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USGS2019

Enhancing reproductive assessments of the Florida manatee Trichechus manatus latirostris by establishing optimal time period and inhibin B baseline concentrations

The Florida manatee Trichechus manatus latirostris occupies coastal and riverine habitats that may influence the species’ endogenous biological rhythms, including its reproductive potential. Inhibin B provides a biomarker of gonadal function and reproductive potential in humans and other eutherian mammals. This study examined the influence of size, sex, and time of year on inhibin B levels in manatees sampled among 3 habitats with varying degrees of environmental stress in Florida. Inhibin B levels in 38 males averaged (±SE) 4.90 ± 0.23 pg ml -1 ; the average level in 31 females was 5.63 ± 0.46 pg ml -1 . Elevated patterns in inhibin B were exhibited between mid-March and mid-August corresponding to increased mating activity and testicular function, with significant differences in inhibin B levels between male and female manatees (p = 0.03) throughout the year. No significant differences in inhibin B were detected between low- and high-impacted sampling locations during winter, suggesting the potential influence of environmental stress on manatee reproduction may be best examined between mid-March and mid-August—the midpoint of the reproductively active, non-winter time period. Establishing temporal baselines for inhibin B values may be useful in assessing manatee reproductive status and potential conservation threats, shedding light on fertility potential, and enabling future assessment of the effects of stressors on reproduction in Florida manatees.

Florida↗

USGS2003

Sediment DIN fluxes and preferential recycling of benthic microalgal nitrogen in a shallow macrotidal estuary

Sediment -water fluxes of NH 4 + , NO 3 - , dissolved inorganic carbon, and O 2 were measured in cores collected from the upper Rowley River estuary , Massachusetts, and used to calculate rates of organic nitrogen (N) mineralization, nitrification, and coupled and direct denitrification (DNF). The cores contained 15 N label in benthic microalgae (BMA) and in NO 3 - in the overlying water as a result of an ongoing whole- estuary 15 NO 3 - enrichment study (NISOTREX II). The tracer allowed for estimation of gross NO 3 - regeneration in sediments and the contribution of BMA derived N to total mineralization. The mean mineralization rate between sites was 16.0 ± 2.0 mmol N m -2 d -1 . Approximately 13 to 56% of the mineralized N was nitrified at rates ranging from 1.8 to 10.1 mmol N m -2 d -1 . Total denitrification was dominated by direct DNF (3.6 mmol N m -2 d -1 ) furthest upstream, where NO 3 - concentrations were highest. Coupled DNF was most important (8.0 mmol N m -2 d -1 ) in the sediments with high nitrification and low water column NO 3 - . A gross NO 3 - flux from sediments to water of 0.9 to 2.1 mmol N m -2 d -1 was estimated from the isotope dilution of δ 15 NO 3 - in the overlying water of the cores. The isotope dilution seen in the cores was also detected as a deviation from conservative δ 15 NO 3 - mixing along estuarine transects. Incorporation of this NO 3 - regeneration into the DNF calculations effectively increased the estimate of direct DNF by up to 50% and decreased the coupled DNF estimate by up to 220%. Increasing δ 15 NH 4 + in the water of the cores indicated that the 15 N-labelled BMA were preferentially mineralized over bulk sediment organic N. Additional 15 N enrichments in the sediment bacterial biomarker diaminopimelic acid showed a link among 15 N-labeled BMA, active bacteria, and 15 NH 4 + released to the overlying water. Based on δ 15 NH 4 + enrichments in the cores, BMA accounted for approximately 50 to 100% of the N mineralized. An isotopic enrichment of δ 15 NH 4 + above background in the estuary was observed at a magnitude consistent with the core-based rates of BMA mineralization. These results provide further evidence that BMA are not unidirectional sinks for water column-dissolved organic nitrogen , but instead act to turn over N between sediments and estuarine water on the scale of days.

