Novel genetic data for conservation monitoring of the false catshark (Pseudotriakis microdon)

South American fur seals, Arctocephalus australis, were intensively hunted for centuries, leaving the species at the edge of extinction. After the cessation of commercial hunting in the 20th century the overall population has increased to an estimated population of 250 000–300 000 individuals, with Guafo Island being the largest breeding colony in Southern Chile with Guafo Island in Southern Chile being the largest breeding colony. The genetic diversity of the South American fur seal population on Guafo Island and the possible genetic connectivity among populations from the Atlantic and Pacific oceans were studied in order to assess the importance of the Southern Chile Pacific population for the management of the species. Mitochondrial DNA sequences from the Guafo Island population were compared with those from various Atlantic (Brazil, Uruguay, and Argentina) and Pacific (Peru) populations previously studied. The results indicate the occurrence of historical and/or current gene flow among the populations of Guafo Island in the Pacific Ocean and the populations of the Atlantic Ocean, displaying a lack of genetic structure within these areas. In contrast, the Peruvian population is highly divergent compared with the Chilean and Atlantic populations. The lack of genetic structure of Guafo Island fur seals suggests that this group is connected to populations in the Atlantic Ocean. Thus, the significant genetic diversity pool harboured by the Guafo Island population represents the northernmost point of expansion of this species from the Atlantic Ocean to the Pacific Ocean, which could be important for the eventual dispersal of the species to more northern areas of the Pacific and to the future adaptation of the species to changing environmental conditions on the Pacific coasts.

Zooxanthellate corals live in symbiosis with phototrophic dinoflagellates of the family Symbiodiniaceae, enabling the host coral to dwell in shallow, nutrient-poor marine waters. The South Atlantic Ocean is characterized by low coral diversity with high levels of endemism. However, little is known about coral–dinoflagellate associations in the region. This study examined the diversity of Symbiodiniaceae associated with the scleractinian coral Favia gravida across its distributional range using the ITS-2 marker. This brooding coral endemic to the South Atlantic can be found across a wide range of latitudes and longitudes, including the Mid-Atlantic islands. Even though it occurs primarily in shallower environments, F. gravida is among the few coral species that live in habitats with extreme environmental conditions (high irradiance, temperature, and turbidity) such as very shallow tide pools. In the present study, we show that F. gravida exhibits some degree of flexibility in its symbiotic association with zooxanthellae across its range. F. gravida associates predominantly with Cladocopium C3 (ITS2 type Symbiodinium C3) but also with Symbiodinium A3, Symbiodinium linucheae (ITS2 type A4), Cladocopium C1, Cladocopium C130, and Fugacium F3. Symbiont diversity varied across biogeographic regions (Symbiodinium A3 and S. linucheae were found in the Tropical Eastern Atlantic, Cladocopium C1 in the Mid-Atlantic, and other subtypes in the Southwestern Atlantic) and was affected by local environmental conditions. In addition, Symbiodiniaceae diversity was highest in a southwestern Atlantic oceanic island (Rocas Atoll). Understanding the relationship between corals and their algal symbionts is critical in determining the factors that control the ecological niches of zooxanthellate corals and their symbionts, and identifying host-symbiont pairs that may be more resistant to environmental changes.

Some top predator populations in the South Atlantic and South Indian oceans are in decline, presumably contingent upon reduced food availability, precipitated by climate change. This phenomenon impacts on the positions of major ocean frontal zones which are hypothesised to act as natural dispersal borders for fish in the Southern Ocean. We investigate this hypothesis by establishing the fish diet of sub-Antarctic fur seals, Arctocephalus tropicalis, at Tristan da Cunha Island (37°15′S, 12°25′W) and Gough Island (40°19′S, 9°57′W), South Atlantic Ocean. The diets of these island populations, located on either side of the Subtropical Convergence, are compared with published dietary information from populations further south on islands located within the Polar Frontal Zone. To this end, fur seal scats were collected and analysed for remains of hard parts from prey in 2012–2013. The myctophid fish Gymnoscopelus piabilis, Protomyctophum tenisoni and Symbolophorus barnardi predominated in the diet. Lampichthys gemellarii, Myctophum aurolaternatum, S. barnardi and the Diaphus genus are recorded for the first time in the diet of A. tropicalis. Sub-Antarctic fur seal populations clustered around the Subtropical Convergence (~ 41°40′S), compared with those in the Polar Frontal Zone (~ 47°25′S to ~ 50°47′S), showed a considerable difference in the myctophid fish prey taken. The latitudinal differences in the fish diet of sub-Antarctic fur seals support suggestions that major frontal zones act as natural dispersal borders for fish in the Southern Ocean.

