USGS - science for a changing world

Ecosystems - Genetics and Genomics

Maps, Imagery, and Publications Hazards Newsroom Education Jobs Partnerships Library About USGS Social Media

Genetics Science in Invasive Species Research

Invasive and exotic species can harm native populations, disrupt natural ecosystems, and potentially transmit nonindigenous diseases to people and wildlife.  USGS geneticists employ molecular tools and techniques to assist in identification, monitoring, and managing non-native species.  Molecular methods are well suited to address the prevention of invasive species introductions, detecting new invasions, identifying impacts to native species, and controlling and managing invasive populations.  Geneticists can use mitochondrial and nuclear DNA to trace the probable origin of the species, whether it came into the environment unintentionally, or was released or escaped from captivity or aquaculture.  Identification of individual animals, estimating population size, and determining the gene flow and population structure of non-native species can be accomplished through genetic research.  Future genetic tools include the use of genes of known function to address reproduction and adaptability. 

 

Photo: Deepwater sculpin from the Great Lakes. Photo Credit: Justin Londer. Photo: Rainbow trout from the South Fork Boise River. Photo Credit: Jason Dunham, USGS. Photo: Lythrum Flowers (Lythrum salicaria). Photo Credit: Photo by Evelyn Anermaet. Photo: Invasive Burmese Python on Her Nest in South Florida. Photo Credit: Photo by Jemeema Carrigan, University of Florida. Courtesy of Skip Snow, National Park Service. Island applesnail shells. Photo credit: Cassie Thibodeaux, USGS National Wetlands Research Center Northern snakehead (Channa argus). Photo credit: USGS Florida Integrated Science Center Photo Library
Burmese Python
(Hunter, Hart)
Nutria in cage. Photo credit: USGS Photo: Young wild-caught Black Carp from Louisiana.  Credit: Leo Nico/USGS; Field# LGN10-59 Photo: native invasive Oriental bittersweet (Celastrus orbiculatus) Photo: Invasive Burmese Python on Her Nest in South Florida. Photo Credit: Photo by Jemeema Carrigan, University of Florida. Courtesy of Skip Snow, National Park Service. Photo: Invasive Burmese Python on Her Nest in South Florida. Photo Credit: Photo by Jemeema Carrigan, University of Florida. Courtesy of Skip Snow, National Park Service.  
Nutrias
Carter)
Black Carp (Hunter, Nico)
 

 

Using Diets to Reveal Overlap and Egg Predation among Benthivorous Fishes in Lake Michigan
Photo: Rainbow trout from the South Fork Boise River. Photo Credit: Jason Dunham, USGS.

Photo: Deepwater sculpin from the Great Lakes. Photo Credit: Justin Londer.

Ecological stability in the Laurentian Great Lakes has been altered by nonindigenous species, such as the round goby Neogobius melanostomus and dreissenid mussels, and by declines in native amphipods Diporeia spp. We evaluated whether these changes could influence diet overlap between three benthivorous fishes (slimy sculpin Cottus cognatus, deepwater sculpin Myoxocephalus thompsonii, and round goby) and whether predation on eggs of native species was occurring. We determined diets of fish collected from Lake Michigan between January and May in 2009 and 2010 using morphological and genetic species identification. Important prey for slimy sculpin were Mysis, Diporeia, and Limnocalanus macrurus; important prey for deepwater sculpin were Mysis and Diporeia. Round goby consumed mainly bivalves and Mysis. Genetic analyses revealed that the two sculpin species consumed the eggs of bloaters (Coregonus hoyi) and deepwater sculpin between February and May at all sites. Round goby also consumed eggs of these species but at lower levels. Diet overlap was identified between sculpin species at Frankfort and Sturgeon Bay, suggesting possible interspecific competition; diet overlap was never observed between round goby and either sculpin species. Given that (1) diet overlap varied by site and (2) diet proportions varied spatially more than temporally, benthivores appear to be exhibiting localized responses to recent ecological changes. Overall, these results reveal that egg predation and interspecific competition could be important interactions to consider in future examinations of the population dynamics of these species or in ecosystem models that forecast how fisheries will respond to possible perturbations or management scenarios.

Mychek-Londer, J. et al. 2013. Diet overlap and food habits of slimy sculpin, deepwater sculpin, and round goby during winter and spring in offshore Lake Michigan. Transactions of the American Fisheries Society. 142:492-504.