Marine Ecology Progress Series↗

USGS2022

Using paleoecological data to inform decision making: A deep-time perspective

Latest climate models project conditions for the end of this century that are generally outside of the human experience. These future conditions affect the resilience and sustainability of ecosystems, alter biogeographic zones, and impact biodiversity. Deep-time records of paleoclimate provide insight into the climate system over millions of years and provide examples of conditions very different from the present day, and in some cases similar to model projections for the future. In addition, the deep-time paleoecologic and sedimentologic archives provide insight into how species and habitats responded to past climate conditions. Thus, paleoclimatology provides essential context for the scientific understanding of climate change needed to inform resource management policy decisions. The Pliocene Epoch (5.3–2.6 Ma) is the most recent deep-time interval with relevance to future global warming. Analysis of marine sediments using a combination of paleoecology, biomarkers, and geochemistry indicates a global mean annual temperature for the Late Pliocene (3.6–2.6 Ma) ∼3°C warmer than the preindustrial. However, the inability of state-of-the-art climate models to capture some key regional features of Pliocene warming implies future projections using these same models may not span the full range of plausible future climate conditions. We use the Late Pliocene as one example of a deep-time interval relevant to management of biodiversity and ecosystems in a changing world. Pliocene reconstructed sea surface temperatures are used to drive a marine ecosystem model for the North Atlantic Ocean. Given that boundary conditions for the Late Pliocene are roughly analogous to present day, driving the marine ecosystem model with Late Pliocene paleoenvironmental conditions allows policymakers to consider a future ocean state and associated fisheries impacts independent of climate models, informed directly by paleoclimate information.

Frontiers in Ecology and Evolution↗

USGS2023

Spatial and individual factors mediate the tissue burden of polycyclic aromatic hydrocarbons in adult and chick brown pelicans in the northern Gulf of Mexico

The northern Gulf of Mexico supports a substantial level of oil and gas extraction in marine waters and experiences acute and chronic exposure to marine pollution events. The region also supports a diverse array of breeding and migratory seabirds that are exposed to these pollutants during foraging and other activities. Among the pollutants of highest concern within the region are polycyclic aromatic hydrocarbons (PAHs) which tend to be toxic, carcinogenic, mutagenic, or teratogenic. We assessed PAH loads in blood from adult brown pelicans and from feathers of adults and chicks of brown pelicans in relation to individual (e.g., body condition, sex) and spatial (e.g., breeding location within the Gulf, home range size, migration distance) factors. Of the 24 PAHs assessed, 17 occurred at least once among all samples. There were no PAHs found in chicks that were not also found in adults. Alkylated PAHs occurred more commonly and were measured at higher summed concentrations compared to parent PAHs in all samples, indicating that exposure to oil and/or byproducts of oil may have been a substantial source of PAH contamination for brown pelicans during this study. Within adults, PAHs were more likely to occur, and to increase in concentration, in blood samples of females compared to males, although no difference was found in feather samples. We also found that occurrence of and concentration of PAHs increased in adults that migrated longer distances. In adults and chicks, the background levels of oil and gas development within the region of the colony was not a consistent predictor of the presence of or concentration of PAHs. We also found correlations of PAHs with hematological and biochemical biomarkers that suggested compromised health. Our results indicate that both short- and long-term exposure (i.e., blood and feathers, respectively) are occurring for this species and that even nest-bound chicks can accumulate high levels of PAHs. Long-term tracking of PAHs, as well as an assessment of sublethal effects of PAHs on pelicans, could enhance our understanding of the persistence and effects of this contaminant in the northern Gulf as could increasing the breadth of species studied.

Frontiers in Ecology and Conservation↗

USGS2022

Advances in coral immunity ‘omics in response to disease outbreaks

Coral disease has progressively become one of the most pressing issues affecting coral reef survival. In the last 50 years, several reefs throughout the Caribbean have been severely impacted by increased frequency and intensity of disease outbreaks leading to coral death. A recent example of this is stony coral tissue loss disease which has quickly spread throughout the Caribbean, devastating coral reef ecosystems. Emerging from these disease outbreaks has been a coordinated research response that often integrates ‘omics techniques to better understand the coral immune system. ‘Omics techniques encompass a wide range of technologies used to identify large scale gene, DNA, metabolite, and protein expression. In this review, we discuss what is known about coral immunity and coral disease from an ‘omics perspective. We reflect on the development of biomarkers and discuss ways in which coral disease experiments to test immunity can be improved. Lastly, we consider how existing data can be better leveraged to combat future coral disease outbreaks.

