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At least 37 records · Page 2Linked to original sources
USGS2023

Assessing arthropod diversity metrics derived from stream environmental DNA: Spatiotemporal variation and paired comparisons with manual sampling

Background Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods. Methods We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment. Results Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.

PeerJ↗
USGS2023

Accounting for spatial habitat and management boundaries when estimating forest bird population distribution and density: Inferences from a soap film smoother

Birds are often obligate to specific habitats which can result in study areas with complex boundaries due to sudden changes in vegetation or other features. This can result in study areas with concave arcs or that include holes of unsuitable habitat such as lakes or agricultural fields. Spatial models used to produce species’ distribution and density estimates need to respect such boundaries to make informed decisions for species conservation and management. The soap film smoother is one model for complex study regions which controls the boundary behaviour, ensuring realistic values at the edges of the region. We apply the soap film smoother to account for boundary effects and compare it with thin plate regression spline (TPRS) smooth and design-based conventional distance sampling methods to produce abundance estimates from point-transect distance sampling collected data on Hawai‘i ‘Ākepa Loxops coccineus in the Hakalau Forest Unit of the Big Island National Wildlife Refuge Complex, Hawai‘i Island, USA. The soap film smoother predicted zero or near zero densities in the northern part of the domain and two hotspots (in the southern and central parts of the domain). Along the boundary the soap film model predicted relatively high densities where ‘Ākepa occur in the adjacent forest and near zero elsewhere. The design-based and soap film abundance estimates were nearly identical. The width of the soap film confidence interval was 16.5% and 0.8% wider than the width of the TPRS smooth and design-based confidence intervals, respectively. The peaks in predicted densities along the boundary indicates leakage by the TPRS smooth. We provide a discussion of the statistical methods, biological findings and management implications of applying soap film smoothers to estimate forest bird population status.

Hawaii↗
USGS2023

Bighorn sheep associations: Understanding tradeoffs of sociality and implications for disease transmission

Sociality directly influences mating success, survival rates, and disease, but ultimately likely evolved for its fitness benefits in a challenging environment. The tradeoffs between the costs and benefits of sociality can operate at multiple scales, resulting in different interpretations of animal behavior. We investigated the influence of intrinsic ( e.g. , relatedness, age) and extrinsic factors ( e.g. , land cover type, season) on direct contact (simultaneous GPS locations ≤ 25 m) rates of bighorn sheep ( Ovis canadensis ) at multiple scales near the Waterton-Glacier International Peace Park. During 2002–2012, male and female bighorn were equipped with GPS collars. Indirect contact (GPS locations ≤ 25 m regardless of time) networks identified two major breaks whereas direct contact networks identified an additional barrier in the population, all of which corresponded with prior disease exposure metrics. More direct contacts occurred between same-sex dyads than female-male dyads and between bighorn groups with overlapping summer home ranges. Direct contacts occurred most often during the winter-spring season when bighorn traveled at low speeds and when an adequate number of bighorn were collared in the area. Direct contact probabilities for all dyad types were inversely related to habitat quality, and differences in contact probability were driven by variables related to survival such as terrain ruggedness, distance to escape terrain, and canopy cover. We provide evidence that probabilities of association are higher when there is greater predation risk and that contact analysis provides valuable information for understanding fitness tradeoffs of sociality and disease transmission potential.

Alberta, British Columbia, Montana↗
USGS2023

Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)

Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy “receiver” coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the presence of numerous previously identified SCTLD bioindicators within our mesocosms. The identification in our mesocosms of specific bacterial amplicon sequence variants that also appear across prior studies spanning different collection years, geographic regions, source material, and coral species, suggests that bacteria may play some role in the disease.

PeerJ↗
USGS2023

Assessing the ecological risk of heavy metal sediment contamination from Port Everglades Florida USA