For more information, contact Justin Mycheck-Londer, David ‘Bo’ Bunnell or Wendylee Stott at the Great Lakes Science Center.

 

back to top

Meet the Parents: Hybridization Poses a Threat to Native Redband Trout
Photo: Rainbow trout from the South Fork Boise River. Photo Credit: Jason Dunham, USGS.

Photo: Rainbow trout from the South Fork Boise River. Photo Credit: Jason Dunham, USGS.

Hybridization between native fish and hatchery fish of the same species and hybridization with closely related non-native species are growing problems. Resulting genetic changes pose serious threats to native fishes and many other species. Researchers from USGS and Trout Unlimited documented hybridization in native redband trout in the Boise River in Idaho. Redband trout is an inland form of rainbow trout; both are the same species, but historically they occupied different geographic ranges. The study used genetic techniques to show that native redband trout are hybridizing with both non-native cutthroat trout and hatchery rainbow trout in the system. Hybridization with hatchery trout was particularly prevalent, and has contributed to replacement of the native redband trout genome.

Additional Research:
Monitoring the Effectiveness of Restored Road-Stream Crossings

FRESC Aquatic Ecology Laboratory
Corvallis Research Group

Neville, H.M., Dunham, J.B., 2011, Patterns of hybridization of nonnative cutthroat trout and hatchery rainbow trout with native redband trout in the Boise River, Idaho: North American Journal of Fisheries Management, v. 31, p. 1163-1176. [Abs] [FullText] Catalog No: 2783

For more information, contact Jason Dunham at the USGS Forest and Rangeland Ecosystem Science Center.

 

back to top

Molecular basis of Lythrum salicaria growth pattern in common gardens in the northern Europe versus southern North America
Photo: Lythrum Flowers (Lythrum salicaria). Photo Credit: Photo by Evelyn Anermaet.

Photo: Lythrum Flowers (Lythrum salicaria). Photo Credit: Photo by Evelyn Anermaet.

Researchers from the National Wildlife Health Center worked on a study led by collaborators in the Czech Republic that makes genetic comparisons of an invasive species in northern wetlands of North America (Lythrum salicaria). Common garden studies were conducted simultaneously by the National Wetlands Research Center (Louisiana) and the University of Czeske Budovisky (Czech Republic). The researchers in the two labs measured the growth of L. salicaria from populations collected along latitudinal gradients in North America and Europe.

For more information, contact Beth Middleton at the USGS National Wetlands Research Center.

 

 

back to top

Developing genetic tools to inform control of invasive Burmese pythons in the Greater Everglades Ecosystem
Burmese python in Everglades National Park. Photo by Roy Wood, National Park Service

Photo: Invasive Burmese Python on Her Nest in South Florida. Photo Credit: Photo by Jemeema Carrigan, University of Florida. Courtesy of Skip Snow, National Park Service.

The invasive and exotic Burmese python is established and breeding in the Everglades National Park (ENP) and has the potential to occupy the entire greater Everglades area.  Pythons can adversely affect populations of native and endangered species and threaten the success of the Comprehensive Everglades Restoration Project (CERP).  Previous studies found very little genetic diversity and lack of population division in the ENP, therefore, additional nuclear microsatellite markers are being developed using massively parallel pyrosequencing techniques.  With these additional tools, we hope to (1) identify the genetic diversity of pythons (including “core” and “periphery” samples) and compare the results to those analyzed in Collins et al. (2008), (2) identify the size of the effective breeding population, (3) identify whether Everglades National Park pythons are a genetically homogeneous population, and (4) prepare for rapid analysis and interpretation of new genetic samples from outside of the Park.  Additionally, gut contents will be genetically analyzed to identify the python prey species.

For more information, contact Dr. Margaret E. Hunter and Dr. Kirsten Hart at the Southeast Ecological Science Center.

