Estimates Of Relative Abundance Research Articles

Suitability of passive integrated transponder tags and a new monitoring technique for at-risk madtoms (Noturus spp.)

Representative indices of population abundance for at-risk species are necessary to inform conservation decision-making. Many madtoms (Noturusspp.) are considered imperiled; however, the efficacy of frequent monitoring efforts has been questioned due to their cryptic and nocturnal behaviors. We systematically evaluated a madtom monitoring tool by (1) evaluating the use of small (8 × 2 mm), surgically implanted 125 kHz passive integrated transponder (PIT) tags for frecklebelly madtomN. munitusand (2) assessing the effectiveness of a radio-frequency identification (RFID)-enhanced artificial cover unit to index madtom abundance. Surgically implanted PIT tags had no apparent influence on madtom survival between 45 and 110 mm total length, and all tags were retained throughout a 21 d laboratory study. In experimental mesocosms, the enhanced cover units confirmed occupancy during nearly all replicates (77.6%), even at extremely low densities (n = 2 madtoms). The enhanced cover units provided representative estimates of madtom relative abundance (p < 0.01), whereas catch per unit effort was not significantly associated with previously validated visual observations (p = 0.12). Although madtom density and the number detected using the enhanced cover units were correlated, the gear was potentially saturated at relatively high densities (~20 fish per mesocosm) when deploying a single unit. In most cases, occupancy was confirmed within 12 h, and nearly half of the individuals were detected within ~72 h. Small PIT tags and RFID-enhanced artificial cover units offer novel opportunities to efficiently describe the ecology and population dynamics of madtoms.

Abundance estimates of Southern Hemisphere Breeding Stock ‘D’ humpback whales from aerial and land-based surveys off Shark Bay, Western Australia, 2008

Single platform aerial line transect and land-based surveys of Southern Hemisphere Breeding Stock ‘D’ humpback whales Megaptera novaeangliaewere undertaken off Shark Bay, Western Australia to provide absolute abundance estimates of animals migrating northward along the westernAustralian coast. The aerial survey flew a total of 28 flights, of which 26 were completed successfully, from 24 June–19 August 2008. The landbased survey was undertaken from Cape Inscription, Dirk Hartog Island, Shark Bay, during the expected peak of the whales’ northward migration,from 8–20 July. During the first week of the land-based survey, some double count effort was undertaken to provide information on the numbersof pods missed from the land station. The assumed period of northward migration was 2 June–7 September. Estimated abundance of northwardmigrating whales during that time is 34,290 (95% CI: (27,340–53,350)), representing an annual rate of increase of 12.9% (CV = 0.20) since anestimate of 11,500 in 1999. This estimate is based on an estimate of relative abundance of surface-available whales of 10,840 (8,640–16,860), andan estimated g(0) of 0.32. There were considerable practical difficulties encountered during the land-based survey which reduced the effectivenessof the dual-survey approach for estimating g(0) for the aerial survey. Furthermore only about 15% of whales were estimated to be within the visualrange of the land-based station. Alternative approaches for estimating g(0) from these data are therefore also presented, resulting in considerablyhigher estimates of around 0.6–0.7, and yielding a conservative abundance estimate of 17,810 (14,210–27,720).

Absolute and relative abundance estimates of Australian east coast humpback whales (Megaptera novaeangliae)

The humpback whales that migrate along the east coast of Australia were hunted to near-extinction in the 1950s and early 1960s. Two independentseries of land-based surveys conducted over the last 25 years during the whales’ northward migration along the Australian coastline havedemonstrated a rapid increase in the size of the population. In 2004 we conducted a survey of the migratory population as a continuation of theseseries of surveys. Two methods of data analysis were used in line with the previous surveys, both for calculation of absolute and relative abundance.We consider the best estimates for 2004 to be 7,090±660 (95% CI) whales with an annual rate of increase of 10.6±0.5% (95% CI) for 1987–2004.The rate of increase agrees with those previously obtained for this population and demonstrates the continuation of a strong post-exploitationrecovery. While there are still some uncertainties concerning the absolute abundance estimate and structure of this population, the rate of annualincrease should be independent of these and highly robust.

