The geometric mean of relative abundance indices: a biodiversity measure with a difference

Abstract In many marine fisheries assessments, population abundance indices from surveys collected by different states and agencies do not always agree with each other. This phenomenon is often due to the spatial synchrony/asynchrony. Those indices that are asynchronous may result in discrepancies in the assessment of temporal trends. In addition, commonly employed stock assessment models, such as the statistical catch-at-age (SCA) models, do not account for spatial synchrony/asynchrony associated with spatial autocorrelation, dispersal, and environmental noise. This limits the value of statistical inference on key parameters associated with population dynamics and management reference points. To address this problem, a set of geospatial analyses of relative abundance indices is proposed to model the indices from different surveys using spatial hierarchical Bayesian models. This approach allows better integration of different surveys with spatial synchrony and asynchrony. We used Atlantic weakfish (Cynoscion regalis) as an example for which there are state-wide surveys and expansive coastal surveys. We further compared the performance of the proposed spatially structured hierarchical Bayesian SCA models with a commonly used Bayesian SCA model that assumes relative abundance indices are spatially independent. Three spatial models developed to mimic different potential spatial patterns were compared. The random effect spatially structured hierarchical Bayesian model was found to be better than the commonly used SCA model and the other two spatial models. A simulation study was conducted to evaluate the uncertainty resulting from model selection and the robustness of the recommended model. The spatially structured hierarchical Bayesian model was shown to be able to integrate different survey indices with/without spatial synchrony. It is suggested as a useful tool when there are surveys with different spatial characteristics that need to be combined in a fisheries stock assessment.

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Comparison of odontocete populations of the Marquesas and Society Islands (French Polynesia)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315408002713 ◽

2008 ◽

Vol 89 (5) ◽

pp. 931-941 ◽

Cited By ~ 6

Author(s):

Alexandre Gannier

Keyword(s):

Relative Abundance ◽

Bottlenose Dolphin ◽

Bottlenose Dolphins ◽

Sperm Whale ◽

French Polynesia ◽

Society Islands ◽

Spotted Dolphin ◽

Abundance Indices ◽

Beaked Whales ◽

Using Data

Small boat surveys were organized to study cetaceans of the Marquesas (9°S and 140°W) and the Society Islands (17°S and 150°W) in French Polynesia. Prospecting took place from 12–15 m sailboats, between 1996 and 2001 with systematic visual searching. Boats moved according to sea conditions, at a mean speed of 10 km/h. Effective effort of 4856 km in the Marquesas and 10,127 km in the Societies were logged. Relative abundance indices were processed for odontocetes using data obtained with Beaufort 4 or less. In the Marquesas, 153 on-effort sightings were obtained on 10 delphinids species including the spotted dolphin, spinner dolphin, bottlenose dolphin, melon-headed whale and rough-toothed dolphin. In the Societies, 153 sightings of 12 odontocetes included delphinids (spinner, rough-toothed and bottlenose dolphins, short-finned pilot and melon-headed whales, Fraser's dolphin, Risso's dolphin and pygmy killer whale) and two species of beaked whales, the sperm whale and dwarf sperm whale. Relative abundance indices were higher in the Marquesas than in the Societies both inshore (0.93 ind/km2 against 0.36 ind/km2) and offshore (0.28 ind/km2 against 0.14 ind/km2). Differences in remote-sensed primary production were equally important, the Marquesas waters featuring an annual average of 409 mgC.m−2 · day−1 and the Societies of only 171 mgC · m−2 · day−1. The presence of a narrow shelf around the Marquesas also accounted for differences in odontocete populations, in particular the delphinids.

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Landscape-wide changes in land use and land cover correlate with, but rarely explain local biodiversity change

Landscape Ecology ◽

10.1007/s10980-020-01109-2 ◽

2020 ◽

Vol 35 (10) ◽

pp. 2255-2273

Author(s):

Martin Jung ◽

Jörn P. W. Scharlemann ◽

Pedram Rowhani

Keyword(s):

Land Use ◽

Land Cover ◽

Functional Groups ◽

Relative Abundance ◽

Photosynthetic Activity ◽

Landsat Imagery ◽

Geometric Mean ◽

Bird Diversity ◽

Assemblage Composition ◽

Biodiversity Change

Abstract Context There is an ongoing debate whether local biodiversity is declining and what might drive this change. Changes in land use and land cover (LULC) are suspected to impact local biodiversity. However, there is little evidence for LULC changes beyond the local scale to affect biodiversity across multiple functional groups of species, thus limiting our understanding of the causes of biodiversity change. Objectives Here we investigate whether landscape-wide changes in LULC, defined as either trends in or abrupt changes in magnitude of photosynthetic activity, are driving bird diversity change. Methods Linking 34 year (1984–2017) time series at 2745 breeding bird survey (BBS) routes across the conterminous United States of America with remotely-sensed Landsat imagery, we assessed for each year what proportion of the landscape surrounding each BBS route changed in photosynthetic activity and tested whether such concomitant or preceding landscape-wide changes explained changes in bird diversity, quantified as relative abundance (geometric mean) and assemblage composition (Bray–Curtis index). Results We found that changes in relative abundance was negatively, and assemblage composition positively, correlated with changes in photosynthetic activity within the wider landscape. Furthermore, landscape-wide changes in LULC in preceding years explained on average more variation in bird diversity change than concomitant change. Overall, landscape-wide changes in LULC failed to explain most of the variation in bird diversity change for most BBS routes regardless whether differentiated by functional groups or ecoregions. Conclusions Our analyses highlight the influence of preceding and concomitant landscape-wide changes in LULC on biodiversity.

