Geology topics

Margaret Hunter

Publications and source records attributed to Margaret Hunter.

64 records · Page 4Linked to original sources

USGS2019

Environmental DNA (eDNA) detection of nonnative bullseye snakehead in southern Florida

Bullseye Snakehead Channa marulius (Hamilton 1822) was first detected in the southern Florida town of Tamarac in 2000 and has been expanding its geographic range since. Environmental DNA (eDNA) analysis is a newly-developed technique used to noninvasively 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 using 222 water samples collected from 2015 to 2018. Positive eDNA detections were obtained at all six locations that were within the known geographic range of Bullseye Snakehead. Furthermore, eDNA was detected in six of 10 locations that were previously thought to be outside the periphery of the range but hydrologically connected through the extensive canal system. Over the four years of sampling, estimated occurrence rates (ψ) remained stable and relatively high (ψ = 0.67 [95% credible interval (CI) 0.33–0.95]) near Tamarac, Florida, as compared to the most southern sampling locations (ψ = 0.0–0.37). Bulls- eye Snakehead eDNA estimated occurrence rates in the middle region increased between 2016 (0.28 [95% CI 0.03–0.94]) and 2017 (0.66 [95% CI 0.24–0.98]), potentially reflecting eDNA detections related to a growing or expanding population. Bullseye Snakehead eDNA was detected at low concentrations on the northern and eastern borders of Everglades National Park, which is an important conservation area and UNESCO World Heritage Site. Despite extensive sampling via electrofishing, no Bullseye Snakehead were visually detected in several locations that yielded positive eDNA samples. It is unclear whether eDNA was transported through flowing water or another vector. To date, collection records for this species are confined to urban canals; however, Bullseye Snakehead may use the interconnected system of canals to disperse to natural conservation areas such as Everglades National Park, Big Cypress National Preserve, and Water Conservation Areas, where it may impact native species via predation and competition.

Florida↗

USGS2018

Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons

Invasive species provide powerful in situ experimental systems for studying evolution in response to selective pressures in novel habitats. While research has shown that phenotypic evolution can occur rapidly in nature, few examples exist of genome‐wide adaptation on short ‘ecological’ timescales. Burmese pythons ( Python molurus bivittatus ) have become a successful and impactful invasive species in Florida over the last 30 years despite major freeze events that caused high python mortality. We sampled Florida Burmese pythons before and after a major freeze event in 2010 and found evidence for directional selection in genomic regions enriched for genes associated with thermosensation, behavior, and physiology. Several of these genes are linked to regenerative organ growth, an adaptive response that modulates organ size and function with feeding and fasting in pythons. Independent histological and functional genomic datasets provide additional layers of support for a contemporary shift in invasive Burmese python physiology. In the Florida population, a shift towards maintaining an active digestive system may be driven by the fitness benefits of maintaining higher metabolic rates and body temperature during freeze events. Our results suggest that a synergistic interaction between ecological and climatic selection pressures have driven adaptation in Florida Burmese pythons, demonstrating the often‐overlooked potential of rapid adaptation to influence the success of invasive species.

Florida↗

USGS2018

A novel technique for isolating DNA from Tempus™ blood RNA tubes after RNA isolation

Objective We use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose ( Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA integrity number from a genomic DNA ScreenTape assay (Agilent), and running the isolated DNA on an agarose gel. Results Of the 23 samples analyzed, the average DNA concentration was 121 ng/µl (range 4–337 ng/µl) and a genomic DNA ScreenTape assay of seven samples indicated high DNA integrity values for 6 of the 7 samples (range 9.1–9.4 out of 10). Of the DNA sent for genotyping by sequencing, all proved to be of sufficient integrity to yield high-quality next-generation sequence results. We recommend this simple procedure to maximize the yield of both RNA and DNA from blood samples.

BMC Research Notes↗

USGS2018

The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution

The Florida manatee ( Trichechus manatus latirostris ) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. M anatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB l oci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.

Developmental and Comparative Immunology↗

USGS2018

Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

Environmental DNA (eDNA) detection is a technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. For eDNA measurement, genetic material shed into the environment is concentrated from water samples and analyzed for the presence of target species. Cytochrome b quantitative PCR and droplet digital PCR eDNA assays were developed for the 3 Vulnerable manatee species: African, Amazonian, and both subspecies of the West Indian (Florida and Antillean) manatee. Environmental DNA assays can help to delineate manatee habitat ranges, high use areas, and seasonal population changes. To validate the assay, water was analyzed from Florida’s east coast containing a high-density manatee population and produced 31564 DNA molecules l -1 on average and high occurrence (ψ) and detection (p) estimates (ψ = 0.84 [0.40-0.99]; p = 0.99 [0.95-1.00]; limit of detection 3 copies µl -1 ). Similar occupancy estimates were produced in the Florida Panhandle (ψ = 0.79 [0.54-0.97]) and Cuba (ψ = 0.89 [0.54-1.00]), while occupancy estimates in Cameroon were lower (ψ = 0.49 [0.09-0.95]). The eDNA-derived detection estimates were higher than those generated using aerial survey data on the west coast of Florida and may be effective for population monitoring. Subsequent eDNA studies could be particularly useful in locations where manatees are (1) difficult to identify visually (e.g. the Amazon River and Africa), (2) are present in patchy distributions or are on the verge of extinction (e.g. Jamaica, Haiti), and (3) where repatriation efforts are proposed (e.g. Brazil, Guadeloupe). Extension of these eDNA techniques could be applied to other imperiled marine mammal populations such as African and Asian dugongs.

