Molecular analysis of the efficiency of sloughed skin sampling in whale population genetics

Relationship between skin and body condition in three species of baleen whales

The assessment of free-ranging cetacean health through the study of skin conditions using photographs has gained prominence in recent years. However, little attention has been given to the relationships between cetacean skin conditions, species, and body condition. To explore this relationship among baleen whale species along the northwestern coast of Spain, we employed a non-invasive method involving photograph analysis. In this study, we examined skin conditions (including injuries, epizoites and ectoparasites, pigmentation disorders, skin lesions, and anatomical malformations) and body condition (overall physical contours and form, as an indicator of nutritional status and health) in 3 species of whales (blue, fin, and minke whales). This methodology facilitated the identification of 29 subcategories of distinct skin conditions and an assessment of body condition over a 5 yr period (2017 to 2021). In our study, we present evidence linking hypopigmentation, protruding pieces of tissue, and tattoo-like lesions to 'Poor' body condition in the 3 baleen whale species. Fin whales exhibited a higher susceptibility to mottling (prevalence = 17.7%), while blue whales were more prone to starbursts (prevalence = 90.5%). Additionally, we found a significant relationship between skin condition diversity and individual body condition. Our findings contribute valuable information to the broader understanding of the health status of baleen whales. Further investigations are necessary to delve into the etiology of the documented skin conditions and their potential implications for individual survival. This study serves as a foundation for ongoing research aimed at advancing our comprehension of these findings.

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.

Endo- and ectoparasites of large whales (Cetartiodactyla: Balaenopteridae, Physeteridae): Overcoming difficulties in obtaining appropriate samples by non- and minimally-invasive methods

Baleen and sperm whales, belonging to the Order Cetartiodactyla, are the largest and heaviest existent mammals in the world, collectively known as large whales. Large whales have been subjected to a variety of conservation means, which could be better monitored and managed if physiological and pathophysiological information, such as pathogen infections, could already be gathered from free-swimming animals instead of carcasses. Parasitic diseases are increasingly recognized for their profound influences on individual, population, and even ecosystem health. Furthermore, a number of parasite species have gained importance as opportunistic neozoan infections in the marine environment. Nonetheless, traditional approaches to study parasitic diseases have been impractical for large whales, since there is no current routine method for the capture and handling of these large animals and there is presently no practical method to obtain blood samples remotely from free-ranging whales. Therefore, we here not only intend to review the endo- and ectoparasite fauna of large whales but also to provide new insights in current available methods for gathering parasitological data by using non- or minimally invasive sampling techniques. We focus on methods, which will allow detailed parasitological studies to gain a broader knowledge on parasitoses affecting wild, free-swimming large whale populations.

Overcoming the challenges of studying conservation physiology in large whales: a review of available methods

Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples ('blow'), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.

Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.

Social structure in migrating humpback whales (Megaptera novaeangliae)

Although largely solitary, humpback whales exhibit a number of behaviours where individuals co-operate with one another, for example during bubble net feeding. Such cases could be due to reciprocal altruism brought on by exceptional circumstances, for example the presence of abundant shoaling fish. An alternative explanation is that these behaviours have evolved through kin selection. With little restriction to either communication or movement, diffuse groups of relatives could maintain some form of social organization without the need to travel in tight-nit units. To try to distinguish between these hypotheses, we took advantage of the fact that migrating humpback whales often swim together in small groups. If kin selection is important in humpback whale biology, these groups should be enriched for relatives. Consequently, we analysed biopsy samples from 57 groups of humpback whales migrating off Eastern Australia in 1992. A total of 142 whales were screened for eight microsatellite markers. Mitochondrial DNA sequences (371 bp) were also used to verify and assist kinship identification. Our data add support to the notion that mothers travel with their offspring for the first year of the calf's life. However, beyond the presence of mother-calf/yearling pairs, no obvious relatedness pattern was found among whales sampled either in the same pod or on the same day. Levels of relatedness did not vary between migratory phases (towards or away from the breeding ground), nor between the two sexes considered either overall or in the north or south migrations separately. These findings suggest that, if any social organization does exist, it is formed transiently when needed rather than being a constant feature of the population, and hence is more likely based on reciprocal altruism than kin selection.