Estimates Of Absolute Abundance Research Articles

Absolute Abundance Estimates of Atlantic Goliath Grouper (Epinephelus itajara) on Spawning Aggregation Sites

Reliable data on Atlantic Goliath Grouper abundance are prerequisite to informed management decisions, particularly as the State of Florida reopened a limited harvest on the species in 2023 after a 32-year moratorium. Limited data exist for this purpose and fisheries data have been unavailable for over three decades due to a fishery closure that began in 1990. The purpose of this study was to compare absolute abundance estimates of Goliath Grouper between two years using an efficient, cost-effective method developed by Koenig. An underwater tagging method was used to collect mark and resight data for use in a Peterson deterministic model. These data were collected at the same spawning aggregation sites off Jupiter, Florida near the time of the new moon in September 2013 and August 2022. We found that Goliath Grouper abundance had declined at all but one of six sites since 2013. Because data were not collected during the intervening years, interannual variability is unknown. However, given the highly age-structured spawning stock of adult Goliath Grouper on the spawning grounds, the lower abundances measured in 2022 may reflect a real decline in the population rather than just representing a weak year of adult recruitment to these spawning sites.

A standardized quantitative analysis strategy for stable isotope probing metagenomics.

Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.

Detecting and analysing intraspecific genetic variation with eDNA: From population genetics to species abundance.

Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections in diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies have explored the potential for these approaches to detect within-species genetic variation, allowing for population genetic assessments and abundance estimates from environmental samples. However, we currently lack a framework outlining the key considerations specific to generating, analysing and applying eDNA data for these two purposes. Here, we discuss how various genetic markers differ with regard to genetic information and detectability in environmental samples and how analysis of eDNA samples differs from common tissue-based analyses. We then outline how it may be possible to obtain species absolute abundance estimates from eDNA by detecting intraspecific genetic variation in mixtures of DNA under multiple scenarios. We also identify the major causes contributing to allele detection and frequency errors in eDNA data, discuss their consequences for population-level analyses and outline bioinformatic approaches to detect and remove erroneous sequences. This review summarizes the key advances required to harness the full potential of eDNA-based intraspecific genetic variation to inform population-level questions in ecology, evolutionary biology and conservation management.

Reconciling data on the trends and abundance of North Atlantic humpback whales within a population modelling framework

Populations of humpback whales (Megaptera novaeangliae) in the North Atlantic appear to have been increasing at least during the last few decades, following the cessation of substantial hunting almost 100 years ago. Several sources of data are available for these populations (survey and mark-recapture estimates of absolute and relative abundance, estimated catches, and estimates of the proportion of the animals on two feeding grounds that are from the West Indies breeding ground). These data were analysed using an age- and sex-structured population dynamics model that is spatially-explicit to the extent that abundance is tracked on five feeding and two breeding grounds. Several alternative hypotheses, including depensation and changes over time in carrying capacity, were captured within the model framework. Two scenarios form the focus of the analyses, based on alternative interpretations of the size of the breeding population off the Cape Verde Islands. The results of these analyses confirm the increase in the number of humpback whales in the North Atlantic, although it is not possible to determine the extent of such increases. Whether both the West Indies and Cape Verde Islands breeding stocks have increased depends on whether the estimate of abundance for the Cape Verde Islands population of approximately 100 animals is valid. Although many of the data sources can be reconciled given the model applied, some conflicts remain; resolution of these conflicts will require collection of additional data.

Assessment of Antarctic minke whales using statistical catch-at-age analysis (SCAA)

Statistical catch-at-age analysis (SCAA) is applied to data for Antarctic minke whales. The SCAA model is spatially-structured, can model multiple stocks of minke whales, and can utilise several data types for parameter estimation. The application to Antarctic minke whales considers two stocks (I and P) in five areas which cover Antarctic Areas III–E to VI–W. The parameters of the model (annual deviations about the stock-recruitment relationship, changes over time in carrying capacity, density-dependence parameters related to productivity and carrying capacity, and the parameters which determine growth by stock, age-specific natural mortality by stock, and vulnerability by area and ‘fleet’) are estimated by fitting the model to data on catches, catch-at-length, conditional age-at-length, and estimates of absolute and relative abundance. A reference case analysis is selected, and sensitivity explored using retrospective analyses and by varying the assumptions on which the reference case analysis is based. The reference case analysis is able to mimic all of the data sources adequately. Most of the analyses (reference and sensitivity) indicates that Antarctic minke whales in the assessed area increased from 1930 until the mid-1970s and have declined thereafter, with the extent of the decline greater for minke whales in Antarctic Areas III–E to V–W than for those further east. Natural mortality is consistently estimated to be higher for younger and older individuals than for individuals of intermediate age. Estimates of MSYR1+ (the exploitation rate on animals 1 and older at which sustainable yield is maximised) are presented, but are unreliable owing to the lack of contrast.

