Innovative monitoring scheme adapted to remote, scattered nesting aggregation reveals a major loggerhead turtle rookery in New Caledonia, South Pacific.

The loggerhead turtle Caretta caretta is a large marine turtle with a cosmopolitan repartition in warm and temperate waters of the planet. The South Pacific subpopulation is classified as 'Critically Endangered' on the IUCN Red List, based on the estimated demographic decline. This precarious situation engages an urgent need to monitor nesting populations in order to highlight conservation priorities and to ensure their efficiency over time. New Caledonia encompasses a large number of micro and distant nesting sites, localized on coral islets widely distributed across its large lagoon. Adequately surveying nesting activities on those hard-to-reach beaches can prove to be challenging. As a result, important knowledge gaps prevail in those high-potential nesting habitats. For the first time, an innovative monitoring scheme was conducted to assess the intensity of nesting activities, considered as a proxy of the population size, on an exhaustive set of islets located in the 'Grand Lagon Sud' area. These data were analyzed using a set of statistical methods specially designed to produce phenology and nesting activity estimates using Bayesian methods. This analysis revealed that this rookery hosts a large nesting colony, with a mean annual estimate of 437 nests (95% Credible Interval = 328-582). These numbers exceed that of the previous estimated annual number of loggerhead turtle nests in New Caledonia, highlighting the exceptional nature of this area. Considering the fact that similar high-potential aggregations have been identified in other parts of New Caledonia, but failed to be comprehensively assessed to this day, we recommend carrying out this replicable monitoring scheme to other locations. It could allow a significant re-evaluation of the New Caledonian nesting population importance and, ultimately, of its prevailing responsibility for the protection of this patrimonial yet endangered species.

Extremely Low mtDNA Diversity and High Genetic Differentiation Reveal the Precarious Genetic Status of Dugongs in New Caledonia, South Pacific.

New Caledonia is home to one of the largest remaining populations of dugongs (Dugong dugon) and is located at the southeastern limit of the species range. Local knowledge suggests that current levels of removal due to anthropogenic pressures are unsustainable, whereas trends suggest an ongoing decline in the population. Considering this unfavorable conservation context, this study aimed to assess the New Caledonian dugong population's resilience by determining its level of genetic diversity and degree of isolation relative to other populations. Mitochondrial DNA (mtDNA) control region sequences (n = 55) collected from live and dead dugongs in New Caledonia were compared with a global data set of previously published sequences (n = 631) representing dugong populations throughout the species range. The New Caledonian dugong population displayed the lowest level of mtDNA diversity documented worldwide (3 haplotypes with 1-bp difference), suggesting a recent origin of the current population through limited colonization events. Population structure analyses indicate a strong genetic differentiation with all the putative populations represented in the global data set, including large neighboring Australian populations. These results show that the dugong population in New Caledonia is particularly isolated, fragile, and vulnerable to anthropogenic threats and diseases with low potential for resilience through incoming gene flow. Our findings call for an instant conservation response and consideration for IUCN population assessment to support the long-term survival of the New Caledonian dugong population.

Horizontal and vertical movements of humpback whales inform the use of critical pelagic habitats in the western South Pacific.

Humpback whales (Megaptera novaeangliae) are known for their nearshore distribution during the breeding season, but their pelagic habitat use patterns remain mostly unexplored. From 2016 to 2018, 18 humpback whales were equipped with depth-recording satellite tags (SPLASH10) to shed light on environmental and social drivers of seamount association around New Caledonia in the western South Pacific. Movement paths were spatially structured around shallow seamounts (<200 m). Indeed, two males stopped over the Lord Howe seamount chain during the first-ever recorded longitudinal transit between New Caledonia and the east coast of Australia. Residence time significantly increased with proximity to shallow seamounts, while dive depth increased in the vicinity of seafloor ridges. Most of the 7,986 recorded dives occurred above 80 m (88.5%), but deep dives (>80 m, max 616 m) were also recorded (11.5%), including by maternal females. Deep dives often occurred in series and were characterized by U-shapes suggesting high energy expenditure. This study provides new insights into the formerly overlooked use of pelagic habitats by humpback whales during the breeding season. Given increasing anthropogenic threats on deep sea habitats worldwide, this work has implications for the conservation of vulnerable marine ecosystems.

Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short-finned pilot whale.

Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short-finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally-distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.

Whales in warming water: Assessing breeding habitat diversity and adaptability in Oceania's changing climate.

