Effects of stratification and misspecification of covariates on species distribution models for abundance estimation from virtual line transect survey data

The aim of this study was to examine the effects of stratification of the survey region on the performance of species distribution models (SDMs) described by generalized linear models or generalized additive models when estimating school abundance by using a line transect survey. True covariates that define spatial school distribution are not always obtainable explanatory variables. When the true covariates differ from explanatory variables in the model, the explanatory variables are determined to be misspecified. We evaluated the performance of SDMs in abundance estimation with misspecified covariates by using dummy datasets for which the true abundance was known. Simulated replicates of spatial distributions of a whale school and sighting data were generated from possible scenarios motivated by the spatial school distribution of Antarctic minke whales Balaenoptera bonaerensis. This distribution was obtained from the Japanese Whale Research Program under Special Permit in the Antarctic. Our results showed that the relative bias of the abundance estimators was large when covariates were misspecified and a survey region was stratified. Although stratification of the survey region is intended to produce a conventional line transect estimator with a smaller variance than that of non-stratified survey region, it also acts to increase the bias of the abundance estimate obtained from SDMs.     

Habitat differentiation between sei (Balaenoptera borealis) and Bryde's whales (B. brydei) in the western North Pacific

Two closely related baleen whale species, sei and Bryde's whales, in the western North Pacific were studied to identify differences in habitat use. Data were obtained from May to August 2004 and 2005. This study examined the relationship between oceanographic features derived from satellite data and the distribution of sei and Bryde's whales using basic statistics. We investigated oceanographic features including sea surface temperature (SST), sea surface chlorophyll a (Chl‐a), sea surface height anomalies (SSHAs), and depth of the habitat. These two whale species used habitats with different SST, Chl‐a, and SSHA ranges. The 0.25 mg m^?3 Chl‐a contour (similar to the definition of the Transition Zone Chlorophyll Front) was a good indicator that separated the habitats of sei and Bryde's whales. Then generalized linear models were used to model the probabilities that the whale species would be present in a habitat and to estimate their habitat distribution throughout the study area as a function of environmental variables. The potential habitats of the two species were clearly divided, and the boundary moved north with seasonal progression. The habitat partitioning results indicated that SST contributed to the patterns of habitat‐use and might reflect differences in prey species between the two whales. This study showed that the habitats of the sei and Bryde's whales were clearly divided and their potential habitat‐use changed seasonally.     

Prey selection of common minke (Balaenoptera acutorostrata) and Bryde's (Balaenoptera edeni) whales in the western North Pacific in 2000 and 2001

A study of common minke and Bryde's whales was conducted in the western North Pacific in the 2000 and 2001 summer seasons to estimate prey selection of cetaceans as this is an important parameter in ecosystem models. Whale sighting and sampling surveys and prey surveys using quantitative echosounder and mid‐water trawl were carried out concurrently in the study. Biomasses of Japanese anchovy, walleye pollock and krill, which were major prey species of common minke and Bryde's whales, were estimated using an echosounder. The results suggested that common minke whale showed prey selection for Japanese anchovy while they seemed to avoid krill in both the offshore and coastal regions and walleye pollock in the continental shelf region. Selection for shoaling pelagic fish was similar to that in the eastern North Atlantic. Bryde's whale showed selection for Japanese anchovy in August 2000 and July 2001, while it showed prey selection for krill in May and June in 2001.     

Modeling environmental,temporal and spatial effects on twaite shad (Alosa fallax) by‐catches in the central Mediterranean Sea

Modeling the relationships between environmental factors and the distribution at sea of species of conservation interest can be useful in predicting their occurrence from a local to a regional scale. This information is essential for planning management and conservation initiatives. In this study, generalized additive models (GAMs) were applied to investigate the influence of environmental, temporal and spatial variables on the catch rates of the twaite shad Alosa fallax (Lacepède) by the pelagic trawl fishery in the north‐central Adriatic Sea. Presence/absence and abundance [catch per unit effort (CPUE)] data between 2006 and 2012 were separately modeled, and the two models were then validated using a test data set. The most important factor influencing the presence and abundance of adult twaite shads was the spatial predictor (latitude × longitude). Two areas of major shads aggregations were observed, the most important of which being located near the estuaries of three main river systems of northern Italy. The twaite shad presence was also significantly affected by season, the largest and lowest occurrences being observed in autumn and spring, respectively. Among the environmental variables tested, only sea surface temperature was included in both models. Alosa fallax showed a wide thermal tolerance (6–27°C) with preference for temperature around 23°C. The model developed from the abundance data showed a moderate predictive power, whereas the accuracy of the presence/absence model was rather low. Some conclusions on the ecological requirements of A. fallax at sea arising from this study are useful to orient future monitoring and research programs and to develop effective conservation actions.     