Frontiers in Marine Science↗

USGS2020

Reconnaissance of surface water estrogenicity and the prevalence of intersex in smallmouth bass (Micropterus dolomieu) inhabiting New Jersey

The observation of testicular oocytes in male fishes has been utilized as a biomarker of estrogenic endocrine disruption. A reconnaissance project led in the Northeastern United States (US) during the period of 2008–2010 identified a high prevalence of intersex smallmouth bass on or near US Fish & Wildlife Service National Wildlife Refuges that included the observation of 100% prevalence in smallmouth bass males collected from the Wallkill River, NJ, USA. To better assess the prevalence of intersex smallmouth bass across the state of New Jersey, a tiered reconnaissance approach was initiated during the fall of 2016. Surface water samples were collected from 101 (85 river, 16 lake/reservoir) sites across the state at base-flow conditions for estrogenicity bioassay screening. Detectable estrogenicity was observed at 90% of the sites and 64% were above the US Environmental Protection Agency trigger level of 1 ng/L. Median surface water estrogenicity was 1.8 ng/L and a maximum of 6.9 ng/L E2EqBLYES was observed. Adult smallmouth bass were collected from nine sites, pre-spawn during the spring of 2017. Intersex was identified in fish at all sites, and the composite intersex prevalence was 93.8%. Prevalence across sites ranged from 70.6% to 100%. In addition to intersex, there was detectable plasma vitellogenin in males at all sites. Total estrogenicity in surface water was determined at these fish collection sites, and notable change over time was observed. Correlation analysis indicated significant positive correlations between land use (altered land; urban + agriculture) and surface water estrogenicity. There were no clear associations between land use and organismal metrics of estrogenic endocrine disruption (intersex or vitellogenin). This work establishes a baseline prevalence of intersex in male smallmouth bass in the state of New Jersey at a limited number of locations and identifies a number of waterbodies with estrogenic activity above an effects-based threshold.

New Jersey↗

USGS2016

Gene transcript profiling in sea otters post-Exxon Valdez oil spill: A tool for marine ecosystem health assessment

Using a panel of genes stimulated by oil exposure in a laboratory study, we evaluated gene transcription in blood leukocytes sampled from sea otters captured from 2006–2012 in western Prince William Sound (WPWS), Alaska, 17–23 years after the 1989 Exxon Valdez oil spill (EVOS). We compared WPWS sea otters to reference populations (not affected by the EVOS) from the Alaska Peninsula (2009), Katmai National Park and Preserve (2009), Clam Lagoon at Adak Island (2012), Kodiak Island (2005) and captive sea otters in aquaria. Statistically, sea otter gene transcript profiles separated into three distinct clusters: Cluster 1, Kodiak and WPWS 2006–2008 (higher relative transcription); Cluster 2, Clam Lagoon and WPWS 2010–2012 (lower relative transcription); and Cluster 3, Alaska Peninsula, Katmai and captive sea otters (intermediate relative transcription). The lower transcription of the aryl hydrocarbon receptor (AHR), an established biomarker for hydrocarbon exposure, in WPWS 2010–2012 compared to earlier samples from WPWS is consistent with declining hydrocarbon exposure, but the pattern of overall low levels of transcription seen in WPWS 2010–2012 could be related to other factors, such as food limitation, pathogens or injury, and may indicate an inability to mount effective responses to stressors. Decreased transcriptional response across the entire gene panel precludes the evaluation of whether or not individual sea otters show signs of exposure to lingering oil. However, related studies on sea otter demographics indicate that by 2012, the sea otter population in WPWS had recovered, which indicates diminishing oil exposure.

Alaska↗

USGS2022

Baseline gene expression levels in Falkland-Malvinas Island penguins: Towards a new monitoring paradigm

Health diagnostics of wildlife have historically relied on the evaluation of select serum biomarkers and the identification of a contaminant or pathogen burden within specific tissues as an indicator of a level of insult. However, these approaches fail to measure the physiological reaction of the individual to stressors, thus limiting the scope of interpretation. Gene-based health diagnostics provide an opportunity for an alternate, whole-system, or holistic assessment of health, not only in individuals or populations but potentially in ecosystems. Seabirds are among the most threatened marine taxonomic groups in the world, with ~25% of this species currently listed as threatened or considered of special concern; among seabirds, the penguins (Family Spheniscidae) are the most threatened seabird Family. We used gene expression to develop baseline physiological indices for wild penguins in the Falkland-Malvinas Islands, and captive zoo penguins. We identified the almost complete statistical separation of penguin groups (gentoo Detroit Zoo, gentoo Falkland-Malvinas Islands, rockhopper Detroit Zoo, and rockhopper Falkland-Malvinas Islands) based on gene expression profiles. Implementation of long-term longitudinal studies would allow for the assessment of temporal increases or decreases of select transcripts and would facilitate interpretation of the drivers of change.

