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USGS2014

The story of invasive algae, arginine, and turtle tumors does not make sense

We are presenting a rebuttal letter to the following article that appeared recently on PeerJ: Van Houtan KS, Smith CM, Dailer ML, and Kawachi M. 2014. Eutrophication and the dietary promotion of sea turtle tumors. PeerJ 2:e602. This article is available at the following URL: https://peerj.com/articles/602/. We argue that the article lacks an inferential framework to answer the complex question regarding the drivers of the turtle tumor disease fibropapillomatosis in Hawaii. The article also contains procedural flaws and does not provide any compelling evidence of a link between algae, arginine, and turtle tumors.

Hawaii↗

USGS2016

Clawpack: Building an open source ecosystem for solving hyperbolic PDEs

Clawpack is a software package designed to solve nonlinear hyperbolic partial differential equations using high-resolution finite volume methods based on Riemann solvers and limiters. The package includes a number of variants aimed at different applications and user communities. Clawpack has been actively developed as an open source project for over 20 years. The latest major release, Clawpack 5, introduces a number of new features and changes to the code base and a new development model based on GitHub and Git submodules. This article provides a summary of the most significant changes, the rationale behind some of these changes, and a description of our current development model.

PeerJ Computer Science↗

USGS2016

Daniel Goodman’s empirical approach to Bayesian statistics

Bayesian statistics, in contrast to classical statistics, uses probability to represent uncertainty about the state of knowledge. Bayesian statistics has often been associated with the idea that knowledge is subjective and that a probability distribution represents a personal degree of belief. Dr. Daniel Goodman considered this viewpoint problematic for issues of public policy. He sought to ground his Bayesian approach in data, and advocated the construction of a prior as an empirical histogram of “similar” cases. In this way, the posterior distribution that results from a Bayesian analysis combined comparable previous data with case-specific current data, using Bayes’ formula. Goodman championed such a data-based approach, but he acknowledged that it was difficult in practice. If based on a true representation of our knowledge and uncertainty, Goodman argued that risk assessment and decision-making could be an exact science, despite the uncertainties. In his view, Bayesian statistics is a critical component of this science because a Bayesian analysis produces the probabilities of future outcomes. Indeed, Goodman maintained that the Bayesian machinery, following the rules of conditional probability, offered the best legitimate inference from available data. We give an example of an informative prior in a recent study of Steller sea lion spatial use patterns in Alaska.

PeerJ↗

USGS2017

Experts correctly describe demography associated with historical decline of the endangered Indiana bat, but not recent period of stationarity

Demographic characteristics of bats are often insufficiently described for modeling populations. In data poor situations, experts are often relied upon for characterizing ecological systems. In concert with the development of a matrix model describing Indiana bat ( Myotis sodalis ) demography, we elicited estimates for parameterizing this model from 12 experts. We conducted this elicitation in two stages, requesting expert values for 12 demographic rates. These rates were adult and juvenile seasonal (winter, summer, fall) survival rates, pup survival in fall, and propensity and success at breeding. Experts were most in agreement about adult fall survival (3% Coefficient of Variation) and least in agreement about propensity of juveniles to breed (37% CV). The experts showed greater concordance for adult ( mean CV, adult = 6.2%) than for juvenile parameters ( mean CV, juvenile = 16.4%), and slightly more agreement for survival (mean CV, survival = 9.8%) compared to reproductive rates ( mean CV, reproduction = 15.1%). However, survival and reproduction were negatively and positively biased, respectively, relative to a stationary dynamic. Despite the species exhibiting near stationary dynamics for two decades prior to the onset of a potential extinction-causing agent, white-nose syndrome, expert estimates indicated a population decline of -11% per year (95% CI = -2%, -20%); quasi-extinction was predicted within a century ( mean = 61 years to QE, range = 32, 97) by 10 of the 12 experts. Were we to use these expert estimates in our modeling efforts, we would have errantly trained our models to a rapidly declining demography asymptomatic of recent demographic behavior. While experts are sometimes the only source of information, a clear understanding of the temporal and spatial context of the information being elicited is necessary to guard against wayward predictions.

PeerJ↗

USGS2021

Composition and distribution of fish environmental DNA in an Adirondack watershed

Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish ( Ictalurus punctatus ) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.

New York↗

USGS2015

Oyster reef restoration supports increased nekton biomass and potential commercial fishery value

Across the globe, discussions centered on the value of nature drive many conservation and restoration decisions. As a result, justification for management activities increasingly asks for two lines of evidence: (1) biological proof of augmented ecosystem function or service, and (2) monetary valuation of these services. For oyster reefs, which have seen significant global declines and increasing restoration work, the need to provide both biological and monetary evidence of reef services on a local-level has become more critical in a time of declining resources. Here, we quantified species biomass and potential commercial value of nekton collected from restored oyster ( Crassostrea virginica ) reefs in coastal Louisiana over a 3-year period, providing multiple snapshots of biomass support over time. Overall, and with little change over time, fish and invertebrate biomass is 212% greater at restored oyster reefs than mud-bottom, or 0.12 kg m −2 . The additional biomass of commercial species is equivalent to an increase of local fisheries value by 226%, or $0.09 m −2 . Understanding the ecosystem value of restoration projects, and how they interact with regional management priorities, is critical to inform local decision-making and provide testable predictions. Quantitative estimates of potential commercial fisheries enhancement by oyster reef restoration such as this one can be used directly by local managers to determine the expected return on investment.

