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.
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.
Investigating Current and Historic White-tailed Kite Population Trends Using Genetic Techniques
A White-tailed kite. Photo by Heather Mohan.
The White‑tailed Kite has demonstrated large population fluctuations over the last 150 years. Once common in California, Texas, and the southeast United States, kite numbers declined to very low levels in the 1900s and was thought to be on the verge of extinction by the 1930s. In the 1940s populations began to expand and increasing numbers were observed during the following decades. Today, the White-tailed Kites are common residents throughout much of California, with slow but steady increases in population numbers in the Central Plains states, Texas and Florida. It is unknown whether current U.S. populations suffered a severe genetic bottleneck in the early 1900s and have rebounded since, or whether current U.S. population growth has been related to immigration from Central and South America populations. We are using genetic techniques to examine museum specimens collected before 1930 and modern samples collected in the 1990s from California to provide clues as to whether modern Kites in California in fact have low diversity due to a genetic bottleneck or whether they were founded and sustained by immigrants from other continents.
Observations of two non-native snake species in the same remote area of southern Florida
Hanslowe, E.B., B.G. Falk, M.A. McEachern, and R.N. Reed
Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. 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%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. 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. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.
Marsh rabbit mortalities tie pythons to the precipitous decline of mammals in the Everglades
McCleery, R.A., A. Sovie, R.N. Reed, M.W. Cunningham, M.E. Hunter, and K.M. Hart
Biomonitoring of environmental status and trends (BEST) program: environmental contaminants, health indicators, and reproductive biomarkers in fish from the Mobile, Apalachicola-Chattahoochee-Flint, Savannah, and Pee Dee River basins
Hinck, J.E., V.S. Blazer, N.D. Denslow, K.R. Echols, R.W. Gale, T.W. May, R. Claunch, C.Wieser, P.J. Anderson, J.J. Coyle, T.S. Gross, and D.E. Tillitt
Largemouth bass (Micropterus salmoides) and common carp (Cyprinus carpio) were collected from 13 sites in 4 river basins in the southeastern United States to document spatial trends in accumulative contaminants, health indicators, and reproductive biomarkers. Organochlorine residues, 2,3,7,8- tetrachlorodibenzo-p-dioxin-like activity (TCDD-EQ), and elemental contaminants were measured in composite samples of whole fish, grouped by species and gender, from each site. Fish were field-examined for external and internal anomalies, selected organs were weighed to compute somatic indices, and tissue and fluid samples were preserved for fish health and reproductive biomarker analyses.
Mercury concentrations in bass samples from all sites exceeded toxicity thresholds for mammals [>0.1 micrograms per gram wet weight (μg/g ww)], fish (>0.2 μg/g ww), and birds (>0.3 μg/g ww) and were greatest (>0.5 μg/g ww) in samples from the Alabama River at Eureka Landing, Alabama; the Mobile River at Bucks, Alabama; the Apalachicola River at Blountstown, Florida; the Savannah River at Sylvania, Georgia; and the Pee Dee River at Bucksport, South Carolina. Selenium concentrations were relatively high (>0.75 μg/g ww) in fish from the Tombigbee River at Lavaca, Alabama; the Mobile River at Bucks; and the Chattahoochee River at Omaha, Georgia compared to those from other sites. Concentrations of 2,2-bis (p-chlorophenyl)- 1,1-dichloroethylene (p,p’-DDE) were high in fish from the Chattahoochee River at Omaha and the Mobile River near Bucks, which was near a 2,2-bis (p-chlorophenyl)-1,1- dichloroethylene (DDT) formulating facility that historically discharged into the lower Mobile River.
Toxaphene concentrations in fish from the Flint River near Albany, Georgia (60-100 nanograms per gram (ng/g) ww) may pose a risk to fish. Concentrations of other formerly used (total chlordanes, dieldrin, endrin, aldrin, mirex, and hexachlorobenzene) and currently used (pentachlorobenzene, pentachloroanisole, dacthal, endosulfan, γ-HCH, and methoxychlor) organochlorine residues generally were low or did not exceed toxicity thresholds. Total polychlorinated biphenyls concentrations in samples from the Coosa River at Childersburg, Alabama; the Apalachicola River at Omaha; the Apalachicola River at Blountstown; and the Pee Dee River at Bucksport were >480 ng/g ww and may be a risk to piscivorous wildlife. Dioxin-like activity as measured by TCDD-EQ was greatest [>10 picograms per gram (pg/g)] in male fish from the Coosa River at Childersburg and the Mobile River at Bucks. Hepatic ethoxyresorufin O-deethylase activity generally was greatest in carp from the Mobile River Basin [means >10 picomols per minute per milligram of protein (pmol/min/mg)] and in bass from the Tombigbee River at Lavaca and Pee Dee River at Pee Dee, South Carolina (means >65 pmol/min/mg). Altered biomarkers were noted in fish from all basins.
The field necropsy and histopathological examination determined that fish from the Mobile River Basin generally were in poorer health than those from the other basins. In bass, health assessment index scores were correlated with mercury and p,p’-DDE concentrations. High health assessment index scores in Mobile River Basin fish were widespread and caused primarily by parasitic infestations, which were most severe in fish from the Tombigbee River at Lavaca and the Alabama River at Eureka Landing. Tumors were present in few fish (n = 5; 0.01%). Ovarian tumors of the same origin (smooth muscle) were present in two older carp from the Chattahoochee River near Omaha, Georgia and may be contaminant related. Reproductive biomarkers including gonadosomatic index, vitellogenin concentrations, and steroid hormone concentrations were anomalous in fish from various sites but were not consistently related to any particular chemical contaminant. Intersex gonads were identified in 47 male bass (42%) representing 12 sites and may indicate exposure to endocrine disrupting compounds. The incidence of intersex male bass was greatest in the Pee Dee River Basin and least severe in the Mobile River Basin. Male bass and carp with low concentrations of vitellogenin were common in all basins. Comparatively high vitellogenin concentrations [>0.35 milligram per milliliter (mg/mL)] in male fish from the Coosa River at Childersburg, the Savannah River at Sylvania, and the Pee Dee River at Rockingham and Bucksport indicate exposure to estrogenic or anti-androgenic chemicals.
Python molurus bivittatus (Burmese python). Minimum size at maturity
Willson, J.D., R.W. Snow, R.N. Reed, and M.E. Dorcas