Geology topics

Caitlin E. Beaver

Publications and source records attributed to Caitlin E. Beaver.

13 recordsLinked to original sources

USGS2026

Accounting for temporal variation and correlation in environmental DNA sampling can improve ecological inferences

Environmental DNA (eDNA) concentration varies through space and time, and measurements collected close together are often correlated. Ignoring this dependence can inflate the rate of incorrect ecological inferences (Type I error rate). Although spatial correlation in eDNA has received considerable attention, temporal correlation has been less well studied. Statistical models and study designs that account for temporal correlation are increasingly important to understand time-dependent effects in complex systems. We developed a hierarchical model that separates temporal ecological variation from variability stemming from sampling and laboratory processes and applied it to four single-site eDNA time series collected over 17–24 days, three of which provided sufficient information for parameter estimation. We then used the empirically estimated parameter magnitudes in a simulation study to evaluate alternative temporal sampling designs that considered (1) how a fixed number of samples are allocated across different numbers of sampling times with different levels of temporal replication and (2) equally spaced versus cluster-spaced sampling (short bursts separated by longer gaps). Across the three time series sufficient for analysis, we observed substantial sampling variability, temporal variability, and temporal correlation, although correlation was estimated imprecisely (large coefficient of variation). Simulations showed that when sampling intervals were shorter than the effective temporal correlation range, models that ignored temporal dependence produced inflated Type I error rates and frequently detected spurious temporal trends. Accounting for temporal correlation substantially reduced this inflated Type I error rate. Optimal sampling strategies depended on study objectives. Clustered sampling most effectively estimated temporal correlation. When temporal dependence was negligible, evenly spaced sampling maximized power to detect trends. Estimating sampling variability required concentrating effort into fewer sampling times with more replicates per time, whereas estimating temporal variance was most precise with intermediate levels of replication. Together, these results indicate that temporal dependence can strongly affect inference from quantitative eDNA time series when sampling intervals approach the correlation timescale. Designs that ignore this dependence risk inferring ecological change or difference where none exists. Our framework provides practical guidance for allocating sampling effort in temporally intensive eDNA monitoring and for interpreting trends from short time series.

Idaho, Florida, Montana, Wisconsin↗

USGS2025

Environmental DNA monitoring of invasive Central American boas in St. Croix at Salt River Bay National Historical Park and Ecological Preserve (SARI)

Invasive Central American boas ( Boa imperator ) have established a reproducing population on the western side of St. Croix, U.S. Virgin Islands but prevalence throughout the island is largely unknown. The large snakes threaten endemic and endangered species through competition and predation, jeopardizing island biodiversity. Environmental DNA (eDNA) methods were used to investigate occurrence and focal areas for management efforts in the Salt River Bay National Historical Park and Ecological Preserve (SARI). To validate a previously developed assay, we collected tissue samples and 13 × 60 mL water samples from a captive boa enclosure in St. Croix. We implemented this assay for both a pilot and main field sampling effort. The pilot in December 2023 resulted in analysis of 7 × 60 mL water samples per site from SARI (3 sites) and from the western forests where boas are established (1 site). The main sampling event in July 2024 collected 15 × 60 mL water samples per site within SARI (11 sites) and western forests (4 sites). Pilot sample replicates were filtered individually, while main samples were consolidated into groups, resulting in seven replicates for pilot sites and five replicates for main event sites, totaling 103 environmental samples. eDNA was isolated using a modified phenol-chloroform isolation method to remove PCR inhibitors, and target eDNA was amplified using droplet digital PCR technology. Water samples from the captive boa amplified target eDNA in 12 of 13 samples, indicating assay effectiveness ex-situ. Low concentrations of eDNA (below the 95% limit of detection) were amplified in 4 of 5 sites in the western forest and in 8 of 14 sites within the National Historic Park. Overall, boa eDNA concentrations were consistently low, as expected in water samples targeting a semi-arboreal snake species with a low rate of eDNA shedding. Further optimization of methods could enable recovery of greater eDNA concentrations in future studies. Additional eDNA method testing and ground-truthing may help to improve the assessment of invasive Boa imperator in St. Croix.

