Geology topics

Jennifer Rowe

Publications and source records attributed to Jennifer Rowe.

14 recordsLinked to original sources

USGS2026

Genomics reveals extensive population structure and undescribed phylogenetic relationships in the Cascade torrent salamander (Rhyacotriton cascadae)

Aim Aims of the study are to examine patterns of range-wide genetic differentiation and population structure in a headwater obligate salamander living in a geologically rich region, to identify genetically distinct populations and areas of gene flow between them. Location Oregon and Washington in the Pacific Northwest, United States of America. Time Period Tissue samples were collected in 2022 and 2023. Major Taxa Studied The Cascade torrent salamander Rhyacotriton cascadae. Methods Utilisation of a genome-wide single nucleotide polymorphism (SNP) dataset from across the species range to conduct a principal components analysis (PCA), Bayesian model of population structure, co-ancestry matrix, phylogenetic tree and estimate genetic diversity. Results There are extensive levels of population structure within R. cascadae , including a previously unknown and highly differentiated clade. Structure is characterised by an island-like pattern wherein the species is comprised of six populations that function as independent demographic units, with gene flow largely constrained within populations. Main Conclusions Our findings reveal cryptic population structure within R. cascadae , identifying six distinct populations across the range. The northernmost population in the northwest of the species range in Washington is surprisingly highly divergent from the other five populations, and the divergence was not previously known to science. While major rivers act as phylogeographic boundaries between some populations, these boundaries appear to not always be complete.

Oregon, Washington↗

USGS2025

Simulated soundscapes and transfer learning boost the performance of acoustic classifiers under data scarcity

1. The biodiversity crisis necessitates spatially extensive methods to monitor multiple taxonomic groups for evidence of change in response to evolving environmental conditions. Programs that combine passive acoustic monitoring and machine learning are increasingly used to meet this need. These methods require large, annotated datasets, which are time-consuming and expensive to produce, creating potential barriers to adoption in data- and funding-poor regions. Recently released pre-trained avian acoustic classification models provide opportunities to reduce the need for manual labelling and accelerate the development of new acoustic classification algorithms through transfer learning. Transfer learning is a strategy for developing algorithms under data scarcity that uses pre-trained models from related tasks to adapt to new tasks. 2. Our primary objective was to develop a transfer learning strategy using the feature embeddings of a pre-trained avian classification model to train custom acoustic classification models in data-scarce contexts. We used three annotated avian acoustic datasets to test whether transfer learning and soundscape simulation-based data augmentation could substantially reduce the annotated training data necessary to develop performant custom acoustic classifiers. We also conducted a sensitivity analysis for hyperparameter choice and model architecture. We then assessed the generalizability of our strategy to increasingly novel non-avian classification tasks. 3. With as few as two training examples per class, our soundscape simulation data augmentation approach consistently yielded new classifiers with improved performance relative to the pre-trained classification model and transfer learning classifiers trained with other augmentation approaches. Performance increases were evident for three avian test datasets, including single-class and multi-label contexts. We observed that the relative performance among our data augmentation approaches varied for the avian datasets and nearly converged for one dataset when we included more training examples. 4. We demonstrate an efficient approach to developing new acoustic classifiers leveraging open-source sound repositories and pre-trained networks to reduce manual labelling. With very few examples, our soundscape simulation approach to data augmentation yielded classifiers with performance equivalent to those trained with many more examples, showing it is possible to reduce manual label-ling while still achieving high-performance classifiers and, in turn, expanding the potential for passive acoustic monitoring to address rising biodiversity monitoring needs.

