Characterization and isolation of DNA microsatellite primers in the spiny dogfish (Squalus acanthias)

The North Atlantic spiny dogfish (Squalus acanthias) population has been declining since the 1980s. Proper management of this population is essential as dogfish are prone to rapid collapse based on the unique biology of this species. We characterized eight microsatellite loci for spiny dogfish to use in determining the genetic structure of this species along the Atlantic coast of the USA.     

Evidence of multiple paternity in spiny dogfish (Squalus acanthias) broods based on microsatellite analysis

An understanding of alternative mating systems is a fundamental requirement for the effective management of vulnerable species. Microsatellite analysis of spiny dogfish Squalus acanthias broods from the north‐west Atlantic provides novel evidence of polyandry in this species.     

Phylogeography of a pan-Atlantic abyssal protobranch bivalve: implications for evolution in the Deep Atlantic

The deep sea is a vast and essentially continuous environment with few obvious barriers to gene flow. How populations diverge and new species form in this remote ecosystem is poorly understood. Phylogeographical analyses have begun to provide some insight into evolutionary processes at bathyal depths (<3000 m), but much less is known about evolution in the more extensive abyssal regions (>3000 m). Here, we quantify geographical and bathymetric patterns of genetic variation (16S rRNA mitochondrial gene) in the protobranch bivalve Ledella ultima, which is one of the most abundant abyssal protobranchs in the Atlantic with a broad bathymetric and geographical distribution. We found virtually no genetic divergence within basins and only modest divergence among eight Atlantic basins. Levels of population divergence among basins were related to geographical distance and were greater in the South Atlantic than in the North Atlantic. Ocean‐wide patterns of genetic variation indicate basin‐wide divergence that exceeds what others have found for abyssal organisms, but considerably less than bathyal protobranchs across similar geographical scales. Populations on either side of the Mid‐Atlantic Ridge in the North Atlantic differed, suggesting the Ridge might impede gene flow at abyssal depths. Our results indicate that abyssal populations might be quite large (cosmopolitan), exhibit only modest genetic structure and probably provide little potential for the formation of new species.     

Global population genetic dynamics of a highly migratory,apex predator shark

Knowledge of genetic connectivity dynamics in the world's large‐bodied, highly migratory, apex predator sharks across their global ranges is limited. One such species, the tiger shark (Galeocerdo cuvier), occurs worldwide in warm temperate and tropical waters, uses remarkably diverse habitats (nearshore to pelagic) and possesses a generalist diet that can structure marine ecosystems through top‐down processes. We investigated the phylogeography and the global population structure of this exploited, phylogenetically enigmatic shark by using 10 nuclear microsatellites (n = 380) and sequences from the mitochondrial control region (CR, n = 340) and cytochrome oxidase I gene (n = 100). All three marker classes showed the genetic differentiation between tiger sharks from the western Atlantic and Indo‐Pacific ocean basins (microsatellite F_ST > 0.129; CR Φ_ST > 0.497), the presence of North vs. southwestern Atlantic differentiation and the isolation of tiger sharks sampled from Hawaii from other surveyed locations. Furthermore, mitochondrial DNA revealed high levels of intraocean basin matrilineal population structure, suggesting female philopatry and sex‐biased gene flow. Coalescent‐ and genetic distance‐based estimates of divergence from CR sequences were largely congruent (d_corr = 0.0015–0.0050), indicating a separation of Indo‐Pacific and western Atlantic tiger sharks <1 million years ago. Mitochondrial haplotype relationships suggested that the western South Atlantic Ocean was likely a historical connection for interocean basin linkages via the dispersal around South Africa. Together, the results reveal unexpectedly high levels of population structure in a highly migratory, behaviourally generalist, cosmopolitan ocean predator, calling for management and conservation on smaller‐than‐anticipated spatial scales.     

