Two cetacean species reveal different long-term trends for toxic trace elements in European Atlantic French waters.

Cetaceans have been naturally exposed to toxic trace elements (TEs) on an evolutionary time scale. Hence, they have developed mechanisms to control and/or mitigate their toxic effects. These long-lived species located at high trophic positions and bioaccumulating toxic elements are assumed to be good biomonitoring organisms. However, anthropogenic emissions have strongly increased environmental levels of toxic TEs in the last decades, questioning the efficiency of the detoxication mechanisms in cetaceans. In this context, temporal trends of mercury (Hg), cadmium (Cd) and lead (Pb) concentrations were studied through the analysis of 264 individuals from two cetacean species the common dolphin (Delphinus delphis) and the harbour porpoise (Phocoena phocoena) and belonging to two different Management Units (MUs) for the latter. These individuals stranded along the French Atlantic coasts from 2000s to 2017. All the trends presented were age- and sex-corrected and stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) were measured as proxies of their feeding ecology. Results showed that Pb concentrations clearly decreased over time in both species and MUs. This decrease agrees with the lead petrol regulation after 2000s, supporting the use of these species as valuable bioindicators of changes for TE levels in the marine environment. A significant long-term increase of total Hg concentrations was only observed in common dolphins. Cadmium concentrations also revealed different trends over the period in both species. The different Hg and Cd trends observed in the two species, probably reflected a contrasted contamination of habitat and prey species than a global increase of the contamination in the environment. These results highlight the necessity and gain of using different species to monitor changes in marine environments, each of them informing on the contamination of its own ecological niche. Lastly, the Se:Hg molar ratios of species suggested a low risk for Hg toxicity over time.

Postglacial Colonization of Northern Coastal Habitat by Bottlenose Dolphins: A Marine Leading-Edge Expansion?

Oscillations in the Earth's temperature and the subsequent retreating and advancing of ice-sheets around the polar regions are thought to have played an important role in shaping the distribution and genetic structuring of contemporary high-latitude populations. After the Last Glacial Maximum (LGM), retreating of the ice-sheets would have enabled early colonizers to rapidly occupy suitable niches to the exclusion of other conspecifics, thereby reducing genetic diversity at the leading-edge. Bottlenose dolphins (genus Tursiops) form distinct coastal and pelagic ecotypes, with finer-scale genetic structuring observed within each ecotype. We reconstruct the postglacial colonization of the Northeast Atlantic (NEA) by bottlenose dolphins using habitat modeling and phylogenetics. The AquaMaps model hindcasted suitable habitat for the LGM in the Atlantic lower latitude waters and parts of the Mediterranean Sea. The time-calibrated phylogeny, constructed with 86 complete mitochondrial genomes including 30 generated for this study and created using a multispecies coalescent model, suggests that the expansion to the available coastal habitat in the NEA happened via founder events starting ~15 000 years ago (95% highest posterior density interval: 4 900-26 400). The founders of the 2 distinct coastal NEA populations comprised as few as 2 maternal lineages that originated from the pelagic population. The low effective population size and genetic diversity estimated for the shared ancestral coastal population subsequent to divergence from the pelagic source population are consistent with leading-edge expansion. These findings highlight the legacy of the Late Pleistocene glacial cycles on the genetic structuring and diversity of contemporary populations.

Killer whale genomes reveal a complex history of recurrent admixture and vicariance.

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

Beached bachelors: An extensive study on the largest recorded sperm whale Physeter macrocephalus mortality event in the North Sea.

Between the 8th January and the 25th February 2016, the largest sperm whale Physeter macrocephalus mortality event ever recorded in the North Sea occurred with 30 sperm whales stranding in five countries within six weeks. All sperm whales were immature males. Groups were stratified by size, with the smaller animals stranding in the Netherlands, and the largest in England. The majority (n = 27) of the stranded animals were necropsied and/or sampled, allowing for an international and comprehensive investigation into this mortality event. The animals were in fair to good nutritional condition and, aside from the pathologies caused by stranding, did not exhibit significant evidence of disease or trauma. Infectious agents were found, including various parasite species, several bacterial and fungal pathogens and a novel alphaherpesvirus. In nine of the sperm whales a variety of marine litter was found. However, none of these findings were considered to have been the primary cause of the stranding event. Potential anthropogenic and environmental factors that may have caused the sperm whales to enter the North Sea were assessed. Once sperm whales enter the North Sea and head south, the water becomes progressively shallower (<40 m), making this region a global hotspot for sperm whale strandings. We conclude that the reasons for sperm whales to enter the southern North Sea are the result of complex interactions of extrinsic environmental factors. As such, these large mortality events seldom have a single ultimate cause and it is only through multidisciplinary, collaborative approaches that potentially multifactorial large-scale stranding events can be effectively investigated.