Life↗

USGS2018

High latitude Southern Hemisphere fire history during the mid-late Holocene (750- 6000 yr BP)

We determined the specific biomass burning biomarker levoglucosan in an ice core from the TALos Dome Ice CorE drilling project (TALDICE) during the mid- to late Holocene (6000–750 BP). The levoglucosan record is characterized by a long-term increase with higher rates starting at ∼ 4000 BP and peaks between 2500 and 1500 BP. The anomalous increase in levoglucosan centered at ∼ 2000 BP is consistent with other Antarctic biomass burning records. Multiple atmospheric phenomena affect the coastal Antarctic Talos Dome drilling site, where the Southern Annular Mode (SAM) is the most prominent as the Southern Annular Mode Index (SAMA) correlates with stable isotopes in precipitation throughout the most recent 1000 years of the ice core. If this connection remains throughout the mid- to late Holocene, then our results demonstrate that changes in biomass burning, rather than changes in atmospheric transport, are the major influence on the TALDICE levoglucosan record. Comparisons with charcoal syntheses help evaluate fire sources, showing a greater contribution from southern South American fires than from Australian biomass burning. The levoglucosan peak centered at ∼ 2000 BP occurs during a cool period throughout the Southern Hemisphere, yet during a time of increased fire activity in both northern and southern Patagonia. This peak in biomass burning is influenced by increased vegetation in southern South America from a preceding humid period, in which the vegetation desiccated during the following cool, dry period. The Talos Dome ice core record from 6000 to ∼ 750 BP currently does not provide clear evidence that the fire record may be strongly affected by anthropogenic activities during the mid- to late Holocene, although we cannot exclude at least a partial influence.

Climate of the Past↗

USGS2023

Assessing environmental change associated with early Eocene hyperthermals in the Atlantic Coastal Plain, USA

Eocene transient global warming events (hyperthermals) can provide insight into a future warmer world. While much research has focused on the Paleocene–Eocene Thermal Maximum (PETM), hyperthermals of a smaller magnitude can be used to characterize climatic responses over different magnitudes of forcing. This study identifies two events, namely the Eocene Thermal Maximum 2 (ETM2 and H2), in shallow marine sediments of the Eocene-aged Salisbury Embayment of Maryland, based on magnetostratigraphy, calcareous nannofossil, and dinocyst biostratigraphy, as well as the recognition of negative stable carbon isotope excursions (CIEs) in biogenic calcite. We assess local environmental change in the Salisbury Embayment, utilizing clay mineralogy, marine palynology, δ 18 O of biogenic calcite, and biomarker paleothermometry (TEX 86 ). Paleotemperature proxies show broad agreement between surface water and bottom water temperature changes. However, the timing of the warming does not correspond to the CIE of the ETM2 as expected from other records, and the highest values are observed during H2, suggesting factors in addition to p CO 2 forcing have influenced temperature changes in the region. The ETM2 interval exhibits a shift in clay mineralogy from smectite-dominated facies to illite-rich facies, suggesting hydroclimatic changes but with a rather dampened weathering response relative to that of the PETM in the same region. Organic walled dinoflagellate cyst assemblages show large fluctuations throughout the studied section, none of which seem systematically related to CIE warming. These observations are contrary to the typical tight correspondence between climate change and assemblages across the PETM, regionally and globally, and ETM2 in the Arctic Ocean. The data do indicate very warm and (seasonally) stratified conditions, likely salinity-driven, across H2. The absence of evidence for strong perturbations in local hydrology and nutrient supply during ETM2 and H2, compared to the PETM, is consistent with the less extreme forcing and the warmer pre-event baseline, as well as the non-linear response in hydroclimates to greenhouse forcing.