 

 

back to top

Island Applesnails (Pomacea insularum)
Island applesnail shells. Photo credit: Cassie Thibodeaux, USGS National Wetlands Research Center
Island applesnail shells (Pomacea insularum). Photo credit: Cassie Thibodeaux, USGS National Wetlands Research Center

The exotic applesnails significantly impact wetland plant communities and rice agriculture due to their voracious grazing. They are also a potential vector for disease transmission to humans and animals. The snail tolerates a range of salinities and temperatures and can forage both in and out of water through the use of a gill and lung. Egg masses are laid on solid surfaces (e.g. dock pilings, plants) just above the water line. Once established, they are very difficult to remove. However, applesnails are species complex of similar looking but distinct species. Each species can have very different environmental tolerances and life history. For example some species are algae eaters while others will eat vascular plants. Because it can be very difficult to accurately identify applesnails species through their external morphology genetic tools are the most reliable way to correctly identify which species of applesnails is invading a system.

For photographs of Island applesnails, go to: http://www.nwrc.usgs.gov/invasive_species/applesnail_images1.htm and http://www.nwrc.usgs.gov/invasive_species/applesnail_images2.htm

For more information view Island Applesnails (Pomacea insularum) in Louisiana: A Rapid Assessment of Status and Risk (PDF; 1.72 MB) and contact Jacoby Carter, National Wetlands Research Center.

 

back to top

Assessing Reproductively-Effective Movement (i.e., Gene Flow) of the Northern Snakehead in the Tidal Potomac River
Northern snakehead (Channa argus). Photo credit: USGS Florida Integrated Science Center Photo Library
Northern snakehead (Channa argus). Photo credit: USGS Florida Integrated Science Center Photo Library

Introduction and establishment of northern snakehead (Channa argus) populations in the tidal Potomac River is expected to have significant ecological impacts. To develop management strategies in northern snakeheads that will ensure long-term success (i.e., eradication), a thorough understanding of the level of dispersal and gene exchange (effective movement) among tributaries is essential.  Leetown Science Center geneticists have developed microsatellite DNA markers for the northern snakehead and are determining movement patterns of the invasive fish within the Little Hunting Creek, Dogue Creek, Accotink-Pohick Creek, Piscataway Creek, and Pomonkey Creek complex in the Potomac River.  Movements will be confirmed by use of contemporary genetic analyses.  Specific sub-objectives are to: 1) compare the genetic population structure observed in the Potomac River; 2) delineate management units within the Potomac River and attempt to define genetically independent populations that may respond differently to particular control techniques; 3) estimate the effective population size, identify social structure within each geographic population, and determine if dispersal shows a sex bias;  and upon funding approval, 4) use contemporary molecular genetic techniques to test the utility of novel DNA constructs for preventing embryogenesis (e.g., daughterless technology) or direct lethal effects (e.g., engineered underdominance)  in northern snakehead.  Determining the presence, direction, and intensity of gene flow among geographic populations will provide the necessary background to understand the ecological effects of snakehead invasion.

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

back to top

 
Nutria (Myocastor coypus)
Nutria in cage. Photo credit: USGS
Nutria in cage at a trip to put telemetry transmitters and collect DNA from nutria. Photo credit: USGS National Wetlands Research Center
Aerial view of marsh. Photo credit: USGS
Nutria impact on marsh, with view of normal marsh, denuded marsh, and enclosure. Photo credit: USGS National Wetlands Research Center
Boat on a marsh. Photo credit: USGS
Netting nutria at a trip to put telemetry transmitters and collect DNA from nutria. Photo credit: USGS National Wetlands Research Center

The invasive nutria, or coypu, causes problems in coastal marshes and bald cypress swamps, especially in Louisiana. Introduced from South America for their fur, they now number in the millions because of the fur trade collapse. Nutria feed on the tender roots of plants, seedlings, and saplings, completely stripping vegetation in areas where they are concentrated (figure Nutria impact on marsh). The USGS studies worldwide nutria distribution and eradication, maps nutria destruction, and develops computer models to predict damage and simulate management options. We are developing several genomic tools to address the nutria problem. These include: DNA finger printing for mark-recapture population estimation. Every nutria's DNA is unique and can be used to identify it. Nutrias are often difficult to catch in live traps and also have low recapture rates. This makes estimating their population difficult. Instead of catching the animal, we are experimenting with hair traps, devices that catch a portion of their hair as they go by. From the DNA in the hair we can identify individuals and make population estimations. DNA can also be used to identify "effective" population size that is how different and how related different populations are. This is useful in understanding how new nutria populations become established. What are the source populations and what pathways they took. Finally we are using DNA to compare nutria populations across the United States and in comparison with population in Northern Italy. Populations that are very diverse or very similar might have different responses to disease, changes in climate, etc.

