Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons and Other Constrictor Snakes in Florida
A Burmese python in the water. USGS photo.
Low detection of invasive constrictors has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida. We developed species-specific eDNA assays for the 5 constrictor snakes in Florida. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. This research was in collaboration with the University of Florida.
Tissue Origin of Low-coverage Shotgun Sequencing Libraries Affects Recovery of Mitogenome Sequences
Teal landing on seasonal wetland. Photo by Tom Koerner, NWR.
This study examined how well complete mitochondrial genomes could be constructed from low coverage shotgun sequencing runs and related the results to tissue type. This study revealed that bird tissue is a much better DNA source for mitochondrial genome assembly than bird blood as it has far more nuclear DNA than mitochondrial DNA. This research was in collaboration with the University of Minnesota and the University of Colorado, Denver.
Analysis of the Mountain Plover Mating System Using Microsatellite Analysis
A Mountain plover. Photo by Marcus Martin.
Mountain Plovers have an uncommon parental-care system where males and females tend separate nests. In Montana, males arrive at breeding grounds first, set up territories, and display to attract a female. After mating and laying an initial set of eggs, a female mates with other males, providing eggs for them to incubate. Courtship activity between multiple males and females within a single breeding season has been documented several times but few copulations have been observed. In this study we are examining the prevalence of multiple paternity within male- and female-tended broods using DNA extracted from chicks and the tending adult. This research is in collaboration with Iowa State University.
Sandhill Cranes in Colorado’s San Luis Valley: Exploring Field and Laboratory Technology for Improved Population Assessments
A Sandhill crane (Grus canadensis) grazing in a grass field. John J. Mosesso, USGS Gallery photo.
There are principally two subspecies of sandhill cranes in North America, greater sandhill cranes that breed throughout the inter-mountain west, and Lesser sandhill cranes that breed in Siberia and Alaska. In route to the wintering grounds, these two subspecies mix at important stop-over sites in the San Luis Valley. The proportion of each of these two species in the San Luis Valley is unknown and this information represents a critical need for the management of these populations. This project aims to estimate the proportion of each subspecies by genotyping DNA from feathers collected in the San Luis Valley.
Identifying Patterns of Genetic Divergence and Units for Conservation in the Boreal Toad Species Group (Anaxyrus boreas)
A Boreal toad near a pond. National Park Service photo.
As previous genetic analyses of the boreal toad (particularly in regard to the Eastern Population DPS) have provided inconclusive results that are not sufficient for delineating conservation units, additional research is required that will apply new approaches to identify and delineate groups of boreal toads. DNA sequence data from nuclear and mitochondrial genes combined with new genomic methods using SNPs will refine our understanding of the genetic structure within the Eastern Population and can advance our understanding of taxonomic boundaries and adaptation in the boreal toad. This research is in collaboration with Florida Gulf Coast University and USFWS.
Investigating Prey of Burmese Pythons using eDNA Methods
A Burmese Python (Python bivittatus) in the grass in Florida. Photo by L. Oberhofer, USGS.
The highly invasive Burmese Python is having a devastating effect on the species native to southern Florida, particularly in the Florida Everglades. The goal of this project is to determine whether eDNA methods can be used to identify prey items eaten by Burmese Pythons.
Using Molecular Genetic Techniques to Investigate Colony Dynamics of the Endangered Indiana Bat (Myotis sodalis)
An Indiana bat in the hand of a scientist. FWS photo.
The need for accurate demographic information is great for the management and recovery of the Indiana bat. This project aims to evaluate the use of molecular tagging techniques to estimate population sizes in this species. We are interested in determining whether we can estimate abundance at one roost site throughout the summer using fecal DNA as a unique mark for mark-recapture population estimation models. We are also interested in determining if we can detect new individuals in the later part of the summer that would represent juveniles. This study is revealing that fecal pellets collected from Indiana bats are a good source of DNA that can be used successfully to estimate both colony size and number of juveniles recruiting into the population. This research is in collaboration with Indiana State University.
Effects of hypoxia on consumption, growth, and RNA:DNA ratios of young Yellow Perch
Roberts, J.J., S.B. Brandt, D. Fanslow, S.A. Ludsin, S.A. Pothoven, D. Scavia, T.O. Höök
The mission of the U.S. Geological Survey (USGS) at the Fort Collins Science Center Molecular Ecology Laboratory is to use the tools and concepts of molecular genetics to address a variety of complex management questions and conservation issues facing the management of the Nation's fish and wildlife resources...