Remote video methods for studying juvenile fish populations in challenging environments

Understanding the dynamics of juvenile fish populations is a key component to understanding variation in adult populations, however, juvenile fish are frequently found in a variety of structurally complex habitats which are often not easily sampled. The use of baited (BRUV) and unbaited (RUV) remote underwater stereo-video to study juvenile fish populations is uncommon and thus far, no study has directly compared the efficacy of these two methods solely for juvenile fish assemblages.The macro-tidal Kimberley region in the north-west of Australia is challenging to sample using diver-based methods due to the strong currents and prevalence of saltwater crocodiles (Crocodylus porosus). We sampled 60 Stereo-RUVs and 60 Stereo-BRUVs across four shallow-water (1-6 m) benthic habitats: coral, mangrove, macroalgae, and seagrass, to contrast the effect of the presence or absence of bait, deployment period, in-water visibility and tidally driven water speed on estimates of relative total abundance, species richness, and composition of the juvenile fish assemblage.No difference was detected in the ability of stereo-BRUV or stereo-RUV to quantify the relative total abundance, species richness, or assemblage composition of juvenile fish. We also found little effect of in-water visibility or tidally driven water speed, likely as a result of stratifying our sampling to slack water periods.We found that a deployment period of 10 min for Stereo-BRUVs and 15 min for Stereo-RUVs was optimum for sampling the juvenile fish assemblage across all four contrasting habitats. Since no statistical significance was observed between 10 and 15 min, we recommend that Stereo-RUVs deployed for 15 min during tidal slack water conditions are an optimum way to provide consistent results for comparisons of juvenile fish assemblage metrics across the benthic habitats studied within this region.The controlled video methodologies described here provided an opportunity to access un-sampled juvenile fish habitats and assemblages where traditional diver-based methodologies are impossible. Applying these methods broadly can help to improve our understanding of the status of juvenile fish and infer the reproductive success and viability of their populations across a range of habitat and environments.

Estimating Dredge Catch Efficiencies for the Northern Quahog (Mercenaria mercenaria) Population of Narragansett Bay

The catch efficiency of a hydraulic dredge was tested on a population of the northern quahog Mercenaria mercenaria in Narragansett Bay, RI, to understand gear limitations and correct relative abundance time series data. In 2017 and 2018, 45 hydraulic dredge tows were conducted following a long-standing fisheries-independent survey protocol, with the dredge transects inspected on SCUBA to assess dredge catch efficiency. Bull raking and quadrat samples taken on SCUBA were also conducted alongside the transects to compare sampling methods. The average dredge catch efficiency across samples was 0.64 (±0.29 SD). Bottom type was the most significant determinant of dredge catch efficiency, with higher catch efficiency on hard bottom (0.73 efficiency) than on soft bottom (0.48 efficiency). The quadrat and bull rake samples reflected higher catch rates than the dredge, but relationships between relative abundance estimates from the alternate methods and the dredge were either weak or insignificant. Bottom type, sediment classification, depth, and observed abundance were used to model dredge catch efficiencies and predict fisheries-independent abundance indices to more accurate estimates. Applying corrections using a generalized linear model scaled abundances through time, with trends generally the same between time series both with and without the corrections applied. This work provides an example of addressing gear efficiency concerns through diverse collaborations and improving the science and management for a commercially and recreationally significant marine resource.

Application of environmental DNA methods for the detection and abundance estimation of invasive aquatic plant Egeria densa in lotic habitats

Estimating the presence and abundance of non-native species in the early stage of invasion is important to prevent further spread of non-native species in aquatic systems. Environmental DNA (eDNA) methods have been applied for aquatic plants; however, it is still questionable on the accuracy of the eDNA methods for the detection and abundance estimation of aquatic plants in lotic systems. Here, we studied the invasive aquatic plant Egeria densa in the tributaries of the Gonokawa River in Japan to compare the E. densa detection rate of the eDNA method with that of the three sampling methods and examine the relationships of the eDNA flux to the upstream plant coverage, plant stem fragment flux, and plant tissue DNA flux of E. densa in the study sites on each season. Our results indicated that the eDNA method better detected the presence of E. densa in our study sites than other methods. The eDNA flux was directly related to the coverage rank and the plant tissue DNA flux in the study sites in both months. These results suggest that the eDNA methods have a potential as monitoring tool for early detection and relative abundance estimation of invasive aquatic plants in lotic systems.

