Filters: partyWithName: Wetland and Aquatic Research Center (X) > Categories: Data (X) > partyWithName: Margaret E Hunter (X)
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Bullseye snakehead, Channa marulius, was first detected in 2000 in the southern Florida town of Tamarac and has been expanding its geographic range. Environmental DNA (eDNA) analysis is a newly-developed technique used to non-invasively detect cryptic or low-density species, or those that are logistically difficult to study. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of target species eDNA. To help delineate bullseye snakehead’s geographic range, we developed and validated a species-specific eDNA assay for both quantitative and droplet digital PCR (ddPCR). We then used ddPCR to assess 16 locations in southeast Florida...
These data represent the standard curve values as well as measurements of cytokine and reference gene transcripts from blood samples collected from Florida manatees and quantified using quantitative PCR.
Categories: Data;
Tags: Aquatic Biology,
Crystal River,
Genetics,
Titusville,
USGS Science Data Catalog (SDC),
We analyzed the single nucleotide polymorphisms (SNPs) present in the genomes of moose representing 3 subspecies in the contiguous United States. Blood samples were collected opportunistically from collaborators during field efforts or were supplied to our lab from collaborators' archives, and represented moose sampling occurring between 2009-2017. DNA was extracted, sequenced using next generation sequencing, and SNPs analyzed using the genetics programs Structure and Tess3, and by performing basic population statistics. These analyses were used to determine the population structure of moose at the subspecies level.
Reported here are the metabarcoding read numbers and biomass data assessed from a fish community in a southern Florida pond in Pinecrest Gardens after invasive species eradication and native restocking in 2017 and 2018 in linear regression models. This dataframe contains the number of fish of each species identified, their measured lengths estimated population surface area, and the number of metabarcoding reads (with SD and COV) for each species observed from the sampling date.
Categories: Data;
Tags: Ecology,
Genetics,
Genetics,
Southern Florida,
USGS Science Data Catalog (SDC),
Red lionfish (Pterois volitans) have become a successful invasive predator across the Northwestern Atlantic, Caribbean, and Gulf of Mexico (GoM). Previous investigations have identified the southeast coast of Florida as the original site of introduction, but no region-wide genetic study has directly addressed the question of introduction location(s). This dataset includes previously unpublished red lionfish samples (n = 237) from six locations: The Bahamas, Florida Keys, Northwest Florida, North Carolina, Panama, and Southeast Florida. Sequences archived in NCBI from other locations in the Northern Region, Caribbean, and Gulf of Mexico basins were used in the analyses (N = 1558). Previously published sequences were...
Environmental DNA (eDNA) water samples were collected at 15 tree islands containing wading bird breeding colonies (order Pelecaniformes) and 15 empty control islands in the central Everglades of Florida in spring of 2017 (April through June) and analyzed for the presence of eDNA from invasive Burmese pythons (Python bivittatus). The Burmese python is now established as a breeding population throughout south Florida, USA. Pythons can consume large quantities of prey and may be a particular threat to wading bird breeding colonies in the Everglades. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis—a genetic tool which detects shed DNA in water...
Categories: Data;
Types: Downloadable,
GeoTIFF,
Map Service,
Raster;
Tags: Aquatic Biology,
Broward,
Everglades,
Genetics,
Miami-Dade,
Data represent the metrics measured to validate the novel technique for isolating DNA from the supernatant of an RNA isolation protocol using blood collected into Tempus blood RNA tubes.
The federally endangered Cape Sable seaside sparrow (Ammospiza maritima mirabilis) is endemic to the Greater Everglades ecosystem in southern Florida. The subspecies inhabits the fragmented freshwater marl prairies and contains six subpopulations (A-F), named for management purposes, since genetic information is lacking. To evaluate genetic connectivity and inform management decisions, feather samples were collected between 2011 and 2018 from 108 sparrows across five subpopulations (A-E). Sequence data for four mitochondrial DNA markers (N = 36–69) and 12 nuclear microsatellite loci (N = 55) are provided. The mitochondrial markers used were Cytochrome b (Cytb), control region D-loop, NADH dehydrogenase 2 (ND2),...