Atlantic Coastal Plain↗

USGS2025

Reconstruction of Holocene and Last Interglacial vegetation dynamics and wildfire activity in Southern Siberia

Wildfires are a rapidly increasing threat to boreal forests. While our understanding of the drivers behind wildfires and their environmental impact is growing, it is mostly limited to the observational period. Here we focus on the boreal forests of southern Siberia and exploit a U–Th-dated stalagmite from Botovskaya Cave, located in the upper Lena region of southern Siberia, to document wildfire activity and vegetation dynamics during parts of two warm periods: the Last Interglacial (LIG; specifically part of the Last Interglacial maximum between 124.1 and 118.8 ka) and the Holocene (10–0 ka). Our record is based on levoglucosan (Lev), a biomarker sensitive to biomass burning, and on lignin oxidation products (LOPs) that discriminate between open and closed forest and hard- or softwood vegetation. In addition, we used carbonate carbon stable isotope ratios ( δ 13 C ), which reflect a dominant control of the host rock, to evaluate soil respiration and local infiltration changes. Our LOP data suggest that, during the Last Interglacial, the region around Botovskaya Cave was characterised by open forest, which by ca. 121.5 ka underwent a transition from fire-resistant hardwood to fire-prone softwood. The Lev record indicates that fire activity was high and increased towards the end of Last Interglacial just before 119 ka. In contrast, the Holocene was characterised by a closed-forest environment with mixed hard- and softwood vegetation. Holocene fire activity varied but at a much lower level than during the Last Interglacial. We attribute the changes in wildfire activity during the intervals of interest to the interplay between vegetation and climate. The open forests of the Last Interglacial were more likely to ignite than their closed Holocene equivalents, and their flammability was aided by warmer and drier summers and a stronger seasonal temperature contrast due to the increase in seasonal insolation difference compared to the Holocene. Our comparison of the last two interglacial intervals suggests that, with increasing global temperatures, the boreal forest of southern Siberia may become progressively more vulnerable to higher wildfire activity.

Botovskaya Cave, Siberia↗

USGS2026

Correcting a systematic bias in an ocean drilling project site 882 alkenone sea surface temperature record

Reconstructions of sea surface temperature (SST) in the geologic record are fundamental to our understanding of Earth's climate history and the evaluation of Earth's climate sensitivity to greenhouse gas forcing. SSTs are reconstructed with a variety of methods, including alkenone biomarker lipids produced by certain coccolithophore algae. One such alkenone SST reconstruction from the subpolar northwest Pacific Ocean Drilling Program (ODP) Site 882 (50.21° N, 167.35° E, 3244 m water depth) has played a large role in shaping the paleoclimate science community's view of global climate warmth during the Late Pliocene (3.6–2.6 million years ago) and the subsequent cooling that characterized the intensification of Northern Hemisphere Glaciation (Haug, 1995; Haug et al., 2005; Martínez-Garcia et al., 2010). First, we have found that the values reported in the PANGAEA archive for this ODP Site 882 alkenone dataset were inaccurately reported as U K' 37 values when they are instead U K 37 ( https://doi.org/10.1594/PANGAEA.315092 , Haug and Sarnthein, 2005). This error in the archived data table resulted in the incorporation of inaccurate absolute SST estimates by several studies that applied U K' 37 calibrations to this ODP Site 882 dataset (e.g., Brennan et al., 2022; Clark et al., 2024, 2025; Tierney et al., 2019, 2025b). Second, using other published data from ODP Site 882 (Studer et al., 2012) and nearby Site 883 (51.11° N, 167.46° E, 2384 m water depth; Herbert et al., 2016; Novak et al., 2024), we show that the original Haug (1995) alkenone SST record at ODP Site 882 systematically reports an amplified range of absolute SST values compared to the more recently generated data. This observation is consistent with the known concentration-dependent biases of the gas chromatography chemical ionization mass spectrometry (GC-CI-MS) analytical method used by the original ODP Site 882 study (Chaler et al., 2000, 2003; Haug, 1995; Hefter, 2008; Rosell-Mele et al., 1995). These concentration-dependent analytical biases complicate applying a uniform correction to the entire Haug (1995) dataset. However, we are able to leverage the published datasets to propose a correction and quantification of uncertainty for a subset of the Haug (1995) dataset measured at similar on-column analyte abundance. For these samples, we find an average analytical uncertainty equivalent to ±2.05 °C , which is greater than and in addition to the typical ±1.4 °C 1 σ prediction uncertainty of the U K' 37 sea surface temperature proxy. We then discuss the implications of the corrected dataset for our understanding of late Neogene and Quaternary climate in the Kuroshio Extension region.