A Shallow Water Ferrous-Hulled Shipwreck Reveals a Distinct Microbial Community.

Shipwrecks act as artificial reefs and provide a solid surface in aquatic systems for many different forms of life to attach to, especially microbial communities, making them a hotspot of biogeochemical cycling. Depending on the microbial community and surrounding environment, they may either contribute to the wreck’s preservation or deterioration. Even within a single wreck, preservation and deterioration processes may vary, suggesting that the microbial community may also vary. This study aimed to identify the differences through widespread sampling of the microbial communities associated with the Pappy Lane shipwreck (NC shipwreck site #PAS0001), a shallow water ferrous-hulled shipwreck in Pamlico Sound, North Carolina to determine if there are differences across the wreck as well as from its surrounding environment. Loose shipwreck debris, drilled shipcores, surrounding sediment, and seawater samples were collected from the Pappy Lane shipwreck to characterize the microbial communities on and around the shipwreck. Results indicated that the shipwreck samples were more similar to each other than the surrounding sediment and aquatic environments suggesting they have made a specialized niche associated with the shipwreck. There were differences between the microbial community across the shipwreck, including between visibly corroded and non-corroded shipwreck debris pieces. Relative abundance estimates for neutrophilic iron-oxidizing bacteria (FeOB), an organism that may contribute to deterioration through biocorrosion, revealed they are present across the shipwreck and at highest abundance on the samples containing visible corrosion products. Zetaproteobacteria, a known class of marine iron-oxidizers, were also found in higher abundance on shipwreck samples with visible corrosion. A novel Zetaproteobacteria strain, Mariprofundus ferrooxydans O1, was isolated from one of the shipwreck pieces and its genome analyzed to elucidate the functional potential of the organism. In addition to iron oxidation pathways, the isolate has the genomic potential to perform carbon fixation in both high and low oxygen environments, as well as perform nitrogen fixation, contributing to the overall biogeochemical cycling of nutrients and metals in the shipwreck ecosystem. By understanding the microbial communities associated with shallow water ferrous-hulled shipwrecks, better management strategies and preservation plans can be put into place to preserve these artificial reefs and non-renewable cultural resources.

Abstract 4638: Associations of fecal microbial profiles with non-malignant breast disease and breast cancer in the Ghana Breast Health Study

Abstract Background and objective: Breast cancer burden is rising in Africa; however, breast cancer risk factors remain largely understudied in this population. The gut microbiome may play a role in the etiology of breast cancer through the regulation of estrogen homeostasis and other metabolic or immunologic pathways. We investigated the association of fecal bacteria with breast neoplasms in a case-control study conducted in Accra and Kumasi, Ghana, comprising 102 non-malignant breast disease cases, 379 invasive breast cancer cases, and 414 population-based controls nested within the Ghana Breast Health Study. Methods: We used the MO-BIO PowerMag kit for DNA extraction and sequenced the V4 region of 16S rRNA gene to characterize bacteria in fecal samples. We used DADA2 to process sequencing data. We calculated estimates of alpha diversity (observed sequence variants, Shannon index, and Faith's phylogenetic diversity), beta diversity (Bray Curtis and unweighted/weighted UniFrac), and presence/absence and relative abundance of select taxa. We then estimated the associations of the microbial metrics with non-malignant breast disease and malignant breast cancer using multivariable unconditional logistic regression. Results: Odds of malignant breast cancer were statistically significantly lower with increasing alpha diversity (all Ptrends <0.0001). For example, comparing those in the highest vs. lowest tertile of observed sequence variants, the odds ratio and 95% confidence interval was 0.22 (0.13-0.36). Alpha diversity estimates were also lower for non-malignant breast disease cases compared to controls but were similar to malignant cases. Likewise, based on the multivariable MiRKAT test, which compares kernel similarity matrices based on beta diversity metrics, overall microbiota composition was similar between non-malignant and malignant cases (all p's > 0.1) but was statistically significantly different for both case groups compared controls (all p's <0.001). After correction for multiple testing, 49 taxa were significantly differentially prevalent among non-malignant and malignant cases compared to controls. Cases tended to have a lower prevalence of the Families Lachnospiraceae, Ruminococcaceae, and Prevotellaceae, and the genera Bifidobacterium, Collinsella, Coprococcus, and Mitsuokella. Notably, previous evidence suggests that some of these differentially prevalent taxa encode the enzymes ß-glucuronidase and/or ß-galactosidase, which are involved in estrogen metabolism. Conclusions: Our findings suggest lower fecal alpha diversity, differences in overall microbial composition, and prevalence of certain taxa involved in estrogen metabolism may be associated with both non-malignant breast disease and invasive breast cancer. Given that the gut bacteria are potentially modifiable and targetable, our findings warrant further investigation into the role of the gut microbiota in hormone regulation and etiology of breast cancer in integrative, prospective studies. Citation Format: Doratha Byrd, Emily Vogtmann, Zeni Wu, Autumn Hullings, Xing Hua, Thomas Ahearn, James J. Goedert, Jianxin Shi, Jonine Figueroa, Louise Brinton, Montserrat Garcia-Closas, Rashmi Sinha. Associations of fecal microbial profiles with non-malignant breast disease and breast cancer in the Ghana Breast Health Study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4638.