Endangered Species Research↗

USGS2018

Development and validation of quantitative PCR assays to measure cytokine transcript levels in the Florida manatee (Trichechus manatus latirostris)

Cytokines have important roles in the mammalian response to viral and bacterial infections, trauma, and wound healing. Because of early cytokine production after physiologic stresses, the regulation of messenger RNA (mRNA) transcripts can be used to assess immunologic responses before changes in protein production. To detect and assess early immune changes in endangered Florida manatees ( Trichechus manatus latirostris ), we developed and validated a panel of quantitative PCR assays to measure mRNA transcription levels for the cytokines interferon (IFN)-γ; interleukin (IL)-2, -6, and -10; tumor necrosis factor-α, and the housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-actin (reference genes). Assays were successfully validated using blood samples from free-ranging, apparently healthy manatees from the east and west coasts of central Florida. No cytokine or housekeeping gene transcription levels were significantly different among age classes or sexes. However, the transcription levels for GAPDH, IL-2, IL-6, and IFN-γ were significantly higher ( P <0.05) in manatees from the east coast of Florida than they were from those from the west coast. We found IL-10 and β-actin to be consistent between sites and identified β-actin as a good candidate for use as a reference gene in future studies. Our assays can aid in the investigation of manatee immune response to physical trauma and novel or ongoing environmental stressors.

Florida↗

USGS2017

Genetic composition and connectivity of the Antillean manatee (Trichechus manatus manatus) in Panama

Genetic diversity and haplotype composition of the West Indian manatee (Trichechus manatus) population from the San San Pond Sak wetland in Bocas del Toro, Panama was studied using a segment of mitochondrial DNA (D’loop). No genetic information has been published to date for Panamanian populations. Due to the secretive behavior and small population size of the species in the area, DNA extraction was conducted from opportunistically collected fecal (N=20), carcass tissue (N=4) and bone (N=4) samples. However, after DNA processing only 10 samples provided good quality DNA for sequencing (3 fecal, 4 tissue and 3 bone samples). We found three haplotypes in total; two of these haplotypes are reported for the first time, J02 (N=3) and J03 (N=4), and one J01 was previously published (N=3). Genetic diversity showed similar values to previous studies conducted in other Caribbean regions with moderate values of nucleotide diversity (π= 0.00152) and haplotipic diversity (Hd= 0.57). Connectivity assessment was based on sequence similarity, genetic distance and genetic differentiation between San San population and other manatee populations previously studied. The J01 haplotype found in the Panamanian population is shared with populations in the Caribbean mainland and the Gulf of Mexico showing a reduced differentiation corroborated with Fst value between HSSPS and this region of 0.0094. In contrast, comparisons between our sequences and populations in the Eastern Caribbean (South American populations) and North Western Caribbean showed fewer similarities (Fst =0.049 and 0.058, respectively). These results corroborate previous phylogeographic patterns already established for manatee populations and situate Panamanian populations into the Belize and Mexico cluster. In addition, these findings will be a baseline for future studies and comparisons with manatees in other areas of Panama and Central America. These results should be considered to inform management decisions regarding conservation of genetic diversity, future controlled introductions, connectivity and effective population size of the West Indian manatee along the Central American corridor.

Bocas del Toro↗

USGS2016

Detection limits of quantitative and digital PCR assays and their influence in presence-absence surveys of environmental DNA

A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species’ presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp ( Ctenopharyngodon idella ) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty – indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis, and forensic and clinical diagnostics.

Molecular Ecology Resources↗

USGS2015

Statistical models for the analysis and design of digital polymerase chain (dPCR) experiments

Statistical methods for the analysis and design of experiments using digital PCR (dPCR) have received only limited attention and have been misused in many instances. To address this issue and to provide a more general approach to the analysis of dPCR data, we describe a class of statistical models for the analysis and design of experiments that require quantification of nucleic acids. These models are mathematically equivalent to generalized linear models of binomial responses that include a complementary, log–log link function and an offset that is dependent on the dPCR partition volume. These models are both versatile and easy to fit using conventional statistical software. Covariates can be used to specify different sources of variation in nucleic acid concentration, and a model’s parameters can be used to quantify the effects of these covariates. For purposes of illustration, we analyzed dPCR data from different types of experiments, including serial dilution, evaluation of copy number variation, and quantification of gene expression. We also showed how these models can be used to help design dPCR experiments, as in selection of sample sizes needed to achieve desired levels of precision in estimates of nucleic acid concentration or to detect differences in concentration among treatments with prescribed levels of statistical power.

Analytical Chemistry↗

USGS2015

Convergent evolution of the genomes of marine mammals

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Nature Genetics↗