Ana Cañadas

Using Hidden Markov Models to Deal with Availability Bias on Line Transect Surveys

We develop estimators for line transect surveys of animals that are stochastically unavailable for detection while within detection range. The detection process is formulated as a hidden Markov model with a binary state-dependent observation model that depends on both perpendicular and forward distances. This provides a parametric method of dealing with availability bias when estimates of availability process parameters are available even if series of availability events themselves are not. We apply the estimators to an aerial and a shipboard survey of whales, and investigate their properties by simulation. They are shown to be more general and more flexible than existing estimators based on parametric models of the availability process. We also find that methods using availability correction factors can be very biased when surveys are not close to being instantaneous, as can estimators that assume temporal independence in availability when there is temporal dependence.

The Devil We Don't Know: Investigating Habitat and Abundance of Endangered Giant Devil Rays in the North-Western Mediterranean Sea

The giant devil ray Mobula mobular, the only Mediterranean mobulid, is subject to mortality caused by directed and accidental captures in fisheries throughout the region. Whilst the combination of human impacts, limited range and a low reproductive potential is not inconsistent with its endangered listing, there are insufficient data to enable a quantitative assessment of trends. Without this, it is difficult to assess and prioritise threats and develop effective conservation actions. Using results from aerial surveys conducted between 2009 and 2014 over the Ligurian, Corsican, Sardinian, northern and central Tyrrhenian seas (626,228 km2), this study provides the first quantitative information on giant devil ray abundance and habitat choice in the western Mediterranean. Devil rays were observed in all seasons except winter, with their estimated abundance in the study area peaking in summer. The overall uncorrected mean density in the study area during summer was estimated at 0.0257 individuals km-2 (range: 0.017–0.044), resulting in a total abundance estimate of 6,092 (12.7%CV) individuals at the surface; once corrected for availability bias, this estimate indicates a summer presence of >12,700 devil rays in the study area. Rays were mostly observed alone even if occasionally, larger aggregations up to a maximum of 18 individuals were observed. Although observed throughout the study area, spatial modelling identified their preferred habitat to be over a broad strip connecting the Tuscan Archipelago to Eastern Sardinia, over a wide range of water depths ranging from 10 to 2000m. The observed seasonal changes in giant devil ray distribution in this study, combined with similar evidence from other areas in the Mediterranean, support the hypothesis that the species undertakes latitudinal migrations across the region, taking advantage of highly productive waters in the north during summer, and warmer southern waters during winter.

New insights into ocean sunfish ( Mola mola ) abundance and seasonal distribution in the northeast Atlantic

The ocean sunfish, Mola mola, is the largest teleost fish in the world. Despite being found in all oceans of the world, little is known about its abundance and factors driving its distribution. In this study we provide the first abundance estimates for sunfish in offshore waters in the northeast Atlantic and the first record of extensive sunfish presence in these waters year-round. Abundance estimates and predictive distributions for sunfish in approximately 300,000 km² of the northeast Atlantic were derived from large scale offshore aerial surveys in 2015–2016 using distance sampling techniques. Generalized additive models of sunfish density were fitted to survey data from 17,360 km of line transect effort resulting in minimum abundance estimates of 12,702 (CI: 9,864-16,357) in the summer (Density = 0.043 ind/km²) and 8,223 individuals (CI: 6,178-10,946) (Density = 0.028 ind/km²) in the winter. Density surface models predicted seasonal shifts in distribution and highlighted the importance of the mixed layer depth, possibly related to thermoregulation following deep foraging dives. The abundance estimate and estimated daily consumption of 2,600 tonnes of jellyfish in the northeast Atlantic highlights the need to re-assess the importance of this species in the pelagic ecosystem, and its role in top-down control of jellyfish blooms.

Conservation Status of Long-Finned Pilot Whales, Globicephala melas, in the Mediterranean Sea

Mediterranean Sea long-finned pilot whales (Globicephala melas) are currently classified as Data Deficient on the International Union for the Conservation of Nature (IUCN) Red List. Multiple lines of evidence, including molecular genetic and photo-identification mark-recapture analyses, indicate that the Strait of Gibraltar population (distributed from 5.8°W longitude to west of Djibouti Bank and Alborán Dorsal in the Alborán Sea) is differentiated from the Mediterranean Sea population (east of Djibouti Bank and the Alborán Dorsal up to the Ligurian Sea). There is low genetic diversity within the Mediterranean population, and recent gene flow with the Strait of Gibraltar population is restricted. Current total abundance estimates are lacking for the species in the Mediterranean. Pilot whales in the Alborán Sea region were negatively affected by a morbillivirus epizootic from 2006 to 2007, and recovery may be difficult. The Strait of Gibraltar population, currently estimated to be fewer than 250 individuals, decreased by 26.2% over 5 years after the morbillivirus epizootic. Population viability analyses predicted an 85% probability of extinction for this population over the next 100 years. Increasing maritime traffic, increased contaminant burdens, and occasional fisheries interactions may severely impair the capacity of the Strait of Gibraltar population to recover after the decline due to the pathogen.