Science Report↗

USGS2024

How, what, and where you sample environmental DNA affects diversity estimates and species detection

Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high-risk scenarios like invasive species management. In this study, we compare two eDNA sampling methods - namely tow net and grab sample, where the tow nets process large volumes of water (3500–7000 L) through a 64 μm pore size and the grab samples process 1 L sample at a single point through 0.45–1.2 μm pore size membranes. We compared these methods to ascertain what most influences (1) the detection of invasive species ( Dreissena mussels and Burmese pythons) using qPCR or ddPCR and (2) total diversity monitoring of metazoan, protist, and fungi community using a COI marker and plant communities using the ITS marker. Sampling was conducted across a wide geography and diverse aquatic environments in Minnesota and Florida, USA, and Switzerland. The tow net samples had significantly higher eDNA yield compared to grab samples; however, they exhibited equal or lower alpha diversity of OTUs (Operational Taxonomic Units). The two sampling methods measured different beta diversity of communities detected with the COI marker across all three regions, highlighting the impact of the sampling method on the diversity of eDNA captured. In comparison, the beta diversity of plant eDNA was less impacted by the sampling method. We found no clear difference in detection for the invasive species targets based on the eDNA sampling method. These results underscore the need for pilot studies before conducting biodiversity inventory and monitoring, and a need for a greater understanding of not just how much, but also what, eDNA is captured depending on method choice, considering both spatial and particle size heterogeneity.

Florida, Minnesota↗

USGS2023

Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex

Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America’s Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia —a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species ( Erimystax dissimilis ) confirmed to serve as a parasitic larval host for P. sintoxia . Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.

Mississippi River basin↗

USGS2023

Genetic analysis of federally endangered Cape Sable seaside sparrow subpopulations in the Greater Everglades, USA

The federally endangered Cape Sable seaside sparrow ( Ammospiza maritima mirabilis ) is endemic to the Greater Everglades ecosystem in southern Florida, inhabiting fragmented marl prairies in six individual subpopulations. The subspecies is threatened by loss of breeding habitat from fire and water management. Genetic information is severely limited for the subspecies but could help inform decisions regarding subpopulation protections and potential translocations for genetic rescue. To provide genetic data and inform management efforts, feather samples were collected across five subpopulations (designated A–E) and protocols were tested to optimize DNA extraction yields. We assessed four mitochondrial DNA markers (N = 36–69) and 12 nuclear microsatellite loci (N = 55) in 108 sparrows. Mitochondrial DNA sequences revealed low haplotype diversity, with NADH dehydrogenase-2 haplotypes matching to most other extant subspecies and to the Atlantic coast subspecies. Nuclear diversity was low compared to other subspecies, but similar across subpopulations. Samples grouped as one population when analyzed by Principal Component Analysis, Bayesian modelling and genetic distance metrics. Limited genetic emigration was detected from one putative migrant. Relatedness was significantly different for sparrows in the most geographically distant subpopulation (A), likely reflecting high self-recruitment and natal site fidelity ( P = 0.003). The low to moderate effective population size (N E = 202.4; N E :N C = 0.06) and generation time estimates indicated that unique genetic variation could be lost quickly during stochastic events. The sample sizes were limited, which reduced the power to comprehensively address recent population size reductions and any subsequent loss of genetic diversity.

Florida↗

USGS2023

Hidden in the hills: Phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species

Inaccurate taxonomy can lead to species in need of conservation being overlooked, which makes revisionary systematics crucially important for imperilled groups. The freshwater mussel genus Alasmidonta is one such group in need of study. Here, we take a multilocus phylogenetic approach to assess species-level taxonomy of Alasmidonta and test monophyly of this genus. Phylogenetic inference resulted in polyphyly of Alasmidonta . Lasmigona , which was included to test monophyly of Alasmidonta , was also polyphyletic. Species delimitation methods disagreed about whether Alasmidonta arcula , Alasmidonta triangulata and Alasmidonta undulata are distinct species, but all delimitation methods agreed that Alasmidonta harbours an undescribed species that would be considered Alasmidonta varicosa under current taxonomy. Given conflict among species delimitation methods and geographical separation, we maintain the current taxonomy for A. arcula and A. triangulata . The undescribed species is restricted to rivers of the Uwharrie Mountains region in North Carolina, USA that flow into the Pee Dee River from the east and can be distinguished morphologically from A. varciosa by higher and wider placed adductor mussels and a hooked pseudocardinal tooth. We offer insights into how supraspecific taxonomy of subtribe Alasmidontina might be resolved and formally describe the lineage from the Uwharrie Mountains region as Uwharrie elktoe, Alasmidonta uwharriensis sp. nov.