Port sediments are often contaminated with metals and organic compounds from anthropogenic sources. Remobilization of sediment during a planned expansion of Port Everglades near Fort Lauderdale, Florida (USA) has the potential to harm adjacent benthic communities, including coral reefs. Twelve sediment cores were collected from four Port Everglades sites and a control site; surface sediment was collected at two nearby coral reef sites. Sediment cores, sampled every 5 cm, were analyzed for 14 heavy metals using inductively coupled plasma-mass spectrometry. Results for all three locations yielded concentration ranges (µg/g): As (0.607–223), Cd (n/d–0.916), Cr (0.155–56.8), Co (0.0238–7.40), Cu (0.004–215), Pb (0.0169–73.8), Mn (1.61–204), Hg (n/d–0.736), Mn (1.61–204), Ni (0.232–29.3), Se (n/d–4.79), Sn (n/d–140), V (0.160–176), and Zn (0.112–603), where n/d = non-detected. The geo-accumulation index shows moderate-to-strong contamination of As and Mo in port sediments, and potential ecological risk indicates moderate-to-significantly high overall metal contamination. All four port sites have sediment core subsamples with As concentrations above both threshold effect level (TEL, 7.24 µg/g) and probable effect level (PEL, 41.6 µg/g), while Mo geometric mean concentrations exceed the background continental crust level (1.5 µg/g) threshold. Control site sediments exceed TEL for As, while the reef sites has low to no overall heavy metal contamination. Results of this study indicate there is a moderate to high overall ecological risk from remobilized sediment due to metal contamination. Due to an imminent dredging at Port Everglades, this could have the potential to harm the threatened adjacent coral communities and surrounding protected habitats.

Florida↗
USGS2023

Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus

Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees ( Apis mellifera ). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues.

PeerJ↗
USGS2023

Understanding fatality patterns and sex ratios of Brazilian free-tailed bats (Tadarida brasiliensis) at wind energy facilities in western California and Texas

Background Operation of wind turbines has resulted in collision fatalities for several bat species, and one proven method to reduce these fatalities is to limit wind turbine blade rotation ( i.e ., curtail turbines) when fatalities are expected to be highest. Implementation of curtailment can potentially be optimized by targeting times when females are most at risk, as the proportion of females limits the growth and stability of many bat populations. The Brazilian free-tailed bat ( Tadarida brasiliensis ) is the most common bat fatality at wind energy facilities in California and Texas, and yet there are few available data on the sex ratios of the carcasses that are found. Understanding the sex ratios of fatalities in California and Texas could aid in planning population conservation strategies such as informed curtailment. Methods We used PCR to determine the sex of bat carcasses collected from wind energy facilities during post-construction monitoring (PCM) studies in California and Texas. In California, we received samples from two locations within the Altamont Pass Wind Resource Area in Alameda County: Golden Hills (GH) ( n = 212) and Golden Hills North (GHN) ( n = 312). In Texas, we received samples from three wind energy facilities: Los Mirasoles (LM) (Hidalgo County and Starr County) ( n = 252), Los Vientos (LV) (Starr County) ( n = 568), and Wind Farm A (WFA) (San Patricio County and Bee County) ( n = 393). Results In California, the sex ratios of fatalities did not differ from 50:50, and the sex ratio remained stable over the survey years, but the seasonal timing of peak fatalities was inconsistent. In 2017 and 2018, fatalities peaked between September and October, whereas in 2019 and 2020 fatalities peaked between May and June. In Texas, sex ratios of fatalities varied between locations, with Los Vientos being female-skewed and Wind Farm A being male-skewed. The sex ratio of fatalities was also inconsistent over time. Lastly, for each location in Texas with multiple years studied, we observed a decrease in the proportion of female fatalities over time. Discussion We observed unexpected variation in the seasonal timing of peak fatalities in California and differences in the sex ratio of fatalities across time and facility location in Texas. In Texas, proximity to different roost types (bridge or cave) likely influenced the sex ratio of fatalities at wind energy facilities. Due to the inconsistencies in the timing of peak female fatalities, we were unable to determine an optimum curtailment period; however, there may be location-specific trends that warrant future investigation. More research should be done over the entirety of the bat active season to better understand these trends in Texas. In addition, standardization of PCM studies could assist future research efforts, enhance current monitoring efforts, and facilitate research on post-construction monitoring studies.

California, Texas↗
USGS2024

Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes

Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered northern tidewater goby, Eucyclogobius newberryi . Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining took twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding has gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining remains the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions.

PeerJ↗
USGS2016

A hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags

Water temperature is a primary driver of stream ecosystems and commonly forms the basis of stream classifications. Robust models of stream temperature are critical as the climate changes, but estimating daily stream temperature poses several important challenges. We developed a statistical model that accounts for many challenges that can make stream temperature estimation difficult. Our model identifies the yearly period when air and water temperature are synchronized, accommodates hysteresis, incorporates time lags, deals with missing data and autocorrelation and can include external drivers. In a small stream network, the model performed well (RMSE = 0.59°C), identified a clear warming trend (0.63 °C decade −1 ) and a widening of the synchronized period (29 d decade −1 ). We also carefully evaluated how missing data influenced predictions. Missing data within a year had a small effect on performance (∼0.05% average drop in RMSE with 10% fewer days with data). Missing all data for a year decreased performance (∼0.6 °C jump in RMSE), but this decrease was moderated when data were available from other streams in the network.