Methods in Ecology and Evolution↗

USGS2025

Pan-amphibia distribution of the fungal parasite Batrachochytrium dendrobatidis varies with species and temperature

Batrachochytrium dendrobatidis (Bd) is a globally distributed fungal pathogen of amphibians that has contributed to one of the largest disease-related biodiversity losses in wildlife. Bd is regularly viewed through the lens of a global wildlife epizootic because the spread of highly virulent genetic lineages has resulted in well-documented declines and extinctions of multiple amphibian species. However, the current state of Bd occurrence, host range, host impacts, and ecological drivers remains poorly understood outside of the most negatively affected amphibian species and regions. Our objective was to describe the macroecology of Bd occurrence and infection intensity on caudates (salamanders) across the United States and to compare these patterns with better-studied anurans (frogs and toads). We collected swabs from 11,183 amphibians at 609 sites from 54 species across the United States from 2015 to 2017. We analyzed the prevalence and intensity of Bd infection jointly using a Bayesian hurdle model with covariates of site-level temperature and precipitation, as well as individual characteristics and species identification. Bd was distributed widely across sites and species sampled across the spatial extent of the conterminous United States. We found that Bd prevalence and intensity were most strongly influenced by temperature in the month preceding sampling and by differences among taxon groups. We estimated that temperature had a strong and nonlinear influence on both Bd prevalence and intensity with peak infection at intermediate temperatures and lower infection at low and high temperatures. We found Caudate hosts tended to have higher prevalence than Anuran hosts and Anuran hosts tended to have higher intensity at optimal temperatures for Bd infection. Our findings suggest that Bd has an amphibian-wide host range, temperature gradients exert a strong influence on Bd, and enzootic transmission likely encompasses a much larger spatial and species distribution than previously recognized across North America.

conterminous United States↗

USGS2023

Broad-scale assessment of methylmercury in adult amphibians

Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg bioaccumulation in 3,241 juvenile and adult amphibians during 2017–2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R 2 ≥ 0.67), whereas total Hg in sediment was not (R 2 ≤ 0.04). Our study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential threats of MeHg to amphibians.

Environmental Science and Technology↗

USGS2023

Population dynamics of the threatened Oregon spotted frog before and after drought mitigation

Amphibians are among the most sensitive taxa to climate change, and species inhabiting arid and semiarid landscapes at the extremes of their range are especially vulnerable to drought. The Jack Creek, Oregon, USA, population of Oregon spotted frogs ( Rana pretiosa ) faces unique challenges because it occupies the highest elevation site in the species' extant range and one that has been transformed by loss of American beavers ( Castor canadensis ), which historically maintained open water. We evaluated the effects of drought mitigation (addition of excavated ponds) on relationships between local and regional water availability, inactive legacy beaver dams, and Oregon spotted frog population dynamics in the Jack Creek system. We conducted egg mass surveys and capture-mark-recapture sampling at a treatment reach with excavated ponds and 3 reference reaches over 13 years; surveys spanned a period before and after pond excavation at the treatment and 1 primary comparison reference reach. We analyzed data using a combination of robust design capture-mark-recapture estimators and generalized linear mixed models to characterize population dynamics. Adult Oregon spotted frog survival was approximately 19.5% higher at the treatment reach than the primary reference reach during the study period. Annual survival was most strongly associated with late summer vegetation greenness, a proxy for water availability, and males had higher survival than females. Among the 4 study reaches, the treatment reach consistently had higher late summer vegetation greenness, and the hydrology functioned more independently of regional precipitation patterns relative to the reference reaches; however, these dynamics were not linked to pond excavation. Breeding was concentrated in 2 legacy beaver ponds that were deepened by excavation during the study compared to an unexcavated beaver pond, 2 excavated ponds without legacy beaver dams, and 9 reference ponds. These results point to the benefit of enhancing existing beaver structures and indicate that management actions aimed at maintaining surface water for breeding in spring and saturated soils and ponded water for adults in late summer would benefit this unique population of Oregon spotted frogs in the face of drought.