A short review of the distribution of short-beaked common dolphins ( Delphinus delphis ) in the central and eastern North Atlantic with an abundance estimate for part of this area

This paper uses data from 3 programmes: (1) the North Atlantic Sightings Surveys (NASS) surveys undertaken throughout much of the central and eastern North Atlantic north of about 40° N in 1987, 1989, 1995 and 2001; (2) the MICA-93 programme; and (3) the north eastern Atlantic segment of the Small Cetacean Abundance in the North Sea (SCANS) survey in 1994. The data from all surveys were used to examine the distribution of common dolphins in the NE Atlantic. No sightings were made north of 57° N. An initial attempt to examine distribution against 4 potential non biological explanatory variables was made. A simple interpretation of the preliminary analyses presented here is that the primary areas for groups of common dolphins were in waters over 15° C and depths of 400-1,000 m (there does appear a link with shelf features), between around 49°-55° N especially between 20°-30°W. An illustrative example of spatial modelling is presented. Only for 1 year (and part of the total survey area) were there sufficient data to attempt to estimate abundance: 1995. The estimated abundance in the W Block of the NASS-95 Faroese survey was 273,159 (cv=0.26; 95% CI=153,392-435,104) short-beaked common dolphins. This estimate is corrected for animals missed on the trackline ( g (0)) and for responsive movement.

Canine mammary tumor risk is associated with polymorphisms in RAD51 and STK11 genes

Cancer is a complex disease involving genetic and phenotypic changes. Several single nucleotide polymorphisms (SNPs) have been associated with the risk of breast cancer development in women; however, little is known regarding their influence on canine mammary tumor risk. We assessed the influence of SNPs in genes related to human breast cancer susceptibility, with respect to the risk of development of mammary tumors in dogs. Sixty-seven canine SNPs in proto-oncogenes, tumor suppressor genes, genes involved in DNA repair, and in hormonal metabolism were evaluated in 212 bitches with mammary tumors and in 161 bitches free of mammary neoplasia. A significant association with mammary neoplasia risk was identified for 2 SNPs in RAD51 (rs23623251 and rs23642734) and one SNP in the STK11 gene (rs22928814). None of the other SNPs were related to the risk of mammary tumor development. The identification of genetic profiles associated with risk of mammary neoplasia is of great importance, supporting the implementation of specific clinical management strategies in high-risk animals.

Using tagging data and aerial surveys to incorporate availability bias in the abundance estimation of blue sharks (Prionace glauca)

There is worldwide concern about the status of elasmobranchs, primarily as a result of overfishing and bycatch with subsequent ecosystem effects following the removal of top predators. Whilst abundant and wide-ranging, blue sharks (Prionace glauca) are the most heavily exploited shark species having suffered marked declines over the past decades, and there is a call for robust abundance estimates. In this study, we utilized depth data collected from two blue sharks using pop-up satellite archival tags, and modelled the proportion of time the sharks were swimming in the top 1-meter layer and could therefore be detected by observers conducting aerial surveys. The availability models indicated that the tagged sharks preferred surface waters whilst swimming over the continental shelf and during daytime, with a model-predicted average proportion of time spent at the surface of 0.633 (SD = 0.094) for on-shelf, and 0.136 (SD = 0.075) for off-shelf. These predicted values were then used to account for availability bias in abundance estimates for the species over a large area in the Northeast Atlantic, derived through distance sampling using aerial survey data collected in 2015 and 2016 and modelled with density surface models. Further, we compared abundance estimates corrected with model-predicted availability to uncorrected estimates and to estimates that incorporated the average time the sharks were available for detection. The mean abundance (number of individuals) corrected with modelled availability was 15,320 (CV = 0.28) in 2015 and 11,001 (CV = 0.27) in 2016. Depending on the year, these estimates were ~7 times higher compared to estimates without the bias correction, and ~3 times higher compared to the abundances corrected with average availability. When the survey area contains habitat heterogeneity that may affect surfacing patterns of animals, modelling animals’ availability provides a robust alternative to correcting for availability bias and highlights the need for caution when applying “average” correction factors.

What is your diagnosis? Cutaneous ulcerated nodule in a geriatric dog

A 17-year-old male Beagle with a history of 2 cutaneous grade II mastocytomas and a cutaneous plasmacytoma (on the pinna) was referred to the veterinarian with a rapidly growing, exophytic, and ulcerated cutaneous nodule on the ventral abdomen. Physical examination revealed no other cutaneous lesion(s) and no lymphadenopathy. The CBC was unremarkable except for a mild lymphopenia (0.97 9 10/L, RI 1.0– 4.8 9 10/L), likely related to a stress response. Biochemical analysis and protein electrophoresis were unremarkable. In bone marrow smears, the cellular morphology of all 3 series and their maturation stages were unremarkable. Fine-needle aspiration of the nodule was performed and smears were stained with Hemacolor (Merck, Darmstadt, Germany) (Figure 1). A