Louisiana↗

USGS2021

Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples

Background Hoary bats ( Lasiurus cinereus ) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here.

PeerJ↗

USGS2021

Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis)

Many mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten ( Martes caurina humboldtensis ) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies’ niche to inform strategic conservation actions.

PeerJ↗

USGS2022

Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: Prominence of thymus expression, immune and metabolic function, and regions of ancient synteny

Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat ( Lasiurus cinereus ) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch ( P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov–Smirnov test ( P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1 -like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.

PeerJ↗

USGS2015

Assessing shoreline exposure and oyster habitat suitability maximizes potential success for sustainable shoreline protection using restored oyster reefs

Oyster reefs provide valuable ecosystem services that contribute to coastal resilience. Unfortunately, many reefs have been degraded or removed completely, and there are increased efforts to restore oysters in many coastal areas. In particular, much attention has recently been given to the restoration of shellfish reefs along eroding shorelines to reduce erosion. Such fringing reef approaches, however, often lack empirical data to identify locations where reefs are most effective in reducing marsh erosion, or fully take into account habitat suitability. Using monitoring data from 5 separate fringing reef projects across coastal Louisiana, we quantify shoreline exposure (fetch + wind direction + wind speed) and reef impacts on shoreline retreat. Our results indicate that fringing oyster reefs have a higher impact on shoreline retreat at higher exposure shorelines. At higher exposures, fringing reefs reduced marsh edge erosion an average of 1.0 m y −1 . Using these data, we identify ranges of shoreline exposure values where oyster reefs are most effective at reducing marsh edge erosion and apply this knowledge to a case study within one Louisiana estuary. In Breton Sound estuary, we calculate shoreline exposure at 500 random points and then overlay a habitat suitability index for oysters. This method and the resulting visualization show areas most likely to support sustainable oyster populations as well as significantly reduce shoreline erosion. Our results demonstrate how site selection criteria, which include shoreline exposure and habitat suitability, are critical to ensuring greater positive impacts and longevity of oyster reef restoration projects.

Louisiana↗

USGS2022

Using a mechanistic framework to model the density of an aquatic parasite Ceratonova shasta

Ceratonova shasta is a myxozoan parasite endemic to the Pacific Northwest of North America that is linked to low survival rates of juvenile salmonids in some watersheds such as the Klamath River basin. The density of C. shasta actinospores in the water column is typically highest in the spring (March–June), and directly influences infection rates for outmigrating juvenile salmonids. Current management approaches require quantities of C. shasta density to assess disease risk and estimate survival of juvenile salmonids. Therefore, we developed a model to simulate the density of waterborne C. shasta actinospores using a mechanistic framework based on abiotic drivers and informed by empirical data. The model quantified factors that describe the key features of parasite abundance during the period of juvenile salmon outmigration, including the week of initial detection (onset), seasonal pattern of spore density, and peak density of C. shasta . Spore onset was simulated by a bio-physical degree-day model using the timing of adult salmon spawning and accumulation of thermal units for parasite development. Normalized spore density was simulated by a quadratic regression model based on a parabolic thermal response with river water temperature. Peak spore density was simulated based on retained explanatory variables in a generalized linear model that included the prevalence of infection in hatchery-origin Chinook juveniles the previous year and the occurrence of flushing flows (≥171 m 3 /s). The final model performed well, closely matched the initial detections (onset) of spores, and explained inter-annual variations for most water years. Our C. shasta model has direct applications as a management tool to assess the impact of proposed flow regimes on the parasite, and it can be used for projecting the effects of alternative water management scenarios on disease-induced mortality of juvenile salmonids such as with an altered water temperature regime or with dam removal.

PeerJ↗

USGS2022

A comparison of non-surgical methods for sexing young gopher tortoises (Gopherus polyphemus)

Many turtle species have temperature-dependent sex determination (TSD), raising the prospect that climate change could impact population dynamics by altering sex ratios. Understanding how climate change will affect populations of animals with TSD requires a reliable and minimally invasive method of identifying the sexes of young individuals. This determination is challenging in many turtles, which often lack conspicuous external sexual dimorphism until years after hatching. Here, we explore four alternatives for sexing three age classes of captive-reared young gopher tortoises ( Gopherus polyphemus ), a terrestrial turtle of conservation concern native to the southeastern United States: (1) naive testosterone levels, (2) testosterone levels following a follicle stimulating hormone (FSH) challenge, (3) linear morphological measurements, and (4) geometric morphometrics. Unlike some other turtle species, male and female neonatal gopher tortoises have overlapping naive testosterone concentration distributions, justifying more complicated methods. We found that sex of neonates (<7 days old) is best predicted by a “random forest” machine learning model with naive testosterone levels and morphological measurements (8% out-of-bag error). Sex of hatchlings (4–8 months old) was predicted with 11% error using a simple threshold on naive testosterone levels, or with 4% error using a simple threshold on post-FSH testosterone levels. Sex of juveniles (approximately 3.5 years old) was perfectly predicted using a simple threshold on naive testosterone levels. Sexing hatchlings at >4 months of age is the easiest and most reliable non-surgical method for sex identification. Given access to a rearing facility and equipment to perform hormone assays, these methods have the potential to supplant laparoscopic surgery as the method of choice for sexing young gopher tortoises.

