The Bottlenose Dolphin Epigenetic Aging Tool (BEAT): A Molecular Age Estimation Tool for Small Cetaceans

Age constitutes a critical parameter for the study of animal populations, providing information about development, environmental effects, survival, and reproduction. Unfortunately, age estimation is not only challenging in large, mobile and legally protected species, but often involves invasive sampling methods. The present work investigates the association between epigenetic modifications and chronological age in small cetaceans. For that purpose, DNA methylation at age-linked genes was characterized in an extensively studied, long-term resident common bottlenose dolphin (Tursiops truncatus) community from Sarasota Bay (FL, United States) for which sampled individuals have a known age. Results led to the identification of several CpG sites that are significantly correlated to chronological age in this species with the potential for sex to play a role in the modulation of this correlation. These findings have allowed for the development and validation of the “Bottlenose dolphin Epigenetic Age estimation Tool” (BEAT), improving minimally-invasive age estimation in free-ranging small cetaceans. Overall, the BEAT proved to be accurate in estimating age in these organisms. Given its minimally-invasive nature and potential large-scale implementation using skin biopsy samples, this tool can be used to generate age data from free-ranging small cetacean populations

Recent expansion of marine protected areas matches with home range of grey reef sharks

Dramatic declines in reef shark populations have been documented worldwide in response to human activities. Marine Protected Areas (MPAs) offer a useful mechanism to protect these species and their roles in coral reef ecosystems. The effectiveness of MPAs notably relies on compliance together with sufficient size to encompass animal home range. Here, we measured home range of 147 grey reef sharks, Carcharhinus amblyrhynchos, using acoustic telemetry in New Caledonia. The distribution of home range was then compared to local MPA sizes. We report a home range of 12 km2 of reef for the species with strong differences between adult males (21 km2), adult females (4.4 km2) and juveniles (6.2 km2 for males, 2.7 km2 for females). Whereas local historic MPA size seemed adequate to protect reef shark home range in general, these were clearly too small when considering adult males only, which is consistent with the reported failure of MPAs to protect sharks in New Caledonia. Fortunately, the recent implementation of several orders of magnitude larger MPAs in New Caledonia and abroad show that recent Indo-Pacific MPAs are now sufficiently large to protect the home ranges of this species, including males, across its geographical range. However, protection efforts are concentrated in a few regions and cannot provide adequate protection at a global scale

Marine megafauna catch in southwestern Indian Ocean small-scale fisheries from landings data

The measurable impacts of small-scale fisheries on coastal marine ecosystems and vulnerable megafauna species (elasmobranchs, marine mammals and sea turtles) within them are largely unknown, particularly in developing countries. This study assesses megafauna catch and composition in handline, longline, bottom-set and drift gillnet fisheries of the southwestern Indian Ocean. Observers monitored 21 landing sites across Kenya, Zanzibar and northern Madagascar for 12 months in 2016–17. Landings (n = 4666) identified 59 species, including three sea turtles, two small cetaceans and one sirenian (Dugong dugon). Primary gear threats to investigated taxa were identified as bottom-set gillnets (marine mammals, sea turtles and batoids), drift gillnets (marine mammals, batoids and sharks) and longlines (sharks). Overall, catch was dominated by small and moderately sized coastal requiem sharks (Carcharhiniformes) and whiprays (Dasyatidae). Larger coastal and oceanic elasmobranchs were also recorded in substantial numbers as were a number of deeper-water species. The diversity of catch demonstrates the potential for small-scale fisheries to have impacts across a number of ecosystems. From the observed catch rates we calculated annual regional elasmobranch landings to be 35,445 (95%CI 30,478–40,412) tonnes, 72.6% more than officially reported in 2016 and 129.2% more than the 10-year average (2006–16), constituting 2.48 (95%CI 2.20–2.66) million individuals. Productivity-Susceptibility Analyses indicate that small and moderately sized elasmobranchs are most vulnerable in the small-scale fisheries. The study demonstrates substantial underreporting of catches in small-scale fisheries and highlights the need to expand efforts globally to assess the extent and impact of small-scale fisheries on vulnerable marine species and their respective ecosystems