Climate of the Past↗

USGS2010

Survival of captive and free-ranging Harlequin Ducks (Histrionicus histrionicus) following surgical liver biopsy

We measured intra- and postoperative mortality rates of captive and free-ranging Harlequin Ducks ( Histrionicus histrionicus ) undergoing surgical liver biopsy sampling for determination of the induction of cytochrome P4501A, a biomarker of oil exposure. Liver biopsies were taken from and radio transmitters were implanted into 157 free-ranging Harlequin Ducks over three winters (55 in 2000, 55 in 2001, and 47 in 2002). No birds died during surgery, but seven (4.5%) died during recovery from anesthesia (three in 2001 and four in 2002). None of the deaths could be attributed directly to the liver biopsy. Four of the 150 (2.7%) birds that were released died in the 2 wk period after surgery. All post-release deaths occurred in 2001; no birds died after release in 2000 or 2002. No mortalities of 36 captive birds occurred during surgery or recovery or in the 2 wk period following surgery. Hemorrhage was a minor problem with one captive bird. Surgical liver biopsies appear to be a safe procedure, but anesthetic complications may occur with overwintering ducks.

Journal of Wildlife Diseases↗

USGS2015

Apparent field safety of a raccoon poxvirus-vectored plague vaccine in free-ranging prairie dogs ( Cynomys spp.), Colorado, USA

Prairie dogs ( Cynomys spp.) suffer high rates of mortality from plague. An oral sylvatic plague vaccine using the raccoon poxvirus vector (designated RCN-F1/V307) has been developed for prairie dogs. This vaccine is incorporated into palatable bait along with rhodamine B as a biomarker. We conducted trials in August and September 2012 to demonstrate uptake and apparent safety of the RCN-F1/V307 vaccine in two prairie dog species under field conditions. Free-ranging prairie dogs and other associated small rodents readily consumed vaccine-laden baits during field trials with no apparent adverse effects; most sampled prairie dogs (90%) and associated small rodents (78%) had consumed baits. Visual counts of prairie dogs and their burrows revealed no evidence of prairie dog decline after vaccine exposure. No vaccine-related morbidity, mortality, or gross or microscopic lesions were observed. Poxviruses were not isolated from any animal sampled prior to bait distribution or on sites that received placebo baits. We isolated RCN-F1/V307 from 17 prairie dogs and two deer mice ( Peromyscus maniculatus ) captured on sites where vaccine-laden baits were distributed. Based on these findings, studies examining the utility and effectiveness of oral vaccination to prevent plague-induced mortality in prairie dogs and associated species are underway.

Colorado↗

USGS2022

Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas

Background The fathead minnow ( Pimephales promelas ) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation. Methods Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950. Results We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow ( P. notatus ) as sister to fathead minnow, with the slim minnow ( P. tenellus ) and bullhead minnow ( P. vigilax ) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (F ST ) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.

PeerJ↗

USGS2018

An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA

Use of environmental DNA (eDNA) to assess distributions of aquatic and semi-aquatic macroorganisms is promising, but sampling schemes may need to be tailored to specific objectives. Given the potentially high variance in aquatic eDNA among replicate grab samples, compositing smaller water volumes collected over a period of time may be more effective for some applications. In this study, we compared eDNA profiles from composite water samples aggregated over three hours with grab water samples. Both sampling patterns were performed with identical autosamplers paired at two different sites in a headwater stream environment, augmented with exogenous fish eDNA from an upstream rearing facility. Samples were filtered through 0.8 μm cellulose nitrate filters and DNA was extracted with a cetyl trimethylammonium bromide procedure. Eukaryotic and bacterial community profiles were derived by amplicon sequencing of 12S ribosomal, 16S ribosomal, and cytochrome oxidase I loci. Operational taxa were assigned to genus with a lowest common ancestor approach for eukaryotes and to family with the RDP Classifier software for prokaryotes. Eukaryotic community profiles were more consistent with composite sampling than grab sampling. Downstream, rarefaction curves suggested faster taxon accumulation for composite samples, and estimated richness was higher for composite samples as a set than for grab samples. Upstream, composite sampling produced lower estimated richness than grab samples, but with overlapping standard errors. Furthermore, a bimodal pattern of richness as a function of sequence counts suggested the impact of clumped particles on upstream samples. Bacterial profiles were insensitive to sample method, consistent with the more even dispersion expected for bacteria compared with eukaryotic eDNA. Overall, samples composited over 3 h performed equal to or better than triplicate grab sampling for quantitative community metrics, despite the higher total sequencing effort provided to grab replicates. On the other hand, taxon-specific detection rates did not differ appreciably and the two methods gave similar estimates of the ratio of the common fish genera Salmo and Coregonus at each site. Unexpectedly, Salmo eDNA dropped out substantially faster than Coregonus eDNA between the two sites regardless of sampling method, suggesting that differential settling affects the estimation of relative abundance. We identified bacterial patterns that were associated with eukaryotic diversity, suggesting potential roles as biomarkers of sample representativeness.