Oregon↗

USGS2023

Adjacent and downstream effects of forest harvest on the distribution and abundance of larval headwater stream amphibians in the Oregon Coast Range

Forest harvest is a primary landscape-scale management action affecting riparian forests. Although concerns about impacts of forest harvest on stream amphibians is generally limited to areas adjacent to harvest, there is a paucity of information regarding potential downstream effects of forest harvest on these species. We designed a before-after, control-impact (BACI) experiment to quantify potential impacts of clearcut logging that included 12-m buffers or smaller variable-width buffers on the distribution and abundance of headwater stream amphibians in adjacent and downstream areas. We sampled larval coastal tailed frogs ( Ascaphus truei ), coastal giant salamanders ( Dicamptodon tenebrosus ), and Columbia torrent salamanders ( Rhyacotriton kezeri ) across 3,915 sampling occasions that spanned 13 study reaches in 2008–2011 (pre-harvest) and 2013–2016 (post-harvest) as part of the Trask River Watershed Study in the Oregon Coast Range, U.S.A. We analyzed these data using occupancy models to estimate occupancy and (when possible) relative abundance, while accounting for various sources of imperfect detection. All species exhibited reduced occupancy adjacent to clearcuts with variable-width buffers (odds ratios [ORs] ranged = 0.24–0.48), and these negative impacts were not always diminished when increasing the buffer size to 12 m (ORs ranged = 0.20–3.56). Dicamptodon tenebrosus was the only species to have occupancy impacted in downstream areas, and this negative impact was related to clearcut logging with uniform 12-m buffers (OR = 0.60). This species was also the only species to have abundance negatively impacted by forest harvest in downstream areas (OR = 0.41 with uniform 12-m buffers, OR = 0.38 with variable-width buffers), albeit impacts to abundance were not evaluated for R. kezeri . Ascaphus truei abundance increased in areas downstream of clearcut logging with uniform 12-m buffers (OR = 2.92). Although we found the direction and magnitude of responses varied by species, our study confirms that clearcut logging can have negative impacts on amphibians that inhabit the adjacent stream areas. Perhaps more importantly, we also found that forest harvest can have negative effects on stream amphibians downstream of the harvested area and that increasing the buffer size to 12 m did not necessarily diminish these impacts in adjacent and downstream areas. Altogether, our study provides a nuanced picture of adjacent and downstream effects of forest harvest on three endemic headwater stream amphibians, and our findings demonstrate that forest management practices should consider downstream effects on aquatic taxa when assessing the impact of harvesting trees near headwater streams.

Oregon↗

USGS2022

Late season movement and habitat use by Oregon spotted frog (Rana pretiosa) in a large reservoir in Oregon, USA

Dam-created reservoirs are common landscape features that can provide habitat for amphibians, but their water level fluctuations and nonnative predators can differ markedly from more natural habitats. We compared fall movement and habitat use by the Oregon Spotted Frog ( Rana pretiosa ) in the reservoir pool with nearby river and pond habitats at Crane Prairie Reservoir in central Oregon, USA. Movement rate of frogs in the river and ponds declined as water temperature cooled. Reservoir frogs moved further than those in the river or ponds, and their movement rate increased as water temperature cooled. Most frog locations across all site types were in aquatic herbaceous vegetation. We did not find shifts in habitat between early and late fall. Increased movement and the lack of habitat shift in our reservoir frogs deeper into fall contrast with R. pretiosa in non-reservoir sites in this study and others. Consistent use of vegetation by reservoir frogs throughout the fall could indicate cover use in presence of fish predators. Our study provides additional detail on the range of habitats used by R. pretiosa in fall and suggests areas for further work to improve survival in constructed sites with abundant fish predators.