Editorial: Small cetacean conservation: Current challenges and opportunities

Dolphins (oceanic and river dolphins; Delphinidae, Iniidae, Lipotidae, Pontoporiidae, Platanistidae) and porpoises (Phocoenidae) are the smallest members of the odontocete suborder. These species have colonized most aquatic ecosystems globally, from rivers to deep oceanic habitats, and from tropical to polar waters. Due to their habitat preferences, high metabolic rates, foraging behaviors, and diets, small cetaceans exhibit a wide range of ecological roles and functions across ecosystems where they occur and have the potential to affect communities via multiple pathways (top-down, bottom-up effects, and a range of behavior-mediated processes, Kiszka et al.). Dolphins and porpoises have also generated significant interest from the scientific community and more broadly by human societies since antiquity, with research on these animals increasing exponentially over the past 40-50 years. Despite protection by a range of international conventions (e.g., Convention on Migratory Species, Convention on the Trade of Endangered Species) and national legislation in most countries, some species are at increasing risk of decline and extirpation in aquatic habitats worldwide, with losses driven by a range of direct and indirect impacts from human activities. Today, more than 20% of species of oceanic dolphins, half of all species of porpoise, and all river dolphins are threatened with extinctionFil: Kiszka, Jeremy J.. Florida International University; Estados UnidosFil: Bejder, Lars. University of Hawaii at Manoa; Estados UnidosFil: Davis, Randall. Texas A&M University; Estados UnidosFil: Harcourt, Rob. Macquarie University; AustraliaFil: Meekan, Mark. University of Western Australia; AustraliaFil: Rodriguez, Diego Horacio. Universidad Nacional de Mar del Plata; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Stockin, Karen A.. Massey University; Nueva Zeland

Unexpected patterns of global population structure in melon-headed whales Peponocephala electra

Foraging specialization, environmental barriers, and social structure have driven the development of strong genetic differentiation within many marine species, including most of the large dolphin species commonly referred to as ‘blackfish’ (subfamily Globicephalinae). We used mitochondrial sequence data (mtDNA) and genotypes from 14 nuclear microsatellite loci (nDNA) to examine patterns of genetic population structure in melon-headed whales Peponocephala electra (MHWs), poorly known members of the blackfish family for which genetic structuring is unknown. MHWs are globally distributed in tropical and subtropical waters, and have formed resident populations around oceanic islands. They frequently mass strand, suggesting strong social cohesion within groups. Based on these characteristics, we hypothesized that MHWs would exhibit strong regional genetic differentiation, similar to that observed in other members of the Globicephalinae subfamily. Instead we found only moderate differentiation (median mtDNA ΦST = 0.204, median nDNA FST = 0.012) among populations both within and between ocean basins. Our results suggest that populations of MHWs that are resident to oceanic islands maintain a higher level of genetic connectivity than is seen in most other blackfish. MHWs may be more behaviorally similar to delphinids from the Delphininae subfamily (particularly the spinner dolphin Stenella longirostris), which are known to form coastal and island-associated resident populations that maintain genetic connectivity either through occasional long-distance dispersal or gene flow with larger pelagic populations. Our results suggest that differences in social organization may drive different patterns of population structure in social odontocete

Identifying barriers to gene flow and hierarchical conservation units from seascape genomics : a modelling framework applied to a marine predator

The ongoing decline of large marine vertebrates must be urgently mitigated, particularly under increasing levels of climate change and other anthropogenic pressures. However, characterizing the connectivity among populations remains one of the greatest challenges for the effective conservation of an increasing number of endangered species. Achieving conservation targets requires an understanding of which seascape features influence dispersal and subsequent genetic structure. This is particularly challenging for adult-disperser species, and when distribution-wide sampling is difficult. Here, we developed a two-step modelling framework to investigate how seascape features drive the genetic connectivity of marine species without larval dispersal, to better guide the design of marine protected area networks and corridors. We applied this framework to the endangered grey reef shark, Carcharhinus amblyrhynchos, a reef-associated shark distributed across the tropical Indo-Pacific. In the first step, we developed a seascape genomic approach based on isolation-by-resistance models involving circuit theory applied to 515 shark samples, genotyped for 4991 nuclear single-nucleotide polymorphisms. We show that deep oceanic areas act as strong barriers to dispersal, while proximity to habitat facilitates dispersal. In the second step, we predicted the resulting genetic differentiation across the entire distribution range of the species, providing both local and global-scale conservation units for future management guidance. We found that grey reef shark populations are more fragmented than expected for such a mobile species, raising concerns about the resilience of isolated populations under high anthropogenic pressures. We recommend the use of this framework to identify barriers to gene flow and to help in the delineation of conservation units at different scales, together with its integration across multiple species when considering marine spatial planning.Peer reviewe