Population structure and possible migratory links of common minke whales, Balaenoptera acutorostrata, in the Southern Hemisphere

Mitochondrial DNA control region sequences were analyzed to investigate population structure and possible migratory links of common minke whales (Balaenoptera acutorostrata) in two ocean basins: western South Atlantic (WSA) and western South Pacific (WSP). The results of several different phylogenetic estimations consistently grouped all haplotypes but one (n = 1) from these two ocean basins into two separate clades. South and North Atlantic haplotypes were more closely related to each other than either was to haplotypes from the WSP. The interpopulation genetic distance between WSA and WSP whales was similar to that reported between North Pacific and North Atlantic common minke whales (0.0234). The migration rate between the two ocean basins was estimated at near-zero using MDIV. The genetic evidence presented here was consistent with the hypothesis of migratory links among Brazil, Chilean Patagonia and the Antarctic Peninsula, and between low-latitude and Antarctic waters of the WSP. The results suggest multiple populations of common minke whales in the Southern Hemisphere, which may have conservation as well as taxonomic implications. Our single locus results should be corroborated by additional analyses in a larger number of samples and at more genetic markers.     

Panbiogeographical analysis of distribution patterns in hagfishes (Craniata: Myxinidae)

Aim To analyse the worldwide distribution patterns of hagfishes using panbiogeographical track analysis, and to attempt to correlate these patterns with the tectonic history of the ocean basins. Location Atlantic and Pacific oceans. Method The distributions of 47 out of 70 species of hagfish (in the genera Eptatretus, Myxine, Nemamyxine, Neomyxine, and Paramyxine) were studied by the panbiogeographical method of track analysis. The analysis was performed using distributional data obtained from the collections included in the Ocean Biogeographic Information System (OBIS, http://www.iobis.org ) and FishBase ( http://www.fishbase.org ), with additional records from the literature. Individual tracks were obtained for each species by plotting localities and connecting them by minimum‐spanning trees. Generalized tracks were determined from the spatial overlap between individual tracks. Results Six generalized tracks were found: in the Gulf of Mexico, Caribbean Sea, South‐eastern Atlantic, Western Pacific, North‐eastern Pacific and South‐eastern Pacific. Main conclusions The distribution patterns of myxinids are marked by a high degree of endemism and vicariance, and are correlated with the tectonic features involved in many of the events that led to the development of oceanic basins. The main massing of the group is around the Pacific Basin. In the Atlantic Ocean, the distribution of Myxine glutinosa seems to correspond to a classic trans‐oceanic track and vicariance resulting from the opening of the Atlantic Ocean during the Cretaceous. In the Pacific Ocean, the distribution of the Eptatretus and Paramyxine species is clearly associated with the margins of the Pacific tectonic plate. The generalized tracks of hagfishes are shared by several other groups of marine organisms, including many from shallow tropical waters, implying a common history for this marine biota. Overall, vicariance is a major feature of hagfish distribution, suggesting vicariant differentiation of widespread ancestors as a result of sea‐floor spreading between continents in connection with ocean formation.     

Inter‐oceanic variation in patterns of host‐associated divergence in a seabird ectoparasite

Aim Parasites with global distributions and wide host spectra provide excellent models for exploring the factors that drive parasite diversification. Here, we tested the relative force of host and geography in shaping population structure of a widely distributed and common ectoparasite of colonial seabirds, the tick Ixodes uriae. Location Two natural geographic replicates of the system: numerous seabird colonies of the North Pacific and North Atlantic Ocean basins. Methods Using eight microsatellite markers and tick samples from a suite of multi‐specific seabird colonies, we examined tick population structure in the North Pacific and compare patterns of diversity and structure to those in the Atlantic basin. Analyses included population genetic estimations of diversity and population differentiation, exploratory multivariate analyses, and Bayesian clustering approaches. These different analyses explicitly took into account both the geographic distance among colonies and host use by the tick. Results Overall, little geographic structure was observed among Pacific tick populations. However, host‐related genetic differentiation was evident, but was variable among host types and lower than in the North Atlantic. Main conclusions Tick population structure is concordant with the genetic structure observed in seabird host species within each ocean basin, where seabird populations tend to be less structured in the North Pacific than in the North Atlantic. Reduced tick genetic structure in the North Pacific suggests that host movement among colonies, and thus tick dispersal, is higher in this region. In addition to information on parasite diversity and gene flow, our findings raise interesting questions about the subtle ways that host behaviour, distribution and phylogeographic history shape the genetics of associated parasites across geographic landscapes.     