PeerJ↗

USGS2001

Ecotoxicology of Wild Mammals

An international group of 32 scientists has critically reviewed the scientific literature on exposure and effects of environmental contaminants in wild mammals. The underlying theme of this text is encompassed by the following four questions: What exactly do we know about environmental contaminants in mammals? What are the commonalities and differences between mammal orders/species in the effects that contaminants have? How and to what degree of accuracy can we predict the adverse effects of environmental contaminants on mammalian wildlife? How significant are contaminant insults compared with other density-independent and -dependent factors such as habitat loss, climatic factors and disease? The book is organized three topical sections including introductory chapters that provide a background on environmental contaminants and the mammalian orders, eight taxonomic chapters discussing all aspects of the exposure to and effects of contaminants in mammalian orders, and four thematic chapters that review and discuss generic issues including biomarkers, prediction and extrapolation of exposure and effects, hazard and risk assessment, and the relative significance of contaminants on mammals compared with other commonly encountered stressors. A final a summary chapter identifies phylogenetic trends, critical data gaps, and overarching research needs. Although the absolute number of toxicological studies in domesticated and wild mammals eclipses that wildlife species, a detailed examination of our knowledge base reveals that information for 'wild' birds is actually greater than that for 'wild' mammals. Of the various mammalian taxa, ecotoxicological data is most noticeably lacking for marsupials and monotremes. In contrast, rodents (comprising 43% of all mammal species) have been studied extensively, despite evidence of their tolerance to some organochlorine compounds, rodenticides, and even radionuclides. Mammalian species at greatest risk of exposure include those that consume a high percentage of their body weight on a daily basis. Aquatic mammals tend to bioaccumulate tremendous burdens of lipophilic contaminants, although storage in their fat depots may actually limit toxicity. Carnivores appear to be more sensitive to adverse effects of environmental contaminants than herbivores. Remarkably few of the thousands of compounds manufactured worldwide have been toxicologically evaluated in wild mammals, and concentrations of even fewer have been monitored in tissues.

Ecological & Environmental Toxicology Series.↗

USGS2001

Investigation of eggshell thickness and biochemical indicators of contaminant exposure in Great Blue Herons(Ardea herodias) from Mason Neck National Wildlife Refuge

Mason Neck National Wildlife Refuge supports the largest great blue heron (Ardea herodias) rookery in the State of Virginia. The presence of bioaccumulative compounds such as polychlorinated biphenyls and DDT in fish collected from the Potomac River and tidal tributaries along the Refuge led to this study. The objective was to determine if there were any indications of pollutant-induced eggshell thinning or evidence of biochemical exposure to contaminants. We examined eggshell thickness and biomarkers of contaminant exposure in livers of embryos collected from the refuge and Coaches Island, a reference location in Chesapeake Bay. There was no evidence of eggshell thinning. Cytochrome P450 activity, measured as ethoxyresomfin-O-dealkylase (EROD) and benzyloxy-resorufin-O-dealkylase (BROD), was not significantly different in embryos from the two colonies. Biochemical indicators of oxidative stress can be reflected as changes in levels of reduced thiols, oxidized glutathione, and thiobarbituric reactive substances (TBARS). Although there were significant differences in the levels of reduced glutathione (GSH) and total thiol (TSH) activities in the embryo livers, there were no statistically significant differences in TBARS, protein-bound sulfhydryls (PBSH), oxidized glutathione (GSSG) and the ratio of GSSG to GSH. In fact, the concentrations of GSH and TSH were higher in the Mason Neck birds relative to Coaches Island. Under conditions of increased oxidative stress at least one or more of the following would be expected: decreased concentrations of reduced thiols (GSH and TSH), increased GSSG, and increased TBARS. In conclusion, we did not detect eggshell thinning or find evidence of a biochemical response to contaminant exposure in the Mason Neck great blue herons.

Report↗