Phylogeography of the copepod Calanoides carinatus s.l. (Krøyer) reveals cryptic species and delimits C. carinatus s.s. distribution in SW Atlantic Ocean

Nuclear deoxyribonucleic acid sequences from approximately 15,000 salmon louse expressed sequence tags (ESTs), the complete mitochondrial genome (16,148bp) of salmon louse, and 16S ribosomal ribonucleic acid (rRNA) and cytochrome oxidase subunit I (COI) genes from 68 salmon lice collected from Japan, Alaska, and western Canada support a Pacific lineage of Lepeophtheirus salmonis that is distinct from that occurring in the Atlantic Ocean. On average, nuclear genes are 3.2% different, the complete mitochondrial genome is 7.1% different, and 16S rRNA and COI genes are 4.2% and 6.1% different, respectively. Reduced genetic diversity within the Pacific form of L. salmonis is consistent with an introduction into the Pacific from the Atlantic Ocean. The level of divergence is consistent with the hypothesis that the Pacific form of L. salmonis coevolved with Pacific salmon (Onchorhynchus spp.) and the Atlantic form coevolved with Atlantic salmonids (Salmo spp.) independently for the last 2.5-11 million years. The level of genetic divergence coincides with the opportunity for migration of fish between the Atlantic and Pacific Ocean basins via the Arctic Ocean with the opening of the Bering Strait, approximately 5 million years ago. The genetic differences may help explain apparent differences in pathogenicity and environmental sensitivity documented for the Atlantic and Pacific forms of L. salmonis.

Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by seven different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcrA gene sequencing coupled with metagenomic analyses. Based on 16S rRNA gene amplicon analyses, these sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and -2 archaeal clades were abundant in the carbonates yet their typical syntrophic partners, sulfate-reducing bacteria, were not significantly present. Based on mcrA amplicon analyses, the Candidatus Methanoperedens clades were also highly abundant. Our metagenome analysis indicated that methane oxidizers affiliated to the ANME-1 and -2, may be capable of performing complete methane- and potentially short-chain alkane oxidation independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds and may be involved in syntrophy with methane-oxidizing archaea. Carbonate structures represent a window for a more diverse utilization of electron acceptors for anaerobic methane oxidation along the Atlantic and Pacific Margin.

Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements.

A previous study detected mixing of two deeply split mtDNA clades (Clade I and Clade II) for Atlantic and Mediterranean populations of the medusozoanPelagia noctiluca. The north hemisphere glaciations and the Messinian salinity crisis have been proposed as the two main biogeographic events related to the isolation between the Atlantic Ocean and the Mediterranean Sea. We tested if the splitting time between Clade I and Clade II ofP. noctilucawas associated with one of these geological events. Our study was based on DNA sequence data of mitochondrial (COI and 16S ribosomal RNA) and nuclear (18S ribosomal RNA, internal transcribed spacer 1 and 5.8S ribosomal RNA) genes from populations of the Atlantic and Pacific Ocean and the Mediterranean Sea. The rise of the Isthmus of Panama was used to calibrate substitution rates for COI. This calibration was based on the detection of a shallow but significant genetic structure betweenP. noctilucapopulations from the Pacific and the Atlantic Oceans. Considering our calibration for COI, we refute a possible origin of Clades I and II during the Messinian salinity crisis. Our estimates suggest the origin for a putative common ancestor of Clades I and II around 2.57 Ma (with 95% 2.91–2.22 HPD), roughly corresponding to the Gelasian stage of the early Pleistocene. These alterations include changes in the sea level and oceanic currents at the Strait of Gibraltar and other regions of the Mediterranean basin, and could explain the origin of the twoP. noctilucaclades.

Quaternary glaciations affected the distribution of many species. Here, we investigate whether the Arctic represented a glacial refugium during the Last Glacial Maximum or an area of secondary contact following the ice retreat, by analyzing the genetic population structure of the thick-billed murre (Uria lomvia), a seabird that breeds throughout the North Atlantic, North Pacific and Arctic Oceans. The thick-billed murre is a species of socio-economic importance and faces numerous threats including hunting, oil pollution, gill netting, and climate change. We compared variation in the mitochondrial DNA (mtDNA) control region (n = 424), supplemented by 4 microsatellite loci (n = 445), among thick-billed murres sampled throughout their range. MtDNA data indicated that colonies comprise 4 genetically differentiated groups (Φst = 0.11-0.81): 1) Atlantic Ocean plus New Siberian Islands region, 2) Cape Parry, 3) Chukchi Sea, and 4) Pacific Ocean. Microsatellite variation differed between Atlantic and Pacific populations. Otherwise, little substructure was found within either ocean. Atlantic and Pacific populations appear to have been genetically isolated since the last interglacial period and should be considered separate evolutionary significant units for management. The Chukchi Sea and Cape Parry appear to represent areas of secondary contact, rather than arctic refugial populations.