Spatial overlap of shark nursery areas and the salmon farming industry influences the trophic ecology of Squalus acanthias on the southern coast of Chile

Potential interactions between marine predators and humans arise in the southern coast of Chile where predator feeding and reproduction sites overlap with fisheries and aquaculture. Here, we assess the potential effects of intensive salmon aquaculture on food habits, growth, and reproduction of a common predator, the spiny dogfish—identified as Squalus acanthias via genetic barcoding. A total of 102 (89 females and 13 males) individuals were collected during winter and summer of 2013–2014 from the Chiloé Sea where salmon aquaculture activities are concentrated. The low frequency of males in our study suggests spatial segregation of sex, while immature and mature females spatially overlapped in both seasons. Female spiny dogfish showed a functional specialist behavior as indicated by the small number of prey items and the relative high importance of the austral hake and salmon pellets in the diet. Immature sharks fed more on pellets and anchovies than the larger hake‐preferring mature females. Our results also indicate that spiny dogfish switch prey (anchovy to hake) to take advantage of seasonal changes in prey availability. Despite differences in the trophic patterns of S. acanthias due to the spatial association with intensive salmon farming, in this region, there appears to be no difference in fecundity or size at maturity compared to other populations. Although no demographic effects were detected, we suggest that a range of additional factors should be considered before concluding that intensive aquaculture does not have any impact on these marine predators.     

Diversity of Diazotrophic Unicellular Cyanobacteria in the Tropical North Atlantic Ocean

We present data on the genetic diversity and phylogenetic affinities of N₂-fixing unicellular cyanobacteria in the plankton of the tropical North Atlantic Ocean. Our dinitrogenase gene (nifH) sequences grouped together with a group of cyanobacteria from the subtropical North Pacific; another subtropical North Pacific group was only distantly related. Most of the 16S ribosomal DNA sequences from our tropical North Atlantic samples were closely allied with sequences from a symbiont of the diatom Climacodium frauenfeldianum. These findings suggest a complex pattern of evolutionary and ecological divergence among unicellular cyanobacteria within and between ocean basins.     

Bomb dating and age validation using the spines of spiny dogfish (Squalus acanthias)

Bomb radiocarbon has previously been used to validate the age of large pelagic sharks based on incorporation into vertebrae. However, not all sharks produce interpretable vertebral growth bands. Here we report the first application of bomb radiocarbon as an age validation method based on date-specific incorporation into spine enamel. Our results indicate that the dorsal spines of spiny dogfish, Squalus acanthias, recorded and preserved a bomb radiocarbon pulse in growth bands formed during the 1960s with a timing which was very similar to that of marine carbonates. Using radiocarbon assays of spine growth bands known to have formed in the 1960s and 1970s as a dated marker, we confirm the validity of spine enamel growth band counts as accurate annual age indicators to an age of at least 45 year. Radiocarbon incorporation into northeast Atlantic dogfish spines occurred in similar years as those in the northwest Atlantic and northeast Pacific, although the amount of radiocarbon differed in keeping with the radiocarbon content of the different water masses. Published reports suggesting that Pacific dogfish are longer lived and slower growing than their Atlantic counterparts appear to be correct, and are not due to errors in interpreting the spine growth bands. Radiocarbon assays of fin spine enamel appears to be well suited to the age validation of sharks with fin spines which inhabit the upper 200 m of the ocean.     