Potential ship strikes and density of humpback whales in the Abrolhos Bank breeding ground,Brazil

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Spatial distribution of Antarctic minke whales (Balaenoptera bonaerensis) in relation to spatial distributions of krill in the Ross Sea,Antarctica

The spatial distribution of Antarctic minke whales in the Ross Sea with relation to spatial distributions of their prey – krill – was investigated in this study using generalized additive models (GAMs). Spatial distributions of two species of krill (ice and Antarctic krill) were estimated by GAMs. Three abiotic factors – distance from the continental shelf break (800 m isobaths), the mean temperature and salinity from the surface to 200 m (MTEM‐200 and MSAL‐200), and latitude and longitude – were used as covariates for models of krill. Estimated spatial distributions of krill were then used with other covariates to model the spatial distribution of Antarctic minke whales. In the selected model of Antarctic minke whales, Antarctic krill were more influential than ice krill. The number of Antarctic minke whales increased as the density of Antarctic krill increased to around 1.5 g m^?2. Beyond that, the number of Antarctic minke whales decreased as the density of Antarctic krill increased. High densities of the Antarctic minke whales were estimated along the sea ice edge in the eastern part of the Ross Sea. Specifically, the densities were high in the north of the continental shelf break where low MTEM‐200 and MSAL‐200 and intermediate densities of Antarctic krill were observed. Further data collection is needed to investigate interannual variations and trends in their relationship. The results show that the spatial distribution of Antarctic minke whales is a function of longitude, distance from the shelf break, oceanographic condition (temperature and salinity), and densities of ice and Antarctic krill.     

Habitat characteristics of skipjack tuna (Katsuwonus pelamis) in the western North Pacific: a remote sensing perspective

Skipjack tuna habitat in the western North Pacific was studied from satellite remotely sensed environment and catch data, using generalized additive models and geographic information systems. Weekly resolved remotely sensed sea surface temperature, surface chlorophyll, sea surface height anomalies and eddy kinetic energy data were used for the year 2004. Fifteen generalized additive models were constructed with skipjack catch per unit effort as a response variable, and sea surface temperature, sea surface height anomalies and eddy kinetic energy as model covariates to assess the effect of environment on catch per unit effort (skipjack tuna abundance). Model selection was based on significance of model terms, reduction in Akaike’s Information Criterion, and increase in cumulative deviance explained. The model selected was used to predict skipjack tuna catch per unit effort using monthly resolved environmental data for assessing model performance and to visualize the basin scale distribution of skipjack tuna habitat. Predicted values were validated using a linear model. Based on the four‐parameter model, skipjack tuna habitat selection was significantly (P < 0.01) influenced by sea surface temperatures ranging from 20.5 to 26°C, relatively oligotrophic waters (surface chlorophyll 0.08–0.18, 0.22–0.27 and 0.3–0.37 mg m^?3), zero to positive anomalies (surface height anomalies 0–50 cm), and low to moderate eddy kinetic energy (0–200 and 700–2500 cm² s^–2). Predicted catch per unit effort showed a trend consistent with the north–south migration of skipjack tuna. Validation of predicted catch per unit effort with that observed, pooled monthly, was significant (P < 0.01, r² = 0.64). Sea surface temperature explained the highest deviance in generalized additive models and was therefore considered the best habitat predictor.     

Analysing the growth of turbot (<Emphasis Type="Italic">Psetta maxima</Emphasis>) in a commercial recirculation system with the use of three different growth models

The growth data of a commercial aquaculture recirculation system were analysed to investigate the growth performance of reared turbot (Psetta maxima). Three common growth models (von Bertalanffy, Gompertz and Schnute) were fitted to the growth data documented over a time period of 6 years. To determine the most suitable model, three different criteria were used: (1) the Akaike index criterion, (2) the sum of squared residuals and (3) the average daily deviation between the estimated final weight and the observed final weight. The evaluation of the growth models showed that the Schnute model had the lowest Akaike index, the lowest sum of squared residuals and the lowest daily deviation between estimated and real weight of all tested growth models. The Schnute model produced sigmoid growth curves. The estimated growth coefficients were the most realistic ones in regard to biological interpretation. In contrast, the von Bertalanffy growth model and the Gompertz model estimated inaccurate exponential growth curves and are therefore unable to simulate the growth data as well as the Schnute model. The results indicate that the von Bertalanffy growth model is not the optimal model to simulate the present growth data and that the growth potential of reared turbot has probably not yet been fully exploited in the aquaculture system(s) examined (so far).     