North Carolina↗

USGS2023

Molecular data validate historical and contemporary distributions of Pleurobema riddellii (Bivalvia: Unionidae) and help guide conservation and recovery efforts

Accurate taxonomic and distributional information are arguably the most critical components of conservation status assessments but can be greatly affected by misidentifications. The Louisiana pigtoe Pleurobema riddellii is a freshwater mussel proposed as threatened under the US Endangered Species Act. The species belongs to the tribe Pleurobemini, which includes multiple taxa that are inherently challenging to identify without molecular data. We validated historical and recent survey records of P. riddellii using a combination of DNA sequence data and morphological characters to provide a more definitive assessment of range and spatiotemporal trends in distribution. Our comprehensive assessment identified specimens collected from the Pearl drainage as P. riddellii , extending the species’ known range into eastern Gulf of Mexico drainages. Contemporary records were unavailable from the Trinity drainage; however, we designed novel minibarcode PCR primers and used historical DNA from a specimen collected in the late 1800s to confirm the historical presence of P. riddellii at the species’ type locality in the Trinity River near Dallas, Texas, USA. Our range-wide genetic diversity assessment provides strong support for 2 main geographic groups, the Ouachita and all remaining populations, with individuals from the Pearl and Trinity drainages sharing haplotypes with conspecifics from other drainages. Available data suggest P. riddellii has been extirpated from a significant portion of the historical range, including the entire Trinity drainage. Additional surveys in Lake Pontchartrain, Trinity, and other drainages in the eastern periphery of the species’ range may provide additional clarity on the distribution and conservation status of P. riddellii .

Endangered Species Research↗

USGS2021

Environmental DNA surveys of Burmese pythons in the Greater Everglades Ecosystem

Improving the probability of detecting invasive giant snakes is vital for the management of emerging or established populations. Burmese pythons occupy thousands of square kilometers of mostly inaccessible habitats in Florida. Environmental DNA (eDNA) methods have been shown to be time and cost effective in a number of systems and may be preferable to traditional detection methods for constrictor snakes, having been shown to be effective at detecting Burmese pythons where traditional and novel detection methods have failed. The purposes of this study were (1) to estimate Burmese python eDNA occurrence in the Greater Everglades Ecosystem based on land-use type; and (2) to conduct preliminary surveys within the Greater Everglades Ecosystem for positive eDNA detections. 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 in samples from 25 of the 28 sites by using droplet digital polymerase chain reaction amplification. Abiotic parameters were collected and explored, but we found no conclusive relationship among them and python eDNA detections. eDNA monitoring of aquatic habitats can assist in identifying newly colonized areas where pythons have not been previously detected, as well as movement corridors and pathways of dispersal. This information could be used to delimit a population boundary as it expands further to the north in peninsular Florida.

Florida↗

USGS2021

Novel insights into the genetic population connectivity of transient whale sharks (Rhincodon typus) in Pacific Panama provide crucial data for conservation efforts

The whale shark ( Rhincodon typus ) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity ( H d = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2 , were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3 , PTY4 , and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

Gulf of Chiriqu↗

USGS2021

Genetic connectivity of the West Indian manatee in the southern range and limited evidence of hybridization with Amazonian manatees

The Antillean subspecies of the West Indian manatee is classified as endangered by the International Union for the Conservation of Nature (IUCN) Red List. In Brazil, the manatee population is listed as endangered with an estimated population size of 500–1,000. Historic hunting, recent habitat degradation, and fisheries bycatch have decreased the population size. The Amazonian manatee is listed as vulnerable by the IUCN with unknown population sizes within Brazil. The Antillean manatee occurs in sympatry with the Amazonian manatee in Brazil and hybridization has been previously indicated. To provide information on the genetic structure, diversity, and degree of hybridization in the sympatric zone near the Amazon River mouth, the mitochondrial DNA control region and 13 nuclear microsatellite markers were assessed on the two species. Samples were analyzed from the Antillean subspecies across its distribution in Brazil ( n = 78) and from the Amazonian species ( n = 17) at the Amazon River mouth and inland mainstem river. To assess the previously defined evolutionary significant units of Antillean manatees in the area, an additional 11 samples from Venezuela and Guyana were included. The Antillean manatee was found to be a single population in Brazil and had lower than average number of alleles (3.00), expected heterozygosity (0.34), and haplotype diversity (0.15) when compared to many other manatee populations. The low values may be influenced by the small population size and extended pressures from anthropogenic threats. Gene flow was identified with Venezuela/Guyana in admixed Antillean Brazil samples, although the two populations were found to be moderately divergent. The nuclear loci in Venezuela/Guyana Antillean manatee samples indicated high differentiation from the samples collected in the Amazon River ( F ST = 0.35 and R ST = 0.18, p = 0.0001). No indication of nuclear hybridization was found except for a single sample, “Poque” that had been identified previously. The distribution of Antillean manatees in Brazil is extensive and the areas with unique habitat and threats would benefit from independent management and conservation actions. Gene flow, resulting in genetic diversity and long-term population stability, could be improved in the southern range through habitat restoration, and the establishments of travel corridors and protected areas, which are particularly important for successful parturition and neonatal calf survival.