The data were collected by U.S.G.S. biologists and their partners during several field trips from March 2013 to April 2014 in Guantanamo Bay, Cuba. Data were collected during the manatee health assessments. The U.S. Geological Survey’s Sirenia Project is a federal research effort focusing on manatee biology and ecology with a long history of studies in the U.S., Puerto Rico, and the international arena. The status of the Antillean manatee in Cuba is not well known. Manatee population census techniques are mostly prohibited due to regulation of the airspace, but it is speculated that the population of manatee in Cuba is not very large. Manatee captures will enable health assessments and radio tagging to determine...
Environmental DNA (eDNA) detection is a rapidly expanding technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of targeted eDNA. To help delineate manatee habitat ranges, high use areas, and seasonal population changes, a cytochrome-b quantitative PCR and state-of-the-art droplet digital PCR (ddPCR) eDNA assay was developed for the three extant and vulnerable manatee species: both subspecies of the West Indian manatee (Florida and Antillean), the African manatee and Amazonian manatee. Occurrence...
Data files for manuscript "Improving eDNA yield and inhibitor reduction through increased water volumes and modified multi-filter isolation techniques". These include the results of different treatments for inhibitor removal from a water sample and DNA yield quantities from such tests. Environmental DNA (eDNA) methods detect genetic material that is shed into the environment through skin cells and excrement by plants and animals. These methods are increasingly being applied to detect imperiled and invasive species for range assessment and occurrence estimates. To improve the recovery and detection of eDNA, we tested and optimized three basic protocols to 1) assess whether eDNA concentration increase in a linear...
Categories: Data;
Tags: Aquatic Biology,
Florida,
Genetics,
USGS Science Data Catalog (SDC),
Wildlife Biology,
Environmental DNA water samples were collected in the Greater Everglades Ecosystem between May 20-22, 2019 and analyzed to estimate Burmese python (Python bivittatus) occurrence. Twenty-eight sites were sampled in the Greater Everglades Ecosystem, with 5 field replicate samples per site, for a total of 140 water samples collected. Python eDNA was detected at 25 of the 28 sampling sites using Droplet Digital PCR amplification. Data either are not available or have limited availability owing to sensitivity concerns. Contact the Wetland and Aquatic Research Center for more information.
Categories: Data;
Tags: Genetics,
Southern Florida,
USGS Science Data Catalog (SDC),
environment,
environmental DNA,
Invasive Burmese pythons (Python bivittatus) have been reproducing in the Florida Everglades since the 1980s. Introduction of the species was either due to unintentional escapes or intentional releases from snakes obtained through the commercial pet trade. Burmese pythons have caused a precipitous decline in small mammal populations in south Florida. To better understand the invasive population, two mitochondrial loci (mtDNA; 1398 bps) were sequenced on 426 snakes and 22 microsatellites were genotyped on 389 snakes. Concatenated cytochrome b and cytochrome oxidase 1 mtDNA sequences produced six haplotypes with a nucleotide and haplotype diversity of π=0.002 and h=0.097, respectively. The dominant haplotype was highly...
Categories: Data;
Types: Citation;
Tags: Big Cypress National Preserve,
Everglades,
Everglades National Park,
Florida,
Florida Keys,
Environmental DNA (eDNA) detection of invasive species can be used to delimit occupied ranges and estimate probabilities to inform management decisions. Environmental DNA is shed into the environment through skin cells and bodily fluids and can be detected in water samples collected from lakes, rivers, and swamps. In south Florida, invasive Burmese pythons occupy much of the Greater Everglades in mostly inaccessible habitat and are credited with causing severe declines of native species’ populations. Detection of Burmese pythons by traditional methods, such as trapping and visual searching, have been largely ineffective, making eDNA a superior method for differentiating invaded habitat. We adapted a quantitative...
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