The patterns of genetic differentiation and levels of genetic diversity among striped dolphin (Stenella coeruleoalba) populations from the North Atlantic Ocean (N=45 individuals) and the central and western Mediterranean Sea (N=78) were investigated using five polymorphic microsatellite loci. A North Pacific sample (N=14) was added as an out-group. Two of the markers were tetranucleotide repeats tested for the first time in this species. The Mediterranean, Atlantic and Pacific samples displayed a mean number of alleles per locus of 11.2, 13.4, and 9.6 respectively, suggesting a high but variable polymorphism across loci. The Mediterranean sample displayed particular characteristics: (i) the lowest allelic richness and expected heterozygosity (HeMediterranean=0.76, while HeAtlantic=0.83 and HePacific=0.85); (ii) a significant departure from Hardy–Weinberg equilibrium (P<0.001; FIS=0.050); and (iii) a significant linkage disequilibrium between two pairs of loci. These last two features, present neither in the Atlantic sample nor in the Pacific one, suggest that the western Mediterranean population might possibly be further subdivided. Significant genetic differentiation was detected between the Mediterranean and Pacific populations, and between the Mediterranean and Atlantic populations. However, pairwise Wright's FST was not significantly different from zero between the two geographically isolated Atlantic and Pacific populations.

Avicennia germinans L. is a widespread mangrove species occupying the west coast of Africa and the Atlantic and Pacific coasts of the Americas from the Bahamas to Brazil and Baja California to Peru. An amplified fragment length polymorphism (AFLP) molecular analysis was carried out to assess genetic architecture within this species and to evaluate the effects of the Atlantic Ocean and the Central American Isthmus (CAI) on population and regional genetic diversity and differentiation. In total, 349 polymorphic AFLP fragments were identified among 144 individuals from 14 populations from the east Atlantic, west Atlantic and east Pacific. Levels of genetic diversity varied considerably among populations, but were generally higher in populations from the east Atlantic. Regional differentiation between the Pacific coast and Atlantic populations was greater than between east and west Atlantic populations, suggesting that the CAI has had an important influence on population genetic structure in this species. The lower level of divergence of east Atlantic from west Atlantic populations suggests some dispersal across the Atlantic Ocean, although migration rates are probably low; Nm from GST equal to 0.41 and accumulation of private and rare alleles in the east Atlantic. Population differentiation did not appear to follow an isolation by distance model and has probably resulted from complex patterns of population bottlenecks, and founder events due to landscape changes during the Pleistocene, particularly in the west Atlantic. The molecular data provide no support for the treatment of east Atlantic populations as a separate species A. africana.

Southern Africa is a marine biodiversity hotspot that not only comprises faunal elements from the Atlantic and Indian Oceans, but also large numbers of endemic species. Using mitochondrial and nuclear DNA sequence data, we explored whether genetic structure in the endemic coastal goby Psammogobius knysnaensis, a species whose range straddles both biomes, is linked to the boundary between the two oceans. Subtle genetic structure was identified between Atlantic and Indian Ocean populations, with genetic diversity being lower in the Atlantic, and particularly on the west coast. Our results point to partial isolation between the populations associated with each biome that is most likely driven by the region’s oceanography, but unlike in other species, there is no evidence for distinct regional evolutionary lineages that are likely adapted to the environmental conditions prevalent in each region. The exclusive presence of P. knysnaensis in sheltered habitats (estuaries and lagoons) may protect this species from the severe impacts of cold water upwelling on the west coast.

Aim The life cycle of many organisms is all but fixed across their distribution range. Most commonly, populations respond to environmental variation by shifting the timing of reproductive events (phenology). More profoundly, populations may (partly) shift their mode of reproduction from sexual to asexual. Life cycle variation can impact reproductive success, gene flow, genetic diversity and, ultimately, the evolutionary trajectory of populations. Understanding the factors that influence life cycle variation is essential for grasping the biology and ecological roles of species. This study investigates the variation in life cycles and its effects on the genetic diversity of a brown seaweed, Dictyota , across its European range. Location North‐East Atlantic Ocean and the Mediterranean Sea. Taxon Dictyota dichotoma (Hudson) J.V. Lamouroux (Phaeophyceae, Dictyotales). Methods We monitored phenology, fertility and lifespan in Atlantic and Mediterranean populations at its northern and southern boundaries and used microsatellite markers to assess how these factors influence genetic and genotypic diversity. Results We observed significant differences in phenology, reproductive strategies and genetic diversity among northern and southern European populations. In Mediterranean populations, D. dichotoma exhibited sporophytic dominance with gametophytes being extremely rare, suggesting a shift towards asexual reproduction. In contrast, North‐East Atlantic populations displayed more pronounced seasonal reproductive patterns with higher frequencies of gametophytes, indicating predominant sexual reproduction. However, genetic analysis showed lower allelic richness and unique alleles in northern populations, whereas southern populations were genetically more diverse, reflecting historical biogeographic processes. Clonal reproduction was more pronounced in the Mediterranean populations, influencing the spatial genetic substructure and contributing to locally lower genotypic diversity compared to Atlantic populations. Main Conclusions Our findings demonstrate that life cycle variation and phenology in D. dichotoma are closely tied to regional environmental conditions and have significant implications for population structure and genetic diversity. Results highlight how shifts in reproductive strategies contribute to the evolutionary and ecological dynamics of marine macroalgae across biogeographical gradients.

Fitness of early life stages in F1 interspecific hybrids between Dicentrarchus labrax and D. punctatus

Stock identity of horse mackerel ( Trachurus trachurus) in the Northeast Atlantic and Mediterranean Sea: Integrating the results from different stock identification approaches