Frontiers in Marine Science↗

USGS2021

Genome-wide SNP analysis reveals multiple paternity in Burmese pythons invasive to the Greater Florida Everglades

Reproductive strategies are an essential component of invasion ecology that influence invasion success and rates of population growth. Burmese Pythons ( Python bivittatus ) are large constrictor snakes that were introduced to the Greater Everglades Ecosystem of southern Florida, USA, from Asia. Since their introduction, these giant constrictors have spread throughout wetlands of southern Florida while increasing in abundance and causing declines in the native species upon which they prey. Multiple paternity in reproduction could facilitate invasion success by increasing the genetic diversity produced within each reproductive event. We used Diversity Arrays Technology genome-wide genotyping to assess multiple paternity in the progeny of wild Burmese Pythons in Florida. We analyzed >4,000 single nucleotide polymorphisms from 153 neonates belonging to 4 clutches collected in southwestern Florida. Complementary hierarchical and K -means clustering analyses of the genetic distances within clutches revealed that three clutches were each fertilized by two sires, with a fourth fertilized by a single sire. The proportions of offspring attributable to each sire within multiple paternity clutches ranged from nearly even to highly skewed. Analysis of multivariate dispersion showed significantly increased genetic variability in the multiple paternity clutches. These results improve our understanding of the reproductive strategy and invasion potential of a giant constrictor with significant ecological impacts.

Florida↗

USGS2021

Genetic analysis of red lionfish Pterois volitans from Florida, USA, leads to alternative North Atlantic introduction scenarios

The red lionfish Pterois volitans is a successful invasive predator across the western North Atlantic, Caribbean, and Gulf of Mexico. The southeast coast of Florida (USA) has been identified as the original introduction location, but genetic analyses including Florida lionfish have yet to investigate introduction scenarios. Here, we assessed the potential lionfish invasion pathways using 1795 sequences from previously published mitochondrial D-loop sequences (n = 1558) and new samples (n = 237) from 6 locations: The Bahamas, Florida Keys, northwest Florida, North Carolina, Panamá, and southeast Florida. None of the assessed Florida lionfish (n = 394) contained the H05-H09 D-loop haplotypes found in The Bahamas, North Carolina, and Bermuda (the Northern Region), indicating that Florida was not the source for these haplotypes. Assessing the mitochondrial population structure, the Florida east coast lionfish grouped with the Caribbean/Gulf of Mexico, as opposed to the Northern Region. To further explore connectivity and invasion pathways, 14 nuclear microsatellite loci were multiplexed on lionfish collected from 15 locations (n = 394). As found in other nuclear lionfish studies, the analyses identified a lack of population structure likely due to founding effects and/or inbreeding in aquaculture brood stocks. Together, the significant haplotype differences and H01-H04 haplotypes refute Florida as the sole source of red lionfish introduction. The results of this study support alternative invasion scenarios, in which Florida was colonized as a secondary introduction site or by individuals from the Northern Region. Understanding invasive species’ population boundaries and dispersal patterns informs local control efforts and management planning for future invasive species introductions.

Florida↗

USGS2021

Genetics as a tool for conservation and management of West Indian manatee populations in Brazil

A study conducted by the National Center for Research and Conservation of Aquatic Mammals (CMA), United States Geological Survey Wetland and Aquatic Research Center, and partner researchers found that the marine Antillean manatee ( Trichechus manatus manatus ) has low genetic diversity in regions where there are territorial interfaces with the Amazonian manatee ( Trichechus inunguis ). The study was published as an article in the journal, Frontiers in Marine Science.

Sirenews↗