Oregon↗

USGS2021

Demography of the Oregon spotted frog along a hydrologically modified river

Altered flow regimes can contribute to dissociation between life history strategies and environmental conditions, leading to reduced persistence reported for many wildlife populations inhabiting regulated rivers. The Oregon spotted frog ( Rana pretiosa ) is a threatened species occurring in floodplains, ponds, and wetlands in the Pacific Northwest with a core range in Oregon, USA. All life stages of R. pretiosa are reliant on aquatic habitats, and inundation patterns across the phenological timeline can have implications for population success. We conducted capture–mark–recapture (CMR) sampling of adult and subadult R. pretiosa at three sites along the Deschutes River downstream from two dams that regulate flows. We related the seasonal extent of inundated habitat at each site to monthly survival probabilities using a robust design CMR model. We also developed matrix projection models to simulate population dynamics into the future under current river flows. Monthly survival was strongly associated with the extent and variability of inundated habitat, suggesting some within-season fluctuations at higher water levels could be beneficial. Seasonal survival was lowest in the winter for all three sites, owing to limited water availability and the greater number of months within this season relative to other seasons. Population growth for the two river-connected sites was most strongly linked to adult survival, whereas population growth at the river-disconnected site was most strongly tied to survival in juvenile stages. This research identifies population effects of seasonally limited water and highlights conservation potential of enhancing survival of particularly influential life stages.

Oregon↗

USGS2021

Monitoring wetland water quality related to livestock grazing in amphibian habitats

Land use alteration such as livestock grazing can affect water quality in habitats of at-risk wildlife species. Data from managed wetlands are needed to understand levels of exposure for aquatic life stages and monitor grazing-related changes afield. We quantified spatial and temporal variation in water quality in wetlands occupied by threatened Oregon spotted frog ( Rana pretiosa ) at Klamath Marsh National Wildlife Refuge in Oregon, United States (US). We used analyses for censored data to evaluate the importance of habitat type and grazing history in predicting concentrations of nutrients, turbidity, fecal indicator bacteria (FIB; total coliforms, Escherichia coli ( E. coli ), and enterococci), and estrogenicity, an indicator of estrogenic activity. Nutrients (orthophosphate and ammonia) and enterococci varied over time and space, while E. coli , total coliforms, turbidity, and estrogenicity were more strongly associated with local livestock grazing metrics. Turbidity was correlated with several grazing-related constituents and may be particularly useful for monitoring water quality in landscapes with livestock use. Concentrations of orthophosphate and estrogenicity were elevated at several sites relative to published health benchmarks, and their potential effects on Rana pretiosa warrant further investigation. Our data provided an initial assessment of potential exposure of amphibians to grazing-related constituents in western US wetlands. Increased monitoring of surface water quality and amphibian population status in combination with controlled laboratory toxicity studies could help inform future research and targeted management strategies for wetlands with both grazing and amphibians of conservation concern.

Oregon↗

USGS2021

An updated assessment of status and trend in the distribution of the Cascades frog (Rana cascadae) in Oregon, USA

Conservation efforts need reliable information concerning the status of a species and their trends to help identify which species are in most need of assistance. We completed a comparative evaluation of the occurrence of breeding for Cascades Frog ( Rana cascadae ), an amphibian that is being considered for federal protection under the U.S. Endangered Species Act. Specifically, in 2018–2019 we resurveyed 67 sites that were surveyed approximately 15 y prior and fit occupancy models to quantify the distribution of R. cascadae breeding in the Cascade Range, Oregon, USA. Furthermore, we conducted a simulation exercise to assess the power of sampling designs to detect declines in R. cascadae breeding at these sites. Our analysis of field data combined with our simulation results suggests that if there was a decline in the proportion of sites used for R. cascadae breeding in Oregon, it was likely a < 20% decline across our study period. Our results confirm that while R. cascadae detection probabilities are high, methods that allow the sampling process to be explicitly modeled are necessary to reliably track the status of the species. This study demonstrates the usefulness of investing in baseline information and data quality standards to increase capacity to make similar comparisons for other species in a timeframe that meet the needs of land managers and policy makers.

