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The food and feeding ecology of the poorly known southern long-finned pilot whale (Globicephala melas edwardii) was investigated using ecological tracers (muscle and skin δ[sup.13]C and δ[sup.15]N, and total mercury, Hg) on individuals from two mass strandings together with at-sea observations of live animals in Kerguelen waters, southern Indian Ocean. Sightings of cetaceans from longliners over 9 years (2003-2012) emphasized the regular occurrence of pilot whales in slope waters surrounding the archipelago. Tissue δ[sup.13]C values (a proxy of consumer foraging habitat) suggest that pilot whales fed in slope waters and in oceanic subantarctic waters over the last months preceding stranding. Tissue δ[sup.15]N values and Hg concentration (dietary proxies) indicate a high trophic position (~4.7) for the pilot whales, likely corresponding to a mixed diet of fish and squid (not crustaceans) of undetennined species. Both skin and muscle Hg concentrations were positively and linearly correlated to individual size with no concomitant δ[sup.15]N changes, which can be interpreted as a progressive Hg accumulation in tissues of individuals throughout life with no parallel dietary shift. Skin and muscle Hg concentrations were linearly and positively related; hence, Hg skin could be used as a proxy of Hg concentration in muscle (a main Hg reservoir of the body). Kerguelen southern long-finned pilot whales were less Hg contaminated than most pilot whale populations studied so far, thus suggesting that they are not at a high risk to Hg-induced damages in the remote islands of the Southern Ocean., Introduction Understanding the role of cetaceans in the structure and functioning of ecosystems is directly linked to a better knowledge of their foraging ecology that is often difficult to assess [...]

Studies focusing on the effect of invasive species on the genetic diversity of native marine invertebrates remain scant. Here we report diversity among French populations of the intertidal gastropod Ocenebra erinacea (Linnaeus, 1758) sampled in the presence and absence of the invasive Ocenebra inornata (Recluz, 1851). Between 1999 and 2004, a total of 352 individuals of O. erinacea was collected from 15 sites (five of which had the invasive present) and was genotyped at the mitochondrial locus Cytochrome Oxidase 1 (cox1). No statistical difference was observed between polymorphism levels recorded within native populations exposed to the invasive, compared with populations sampled in the absence of O. inornata. No sign of native population decline was detected in response to the invader. While significant shifts in native O. erinacea population sizes have previously been reported in the literature, genetic effects may take longer to accumulate, or may be undetectable without a larger panel of genetic markers. By contrast, large genetic distances and significant population differentiation were recorded between Atlantic and Mediterranean O. erinacea samples, suggesting that these populations have distinct evolutionary histories. Comparison of genetic divergence within the closely related genus Nucella suggests that the Atlantic populations of O. erinacea and those from Thau Lagoon in the Mediterranean may belong to different species or subspecies. [ABSTRACT FROM AUTHOR]

We used mitochondrial DNA control region sequences to genetically identify to the species level 23 pilot whales (genus Globicephala) that stranded on the French coasts between 1996 and 2011. Genetic analysis complemented morphological diagnoses, often hampered by an overlap in morphological characters between the two species or incomplete measurements. Mitochondrial DNA data allowed identification of 21 long-finned pilot whales ( Globicephala melas) and two unusual stranding events of the more tropical species ( Globicephala macrorhynchus). In pilot whales as in most cetaceans, shifts in species range are expected to occur due to global climate change. In this context, our study contributes to the long-term monitoring of pilot whale stranding events, providing indirect information on species occurrence. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The article discusses a study which investigated the non-breeding spatial and temporal overlap between two subspecies of the black-tailed godwit Limosa limosa on the central Atlantic coast of France. Topics discussed include the differences in the wintering distribution of the species, the high proportion of juveniles among the individuals caught by mist-net throughout the winter period, and the significant predominance of males in both age classes.

Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.