Georgia↗

USGS2022

Hydrological and lock operation conditions associated with paddlefish and bigheaded carp dam passage on a large and small scale in the Upper Mississippi River (Pools 14–18)

Movement and dispersal of migratory fish species is an important life-history characteristics that can be impeded by navigation dams. Although habitat fragmentation may be detrimental to native fish species, it might act as an effective and economical barrier for controlling the spread of invasive species in riverine systems. Various technologies have been proposed as potential fish deterrents at locks and dams to reduce bigheaded carp (i.e., silver carp and bighead carp ( Hypophthalmichthys spp.)) range expansion in the Upper Mississippi River (UMR). Lock and Dam (LD) 15 is infrequently at open-river condition (spillway gates completely open; hydraulic head across the dam <0.4 m) and has been identified as a potential location for fish deterrent implementation. We used acoustic telemetry to evaluate paddlefish passage at UMR dams and to evaluate seasonal and diel movement of paddlefish and bigheaded carp relative to environmental conditions and lock operations at LD 15. We observed successful paddlefish passage at all dams, with the highest number of passages occurring at LDs 17 and 16. Paddlefish residency events in the downstream lock approach of LD 15 occurred more frequently and for longer durations than residency events of bigheaded carp. We documented upstream passages completed by two individual paddlefish through the lock chamber at LD 15, and a single bighead carp completed upstream passage through the lock chamber during two separate years of this study. We identified four bigheaded carp and 19 paddlefish that made upstream passages through the spillway gates at LD 15 during this study. The majority of the upstream passages through the spillway gates for both species occurred during open river conditions. When hydraulic head was approximately 1-m or greater, we observed these taxa opt for upstream passage through the lock chamber more often than the dam gates. In years with infrequent open-river condition, a deterrent placed in the downstream lock approach may assist in meeting the management goal of reducing upstream passage of bigheaded carps but could also potentially affect paddlefish residency and passage. Continued study to understand the effects of deterrents on native fish could be beneficial for implementing an integrated bigheaded carp control strategy. Understanding fish behavior at UMR dams is a critical information need for river managers as they evaluate potential tools or technologies to control upstream expansion of bigheaded carp in the UMR.

Illinois, Iowa↗

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↗

USGS2022

Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration

Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at −80 °C to −20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during collection, preservation, and archiving maximizes the research potential of coral specimens and allows for the greatest number of possible downstream analyses.

PeerJ↗

USGS2022

Regularizing priors for Bayesian VAR applications to large ecological datasets

Using multi-species time series data has long been of interest for estimating inter-specific interactions with vector autoregressive models (VAR) and state space VAR models (VARSS); these methods are also described in the ecological literature as multivariate autoregressive models (MAR, MARSS). To date, most studies have used these approaches on relatively small food webs where the total number of interactions to be estimated is relatively small. However, as the number of species or functional groups increases, the length of the time series must also increase to provide enough degrees of freedom with which to estimate the pairwise interactions. To address this issue, we use Bayesian methods to explore the potential benefits of using regularized priors, such as Laplace and regularized horseshoe, on estimating interspecific interactions with VAR and VARSS models. We first perform a large-scale simulation study, examining the performance of alternative priors across various levels of observation error. Results from these simulations show that for sparse matrices, the regularized horseshoe prior minimizes the bias and variance across all inter-specific interactions. We then apply the Bayesian VAR model with regularized priors to a output from a large marine food web model (37 species) from the west coast of the USA. Results from this analysis indicate that regularization improves predictive performance of the VAR model, while still identifying important inter-specific interactions.

PeerJ↗

USGS2015

Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons

PeerJ↗

USGS2023

Pandemic-driven changes in the nearshore non-commercial fishery in Hawai'i: Catch photos posted to social media capture changes in fisher behavior

Using social media, we collect evidence for how nearshore fisheries are impacted by the global COVID-19 pandemic in Hawai’i. We later confirm our social media findings and obtain a more complete understanding of the changes in nearshore non-commercial fisheries in Hawai’i through a more conventional approach—speaking directly with fishers. Resource users posted photographs to social media nearly three times as often during the pandemic with nearly double the number of fishes pictured per post. Individuals who fished for subsistence were more likely to increase the amount of time spent fishing and relied more on their catch for food security. Furthermore, individuals fishing exclusively for subsistence were more likely to fish for different species during the pandemic than individuals fishing recreationally. Traditional data collection methods are resource-intensive and this study shows that during times of rapid changes, be it ecological or societal, social media can more quickly identify how near shore marine resource use adapts. As climate change threatens additional economic and societal disturbances, it will be necessary for resource managers to collect reliable data efficiently to better target monitoring and management efforts.

Hawaii↗