Chagos feels the pinch: assessment of holothurian (sea cucumber) abundance,illegal harvesting and conservation prospects in British Indian Ocean Territory

• 1. Data are analysed from visual censuses of shallow‐water holothurians (sea cucumbers) in 72 shallow water transects 100 m×2 m within four atolls of Chagos. Mean holothurian abundance in Diego Garcia, where harvesting is absent, was 18.5 individuals/transect (all transects) and 55.4 individuals/transect (only those containing holothurians). In the three exploited atolls, mean abundance did not exceed 3.5 and 5.2 individuals/transect, respectively.
• 2. Comparison with data collected during this study and an earlier investigation reveals a marked decline over four years in both mean and maximum density of commercially valuable Stichopus chloronotus and Holothuria atra in Salomon and Peros Banhos, both exploited atolls, and also for Holothuria nobilis in the latter.
• 3. Holothurian counts were also made along an extensive transect (21 km×4 m) encircling Salomon atoll. Abundance showed highly significant negative correlation with fishing pressure, the latter estimated using an ordinal (0–3) scale (R_s=?0.605, P?0.01). Harvesting effects were not discernible using data from 200 m² transects.
• 4. While recent studies have shown Chagos is virtually pristine regarding contaminant levels, its holothurian resources are under increasing pressure. Results from this study, and examination of Sri Lanka's fishing activity in distant waters, point to heavy and illegal harvesting.
• 5. Stronger measures are needed to control the illegal fishery, to prevent holothurian abundances falling to the non‐sustainable levels now prevalent across much of the Indo‐Pacific, and to ensure that Chagos remains a biodiversity hotspot and environment of international renown. Use of smaller surveillance vessels would facilitate this.Copyright © 2009 John Wiley & Sons, Ltd.

     

A historical feeding ground for humpback whales in the eastern South Pacific revisited: the case of northern Patagonia,Chile

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The abundance of common bottlenose dolphins (Tursiops truncatus) in the former special marine reserve of the Cres‐Lošinj Archipelago,Croatia

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Distribution and ecology of bigeye thresher Alopias superciliosus in the Pacific Ocean

We analyzed records of shark capture by tuna longline vessels during the period 1992–2006 to document the distribution and ecology of bigeye thresher in the Pacific Ocean. Catch per unit effort (CPUE) was highest in the area of 10–15°N in the north and 5–10°S in the south. Juveniles <150 cm were also distributed in this area. Seasonal changes in the distribution of abundance are thought to represent seasonal migrations in latitude. We observed an increase in the ratio of large individuals at high latitude, likely a result of their increased thermal capacity allowing them to migrate further. Males were captured more often than females, suggesting that there is segregation by sex. Pregnant females were observed from 0°N to 36°N in the north Pacific. Neonates were observed between 10–15°N/150–180°W, overlapping with the area in which large numbers of juveniles were captured. Thus, we hypothesize that this area represents the parturition and nursery grounds for bigeye thresher in this region.     

Forecasting of jack mackerel landings (Trachurus murphyi) in central‐southern Chile through neural networks

In the present study, the performance of neuronal networks models in monthly landing forecasting of jack mackerel (Trachurus murphyi) in central‐southern Chile (32°S–42°S) was assessed. Thus, monthly estimations for 10 environmental variables, fishing effort (fe) and jack mackerel landings for the period 1973–2008 were used. A preliminary analysis was done in order to remove strongly correlated variables. Sea surface temperature (SST) and fe are established as input variables, then, a non‐linear cross correlation analysis was performed to estimate the lag between the input variables and jack mackerel landings. Two models were adjusted: model one includes both training and testing cases randomly selected using all data involved in the analysed period; for model 2, the data is divided into two time series: the first from 1973 to 2002 used for training and the second between 2003 and 2008 used for validation. The external validation process for model 1 showed an explained variance of 92%, with a standard forecasting error of 30%. The explained variance for model 2 was 81%, with a standard forecasting error of 38%. Finally, the sensitivity analysis for both models showed the fe as the most influential variable to jack mackerel landings, which presents functionality depending on anthropogenic effects rather than environmental conditions.     

Observations on the influence of temperature on the length of embryonic development in Octopus vulgaris (Senegal)

Observations were made in Senegal between 1997–1998 on the length of embryonic development in Octopus vulgaris. The data were from eggs which had been laid by two females in the open sea and fourteen females in concrete tanks. The observations in natural surroundings are the first concerning this species. Hatching occurred after 15–42 d at 27 °C, 29–49 d at 22–23 °C, 57–65 d at 21 °C and 80–87 d at 17 °C. These values are higher than the few data previously recorded in European aquariums, particularly for temperatures under 20 °C.     