For more information visit http://www.nwrc.usgs.gov/special/nutria/index.htm and contact Jacoby Carter, National Wetlands Research Center.

back to top

Genetic Analysis of Wild and Captive Introduced Black Carp (Mylopharyngodon piceus)
Photo: Young wild-caught Black Carp from Louisiana. Photo credit: Leo Nico/USGS; Field# LGN10-59

Photo: Young wild-caught Black Carp from Louisiana. Photo credit: Leo Nico/USGS; Field# LGN10-59

The black carp (Mylopharyngodon piceus) is a large (>1 m long) riverine fish from eastern Asia introduced into the United States.  Among the four major Asian carp species in North America, black carp was last to be introduced and discovered in the wild.  This species also remains the most enigmatic of the non-native carps, largely because of the paucity of data on introduced populations. In contrast to the other Asian carps present, the black carp is a benthic fish that feeds heavily on mussels and snails, threatening North America's native mollusks, many of which are imperiled presently.  Over the past 15 years, there have been confirmed and unconfirmed reports of black carp captures in the middle and lower portions of the Mississippi Basin.  Wild black carp most likely originated from escape or release of aquaculture fish.  Still, as with most cases involving discovery of non-native aquatic organisms in the wild, definitive proof as to the source of introduction is difficult to establish. The purpose of this study is to use genetic analysis to compare the relatedness of wild and captive black carp.  Population structure, effective population size, and genetic diversity of both groups will be addressed.  These results may provide information or establish a direct link of wild populations to specific introduction pathways. Microsatellite markers were provided by Tim King et al. at the USGS Leetown Science Center. 

For more information visit http://fl.biology.usgs.gov/All_Staff/nico.html or contact Dr. Margaret E. Hunter and Dr. Leo Nico at the Southeast Ecological Science Center.

back to top

Oriental bittersweet (Celastrus orbiculatus)
Invasive oriental bittersweet (Celastrus orbiculatus). Photo: Stacey Leicht Young, USGS
Invasive oriental bittersweet (Celastrus orbiculatus).  Photo: Stacey Leicht Young, USGS
American bittersweet (C. scandens). Photo: Stacey Leicht Young, USGS
American bittersweet (C. scandens). Photo: Stacey Leicht Young, USGS
Bittersweet taking over trees. Photo: Stacey Leicht Young, USGS
Bittersweet taking over trees. Photo: Krystalynn Frohnapple, USGS
Hybrid bittersweet. Photo Credit: David Zaya, Univ. of Illinois, Chicago
Hybrid bittersweet.  Photo Credit: David Zaya, Univ. of Illinois, Chicago

Oriental bittersweet (Celastrus orbiculatus) is an invasive vine that has spread throughout the eastern United States over the last 100 years. It was originally introduced for ornamental and horticultural purposes. It is an aggressive vine that crowds out and kills native vegetation, and has been shown to alter succession. Concurrent with the proliferation of oriental bittersweet, the native congeneric vine American bittersweet (C. scandens) has declined throughout its natural range, especially along the east coast where the oriental bittersweet invasion is oldest and most thorough. Efforts to control oriental bittersweet and conserve American bittersweet are complicated by the potential of hybridization between the two species and the difficulty of distinguishing plants in the absence of reproductive structures. Nuclear microsatellite DNA markers, however, can determine the genetic identity of plants before reproductive maturity or outside of the reproductive season. The goals of this work are to (a) determine how hybridization has aided in the invasion of oriental bittersweet and the decline of American bittersweet, (b) test the hypothesis that hybridization is occurring asymmetrically where American bittersweet is more likely to act as the maternal plant in interspecific crosses, and (c) determine the species identity of individuals sold by horticulture and marketed as “American bittersweet” or “Celastrus scandens”.

For more information, view the fact sheet on identifying these two species at the Great Lakes Science Center website, American and Oriental Bittersweet Identification.  Contact David Zaya, University of Illinois at Chicago, and Dr. Noel Pavlovic and Dr. Stacey Leicht Young at Lake Michigan Ecological Research Station

back to top

Preservation of bull trout in Glacier National Park: Experimental suppression of invasive lake trout in the Quartz Lake system
Radiotagged subadult bull trout (Salvelinus confluentus) in the Flathead River.