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Evaluation of three relative abundance indices for assessing dingo populations

Wildlife Research ◽

10.1071/wr9960197 ◽

1996 ◽

Vol 23 (2) ◽

pp. 197 ◽

Cited By ~ 67

Author(s):

L Allen ◽

R Engeman ◽

H Krupa

Keyword(s):

Relative Abundance ◽

Canis Lupus ◽

Activity Index ◽

Correlation Coefficients ◽

Target Species ◽

Wild Canids ◽

Population Reduction ◽

Abundance Indices ◽

High Level ◽

Level Of Agreement

Three methods of assessing relative abundance of wild canids were evaluated on a population of dingoes, Canis lupus dingo (Corbett), on a cattle station in south-westem Queensland. The tested indices relied on measurements of activity based on spoor. Two of the techniques attracted the target species to tracking stations through the use of a novel (fatty acid scent) or food-based (buried meat) attractant. The third index (activity) measured the number of dingo tracks crossing tracking stations placed at 1-km intervals along a road transect. All three indices had a high level of agreement for detecting differences in relative abundance, with correlation coefficients exceeding 0.85. When the stations were analysed in 1-km segments, the activity index proved the most sensitive, producing proportionally more positive responses than either of the other two indices irrespective of whether the tracking stations were assessed at 1-, 2-, 3- or 4-day intervals. Inconsistencies between indices existed, with the derived abundance indices not showing the anticipated reduction following population reduction. The effect of season and the interaction between dingo activity and index methodology are discussed.

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Evaluation of Potential Overwinter Mortality of Age-0 Walleye and Appropriate Age-1 Sampling Gear

Journal of Fish and Wildlife Management ◽

10.3996/082017-jfwm-062 ◽

2018 ◽

Vol 9 (1) ◽

pp. 65-74 ◽

Cited By ~ 2

Author(s):

Jeffrey D. Grote ◽

Melissa R. Wuellner ◽

Brian G. Blackwell ◽

David O. Lucchesi

Keyword(s):

South Dakota ◽

Body Condition ◽

Relative Abundance ◽

Coefficient Of Variation ◽

First Year ◽

Selective Mortality ◽

Frequency Distributions ◽

Abundance Indices ◽

Overwinter Mortality ◽

First Year Of Life

Abstract Potential recruitment of age-0 Walleye Sander vitreus to adults is often indexed by the relative abundance of age-0 individuals during their first summer or fall. However, relationships between age-0 and adult Walleye abundance are often weak or nonsignificant in many waters. Overwinter mortality during the first year of life has been hypothesized as an important limitation to Walleye recruitment in lakes, but limited evidence of such mortality exists, likely due to difficulties in sampling age-1 Walleye during spring. The objectives of this study were to: 1) compare results from nighttime electrofishing to index relative abundance of age-1 Walleyes with relative abundance indices of minifyke nets in four eastern South Dakota lakes; 2) determine whether size-selective mortality was occurring in those four lakes; and 3) if size-selective mortality was occurring in these lakes, determine whether that mortality was attributed to body condition. We sampled four natural lakes in eastern South Dakota 2 wk after ice-off in 2013 and 2014. Precision of nighttime electrofishing (coefficient of variation = 216.6) was greater than that estimated for minifyke nets (coefficient of variation = 338.5) across both years. We detected no differences in length-frequency distributions of collected spring age-1 Walleye between the two gears. Age-0 fall relative abundance indices from electrofishing were significantly greater (P < 0.01) than spring age-1 nighttime electrofishing indices of relative abundance at three of the four study lakes, indicating that overwinter mortality may occur at a substantial rate during the first year of life for Walleye in these systems. Quantile–quantile regression plots showed evidence of size-selective mortality in three of four lakes sampled. However, body condition of age-0 Walleye appeared to have little to no influence on overwinter mortality. Instead, we suggest that smaller-sized walleye may be more vulnerable to overwinter predation. Collectively, these results provide evidence of previously hypothesized overwinter mortality within the first year for Walleye and indicate possibilities for indexing potential adult recruitment of Walleye just after this critical period.