Review of contemporary cetacean stock assessment models

Model-based methods of analysis are widely used to conduct cetacean stock assessments, and to provide the operating models on which management strategy evaluation is based. This paper reviews recent assessments and management strategy evaluations for cetacean populations, with a view towards establishing ‘best practice’ guidelines for such analyses. The models on which these analyses are based range from simple exponential trend models that ignore density-dependence to complex multi-stock age-sex- and stage-structured models that form the basis for management strategy evaluation. Most analyses assume that density-dependence is on calf survival (which implicitly includes maturity and pregnancy rate), but it could also impact the survival rate of adults or the age-at-maturity. Cetaceans seldom have more than one calf per female each year, which limits the variation in calf numbers, and places an upper limit on the effects of density-dependent calf survival. The models differ in terms of whether the population projections start when substantial catches first occurred or whether allowance is made for time-varying carrying capacity by starting the model in a more recent year. Most of the models are deterministic, but account needs to be taken of variation in cohort strength for analyses that include age-composition data or for species that are relatively short-lived. A limited number of analyses include process variability using a statespace-like modelling framework. For some stocks, abundance is so low that ideally both demographic and environmental variability should be included in models. The primary source of data for parameter estimation is a time-series of estimates of absolute abundance, although some approaches considered used a variety of data types, including relative abundance indices, mark-recapture data and minimum abundance estimates based on haplotype counts. In general, at least one estimate of absolute abundance is needed for parameter estimation; this is because there is a lack of catch-induced declines in abundance captured by indices of relative abundance that could be used to provide information on absolute abundance. Similarly, information on abundance from age- and length- composition data is limited. Most of the analyses quantify uncertainty using Bayesian methods to allow information on biological parameters, particularly the intrinsic rate of growth and the relative population at which maximum production occurs, to be included in the analyses, along with sensitivity testing. The future for the models on which assessments and management strategy evaluations are based will often involve multi-stock models that include age-, sex- and spatial-structure and are fitted as state-space formulations, although at present such models are often too computationally intensive to be feasible for implementation or there is insufficient information in the data to estimate the parameters representing all the processes, leading to simplifications, with the result that the performance of some of the methods of assessment used for cetacean stocks needs to be better understood, including through simulation testing.

Direct estimates of reef fish abundance across an artificial reef network

Fisheries-independent surveys are commonly used to create indices of relative abundance. If properly designed and calibrated, these surveys may also be used to estimate absolute abundance. Here, we demonstrate the efficacy of this approach by estimating the absolute abundance of red lionfish ( Pterois volitans), gray triggerfish ( Balistes capriscus), and red snapper ( Lutjanus campechanus) across an extensive network of artificial reefs using camera counts, indices of relative abundance, calibration factors, and index-removal estimators. From 2012 to 2017, per reef estimates increased for red lionfish (20×), gray triggerfish (2.1×), and red snapper (2.2×). Network-wide absolute abundances were calculated by multiplying the average per reef estimate by the estimated number of reefs in the network. All increases were consistent with predictions of stock assessment (red snapper), management actions (gray triggerfish), or invasive species colonization (red lionfish). Our methodology demonstrates how estimates of absolute abundance can be derived from fishery-independent surveys and used to evaluate the outputs of stock assessments both in direction and magnitude and quantify critical ecosystem components.

N-mixture model-based estimate of relative abundance of sloth bear (Melursus ursinus) in response to biotic and abiotic factors in a human-dominated landscape of central India.