Marine megafauna interactions with small-scale fisheries in the southwestern Indian Ocean: a review of status and challenges for research and management

In developing regions, coastal communities are particularly dependent on small-scale fisheries for food security and income. However, information on the scale and impacts of small-scale fisheries on coastal marine ecosystems are frequently lacking. Large marine vertebrates (marine mammals, sea turtles and chondrichthyans) are often among the first species to experience declines due to fisheries. This paper reviews the interactions between small-scale fisheries and vulnerable marine megafauna in the southwestern Indian Ocean. We highlight an urgent need for proper documentation, monitoring and assessment at the regional level of small-scale fisheries and the megafauna affected by them to inform evidence-based fisheries management. Catch and landings data are generally of poor quality and resolution with compositional data, where available, mostly anecdotal or heavily biased towards easily identifiable species. There is also limited understanding of fisheries effort, most of which relies on metrics unsuitable for proper assessment. Management strategies (where they exist) are often created without strong evidence bases or understanding of the reliance of fishers on resources. Consequently, it is not possible to effectively assess the current status and ensure the sustainability of these species groups; with indications of overexploitation in several areas. To address these issues, a regionally collaborative approach between government and non-governmental organisations, independent researchers and institutions, and small-scale fisheries stakeholders is required. In combination with good governance practices, appropriate and effective, evidence-based management can be formulated to sustain these resources, the marine ecosystems they are intrinsically linked to and the livelihoods of coastal communities that are tied to them

Caribbean Sea Soundscapes: Monitoring Humpback Whales, Biological Sounds, Geological Events, and Anthropogenic Impacts of Vessel Noise

Assessing marine soundscapes provides an understanding of the biological, geological and anthropogenic composition of a habitat, including species diversity, community composition, and human impacts. For this study, nine acoustic recorders were deployed between December 2016 and June 2017 off six Caribbean islands in several Marine Parks: the Dominican Republic (DR), St. Martin (SM), Guadeloupe east and west (GE, GW), Martinique (MA), Aruba (AR), and Bonaire (BO). Humpback whale song was recorded at five sites on four islands (DR, SM, GE, GW, and MA) and occurred on 49–93% of recording days. Song appeared first at the DR site and began 4–6 weeks later at GE, GW, and MA. No song was heard in AR and BO, the southernmost islands. A 2-week period was examined for the hourly presence of vessel noise and the number and duration of ship passages. Hourly vessel presence ranged from low (20% – DR, 30% – SM), medium (52% – MA, 54% – BO, 77% – GE) to near continuous (99% – GW; 100% – AR). Diurnal patterns were observed at BO, GE, and MA with few to no vessels present during night time hours, possibly reflecting the activity of recreational craft and fishing vessels. At the DR and GW sites, vessel traffic was ubiquitous for most of the day, likely reflecting heavy cruise ship and container ship presence. Soundscapes were diverse across islands with persistent fish choruses, sporadic sperm whale (Physeter macrocephalus) and dolphin (Delphinidae) presence at BO, minke whales (Balaenoptera acutorostrata) from late December to late February at MA and an earthquake recorded across all sites. These analyses provide an important first step in characterizing the health and species richness in Caribbean marine parks and demonstrate a surprising high anthropogenic foot print. Vessel traffic in particular contributes adversely to marine soundscapes, masking marine mammal sounds, potentially changing typical animal behavior and raising the risk of ship strike

Population genomics of the white beaked dolphin (Lagenorhynchus albirostris)::Implications for conservation amid climate driven range shifts

Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.</p