Trans‐Pacific and trans‐Arctic pathways of the intertidal macroalga Fucus distichus L. reveal multiple glacial refugia and colonizations from the North Pacific to the North Atlantic

Aim We examined the phylogeography of the cold‐temperate macroalgal species Fucus distichus L., a key foundation species in rocky intertidal shores and the only Fucus species to occur naturally in both the North Pacific and the North Atlantic. Location North Pacific and North Atlantic oceans (42° to 77° N). Methods We genotyped individuals from 23 populations for a mitochondrial DNA (mtDNA) intergenic spacer (IGS) (n = 608) and the cytochrome c oxidase subunit I (COI) region (n = 276), as well as for six nuclear microsatellite loci (n = 592). Phylogeographic structure and connectivity were assessed using population genetic and phylogenetic network analyses. Results IGS mtDNA haplotype diversity was highest in the North Pacific, and divergence between Pacific haplotypes was much older than that of the single cluster of Atlantic haplotypes. Two ancestral Pacific IGS/COI clusters led to a widespread Atlantic cluster. High mtDNA and microsatellite diversities were observed in Prince William Sound, Alaska, 11 years after severe disturbance by the 1989 Exxon Valdez oil spill. Main conclusions At least two colonizations occurred from the older North Pacific populations to the North Atlantic between the opening of the Bering Strait and the onset of the Last Glacial Maximum. One colonization event was from the Japanese Archipelago/eastern Aleutians, and a second was from the Alaskan mainland around the Gulf of Alaska. Japanese populations probably arose from a single recolonization event from the eastern Aleutian Islands before the North Pacific–North Atlantic colonization. In the North Atlantic, the Last Glacial Maximum forced the species into at least two known glacial refugia: the Nova Scotia/Newfoundland (Canada) region and Andøya (northern Norway). The presence of two private haplotypes in the central Atlantic suggests the possibility of colonization from other refugia that are now too warm to support F. distichus. With the continuing decline in Arctic ice cover as a result of global climate change, renewed contact between North Pacific and North Atlantic populations of Fucus species is expected.     

An introduced population of Chorda asiatica (Chordaceae,Laminariales) in Puget Sound,Pacific coast of North America

Northeastern Pacific Ocean and northwestern Atlantic Ocean populations of Chorda species, which have not been examined in previous phylogenetic studies, were investigated. All specimens that were collected in Hood Canal, Puget Sound, WA, USA, Pacific coast of North America, showed identical ITS‐5.8S rDNA sequences, and they were included in the clade of Japanese Chorda asiatica. With morphological data added to the molecular data, they were identified as C. asiatica and were concluded to be non‐indigenous populations, most likely introduced with oyster spat together with Sargassum muticum. Specimens collected in New York, NY, USA, Atlantic coast of North America, were genetically closest to C. filum from Newfoundland and were identified as C. filum. The genetic divergence of the North Atlantic populations of C. filum was relatively small compared to that of Japanese C. asiatica considering their broader distributional ranges on both sides of the Atlantic.     

Reproductive and population parameters of spiny dogfish Squalus acanthias in the south‐western Atlantic Ocean

The objective of this study was to estimate reproductive and population parameters of the spiny dogfish Squalus acanthias for the south‐western Atlantic Ocean. In total, 2714 specimens (1616 males and 1098 females) were collected from surveys carried out using research vessels. Males ranged from 225 to 861 mm total length (L_T) and females from 235 to 925 mm L_T. The size at maturity of females (651 mm) was significantly greater than that of males (565 mm). The maximum proportion of mature individuals (P_max) of the gestation ogive was <1, which indicates that a proportion of mature females was not in gestation. This inactivity may be explained by the occurrence of resting periods between cycles or by the asynchrony of the reproductive cycle. The estimated P_max for the maternity ogive suggested that about one third of mature females were in the maternity stage (i.e. with embryos >156 mm). The temporal and spatial co‐occurrence of non‐gravid adult females at different stages of ovarian development, as well as gravid females at all embryonic development stages would indicate that the female reproductive cycle in the south‐western Atlantic Ocean is asynchronous. The results indicate that S. acanthias is susceptible to fishing pressure on account of its length at maturity, extended reproductive cycles and low fecundity.     