Monitoring freshwater fish communities in large rivers using environmental DNA metabarcoding and a long-term electrofishing survey.

Monitoring freshwater fish communities in a large human-impacted river is a challenging task. The structure of fish assemblages has been monitored yearly in the Marne and the Seine Rivers, across the Paris conurbation, France, using traditional electrofishing (EF) surveys since 1990, in accordance with the European Water Framework Directive. In addition, metabarcoding of DNA extracted from environmental samples (eDNA) was concomitantly conducted in nine sampling sites in 2017 and in 2018 to compare the estimates of species richness and relative abundance among three methods: annual, long-term EF monitoring and eDNA. The present study confirms better detection of fish species using eDNA compared to annual EF. eDNA metabarcoding was also more efficient for species detection than a 3-6-year EF survey but was similar or less efficient than a long-term EF survey of 14 years of monitoring. In addition, the numbers of reads per species relative to the total number of reads significantly increased with (a) increasing relative abundance (relative percentage of individuals caught per species) and (b) increasing number of years that a fish species was detected during the 2000-2018 period. These results suggest that eDNA could reflect local population persistence.

Compositional Lotka-Volterra describes microbial dynamics in the simplex.

Dynamic changes in microbial communities play an important role in human health and disease. Specifically, deciphering how microbial species in a community interact with each other and their environment can elucidate mechanisms of disease, a problem typically investigated using tools from community ecology. Yet, such methods require measurements of absolute densities, whereas typical datasets only provide estimates of relative abundances. Here, we systematically investigate models of microbial dynamics in the simplex of relative abundances. We derive a new nonlinear dynamical system for microbial dynamics, termed "compositional" Lotka-Volterra (cLV), unifying approaches using generalized Lotka-Volterra (gLV) equations from community ecology and compositional data analysis. On three real datasets, we demonstrate that cLV recapitulates interactions between relative abundances implied by gLV. Moreover, we show that cLV is as accurate as gLV in forecasting microbial trajectories in terms of relative abundances. We further compare cLV to two other models of relative abundance dynamics motivated by common assumptions in the literature-a linear model in a log-ratio transformed space, and a linear model in the space of relative abundances-and provide evidence that cLV more accurately describes community trajectories over time. Finally, we investigate when information about direct effects can be recovered from relative data that naively provide information about only indirect effects. Our results suggest that strong effects may be recoverable from relative data, but more subtle effects are challenging to identify.