PeerJ↗
USGS2024

A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus)

Background Previous work found that numerous genes positively selected within the hoary bat ( Lasiurus cinereus ) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. Methods A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo ( www.dnazoo.org ). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Results Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these ( Trpc4 ) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. Discussion This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.

PeerJ↗
USGS2024

Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes

Background Enhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python ( Python bivittatus ) in the Florida Everglades. Methods Using multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus ). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure. Results Time-lapse game cameras detected almost 40 times more snakes ( n = 375, treatment = 245, control = 130) than visual surveys ( n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs. Conclusions Our study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics.

Florida↗
USGS2024

Bayesian multistate models for measuring invasive carp movement and evaluating telemetry array performance

Understanding the movement patterns of an invasive species can be a powerful tool in designing effective management and control strategies. Here, we used a Bayesian multistate model to investigate the movement of two invasive carp species, silver carp ( Hypophthalmichthys molitrix ) and bighead carp ( H. nobilis ), using acoustic telemetry. The invaded portions of the Illinois and Des Plaines Rivers, USA, are a high priority management zone in the broader efforts to combat the spread of invasive carps from reaching the Laurentian Great Lakes. Our main objective was to characterize the rates of upstream and downstream movements by carps between river pools that are maintained by navigation lock and dam structures. However, we also aimed to evaluate the efficacy of the available telemetry infrastructure to monitor carp movements through this system. We found that, on a monthly basis, most individuals of both species remained within their current river pools: averaging 76.2% of silver carp and 75.5% of bighead carp. Conversely, a smaller proportion of silver carp, averaging 14.2%, and bighead carp, averaging 13.9%, moved to downstream river pools. Movements towards upstream pools were the least likely for both species, with silver carp at an average of 6.7% and bighead carp at 7.9%. The highest probabilities for upstream movements were for fish originating from the three most downstream river pools, where most of the population recruitment occurs. However, our evaluation of the telemetry array’s effectiveness indicated low probability to detect fish in this portion of the river. We provide insights to enhance the placement and use of these monitoring tools, aiming to deepen our comprehension of these species’ movement patterns in the system.

Illinois↗
USGS2016

Updating movement estimates for American black ducks (Anas rubripes)

Understanding migratory connectivity for species of concern is of great importance if we are to implement management aimed at conserving them. New methods are improving our understanding of migration; however, banding (ringing) data is by far the most widely available and accessible movement data for researchers. Here, we use band recovery data for American black ducks ( Anas rubripes ) from 1951–2011 and analyze their movement among seven management regions using a hierarchical Bayesian framework. We showed that black ducks generally exhibit flyway fidelity, and that many black ducks, regardless of breeding region, stopover or overwinter on the Atlantic coast of the United States. We also show that a non-trivial portion of the continental black duck population either does not move at all or moves to the north during the fall migration (they typically move to the south). The results of this analysis will be used in a projection modeling context to evaluate how habitat or harvest management actions in one region would propagate throughout the continental population of black ducks. This analysis may provide a guide for future research and help inform management efforts for black ducks as well as other migratory species.

PeerJ↗
USGS2024

Deep-ocean macrofaunal assemblages on ferromanganese and phosphorite-rich substrates in the Southern California Borderland