In the context of a changing climate, understanding the environmental drivers of marine megafauna distribution is important for conservation success. The extent of humpback whale breeding habitats and the impact of temperature variation on their availability are both unknown. We used 19 years of dedicated survey data from seven countries and territories of Oceania (1,376 survey days), to investigate humpback whale breeding habitat diversity and adaptability to climate change. At a fine scale (1 km resolution), seabed topography was identified as an important influence on humpback whale distribution. The shallowest waters close to shore or in lagoons were favored, although humpback whales also showed flexible habitat use patterns with respect to shallow offshore features such as seamounts. At a coarse scale (1° resolution), humpback whale breeding habitats in Oceania spanned a thermal range of 22.3-27.8°C in August, with interannual variation up to 2.0°C. Within this range, both fine and coarse scale analyses of humpback whale distribution suggested local responses to temperature. Notably, the most detailed dataset was available from New Caledonia (774 survey days, 1996-2017), where encounter rates showed a negative relationship to sea surface temperature, but were not related to the El Niño Southern Oscillation or the Antarctic Oscillation from previous summer, a proxy for feeding conditions that may impact breeding patterns. Many breeding sites that are currently occupied are predicted to become unsuitably warm for this species (>28°C) by the end of the 21st century. Based on modeled ecological relationships, there are suitable habitats for relocation in archipelagos and seamounts of southern Oceania. Although distribution shifts might be restrained by philopatry, the apparent plasticity of humpback whale habitat use patterns and the extent of suitable habitats support an adaptive capacity to ocean warming in Oceania breeding grounds.

Interspecific Hybridization in Pilot Whales and Asymmetric Genetic Introgression in Northern Globicephala melas under the Scenario of Global Warming.

Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.

Resumption of traditional drive hunting of dolphins in the Solomon Islands in 2013.

The 'drive hunting' of dolphins has a long history in the Solomon Islands, specifically at the island of Malaita. In 2010, the most active village, Fanalei, suspended hunting in exchange for financial compensation from an international non-governmental organization but resumed hunting again in early 2013. Here, we report on a visit to Fanalei in March 2013 to document the species and number of dolphins killed in the renewed hunting. Detailed records for the 2013 hunting, up to the time of our visit, included at least 1500 pantropical spotted dolphins (Stenella attenuata), 159 spinner dolphins (Stenella longirostris) and 15 'bottlenose' dolphins, probably Tursiops truncatus. Molecular identification confirmed two of the species, pantropical spotted and spinner dolphins. A summary of all available records from 1976 to 2013 documented a minimum total of 15 454 dolphins killed by the Fanalei villagers alone. We also found the local price of a dolphin tooth had increased from about US$0.14 (SBD$1) in 2004 to about US$0.70 (SBD$5) in 2013. The large number of dolphins killed and the apparent incentive for future hunting offered by the increasing commercial value of teeth, highlight an urgent need to monitor hunts and assess the abundance and trends in local populations.

The evolving male: spinner dolphin (Stenella longirostris) ecotypes are divergent at Y chromosome but not mtDNA or autosomal markers.

The susceptibility of the Y chromosome to sexual selection may make this chromosome an important player in the formation of reproductive isolating barriers, and ultimately speciation. Here, we investigate the role of the Y chromosome in phenotypic divergence and reproductive isolation of spinner dolphin (Stenella longirostris) ecotypes. This species contains six known ecotypes (grouped into four subspecies) that exhibit striking differences in morphology, habitat and mating system, despite having adjacent or overlapping ranges and little genetic divergence at previously studied mtDNA and autosomal markers. We examined the phylogeographic structure for all six ecotypes across the species range (n = 261, 17 geographic locations) using DNA sequences from three Y chromosome markers, two maternally inherited mitochondrial (mtDNA) markers, and a biparentally inherited autosomal intron. mtDNA and autosomal analyses revealed low divergence (most Φ(ST) values <0.1) between ecotypes and geographic regions, concordant with previous studies. In contrast, Y intron analyses revealed fixed differences amongst the three most phenotypically divergent groups: S. l. longirostris vs. S. l. roseiventris vs. combined S. l. orientalis/S. l. centroamericana/Tres Marias ecotypes). Another ecotype (whitebelly), previously postulated to be a hybrid between the two phenotypically most divergent ecotypes, had Y haplotypes from both putative parent ecotypes, supporting a hybrid designation. Reduced introgression of the Y chromosome has previously been observed in other organisms ranging from insects to terrestrial mammals, and here we demonstrate this phenomenon in a marine mammal with high dispersal capabilities. These results indicate that reduced introgression of the Y chromosome occurs in a wide taxonomic range of organisms and support the growing body of evidence that rapid evolution of the Y chromosome is important in evolutionary diversification.

Genetic evidence of multiple matrilines and spatial disruption of kinship bonds in mass strandings of long-finned pilot whales, Globicephala melas.