Reliable estimation of abundance is a prerequisite for a species' conservation planning in human-dominated landscapes, especially if the species is elusive and involved in conflicts. As a means of population estimation, the importance of camera traps has been recognized globally, although estimating the abundance of unmarked, cryptic species has always been a challenge to conservation biologists. This study explores the use of the N-mixture model with three probability distributions, i.e., Poisson, negative binomial (NB) and zero-inflated Poisson (ZIP), to estimate the relative abundance of sloth bears (Melursus ursinus) based on a camera trapping exercise in Sanjay Tiger Reserve, Madhya Pradesh from December 2016 to April 2017. We used environmental and anthropogenic covariates to model the variation in the abundance of sloth bears. We also compared null model estimates (mean site abundance) obtained from the N-mixture model to those of the Royle-Nichols abundance-induced heterogeneity model (RN model) to assess the application of similar site-structured models. Models with Poisson distributions produced ecologically realistic and more precise estimates of mean site abundance (λ = 2.60 ± 0.64) compared with other distributions, despite the relatively high Akaike Information Criterion value. Area of mixed and sal forest, the photographic capture rate of humans and distance to the nearest village predicted a higher relative abundance of sloth bears. Mean site abundance estimates of sloth bears obtained from the N-mixture model (Poisson distribution) and the RN model were comparable, indicating the overall utility of these models in this field. However, density estimates of sloth bears based on spatially explicit methods are essential for evaluating the efficacy of the relatively more cost-effective N-mixture model. Compared to commonly used index/encounter-based methods, the N-mixture model equipped with knowledge on governing biotic and abiotic factors provides better relative abundance estimates for a species like the sloth bear. In the absence of absolute abundance estimates, the present study could be insightful for the long-term conservation and management of sloth bears.

Monitoring small mammal abundance using NEON data: are calibrated indices useful?

Abstract Small mammals are important to the functioning of ecological communities with changes to their abundances used to track impacts of environmental change. While capture–recapture estimates of absolute abundance are preferred, indices of abundance continue to be used in cases of limited sampling, rare species with little data, or unmarked individuals. Improvement to indices can be achieved by calibrating them to absolute abundance but their reliability across years, sites, or species is unclear. To evaluate this, we used the US National Ecological Observatory Network capture–recapture data for 63 small mammal species over 46 sites from 2013 to 2019. We generated 17,155 absolute abundance estimates using capture–recapture analyses and compared these to two standard abundance indices, and three types of calibrated indices. We found that neither raw abundance indices nor index calibrations were reliable approximations of absolute abundance, with raw indices less correlated with absolute abundance than index calibrations (raw indices overall R2 < 0.5, index calibration overall R2 > 0.6). Performance of indices and index calibrations varied by species, with those having higher and less variable capture probabilities performing best. We conclude that indices and index calibration methods should be used with caution with a count of individuals being the best index to use, especially if it can be calibrated with capture probability. None of the indices we tested should be used for comparing different species due to high variation in capture probabilities. Hierarchical models that allow for sharing of capture probabilities over species or plots (i.e., joint-likelihood models) may offer a better solution to mitigate the cost and effort of large-scale small mammal sampling while still providing robust estimates of abundance.

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.

Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.

Quantitative insights into effects of intrapartum antibiotics and birth mode on infant gut microbiota in relation to well-being during the first year of life

ABSTRACT Birth mode and maternal intrapartum (IP) antibiotics affect infants’ gut microbiota development, but their relative contribution to absolute bacterial abundances and infant health has not been studied. We compared the effects of Cesarean section (CS) delivery and IP antibiotics on infant gut microbiota development and well-being over the first year. We focused on 92 healthy infants born between gestational weeks 37–42 vaginally without antibiotics (N = 26), with IP penicillin (N = 13) or cephalosporin (N = 7) or by CS with IP cephalosporin (N = 33) or other antibiotics (N = 13). Composition and temporal development analysis of the gut microbiota concentrated on 5 time points during the first year of life using 16S rRNA gene amplicon sequencing, integrated with qPCR to obtain absolute abundance estimates. A mediation analysis was carried out to identify taxa linked to gastrointestinal function and discomfort (crying, defecation frequency, and signs of gastrointestinal symptoms), and birth interventions. Based on absolute abundance estimates, the depletion of Bacteroides spp. was found specifically in CS birth, while decreased bifidobacteria and increased Bacilli were common in CS birth and exposure to IP antibiotics in vaginal delivery. The abundances of numerous taxa differed between the birth modes among cephalosporin-exposed infants. Penicillin had a milder impact on the infant gut microbiota than cephalosporin. CS birth and maternal IP antibiotics had both specific and overlapping effects on infants’ gut microbiota development. The resulting deviations in the gut microbiota are associated with increased defecation rate, flatulence, perceived stomach pain, and intensity of crying in infancy.