Exploratory Surveys of Migratory Birds Breeding in the Western and Central Canadian Arctic 2005–2011

Abstract The Canadian Arctic and subarctic are the primary breeding areas of many species of North American water and land birds. Because of the remote location and the logistical difficulties of working there, wildlife biologists have not systematically surveyed most important areas for wildlife, nor have they surveyed these areas very frequently. During the summers of 2005–2011, various Joint Ventures, and U.S., Canadian, and state wildlife agencies and other partners funded exploratory fixed-wing aircraft surveys of migratory birds (excluding passerines and shorebirds) in important habitats in Canada's western and central Arctic. Our objectives were to provide access to the complete survey dataset (all bird and mammal observations and associated location data) and summarize information on several species. Thus, we produced maps of average relative density and estimates of abundance in the survey area for cackling geese Branta hutchinsii, greater white-fronted geese Anser albifrons, tundra swans Cygnus columbianus, king eiders Somateria spectabilis, long-tailed ducks Clangula hyemalis, white-winged Melanitta fusca and surf Melanitta perspicillatas scoters, and yellow-billed Gavia adamsii, red-throated Gavia stellata, and Pacific Gavia pacifica loons. We reviewed previous survey efforts in the area and, where possible, compared them with our results.

Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data

Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet-multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM-Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.

Combining fisheries surveys to inform marine species distribution modelling

Abstract Ecosystem-scale examination of fish communities typically involves creating spatio-temporally explicit relative abundance distribution maps using data from multiple fishery-independent surveys. However, sampling performance varies by vessel and sampling gear, which may influence estimated species distribution patterns. Using GAMMs, the effect of different gear–vessel combinations on relative abundance estimates at length was investigated using European fisheries-independent groundfish survey data. We constructed a modelling framework for evaluating relative efficiency of multiple gear–vessel combinations. 19 northeast Atlantic surveys for 254 species-length combinations were examined. Space-time variables explained most of the variation in catches for 181/254 species-length cases, indicating that for many species, models successfully characterized distribution patterns when combining data from disparate surveys. Variables controlling for gear efficiency explained substantial variation in catches for 127/254 species-length data sets. Models that fail to control for gear efficiencies across surveys can mask changes in the spatial distribution of species. Estimated relative differences in catch efficiencies grouped strongly by gear type, but did not exhibit a clear pattern across species’ functional forms, suggesting difficulty in predicting the potential impact of gear efficiency differences when combining survey data to assess species’ distributions and highlighting the importance of modelling approaches that can control for gear differences.

<em></em><p><strong>New and interesting aerial diatom assemblages from southwestern Iceland</strong></p>

Examination of algal assemblages from aerial environments around the globe, especially those from pseudoaerial habitats found on moistened rocks underneath waterfalls or around springs and seeps, reveals the presence of unique diatom floras. Yet, diatom assemblages from northern regions like Iceland remain understudied, especially those from the volcanic rock outcrops and boulders that create euaerial habitats where biota receive moisture from the atmosphere or the rock itself. During the summers of 2013 and 2015, we examined the biodiversity of mostly euaerial, but also pseudoaerial, diatom assemblages collected from volcanic rock outcrops or large boulders on the landscape from southwestern Iceland. We used light and scanning electron microscopy to document the biodiversity of common, smaller, new, or interesting specimens, such as Humidophila and Eunotia. We describe one new Humidophila species, H. eldfjallii sp. nov., with triundulate valve margins and include information on another unidentified taxon, Humidophila sp. 1, naviculoid in shape with tapering to rounded ends, continuous striae through the length of the valve, and a circular central area. We formally transfer Diadesmis contenta var. biceps to Humidophila biceps. To correct the nomenclature, we recognized Humidophila parallela at the species level. Relative abundance estimates of diatom populations provided further characterization of the assemblages on these habitats. Humidophila taxa, especially H. gallica dominated the diverse diatom flora. We discuss adaptations for survival with access to mostly atmospheric water. The diatom flora described here adds to the flora for this region, highlights the diversity of diatom assemblages that can inhabit euaerial environments, and provides evidence of adaptive success of diatoms in extreme habitats with limited moisture and nutrients.