Oregon↗

USGS2020

Batrachochytrium salamandrivorans (Bsal) not detected in an intensive survey of wild North American amphibians

The salamander chytrid fungus (Batrachochytrium salamandrivorans [Bsal]) is causing massive mortality of salamanders in Europe. The potential for spread via international trade into North America and the high diversity of salamanders has catalyzed concern about Bsal in the U.S. Surveillance programs for invading pathogens must initially meet challenges that include low rates of occurrence on the landscape, low prevalence at a site, and imperfect detection of the diagnostic tests. We implemented a large-scale survey to determine if Bsal was present in North America designed to target taxa and localities where Bsal was determined highest risk to be present based on species susceptibility and geography. Our analysis included a Bayesian model to estimate the probability of occurrence of Bsal given our prior knowledge of the occurrence and prevalence of the pathogen. We failed to detect Bsal in any of 11,189 samples from 594 sites in 223 counties within 35 U.S. states and one site in Mexico. Our modeling indicates that Bsal is highly unlikely to occur within wild amphibians in the U.S. and suggests that the best proactive response is to continue mitigation efforts against the introduction and establishment of the disease and to develop plans to reduce impacts should Bsal establish.

Continental United States↗

USGS2019

Disentangling effects of invasive species and habitat while accounting for observer error in a long-term amphibian study

The invasive American bullfrog ( Lithobates catesbeianus ) and a variety of non‐native sport fish commonly co‐occur in lowland lentic habitats of the western United States. Both invasive taxa are implicated in declines of native amphibians in this region, but few long‐term studies of communities exist. Further, field studies of invasive–native interactions are complicated by confounding habitat modifications and observation errors. We surveyed amphibians and measured habitat characteristics for 12 yr across 38 wetland sites within the Willamette Valley, Oregon, USA. We assessed the influence of invasive species, habitat, and their interactions on the distributions of five native amphibian species using a multispecies dynamic occupancy model that accounted for false‐negative and false‐positive detections. In general, habitat characteristics—such as within‐pond vegetation cover, surrounding forest, and drought severity—were important for local persistence of native species when bullfrogs co‐occurred. We also found evidence of a cumulative negative effect of bullfrogs and non‐native fish (families Centrarchidae and Ictaluridae) on northern red‐legged frog ( Rana aurora ) local persistence that was mediated by the dominance of invasive reed canarygrass ( Phalaris arundinacea ). Non‐native fish and bullfrogs had variable effects on native amphibian species, but neither invasive taxon appears to be causing declines in occupied sites within our study area. Moreover, species relationships with habitat differed when invaders were present, indicating that certain habitats may increase persistence of native amphibians in the invaded landscape.

Oregon↗

USGS2018

Effect of cattle exclosures on Columbia Spotted Frog abundance

Livestock grazing is an important land use in the western USA and can have positive or negative effects on amphibians. Columbia Spotted Frog ( Rana luteiventris ) often use ponds that provide water for cattle. We conducted a long-term manipulative study on US Forest Service land in northeastern Oregon to determine the effects of full and partial exclosures that limited cattle access to ponds used by frogs. We found weak evidence of a short-term increase in abundance that did not differ between full and partial exclosures and that diminished with continuing exclusion of cattle. The benefit of exclosures was small relative to the overall decline in breeding numbers that we documented. This suggests that some protection can provide a short-term boost to populations.

Wetlands Ecology and Management↗

USGS2018

Late-season movement and habitat use by Oregon spotted frogs (Rana pretiosa) in Oregon, USA

Many amphibians use multiple habitats across seasons. Information on seasonal habitat use, movement between seasonal habitat types, and habitats that may be particularly valuable is important to conservation and management. We used radio-telemetry to study late-season movement and habitat use by Oregon Spotted Frog ( Rana pretiosa ) at nine sites from four populations along the Cascade Mountains in Oregon. Movement rates declined with date and were the lowest at the end of tracking in December and January. Frogs across our sites used vegetated shallows in late summer and early fall. In fall, frogs used a range of habitat types, and at several sites moved to distinctive habitats such as springs, interstices in lava rock, and semi-terrestrial beaver channels. Distance between first and last tracking location was <250 m for 84.5% (49/58) of frogs, ranged up to 1145 m, and was greater for frogs in ditch habitats than those not in ditches. Distinctive features like springs or semi-terrestrial retreats can host multiple frogs and may represent particularly valuable wintering habitat for R. pretiosa in some sites in their Oregon range.

Oregon↗