Mineral-rich hardgrounds, such as ferromanganese (FeMn) crusts and phosphorites, occur on seamounts and continental margins, gaining attention for their resource potential due to their enrichment in valuable metals in some regions. This study focuses on the Southern California Borderland (SCB), an area characterized by uneven and heterogeneous topography featuring FeMn crusts, phosphorites, basalt, and sedimentary rocks that occur at varying depths and are exposed to a range of oxygen concentrations. Due to its heterogeneity, this region serves as an optimal setting for investigating the relationship between mineral-rich hardgrounds and benthic fauna. This study characterizes the density, diversity, and community composition of macrofauna (>300 μm) on hardgrounds as a function of substrate type and environment (depth and oxygen ranges). Rocks and their macrofauna were sampled quantitatively using remotely operated vehicles (ROVs) during expeditions in 2020 and 2021 at depths above, within, and below the oxygen minimum zone (OMZ). A total of 3,555 macrofauna individuals were counted and 416 different morphospecies (excluding encrusting bryozoans and hydrozoans) were identified from 82 rocks at depths between 231 and 2,688 m. Average density for SCB macrofauna was 11.08 ± 0.87 ind. 200 cm −2 and mean Shannon-Wiener diversity per rock (H′ [loge] ) was 2.22 ± 0.07. A relationship was found between substrate type and macrofaunal communities. Phosphorite rocks had the highest H′ of the four substrates compared on a per-rock basis. However, when samples were pooled by substrate, FeMn crusts had the highest H′ and rarefaction diversity. Of all the environmental variables examined, water depth explained the largest variance in macrofaunal community composition. Macrofaunal density and diversity values were similar at sites within and outside the OMZ. This study is the first to analyze the macrofaunal communities of mineral-rich hardgrounds in the SCB, which support deep-ocean biodiversity by acting as specialized substrates for macrofaunal communities. Understanding the intricate relationships between macrofaunal assemblages and mineral-rich substrates may inform effects from environmental disruptions associated with deep-seabed mining or climate change. The findings contribute baseline information useful for effective conservation and management of the SCB and will support scientists in monitoring changes in these communities due to environmental disturbance or human impact in the future.

California↗
USGS2025

Molecular evolution of TRPC4 regulatory sequences supports a role in mammalian thermoregulatory adaptation

Background Proteins encoded by the canonical transient receptor potential (Trpc) gene family form transmembrane channels involved in diverse signal-transduction pathways. Trpc4 has been shown necessary for the induction of nonshivering thermogenesis (NST) in mice, a key component of which is thermogenic brown adipose tissue (BAT). In bats, T rpc4 exhibited diversifying selection within exons encoding regulatory binding sites of TRPC4. Methods To assess whether diversification of these regulatory sequences mirrors the diversification of mammalian thermoregulatory strategies, the ratio of nonsynonymous to synonymous substitutions (ω) was estimated for multiple tetrapod outgroups and eutherian orders. Four questions were addressed: (1) Did the ancestral eutherian Trpc4 diverge under positive selection from nonplacental mammals that lack BAT? (2) Did Trpc4 subsequently become more constrained in descendant eutherian clades? (3) In eutherian clades that subsequently lost BAT by inactivation of the thermogenin gene Ucp1 , did Trpc4 become less constrained? (4) Does the evolutionary rate of Trpc4 differ between quantitatively more heterothermic mammal orders (bats and rodents) relative to quantitatively less heterothermic outgroups (carnivores, artiodactylids, and primates)? Results Coincident with the advent of BAT, Trpc4 evolutionary rate increased significantly in ancestral eutheria after their divergence from nonplacental mammals but a branch-site model did not support a rate class ω > 1 along that branch. In descendant eutherian mammals, Trpc4 became far more constrained, with an evolutionary rate less than half that of tetrapod clades lacking NST, a pattern was not seen in other Trp channel genes. Intensifying selection in descendent eutherian mammals was further supported with the RELAX program, which also indicated reduced constraint on Trpc4 in clades that have secondarily lost BAT. However, no consistent pattern was identified within mammalian orders with strong variation in heterothermy: evidence of increased evolutionary rate was again found in bats for Trpc4 as well as homologs it directly binds in heteromeric membrane channels ( Trpc5 and Trpc1 ), yet all rodent Trpc genes had low evolutionary rates. Evolutionary rates of Trpc4 and Trpc1 in bats were consistent with relaxed constraint whereas bat Trpc5 experienced diversifying selection. Most variation among tetrapod TRPC4 sequences lies within an 85 amino-acid window that is functionally uncharacterized. Sequence alignments demonstrated that the TRPC4 β isoform, which lacks a portion of the C-terminal regulatory region, originated in basal eutherians but appears to be lost in many tip lineages. Collectively, the data indicate that the C-terminal region of TRPC4 has responded to selection on NST thermoregulation during the diversification of eutherian mammals. The drivers of increased diversification of Trpc4 and interacting genes in bats remain to be determined.