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Seasonal variation of striped dolphins, fin- and sperm whales' abundance in the Ligurian Sea (Mediterranean Sea)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315407054719 ◽

2007 ◽

Vol 87 (1) ◽

pp. 345-352 ◽

Cited By ~ 27

Author(s):

Sophie Laran ◽

Violaine Drouot-Dulau

Keyword(s):

Relative Abundance ◽

Sperm Whale ◽

Line Transect ◽

Physeter Macrocephalus ◽

Monthly Basis ◽

Ligurian Sea ◽

Stenella Coeruleoalba ◽

Abundance Indices ◽

Fin Whales ◽

Acoustic Sampling

In order to investigate seasonal changes in cetacean relative abundance, a series of surveys were conducted between the French mainland and Corsica. From February 2001 to February 2004, thirty similar transects were conducted monthly, using the same dedicated boat and a consistent sampling protocol, including visual observation and passive acoustic sampling. A total effort of 5759 km was sampled, conducted at the same speed and in good sighting conditions. Relative abundances of striped dolphins (Stenella coeruleoalba) and fin whales (Balaenoptera physalus) were determined using standard line-transect methodology. The relative abundance of striped dolphins peaked in May and September (>1.3×10-2 ind.km-1), while a consistent minimum value (<0.6×10-2 ind.km-1) was obtained from December to April. A maximum relative abundance of fin whales occurred in August with 5.6×10-2 ind.km-1 and decreased to almost zero from November to January. For sperm whale (Physeter macrocephalus), a long diver species, frequency and abundance indices were determined using acoustic sampling. The highest acoustic relative abundance was observed from August to October, with more than 2×10-2 ind.km-1. Environmental parameters (sea surface temperature and chlorophyll) were computed for the sampling area from remote sensing imagery and pooled on a monthly basis, to correlate with relative abundance indices of the three species.

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Evaluation of quota management policies for developing fisheries

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f98-172 ◽

1998 ◽

Vol 55 (12) ◽

pp. 2691-2705 ◽

Cited By ~ 23

Author(s):

Carl Walters

Keyword(s):

Mortality Rate ◽

Relative Abundance ◽

Cumulative Effect ◽

Mortality Rates ◽

Reference Trajectory ◽

Fishing Mortality ◽

Small Probability ◽

Abundance Indices ◽

Management Policies ◽

Quota Management

Losses can be measured as deviations from a desired reference trajectory of quotas that would be taken if there were no uncertainty and are highly dependent on assessments prior to and during development. Simulations of assessment and quota setting under various quota setting rules indicate that variability in relative abundance indices can cause substantial losses, especially considering cumulative effect of early quota errors on later departures of biomass from that needed to produce the desired quotas, even if optimum fishing mortality rate is known in advance. Conservative assessments (low biomass estimates for which there is only a small probability that biomass is actually lower) are favored during development when loss is measured as the relative departure from the best quota for each year. But if loss is measured as absolute departure from the best quota, it is generally better to base the quota on the biomass estimate for which there is nearly a 50% chance that the stock is smaller. Deliberate overfishing (probing) is not favored under either loss measure. Losses can be reduced with minimum biomass surveys and closed areas that directly cushion fishing mortality rates from being more than 50% too low or high.

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Comparison of relative abundance indices calculated from two methods of generating video count data

Fisheries Research ◽

10.1016/j.fishres.2015.05.011 ◽

2015 ◽

Vol 170 ◽

pp. 125-133 ◽

Cited By ~ 29

Author(s):

Matthew D. Campbell ◽

Adam G. Pollack ◽

Christopher T. Gledhill ◽

Theodore S. Switzer ◽

Douglas A. DeVries

Keyword(s):

Relative Abundance ◽

Count Data ◽

Abundance Indices

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Simulating spatial dynamics to evaluate methods of deriving abundance indices for tropical tunas

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f10-056 ◽

2010 ◽

Vol 67 (9) ◽

pp. 1409-1427 ◽

Cited By ~ 12

Author(s):

Thomas R. Carruthers ◽

Murdoch K. McAllister ◽

Robert N. M. Ahrens

Keyword(s):

Population Dynamics ◽

Relative Abundance ◽

Spatial Dynamics ◽

Selection Criterion ◽

Information Criterion ◽

Fishing Effort ◽

Catch Per Unit Effort ◽

Applied Model ◽

Thunnus Obesus ◽

Abundance Indices

Relative abundance indices derived from nominal catch-per-unit-effort (CPUE) data are a principle source of information for the majority of stock assessments. A particular problem with formulating such abundance indices for pelagic species such as tuna is the interpretation of CPUE data from fleets that have changed distribution over time. In this research, spatial population dynamics are simulated to test the historical pattern of fishing effort as a basis for making inferences about relative abundance. A number of age-structured, spatially disaggregated population dynamics models are described for both Atlantic yellowfin tuna ( Thunnus albacares ) and bigeye tuna ( Thunnus obesus ) to account for uncertainty in spatial distribution and movement. These models are used to evaluate the reliability of standardization methods and a commonly applied model selection criterion, Akaike’s information criterion (AIC). The simulations demonstrate the pitfalls of aggregating CPUE data over spatial areas and highlight the need for data imputation. Simulations support simpler models than those selected using AIC for extracting reliable indices of relative abundance.

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