Cytochrome b marker reveals an independent lineage of Stenella coeruleoalba in the Gulf of Taranto

The Validation of a Non-Invasive Skin Sampling Device for Detecting Cetacean Poxvirus

Simple Summary

The current growing social awareness of animal welfare has led to the development of welfare indicators, which are effective tools for assessing each of the integrated aspects of this multidisciplinary issue. Hence, skin diseases have been suggested as potential general health indicators for use in cetaceans. Particularly cetacean poxvirus causes distinguishable hyperpigmented “ring” or “tattoo” lesions that affect cetaceans both in the wild and in managed facilities. However, most studies have analyzed these characteristic lesions through visual appraisal, while only a few have implemented diagnostic methods to corroborate the presence of the virus. To this end, skin biopsies are usually the sampling method selected, although they are considered to be an intrusive procedure. In this study, we analyzed sloughed skin sampled with cytology cell samplers (CCSs) in 12 tattoo-like lesions from two free-ranging cetaceans stranded in the Canary Islands. We employed two different DNA extraction methods and compared the effectiveness of the device with that of biopsies. All the lesions resulted positive for cetacean poxvirus, obtaining reliable data from the use of this device. Thus, CCS is considered to be a promising non-invasive tool for further assessing skin diseases in cetaceans, particularly those under human care, without affecting their welfare.

Abstract

Poxvirus-like lesions are widely used as a potential health indicator in cetaceans, although for this application, corroboration of Poxvirus skin disease is imperative. Aiming to address skin biopsies intrusiveness, a preliminary investigation of a non-invasive skin sampling procedure to molecularly detect CePV-1 in 12 tattoo-like-lesions from two free-ranging stranded cetaceans in the Canary Islands was performed. Skin lesions were brushed with cytology cell samplers (CCSs) and placed into 1.5 mL microcentrifuge tubes with 1 mL of RNAlater^TM Stabilization Solution. For factual comparisons, DNA extractions from sloughed skin obtained with CCS and biopsies from the same lesions were accomplished with DNA Tissue Kit S^TM (QuickGene, Kurabo, Japan). Moreover, a second DNA extraction from sloughed skin with DNeasy^TM Blood and Tissue Kit (Qiagen, Inc., Valencia, CA, USA) was performed to ascertain kit suitability for CCS. Molecular detection of CePV-1 was performed through a real-time PCR. As a result, a 91.7% and 83.3% rates of positivity were obtained with biopsies and CCS through Quickgene, respectively, compared to the rate of 100% using CCS with Qiagen. Accordingly, CCS is a reliable non-invasive sampling device to obtain sufficient genetic material to be analyzed for CePV-1 in tattoo-skin-lesions as well as for other purposes in cetaceans under human care.

Managing multiple pressures for cetaceans' conservation with an Ecosystem-Based Marine Spatial Planning approach

Despite the recognized important ecological role that cetaceans play in the marine environment, their protection is still scarcely enforced in the Mediterranean Sea even though this area is strongly threatened by local human pressures and climate change. The piecemeal of knowledge related to cetaceans' ecology and distribution in the basin undermines the capacity of addressing cetaceans' protection and identifying effective conservation strategies. In this study, an Ecosystem-Based Marine Spatial Planning (EB-MSP) approach is applied to assess human pressures on cetaceans and guide the designation of a conservation area in the Gulf of Taranto, Northern Ionian Sea (Central-eastern Mediterranean Sea). The Gulf of Taranto hosts different cetacean species that accomplish important phases of their life in the area. Despite this fact, the gulf does not fall within any area-based management tools (ABMTs) for cetacean conservation. We pin down the Gulf of Taranto being eligible for the designation of diverse ABMTs for conservation, both legally and non-legally binding. Through a risk-based approach, this study explores the cause-effect relationships that link any human activities and pressures exerted in the study area to potential effects on cetaceans, by identifying major drivers of potential impacts. These were found to be underwater noise, marine litter, ship collision, and competition and disturbance on preys. We draw some recommendations based on different sources of available knowledge produced so far in the area (i.e., empirical evidence, scientific and grey literature, and expert judgement) to boost cetaceans' conservation. Finally, we stress the need of sectoral coordination for the management of human activities by applying an EB-MSP approach and valuing the establishment of an ABMT in the Gulf of Taranto.

The T Cell Receptor (TRB) Locus in Tursiops truncatus: From Sequence to Structure of the Alpha/Beta Heterodimer in the Human/Dolphin Comparison

The bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and, similarly to other cetaceans, represents the most successful mammalian colonization of the aquatic environment. Here we report a genomic, evolutionary, and expression study of T. truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3' end, its uniqueness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rearranged T cell receptor α (TRA) and TRB cDNA from the peripheral blood of one of the two specimens, and the human/dolphin amino acids multi-sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the complementarity-determining region according to IMGT numbering (CDR-IMGT) of the dolphin variable V-alpha and beta domains were identified. According to comparative modelization, the atom pair contact sites analysis between the human MH1 grove (G) domains and the T cell receptor (TR) V domains confirms conservation of the structure of the dolphin TR/pMH.

Combined Color Semantics and Deep Learning for the Automatic Detection of Dolphin Dorsal Fins

Photo-identification is a widely used non-invasive technique in biological studies for understanding if a specimen has been seen multiple times only relying on specific unique visual characteristics. This information is essential to infer knowledge about the spatial distribution, site fidelity, abundance or habitat use of a species. Today there is a large demand for algorithms that can help domain experts in the analysis of large image datasets. For this reason, it is straightforward that the problem of identify and crop the relevant portion of an image is not negligible in any photo-identification pipeline. This paper approaches the problem of automatically cropping cetaceans images with a hybrid technique based on domain analysis and deep learning. Domain knowledge is applied for proposing relevant regions with the aim of highlighting the dorsal fins, then a binary classification of fin vs. no-fin is performed by a convolutional neural network. Results obtained on real images demonstrate the feasibility of the proposed approach in the automated process of large datasets of Risso’s dolphins photos, enabling its use on more complex large scale studies. Moreover, the results of this study suggest to extend this methodology to biological investigations of different species.