Radiotagged subadult bull trout (Salvelinus confluentus) in the Flathead River. This trout was part of scientific research to understand the seasonal habitat use and movements of bull trout. Photo credit: Clint Muhlfeld, USGS.

Pre-spawning adult captured in the North Fork Flathead River on its way to spawn in its natal tributary.

Photo: Pre-spawning adult captured in the North Fork Flathead River on its way to spawn in its natal tributary. Photo credit: Clint Muhlfeld, USGS.

Populations of the threatened bull trout (Salvelinus confluentus) have dramatically declined throughout much of their native range over the past century. Bull trout declines are largely attributed to introductions of nonnative species, and habitat degradation and fragmentation. Glacier National Park (GNP) supports approximately one-third of the remaining natural habitat supporting the migratory life history of bull trout in the entire Columbia River Basin. The decline of bull trout in GNP is directly attributed to the invasion and establishment of nonnative lake trout Salvelinus namaycush, which consistently displace bull trout in systems where they have been introduced. The goal of this research is to protect GNP's ecologically unique bull trout populations from further declines and potential extinction. This collaborative USGS and NPS research project will assess demographics of the expanding lake trout population, and use this information to inform and implement experimental removal and control alternatives to reduce or eliminate competitive interactions in the Quartz Lake system and other lakes in GNP. This information is critical to understanding the feasibility of suppressing nonnative lake trout in a small, recently invaded lake that contains native bull trout. Results will be applied to management of other lakes in GNP and possibly other systems throughout the native range of bull trout. For more information, contact Clint Muhlfeld, cmuhlfeld@usgs.gov http://nrmsc.usgs.gov/staff/muhlfeld. Collaborators: Chris Downs (GNP) Chris_Downs@nps.gov and Chris Guy (Montana State University). http://nrmsc.usgs.gov/files/norock/products/LakeTrout_03_Info08.pdf

back to top

Hybridization between native westslope cutthroat and non-native rainbow trout
Rainbow trout x Westslope cutthroat trout hybrid, Flathead River, Montana. Photo credit: Clint Muhlfeld, USGS.

Photo: Rainbow trout x Westslope cutthroat trout hybrid, Flathead River, Montana. Photo credit: Clint Muhlfeld, USGS.

Hybridization with introduced salmonids is probably the greatest threat facing westslope cutthroat trout Oncorhynchus clarkii lewisi (WCT). The upper Flathead River system in Montana is considered a regional stronghold for WCT. The long-term persistence of these populations is threatened by the continued spread of introgression with nonnative O. mykiss (RBT). Previous studies indicate increased straying by hybrids contributes to the spread of hybridization in the upper Flathead River. Genetic and ecological factors determining invasion success and establishment of future sources of hybridization remain poorly understood in the natural environment. To examine these potential threats, researchers asked what factors influence successful invasion of WCT x RBT hybrids? Research hypotheses to explain the increase of RBT introgression in the Flathead system are: (1) continued dispersal (i.e., straying) and gene flow from downstream source populations with high proportions of RBT mixing and (2) sufficient reproductive success and survival by hybrid fish and subsequent colonization of stream habitats. For more information, contact Clint Muhlfeld (cmuhlfeld@usgs.gov) and Matthew Boyer Montana Fish, Wildlife and Parks. Additional information can be found at:http://nrmsc.usgs.gov/research/hybrid_trout.

back to top

 

In the Spotlight

Burmese python in Everglades National Park. Photo by Roy Wood, National Park ServicePythons can adversely affect populations of native and endangered species and threaten the success of the Comprehensive Everglades Restoration Project (CERP).  Previous studies found very little genetic diversity and lack of population division in the ENP, therefore, additional nuclear microsatellite markers are being developed using massively parallel pyrosequencing techniques. 


(Photo: Burmese python in Everglades National Park. Photo by Roy Wood, National Park Service)

Accessibility FOIA Privacy Policies and Notices

Take Pride in America logo USA.gov logo U.S. Department of the Interior | U.S. Geological Survey
URL: http://www.usgs.gov/ecosystems/genetics_genomics/genetics_invasive.html
Page Contact Information: Ask USGS
Page Last Modified: Thursday June 06 2013