Documenting Changes in Mammal Communities in the Northern Everglades

Restoration of the Everglades is an ambitious endeavor to revitalize its communities and ecosystem health, but there remain gaps in our understanding of mammal communities due to lack of long-term data synthesis. Using secondary data from long-term surveys, this study examines the potential impacts of changes in hydrological management on mammal communities within a state wildlife management area in the northern Everglades. The installation of a pump station in 1991 began a 15-year period of active water management associated with hydrological restoration. Infrastructural damage in late 2005 resulted in 9 years of no significant active inflows. I calculated non-cervid mammal encounter rates from data gathered during perimeter levee surveys over a 10-year period. Mammal encounter rates showed a strong declining trend during the time after the pump failure. A similar analysis for an adjacent management area, which did not suffer an interruption in pump inflows, also showed a decline in mammal encounter rates. In addition, I replicated a small-mammal trapping survey conducted in the mid 1990s. Results showed a decline in diversity of small mammals in the focal area. Recent confirmation of Python molurus (Burmese Python) in the area and the expansion of Canis latrans (Coyote) are likely to have played a role in these apparent declines. Thus, establishing baseline estimates of relative abundance are critical for conservation efforts. With increasingly limited resources, it is important to maximize the utility of data that has already been collected.

Assessing the blood meal hosts of Culex quinquefasciatus and Aedes taeniorhynchus in Isla Santa Cruz, Gal\xe1pagos

BackgroundBlood meal host selection by mosquito vectors is an important component in understanding disease dynamics of pathogens that threaten endemic fauna in isolated islands such as Galápagos. Research on the feeding behavior of mosquitoes can provide clues to the hosts and vectors involved in disease transmission. This information is particularly critical for endemic wildlife fauna in island systems that have evolved without resistance to novel diseases such as avian malaria. The aims of this study were to determine the blood-feeding patterns of two species of mosquitoes found in Galápagos and discuss how their feeding behavior may influence the transmission of pathogens such as avian malaria.MethodsIn the summer of 2015, we sampled two mosquito species (Aedes taeniorhynchus and Culex quinquefasciatus) across 18 different sites on Isla Santa Cruz, which is the second largest island in Galápagos and has the largest human population. We trapped mosquitoes using CDC light traps and CDC gravid traps and identified sources of blood meals for engorged mosquitoes by sequencing a portion of the vertebrate mitochondrial cytochrome b gene.ResultsOut of 947 female mosquitoes captured, 320 were blood-fed, and PCR amplifications were successful for 301 of the blood meals. Results revealed that both Aedes taeniorhynchus and Culex quinquefasciatus feed from a variety of vertebrate taxa, numerically dominated by humans on Isla Santa Cruz.ConclusionsThe high proportion of mammalian blood meals could represent locally available and abundant hosts on Santa Cruz. However, host surveys and estimates of relative abundances of vertebrate species will need to accompany mosquito trapping studies on non-inhabited and inhabited islands in Galápagos to further validate this.

Density-Dependent Escapement of Rusty Crayfish from Modified Minnow Traps with Varying Throat Configurations

Abstract Modified minnow traps are the most widely used gear for collecting tertiary burrowing crayfishes. The throats of modified minnow traps are often widened more than 60% to accommodate the capture of larger crayfish. However, widening this crucial chokepoint into the trap may facilitate easier escape of captured individuals, especially as density in the trap increases. Increased escapement rates may reduce catch rates and corresponding estimates of relative abundance and lower detection probability. Incorporating a design feature, that is, throat restriction, that allows entry of all sizes of crayfish while reducing escapement would be an improvement over current designs. Here, I present the results of a paired field and laboratory experiment comparing the effectiveness of modified minnow traps with a throat restriction (restricted) and without such a feature (unrestricted) under varying crayfish densities. I chose rusty crayfish Faxonius rusticus as a study organism because it is widespread and abundant in the Laurentian Great Lakes region and commonly the focus of research and removal efforts. Rusty crayfish capture and escapement were strongly influenced by throat design and crayfish densities. The field component demonstrated that both traps performed similarly under low-to-moderate densities; however, at high densities catch in unrestricted traps plateaued at approximately 50 crayfish/trap, while restricted traps kept accumulating catch up to 155 crayfish/trap. Laboratory trials demonstrated that escapement for both trap types was negligible at low density and slightly higher at medium density: 0.8% for restricted and 11.5% for unrestricted. However, at high density, escapement from restricted traps was 8.8 vs. 45.3% for unrestricted traps. Our findings suggest that inclusion of a throat restriction may increase catch of rusty crayfish by reducing escapement and may be of particular use in removal projects or when sampling in high-density populations.