Estimating natural mortality for Atlantic Sea scallops (Placopecten magellenicus) using a size-based stock assessment model

We estimate temporally varying natural mortality within a size-based stock assessment model for U.S. sea scallops in three different regions, and compare the results to corresponding models where natural mortality is not estimated, and (in one case) where only the mean natural mortality is estimated. In one model, for the Georges Bank Closed Areas, natural mortality was estimated by year for all sizes, whereas in the other two models (for the Georges Bank Open Areas and the Mid-Atlantic Bight), annual variation in natural mortality was estimated for juveniles only. Estimating natural mortality by year improved the performance over fixed natural mortality in all three models, as measured by Akaike’s information criterion (AIC) and reduced retrospective patterns. There was evidence that natural mortality is density-dependent. Large recruitment events were associated with substantial increases in juvenile natural mortality, and natural mortality in the Georges Bank Closed Areas tended to increase at high biomass. Estimation of natural mortality was facilitated by survey data that gave estimates of absolute abundance together with low fishing mortality that minimized the confounding between natural and fishing mortality. Natural mortality is an important process that should be estimated when there is sufficient information to do so.

Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens

ObjectivesObservational studies demonstrate an association between vaginal douching and bacterial vaginosis (BV) characterised by Gram stain. We sought to describe the effect of a douching cessation intervention on the composition...

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome.

Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.

Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals

SummaryWhile microbial communities inhabit a wide variety of complex natural environments, in vitro culturing enables highly controlled conditions and high-throughput interrogation for generating mechanistic insights. In vitro assemblies of gut commensals have recently been introduced as models for the intestinal microbiota, which plays fundamental roles in host health. However, a protocol for 16S rRNA sequencing and analysis of in vitro samples that optimizes financial cost, time/effort, and accuracy/reproducibility has yet to be established. Here, we systematically identify protocol elements that have significant impact, introduce bias, and/or can be simplified. Our results indicate that community diversity and composition are generally unaffected by substantial protocol streamlining. Additionally, we demonstrate that a strictly aerobic halophile is an effective spike-in for estimating absolute abundances in communities of anaerobic gut commensals. This time- and money-saving protocol should accelerate discovery by increasing 16S rRNA data reliability and comparability and through the incorporation of absolute abundance estimates.

Mark-release-recapture of ticks: A case study of estimating the abundance of Ixodes persulcatus (Acari, Ixodidae).

In this study, we tested the applicability of three common methods of absolute abundance estimation-Peterson, Bailey and Jolly-Seber-to Ixodes persulcatus ticks based on mark-release-recapture data. The ticks were collected by flagging during the seasonal activity peak of the ticks in the mid-taiga zone of Karelia (62.0697°N, 33.9614°E). In total, 108 females and 92 males of I. persulcatus were marked. The marked individuals were captured 161 times before the end of the study period with their proportion in the samples reaching 50%. Females were recaptured more often than males, 105 versus 56 times. Estimates of adult tick abundance ranged from 0.4 to 2 specimens per m2 depending on the calculation method. The obtained estimates of absolute abundance varied unpredictably depending on the length of the intervals between capture sessions and showed no significant correlations with the number of ticks collected by flagging. The choice of the method of tick abundance estimation mainly depends on the study aims. The Petersen method may be useful for quick estimates of local tick abundance, whereas the Jolly-Seber method allows an estimation of the absolute abundance during the entire period of the tick activity. Individual marking of ticks may improve the accuracy of the estimates.

Pitfalls and pointers: An accessible guide to marker gene amplicon sequencing in ecological applications

Abstract Next‐Generation Sequencing (NGS) is a powerful tool that has been rapidly adopted by many ecologists studying microbial communities. Despite the exciting demonstration of NGS technology as a tool for ecological research, cryptic pitfalls inherent to its use can obscure correct interpretation of NGS data. Here, we provide an accessible overview of a NGS process that uses marker gene amplicon sequences (MGAS) that will allow scientists, particularly community ecologists, to make appropriate methodological choices and understand limits on inference about community composition and diversity that can be drawn from MGAS data. We describe the MGAS pipeline, focusing specifically on cryptic sources of variation that have received less emphasis in the ecological literature, but which may substantially impact inference about microbial community diversity and composition. By simulating communities from published microbiome data, we demonstrate how these sources of variation can generate inaccurate or misleading patterns. We specifically highlight sample dilution without researcher awareness and lane‐to‐lane variability, two cryptic sources of variation arising during the MGAS pipeline. These sources of variation affect estimates of species presence and relative abundance, particularly for species with moderate to low abundances. Each of these sources of bias can lead to errors in the estimation of both absolute and relative abundance within, and turnover among, microbial communities. Awareness and understanding of what happens and, specifically, why it happens during MGAS generation is key to generating a strong dataset and building a robust community matrix. Requesting sample dilution information from the sequencing centre, including technical replicates across sequencing lanes, and understanding how sampling intensity and community taxa distribution patterns shape the measurement of community richness, evenness and diversity are critical for drawing correct ecological inferences using MGAS data.