Mass strandings of whales and dolphins have puzzled biologists since Aristotle. Although environmental factors are often assumed to initiate strandings, social forces must also influence the dynamics of many of these events, particularly for the primary species involved in mass strandings, the long-finned pilot whales (Globicephala melas). Here, we test two hypotheses derived from common assumptions about the social dynamics of long-finned pilot whales by identifying maternal lineages from mtDNA haplotypes and inferring kinship from microsatellite genotypes of 490 individuals from 12 stranding events. Contrary to the "extended matriline" hypothesis, we found that multiple maternal lineages were present in at least 9 of the 12 mass strandings. Contrary to the "kinship cohesion" hypothesis, we found no correlation between spatial distribution and kinship along the stranding beach. Most notably, we documented the spatial disruption of the expected proximity between mothers and their dependent calves. These results challenge the common assumption that kinship-based behavior, such as care-giving, are a primary factor in these mass strandings. We suggest instead that disruption of kinship bonds could result from interactions among unrelated social groups during feeding or mating aggregations, perhaps playing a causal role in these events. Our finding that dependent calves were often spatially separated or absent from their mothers has important implications for humane management of rescue efforts. To improve our understanding of the social causes and consequences of mass strandings, future documentation of strandings should include exhaustive DNA sampling, with accompanying spatial and temporal records.

A worldwide perspective on the population structure and genetic diversity of bottlenose dolphins (Tursiops truncatus) in New Zealand.

Bottlenose dolphins (Tursiops truncatus) occupy a wide range of coastal and pelagic habitats throughout tropical and temperate waters worldwide. In some regions, "inshore" and "offshore" forms or ecotypes differ genetically and morphologically, despite no obvious boundaries to interchange. Around New Zealand, bottlenose dolphins inhabit 3 coastal regions: Northland, Marlborough Sounds, and Fiordland. Previous demographic studies showed no interchange of individuals among these populations. Here, we describe the genetic structure and diversity of these populations using skin samples collected with a remote biopsy dart. Analysis of the molecular variance from mitochondrial DNA (mtDNA) control region sequences (n = 193) showed considerable differentiation among populations (F(ST) = 0.17, Phi(ST) = 0.21, P < 0.001) suggesting little or no female gene flow or interchange. All 3 populations showed higher mtDNA diversity than expected given their small population sizes and isolation. To explain the source of this variation, 22 control region haplotypes from New Zealand were compared with 108 haplotypes worldwide representing 586 individuals from 19 populations and including both inshore and offshore ecotypes as described in the Western North Atlantic. All haplotypes found in the Pacific, regardless of population habitat use (i.e., coastal or pelagic), are more divergent from populations described as inshore ecotype in the Western North Atlantic than from populations described as offshore ecotype. Analysis of gene flow indicated long-distance dispersal among coastal and pelagic populations worldwide (except for those haplotypes described as inshore ecotype in the Western North Atlantic), suggesting that these populations are interconnected on an evolutionary timescale. This finding suggests that habitat specialization has occurred independently in different ocean basins, perhaps with Tursiops aduncus filling the ecological niche of the inshore ecotype in some coastal regions of the Indian and Western Pacific Oceans.

Unconventional ventral attachment of time-depth recorders as a new method for investigating time budget and diving behaviour of seabirds.

We tested the use of commercially available electronic time-depth recorders (TDRs) to quantify activities and thus total time budgets of seabirds. This new method involved first fitting TDRs onto the birds' bellies (not on their backs), and, secondly, analysing continuous recordings of temperature, light and pressure to differentiate activities on land and at sea. The birds studied were 12 common guillemots (Uria aalge) rearing chicks at Hornøya, in northern Norway. The method successfully recorded five different activities: at the colony, flying, diving, and resting or active at the sea surface. Overall, common guillemots spent 68% of their time at the colony and 32% at sea. While at sea, the birds spent the majority (77%) of their time at the surface, during which they were active 64% of the time, and rested only 13%. Birds engaged in the costly behaviours of flying and diving for shorter times (11% and 12% of their time at sea, respectively). The method allowed us to differentiate between two types of trips to sea based on the presence (foraging trips: 77% of the total number of trips) or absence (non-foraging trips: 23%) of dives. On average, foraging trips lasted 3.2 h, but most trips were shorter (<1 h), during which the mean estimated travel distance from the colony was 11 km. Diving occurred in bouts of 7.7+/-6.6 dives (mean +/- S.D.). The mean maximum dive depth was 10.2+/-7.6 m (deepest dive: 37 m), and the mean dive duration and post-dive intervals were 38.7+/-21.3 s (longest dive: 119 s) and 20+/-12 s, respectively. Direct and indirect evidence suggests that common guillemots had no difficulty in finding food during the study period, and that the TDRs had minimal effects on the birds' behaviour and physiology. The method is easy to use in the field and is applicable to many other flying seabird species; it is therefore an efficient way of collecting information on time budgets and diving behaviour in the context of various ecological and monitoring studies.