More than Fish – The Potential of Baited Remote Underwater Video to Assess Freshwater Herpetofauna and Dolphins

We discuss new applications of baited remote underwater video (BRUV) systems based on recordings of Amazonian freshwater fauna during a long-term fish monitoring program in the Xingu River, Brazil. BRUVs facilitated estimates of relative abundance and frequency of occurrence for species of river turtles (Podocnemis unifilis, P. expansa, Rhinoclemmys punctularia), river dolphin (Inia geoffrensis) and spectacled caiman (Caiman crocodilus) in a variety of habitats including rocky rapids, submerged sandy beaches, an artificial reservoir and the Xingu Ria.

Comparison of fish detections, community diversity, and relative abundance using environmental DNA metabarcoding and traditional gears

AbstractBackgroundDetecting species at low abundance, including aquatic invasive species (AIS), is critical for making informed management decisions. Environmental DNA (eDNA) methods have become a powerful tool for rare or cryptic species detection; however, many eDNA assays offer limited utility for community‐level analyses due to their use of species‐specific (presence/absence) ‘barcodes’. Metabarcoding methods provide information on entire communities based on sequencing of all taxon‐specific barcodes within an eDNA sample.AimsEvaluate measures of fish species detections, community diversity, and estimates of relative abundance based on eDNA metabarcoding and traditional fisheries sampling approaches in the context of fish community characterization and AIS survellience.Materials and MethodsIn 2016, eight limnologically diverse lakes (surface area range: 13 – 1,728 ha) in Michigan, USA were sampled using a variety of traditional fisheries gears to characterize fish community composition. Environmental DNAs from surface (33 ± 6, mean ± 1 SD) and benthic (14 ± 2) water samples from each lake were isolated and amplified for two metabarcoding markers (mitochondrial 12S and 16S rDNA loci) using fish‐specific primers. Fish species detected within each lake were determined by comparing the sequencing data to a database of sequences from native Michigan fish species and 19 AIS on the Michigan's Watch List.ResultsAnalysis of species accumulation curves indicated multi‐locus eDNA metabarcoding assays can enhance species detection capacities and characterize 95% of a fish community in fewer sampling efforts than traditional gear (range: 2 – 62, median: 14). In addition, all AIS detected in traditional gear samples were also detected by eDNA, while some AIS detected by eDNA assays were absent from traditional gear samples.DiscussionResults reported here are, in part, driven by the lack of species‐selectivity during eDNA sampling events. Given the efficacy of eDNA assays, we suggest multi‐locus eDNA metabarcoding assays be implemented in early detection efforts.

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance*[S

Multiplexed proteomics has emerged as a powerful tool to measure relative protein expression levels across multiple conditions. The relative protein abundances are inferred by comparing the signals generated by isobaric tags, which encode the samples' origins. Intuitively, the trust associated with a protein measurement depends on the similarity of ratios from the protein's peptides and the signal-strength of these measurements. However, typically the average peptide ratio is reported as the estimate of relative protein abundance, which is only the most likely ratio with a very naive model. Moreover, there is no sense on the confidence in these measurements. Here, we present a mathematically rigorous approach that integrates peptide signal strengths and peptide-measurement agreement into an estimation of the true protein ratio and the associated confidence (BACIQ). The main advantages of BACIQ are: (1) It removes the need to threshold reported peptide signal based on an arbitrary cut-off, thereby reporting more measurements from a given experiment; (2) Confidence can be assigned without replicates; (3) For repeated experiments BACIQ provides confidence intervals for the union, not the intersection, of quantified proteins; (4) For repeated experiments, BACIQ confidence intervals are more predictive than confidence intervals based on protein measurement agreement. To demonstrate the power of BACIQ we reanalyzed previously published data on subcellular protein movement on treatment with an Exportin-1 inhibiting drug. We detect ∼2× more highly significant movers, down to subcellular localization changes of ∼1%. Thus, our method drastically increases the value obtainable from quantitative proteomics experiments, helping researchers to interpret their data and prioritize resources. To make our approach easily accessible we distribute it via a Python/Stan package.