Absolute Abundance Estimates for Red Snapper, Greater Amberjack, and Other Federally Managed Fish on Offshore Petroleum Platforms in the Gulf of Mexico

AbstractOffshore petroleum platforms provide habitat utilized by an array of reef fish that are valuable to both commercial and recreational fishers. However, thousands of offshore platforms have been decommissioned in the Gulf of Mexico over the past decade, with many of the removals being accomplished using explosive severance methods. Here, we estimate the impact of platform removal in the Gulf of Mexico on five stocks of federally managed reef fish based on the percentage of each stock that is resident on platforms. We conclude that the gulfwide impact of removal will be relatively minor (1% to 8% of the estimated stock abundance) for four species, Red Snapper Lutjanus campechanus, Gray Triggerfish Balistes capriscus, Vermilion Snapper Rhomboplites aurorubens, and Cobia Rachycentron canadum. In contrast, losses for the Greater Amberjack Seriola dumerili stock would potentially represent 45% of the known stock. An alternative explanation is that the actual abundance of Greater Amberjack is much larger than the most recent stock size estimate; in either case, we suggest this issue needs further examination. Removal impacts could also be significant for reef‐fish fisheries (especially the Red Snapper fishery) in areas where platforms are presently abundant but other high‐relief natural or artificial reefs are not present. Removal of the platforms from these areas will greatly impact the local fisheries.

Multiple‐model stock assessment frameworks for precautionary management and conservation on fishery‐targeted coastal dolphin populations off Japan

Abstract Stock assessment approaches are often oversimplified due to lack of biological knowledge and insufficient data. In spite of world‐wide attention, fishery‐targeted coastal dolphin species in Japan have lacked in‐depth quantitative stock assessments because of limited time series of population size and an absence of associated biological information. We consequently developed integrated population models that analysed multiple sources of data simultaneously with published biological information within a Bayesian framework. We estimate population status and trends for three main species targeted by fisheries, bottlenose dolphins Tursiops truncatus, Risso's dolphins Grampus griseu, and short‐finned pilot whales Globicephala macrorhynchus, using single‐species age‐aggregated and age‐structured population dynamics models. Models were fit to absolute abundance estimates from systematic line‐transect surveys, four series of abundance indices calculated from fisher's logbooks, and historical catch records. Published biological information was used to develop prior distributions for the biological parameters. We assessed the possible effects of ecological disturbance and competition using state‐space and multispecies models. The multispecies model was selected by the model selection both for the age‐aggregated and the age‐structured approaches. Single‐species assessments found that population size declined 4.2% (Risso's dolphin) to 8.0% (bottlenose dolphin) for three species since the late 1800s based on median posterior values, while the state‐space and multispecies models found that environmental disturbance and an interaction among species could have reduced population size more substantially. Policy implications. Simple single‐species models are often used to provide conservation and management advice for wild animals but, in this case, results from such models are overly optimistic because they overlook important ecological process. In contrast, current population status could be less favorable if environmental disturbance and interspecific competition actually control population dynamics. Even if that is not the case, considering ecological process in the model will provide more precautionary ways. Our approach of combining multiple modelling frameworks is applicable to many other management systems, and offers increased confidence in estimated status and trends over assessments that consider only a single model.

Estimating the sampling efficiencies of a framed midwater trawl and ring net for zooplankton using an acoustic method

It is well known that there is bias using different sampling gear, such as a framed midwater trawl (FMT) and a ring net, when measuring the density and length distribution of target species. This limit is characterized by the sampling efficiency of the gear. Acoustic monitoring can be used to determine the sampling efficiencies of this gear, as its noninvasive, wide-range sweeps provide more reliable estimates of absolute abundance of the target species. The density measured by the gear can then be standardized by multiplying the initial density measurement by the derived sampling efficiency. In this study, we compared the estimated densities of the dominant zooplankton in the sound scattering layer (SSL) from acoustic monitoring to the densities of the same species measured using the FMT and ring net. The respective sampling efficiencies of this gear for zooplankton categories was then determined using linear regression models. For small Euphausiidae and Copepoda, the sampling efficiency of ring net was higher than that of FMT. In contrast, the ring net was less effective than FMT for large Euphausiidae. These results highlight that the entering and retention rates of the species depend on the type and characteristics of the survey gear, as well as the size and swimming ability of the target species.