Ultrastructure of the Odontocete organ of Corti: scanning and transmission electron microscopy.

The morphological study of the Odontocete organ of Corti, together with possible alterations associated with damage from sound exposure, represents a key conservation approach to assess the effects of acoustic pollution on marine ecosystems. By collaborating with stranding networks from several European countries, 150 ears from 13 species of Odontocetes were collected and analyzed by scanning (SEM) and transmission (TEM) electron microscopy. Based on our analyses, we first describe and compare Odontocete cochlear structures and then propose a diagnostic method to identify inner ear alterations in stranded individuals. The two species analyzed by TEM (Phocoena phocoena and Stenella coeruleoalba) showed morphological characteristics in the lower basal turn of high-frequency hearing species. Among other striking features, outer hair cell bodies were extremely small and were strongly attached to Deiters cells. Such morphological characteristics, shared with horseshoe bats, suggest that there has been convergent evolution of sound reception mechanisms among echolocating species. Despite possible autolytic artifacts due to technical and experimental constraints, the SEM analysis allowed us to detect the presence of scarring processes resulting from the disappearance of outer hair cells from the epithelium. In addition, in contrast to the rapid decomposition process of the sensory epithelium after death (especially of the inner hair cells), the tectorial membrane appeared to be more resistant to postmortem autolysis effects. Analysis of the stereocilia imprint pattern at the undersurface of the tectorial membrane may provide a way to detect possible ultrastructural alterations of the hair cell stereocilia by mirroring them on the tectorial membrane.

Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator.

Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation ('pelagic' and 'coastal') of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species.

Harbour porpoises (Phocoena phocoena) stranded along the southern North Sea: an assessment through metallic contamination.

Throughout the last few years, the southern North Sea has witnessed an increase in the number of stranded marine mammals, particularly the harbour porpoise (Phocoena phocoena). This species is subject to several potential threats such as exposure to contaminants, changes in food supply, marine traffic and fishery by-catch. The aims of this study were to investigate potential associations between contaminants and health status and to analyze spatial and temporal trends of metal concentrations in harbour porpoises. Selected trace elements (As, Cd, Cr, Cu, Hg, Mn, Se, V and Zn) were measured in kidneys and livers of 105 harbour porpoises stranded along the southern North Sea (French and Belgian coasts from 2006 to 2013) and 27 stranded along the Bay of Biscay (French coast from 2009 to 2012). Porpoises that died from infectious disease displayed significant higher hepatic concentrations of Cd, Hg, Se and Zn compared to healthy porpoises that died from physical trauma. Adult porpoises displayed significant higher concentrations of Cd, Cr, Hg, Se and V in livers compared to juveniles. No spatial or temporal trends in metal concentrations were detected in our study. The results of the present study suggested that chemical contamination may represent one of many threats encountered by harbour porpoises, but it cannot explain alone the increase in the number of stranded individuals.

Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic.

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.

Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans.

Restriction-site-associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbour porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analysing individuals from the distinct families compared with analyses restricted to intraspecific comparisons (i.e. within D. delphis). Despite relatively stringent quality filters, 3595 polymorphic loci were retrieved from our interfamilial comparison. Cetaceans have undergone rapid diversification, and the estimated divergence time between the two families is relatively recent (14-19 Ma). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions.

The stranding anomaly as population indicator: the case of harbour porpoise Phocoena phocoena in North-Western Europe.

Ecological indicators for monitoring strategies are expected to combine three major characteristics: ecological significance, statistical credibility, and cost-effectiveness. Strategies based on stranding networks rank highly in cost-effectiveness, but their ecological significance and statistical credibility are disputed. Our present goal is to improve the value of stranding data as population indicator as part of monitoring strategies by constructing the spatial and temporal null hypothesis for strandings. The null hypothesis is defined as: small cetacean distribution and mortality are uniform in space and constant in time. We used a drift model to map stranding probabilities and predict stranding patterns of cetacean carcasses under H0 across the North Sea, the Channel and the Bay of Biscay, for the period 1990-2009. As the most common cetacean occurring in this area, we chose the harbour porpoise Phocoena phocoena for our modelling. The difference between these strandings expected under H0 and observed strandings is defined as the stranding anomaly. It constituted the stranding data series corrected for drift conditions. Seasonal decomposition of stranding anomaly suggested that drift conditions did not explain observed seasonal variations of porpoise strandings. Long-term stranding anomalies increased first in the southern North Sea, the Channel and Bay of Biscay coasts, and finally the eastern North Sea. The hypothesis of changes in porpoise distribution was consistent with local visual surveys, mostly SCANS surveys (1994 and 2005). This new indicator could be applied to cetacean populations across the world and more widely to marine megafauna.