Longtail tuna Thunnus tonggol (Bleeker, 1851) shows genetic partitioning across,but not within,basins of the Indo‐Pacific based on mitochondrial DNA

Genetic stock structure is atypical in tuna species, with most species demonstrating geographically‐broad, panmictic populations. Here, genetic data suggest a distinct pattern for Thunnus tonggol across the Indo‐Pacific region. The genetic variation in the coastal tuna T. tonggol sampled from across the South China Sea was examined using the highly variable mitochondrial DNA displacement loop (D‐loop) gene region. One hundred and thirty‐nine specimens were sampled from four locations in Indonesia, Vietnam and the Philippines. Phylogenetic reconstruction of genetic relationships revealed no significant ?_ST statistics and hence no population structure within the South China Sea. However, subsequent analysis with sequence data from coastal northwest India infers discrete genetic stocks between the Indian Ocean and the South China Sea. Consistent with previous genetic analyses of tuna species in the Indo‐Pacific, the findings in this study infer no population structure within each basin, but rather show a significant partitioning across the wider region. Furthermore, these results have implications for the management of the commercially valuable Thunnus tonggol across national boundaries, and thus requiring collaboration among countries to ensure its sustainable use.     

Outlier SNP markers reveal fine‐scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome‐wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large‐ and fine‐scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F_CT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F_CT range 0.275–0.705) and fine‐scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.     

Genetic patterns across multiple introductions of the globally invasive crab genus Carcinus

The European green crab Carcinus maenas is one of the world's most successful aquatic invaders, having established populations on every continent with temperate shores. Here we describe patterns of genetic diversity across both the native and introduced ranges of C. maenas and its sister species, C. aestuarii, including all known non‐native populations. The global data set includes sequences from the mitochondrial cytochrome c oxidase subunit I gene, as well as multilocus genotype data from nine polymorphic nuclear microsatellite loci. Combined phylogeographic and population genetic analyses clarify the global colonization history of C. maenas, providing evidence of multiple invasions to Atlantic North America and South Africa, secondary invasions to the northeastern Pacific, Tasmania, and Argentina, and a strong likelihood of C. maenas × C. aestuarii hybrids in South Africa and Japan. Successful C. maenas invasions vary broadly in the degree to which they retain genetic diversity, although populations with the least variation typically derive from secondary invasions or from introductions that occurred more than 100 years ago.     

Age and growth of spiny dogfish <Emphasis Type="Italic">Squalus acanthias</Emphasis> (Squalidae,Chondrichthyes) in pacific waters off the Kuril Islands

On the basis of materials collected from catches of drift salmon nets in Pacific waters off the Kuril Islands from 2005 to 2006, the age and rate of growth of spiny dogfish Squalus acanthias are considered. Individuals with a length of 67–123 cm and weight of 1140–5970 g aged 10–26 years were represented in catches. In almost all age classes, the length of males was greater and the weight smaller than in females. The lifespan of females is slightly higher as compared to males-26 and 25 years, respectively. The values of K coefficient of the Bertallanffi equation of growth in males and females comprised 0.10 and 0.05 and the calculated values of the asymptotic body length comprised 116.3 cm and 147.2 cm. A relationship was found between the age of spiny dogfish and the spine size: its length (r _s = 0.693), base width (r _s = 0.815), and base length (r _s = 0.823).     

Subtropical migrants in the southwestern part of the Bering Sea

From 2003 to 2008, arrivals (including mass) of sea bream Brama japonica, saury Cololabis saira, and spiny dogfish Squalus acanthias, as well as some cases of catches of Japanese anchovy Engraulis japonicus, and Todarodes pacificus, and Onychoteuthis borealijaponica squids were recorded in Pacific waters of Kamchatka in the southwestern sector of the Bering Sea. The penetration of these species far to the north is related to feeding migrations as well as to the passive transfer of water by currents. Migrations of subtropical species to Pacific waters of Kamchatka and the southern part of the Bering Sea depend on thermal conditions and circulation of currents in each particular year and are determined, first of all, by the intensity of the Western Subarctic gyre, although in some years, the migration flow of B. japonica and C. saira from the northeastern part of the Pacific Ocean increases.     

