGS Native Bee Inventory and Monitoring Lab) has been collaborative work on the Genus Nomada (a group in which almost every current name will be involved in a synonomy or division) and a first paper in what will be a series is due out within a few months.

For more information contact Sam Droege, Patuxent Wildlife Research Center and Seán Brady at the National Museum of Natural History, Smithsonian Institution.

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Rapid Genetic Identification of Southern California Fairy Shrimp Species from Cysts
Endangered fairy shrimp, Branchinecta sandiegonensis. Photo credit: D. Parsick, University of San Diego

The endangered fairy shrimp (Branchinecta sandiegonensis).
Photo credit: D. Parsick, University of San Diego

There are three species of Branchinecta fairy shrimp in southern California, the federally endangered Branchinecta sandiegonensis, the federally threatened Branchinecta lynchi and the more common Branchinecta lindahli which overlaps in distribution with B. sandiegonensis and B. lynchi. Currently, these three species can only readily be distinguished based on morphological characteristics of adults. 

We are developing a rapid genetic test for species identification from cysts which will allow assessment of species presence during the dry season (cysts are present in soils year-round), as well as for verification of morphological identifications of adults.

More information can be viewed at http://www.werc.usgs.gov/Project.aspx?ProjectID=173. For more information contact Amy Vandergast, Western Ecological Research Center.

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Identifying the Basic Unit of Management Among Collections of the Horseshoe Crab
Horseshoe crabs on Florida shore. Photo credit: Thomas A. Hermann/NBII.Gov

Horseshoe crabs on Florida shore. Photo credit: Thomas A. Hermann/NBII.Gov

Thirteen microsatellite DNA loci were surveyed in 1232 horseshoe crabs (Limulus polyphemus) collected from 28 spawning sites ranging from Franklin, ME to the Yucatan Peninsula, Republic of Mexico.  This range-wide survey revealed a high degree of genetic diversity (up to 50 alleles per locus) and heterozygosity (up to 97.2%).  There appeared to be substantial gene flow between each population and its nearest neighbors.  The correlation of genetic distance and geographic distance supported isolation-by-distance as a mechanism underlying structure of L. polyphemus along the Atlantic coast of North America.  Results suggested the presence of male-biased dispersal throughout the study area.  Within the continuum of isolation-by-distance and in the presence of male-biased dispersal, clustering of specific collections on a tree of genetic distances and hierarchical gene diversity analyses demonstrate discrete regional units.  These results suggest the definition of five regional management units within the United States:  Gulf of Maine, Mid-Atlantic, Southeast U.S. (South Carolina and Georgia), Florida-Atlantic, and Florida-Gulf.  Multilocus assignment tests indicate a high probability of correctly assigning individuals back to the proposed management unit from which they were collected, and could serve as a useful tool for identifying the source of animals that are caught at sea.  This mixed-stock research is currently underway.

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

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Loss of Genetic Connectivity Due to Habitat Fragmentation in Southern California Endemic Jerusalem Crickets
Mahogany Jerusalem Cricket. Photo credit: David Weissman, California Academy of Sciences
Mahogany Jerusalem Cricket. Photo credit: David Weissman, California Academy of Sciences

Habitat loss and fragmentation due to urbanization are some of the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. USGS scientists and colleagues have examined genetic variation in remnant populations of endemic Jerusalem crickets. These are large, flightless insects that are found throughout southern California, and are ideal indicator species for monitoring the effects of urban habitat fragmentation. Results show that genetic connectivity has declined across urban barriers such as housing developments and roads. Smaller and more isolated fragments also contain populations with less genetic diversity than those in larger and more contiguous natural areas. Although efforts to restore connectivity among natural areas in southern California are usually focused on larger, wide ranging species, our results also underscore the importance of preserving and restoring landscape connectivity for long-term persistence of smaller native species with low mobility and small home ranges.

For more information view http://www.werc.usgs.gov/Project.aspx?ProjectID=170 and hhttp://www.werc.usgs.gov/Project.aspx?ProjectID=168 and contact Amy Vandergast, Western Ecological Research Center.

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Utilizing Multilocus Genotypes to Reveal Population Connectivity (and Subterranean Water Flow) Among Collections of the Madison Cave Isopod
Madison cave isopod. Photo credit: Courtesy Virginia DCR Natural Heritage Program
Madison cave isopod. Photo credit: Courtesy Virginia DCR Natural Heritage Program

Antrolana lira is a subterranean freshwater crustacean (stygobite) endemic to the karst aquifers of the Shenandoah Valley in Virginia and West Virginia. A. lira was listed as a threatened species in November 1982 primarily due to the groundwater threats posed by urban and agricultural development combined with the absence of basic life history and ecological information on the species.  A detailed understanding of the evolution of the Shenandoah Valley hydrogeologic system is essential to identifying additional populations, developing management and recovery plans for Antrolana lira. In a karst setting, typified by sinkholes, subterranean water-filled conduits, springs and caves, historic groundwater flowpaths can play a significant role in understanding modern hydrologic connections because those flowpaths may still be used during high flow events, directing water across what are, during normal aquifer levels, drainage divides.  These historic connections and high-flow routes can be difficult to detect during standard hydrogeologic examinations that include techniques such as potentiometric surface mapping, dye tracing, and karst feature mapping.  Traditional methods of mark and recapture in subterranean organisms provide limited details about the migratory patterns of a species because so few marked individuals are ever recaptured. Advances in genetic analysis are increasing our ability to detect patterns of connectivity.  The genetic history of stygobite gene flow patterns could be a valuable tool to add to the standard hydrogeologic methods toolbox.  Genetic techniques can provide population-specific data (e.g., levels of genetic diversity, genetic variation, and effective population sizes) and the migratory routes connecting populations.

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

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Genetic Survey on the Riverside Fairy Shrimp (Streptocephalus woottoni)
Photo: Riverside Fairy Shrimp. Photo credit: Chris W. Brown, USGS

Photo: Riverside Fairy Shrimp. Photo credit: Chris W. Brown, USGS

USGS researchers are conducting a comprehensive genetic survey on the Riverside fairy shrimp Streptocephalus woottoni. Understanding patterns of population genetic structure may aid in defining units for conservation, and implementing effective relocation and restoration actions.  For example, soil from extirpated pools is often stored for future mitigation actions such as translocation, or re-establishment.  However, if populations are genetically unique and locally adapted, it may be inadvisable to found new populations with salvaged cysts from distant locations. For more information view http://www.werc.usgs.gov/Project.aspx?ProjectID=211 and contact Amy Vandergast, Western Ecological Research Center.

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