PeerJ↗
USGS2025

Gram staining reveals diverse bacterial associations in coral cell-associated microbial aggregates in the Pacific Ocean

Cell-associated microbial aggregates (CAMAs) (also referred to as coral-associated microbial aggregates) have been observed in 24 coral species from the Pacific Ocean, and studies indicate most contain gram-negative bacilli from the genus Endozoicomonas. Here, we used histology with Gram staining to evaluate the morphology and distribution of CAMAs in six species of scleractinian corals from Hawaii and Palmyra. Within CAMAs, we observed the coexistence of bacteria with differing morphologies and Gram-staining properties both within and among coral species. Pocillopora and Acropora had mostly gram-negative bacilli, whereas gram-negative cocci dominated in Porites . Acropora had the highest abundance of gram-positive CAMAs. The anatomical distribution of CAMAs varied by coral species. CAMAs dominated in the tentacles of Pocillopora meandrina , Pocillopora grandis , and Porites evermanni, were mostly in the coenenchyme of Acropora cytherea , and were found equally between tentacles and coenenchyme in Porites compressa and Porites lobata . Tissue-layer distribution also varied, with CAMAs mainly in the epidermis of Pocillopora but in the gastrodermis of Porites and Acropora . The diversity of bacteria in CAMAs and their anatomic distribution in Pacific corals may be more complex than previously understood. This indicates other bacterial species, in addition to Endozoicomonas, are colonizing CAMAs in corals from the Pacific Ocean.

Hawaii↗
USGS2026

The Appalbees menu: A multiyear, multilocus metagenetic assessment of pollen foraging by Appalachian Bombus affinis workers

Background Detailed studies of foraging behavior are needed for scientific management of the endangered rusty-patched bumblebee ( Bombus affinis ) in the disjunct and ecologically differentiated habitats it presently occupies. Current knowledge gaps hinder recovery planning but are challenging to redress through direct observation of rare interactions in the field. Methods We used genetic metabarcoding to characterize the taxonomic composition of pollen collected by B. affinis workers in the Appalachian mountains of Virginia and West Virginia from 2021–2023. We developed a custom sequence database of the regional flora and compared results for two independent genetic loci, internal transcribed spacer 1 and internal transcribed spacer 2 (ITS1 and ITS2). Results While ITS2 consistently detected more plant diversity, results from the two loci were broadly concordant with a few notable exceptions. The plant genera Hydrangea , Actaea , Rhododendron , Tilia , and (unexpectedly) Laportea were prominent in midsummer samples, with Rubus a consistent contributor in late spring and early summer. Pea flowers (family Fabaceae) were relatively infrequent but the genera Securigera and Trifolium were detected before the Hydrangea bloom and again in late summer afterwards. The diversity of forage plants was highest in late summer, driven primarily by various genera of Asteraceae. Comparing the current data with previous work indicates regional differentiation in forage plants between Appalachia and the upper Midwest, but also allows ‘consensus’ forage sources that are supported by multiple lines of evidence and shared between regions to be tabulated. These results should help managers focus survey efforts for this endangered species and plan habitat enhancements.

Illinois, Virginia, West Virginia, Wisconsin↗
USGS2016

First records of Canis dirus and Smilodon fatalis from the late Pleistocene Tule Springs local fauna, upper Las Vegas Wash, Nevada

Late Pleistocene groundwater discharge deposits (paleowetlands) in the upper Las Vegas Wash north of Las Vegas, Nevada, have yielded an abundant and diverse vertebrate fossil assemblage, the Tule Springs local fauna (TSLF). The TSLF is the largest open-site vertebrate fossil assemblage dating to the Rancholabrean North American Land Mammal Age in the southern Great Basin and Mojave Desert. Over 600 discrete body fossil localities have been recorded from the wash, including an area that now encompasses Tule Springs Fossil Beds National Monument (TUSK). Paleowetland sediments exposed in TUSK named the Las Vegas Formation span the last 250 ka, with fossiliferous sediments spanning ∼100–13 ka. The recovered fauna is dominated by remains of Camelops and Mammuthus , and also includes relatively common remains of extinct Equus and Bison as well as abundant vertebrate microfaunal fossils. Large carnivorans are rare, with only Puma concolor and Panthera atrox documented previously. Postcranial remains assigned to the species Canis dirus (dire wolf) and Smilodon fatalis (sabre-toothed cat) represent the first confirmed records of these species from the TSLF, as well as the first documentation of Canis dirus in Nevada and the only known occurrence of Smilodon in southern Nevada. The size of the recovered canid fossil precludes assignment to other Pleistocene species of Canis . The morphology of the felid elements differentiates them from other large predators such as Panthera , Homotherium , and Xenosmilus , and the size of the fossils prevents assignment to other species of Smilodon . The confirmed presence of S. fatalis in the TSLF is of particular interest, indicating that this species inhabited open habitats. In turn, this suggests that the presumed preference of S. fatalis for closed-habitat environments hunting requires further elucidation.

PeerJ↗