Population structure of North Atlantic and North Pacific sei whales (<Emphasis Type="Italic">Balaenoptera borealis</Emphasis>) inferred from mitochondrial control region DNA sequences and microsatellite genotypes

Currently, three stocks of sei whales (Balaenoptera borealis) are defined in the North Atlantic; the Nova Scotian, Iceland-Denmark Strait and Eastern North Atlantic stocks, which are mainly based upon historical catch and sighting data. We analyzed mitochondrial control region DNA (mtDNA) sequences and genotypes from 7 to 11 microsatellite loci in 87 samples from three sites in the North Atlantic; Iceland, the Gulf of Maine and the Azores, and compared against the North Pacific using 489 previously published samples. No statistically significant deviations from homogeneity were detected among the North Atlantic samples at mtDNA or microsatellite loci. The genealogy estimated from the mtDNA sequences revealed a clear division of the haplotypes into a North Atlantic and a North Pacific clade, with the exception of one haplotype detected in a single sample from the Azores, which was included in the North Pacific clade. Significant genetic divergence between the North Atlantic and North Pacific Oceans was detected (mtDNA Φ_ST?=?0.72, microsatellite Weir and Cockerham’s ? = 0.20; p?<?0.001). The coalescent-based estimate of the population divergence time between the North Atlantic and North Pacific populations from the sequence variation among the mtDNA sequences was at 163,000 years ago. However, the inference was limited by an absence of samples from the Southern Hemisphere and uncertainty regarding mutation rates and generation times. The estimates of inter-oceanic migration rates were low (Nm at 0.007 into the North Pacific and at 0.248 in the opposite direction). Although estimates of genetic divergence among the current North Atlantic stocks were low and consistent with the extensive range of movement observed in satellite tagged sei whales, the high uncertainty of the genetic divergence estimates precludes rejection of multiple stocks in the North Atlantic.     

PHYLOGEOGRAPHY OF THE TRUMPETFISHES (AULOSTOMUS): RING SPECIES COMPLEX ON A GLOBAL SCALE

Abstract.— The distribution of circumtropical marine species is limited by continental boundaries, cold temperate conditions, and oceanic expanses, but some of these barriers are permeable over evolutionary time scales. Sister taxa that evolved in separate ocean basins can come back into contact, and the consequences of this renewed sympatry may be a key to understanding evolutionary processes in marine organisms. The circumtropical trumpetfishes (Aulostomus) include a West Atlantic species (A. maculatus), an Indian‐Pacific species (A. chinensis), and an East Atlantic species (A. strigosus) that may be the product of a recent invasion from the Indian Ocean. To resolve patterns of divergence and speciation, we surveyed 480 bp of mitochondrial DNA cytochrome b in 196 individuals from 16 locations. Based on a conventional molecular clock of 2% sequence divergence per million years, the deepest partitions in a neighbor‐joining tree (d= 0.063‐0.082) are consistent with separation of West Atlantic and Indian‐Pacific species by the Isthmus of Panama, 3–4 million years ago. By the same criteria, trumpetfish in the East Atlantic were isolated from the Indian Ocean about 2.5 million years ago (d= 0.044‐0.054), coincident with the advent of glacial cycles and cold‐water upwelling around South Africa. Continental barriers between tropical oceans have only rarely been surmounted by trumpetfishes, but oceanic barriers do not appear to be substantial, as indicated by weak population partitioning (ø_ST= 0.093) in A. chinensis across the Indian and Pacific Oceans. Finally, morphological and mitochondrial DNA data indicate hybridization of A. strigosus and A. maculatus in Brazil. After 3–4 million years and a globe‐spanning series of vicariant and dispersal events, trumpetfish lineages have come back into contact in the southwest Atlantic and appear to be merging. This ring species phenomenon may occur in a broad array of marine organisms, with clear implications for the production and maintenance of biodiversity in marine ecosystems.