Dynamics of extinction of a small population of the three‐spined stickleback (Gasterosteus aculeatus L) caused by habitat modification

• 1. Abundance of a population of three‐spined stickleback, Gasterosteus aculeatus L., in a small backwater of Afon Rheidol in mid‐Wales (UK) was estimated annually each October from 1972 to 1999 by mark–recapture.
• 2. The population became extinct in 2000, because of land‐use changes in 1995, which modified the drainage pattern through the backwater, causing the backwater to eventually dry up.
• 3. The final decline to extinction started from an estimated abundance of 1550 in 1998 and the abundance in 1999, the year before extinction, was 85. The smallest abundance from which the population showed an increase was 670.
• 4. Two years before extinction (1998), the population was characterized by an anomalously high proportion of small fish.
• 5. There was a significant power relationship between the years to extinction and population size, but if the data were analysed in two periods, 1972–1989 and 1990–1999, the relationship was only significant for the second period.
• 6. There was no relationship between time to extinction and per capita annual rate of increase (k), although values of k were unusually low in the last two years before extinction.
• 7. Time to extinction was not related to mean length, mean mass or the condition of the fish.
• 8. The results suggest that the indicators of impending extinction may vary with the causes of extinction and may be ambiguous, even when a long time‐series of demographic data is available. Copyright © 2010 John Wiley & Sons, Ltd.

     

The influence of protection and temperature on subtropical reef fish assemblages in Cape Byron Marine Park

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From land and sea,long‐term data reveal persistent humpback whale (Megaptera novaeangliae) breeding habitat in New Caledonia

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Stock assessment of Japanese eels using Japanese abundance indices

The paper compiles a catch history of Japanese eels Anguilla japonica in East Asia and some Japanese relative abundance series. Maximum likelihood estimates of stock abundance of eels have been obtained using the abundance series and various biological parameters, such as growth, maturity and natural mortality. Age- and sex-structured models have been used to express the dynamics of stock abundance, and the Beverton and Holt model has been used to express the relationship between stock and recruitment. Data for estimations are standardized catch per unit effort of commercial fishery for exploitable stock (1954–2006 and 1968–2008) and for glass eel (1954–2010, 1972–2004, and 1973–1997). From the results of the base case scenario of estimations, the estimated stock size of individuals aged ≥1 year was 18.7 thousand tons in 2010, which was 24 % of the carrying capacity. The estimated stock size has recovered since 1990. Maximum sustainable yield was 4,180 tons if only the exploitable stock were utilized, and 266 tons if only the glass eel were utilized. These results and issues relating to estimation and management for reducing the fishery impact on stock are discussed.     

Abundance and genetic diversity of the red crab Pleuroncodes planipes along the western coast of the Baja California Peninsula, Mexico

This study reports the distribution, estimated abundance and biomass, and genetic population structure of the red crab Pleuroncodes planipes along the western coast of the Baja California Peninsula, Mexico. Using a hybrid conical net for fish and crustaceans, bottom trawls with stratified depth were performed at transect sites perpendicular to the coast. Red crab was observed to distribute widely in the study area, particularly in upwelling areas such as Bahia Magdalena and its surroundings, and the greatest catches were recorded at depths between 51 and 100 m, and between 201 and 300 m, with values of 2,297 and 3,223 kg/h of trawl, respectively. The population genetic analysis using mitochondrial DNA sequencing revealed no significant population differentiation. The total estimated biomass was 611,525 metric tons, supporting the proposal that the red crab is a viable exploitation resource in the study area.     

Using angling and electric fishing to estimate smallmouth bass abundance in a river

Estimating abundance is fundamental to effective fishery management but can be challenging in a river where spatial and temporal heterogeneity may preclude the consistent use of a single sampling gear and different gears have differing size selectivity and capture probabilities of fish. In this study, the number of smallmouth bass, Micropterus dolomieu Lacepède, was estimated based on mark–recapture data from angling and boat electric fishing in a 4.2‐km regulated section (mean width = 115 m) of the Broad River, South Carolina, USA. Closed‐population capture–mark–recapture models were fit in the Bayesian hierarchical modelling framework with an estimated number of 2,380 fish (95% credible interval: 1,578–3,693) over 200 mm TL, although simulations indicated that abundance would be slightly overestimated (<20%) when two gears selected for different individuals. Integrating two gear types into a mark–recapture study can provide a method for assessing abundance in spatially or temporally heterogeneous habitats.