Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach‐cast, remote‐biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population‐level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as‐yet‐unnamed species off northern Australia).     

Phylogenetic relationships of tropical western Atlantic snappers in subfamily Lutjaninae (Lutjanidae: Perciformes) inferred from mitochondrial DNA sequences

Phylogenetic relationships among 20 nominal species of tropical lutjanine snappers (Lutjanidae) (12 from the western Atlantic, one from the eastern Pacific, and seven from the Indo‐Pacific) were inferred based on 2206 bp (712 variable, 614 parsimony informative) from three protein‐coding mitochondrial genes. Also included in the analysis were DNA sequences from two individuals, identified initially as Lutjanus apodus, which were sampled off the coast of Bahia State in Brazil (western Atlantic), and from three individuals labelled as ‘red snapper’ in the fish market in Puerto Armuelles, Panama (eastern Pacific). Bayesian posterior probabilities and maximum‐likelihood bootstrap percentages strongly supported monophyly of all lutjanines sampled and the hypothesis that western Atlantic lutjanines are derived from an Indo‐Pacific lutjanine lineage. The phylogenetic hypothesis also indicated that oceans where lutjanines are distributed (western Atlantic, eastern Pacific, and Indo‐Pacific) are not reciprocally monophyletic for the species distributed within them. There were three strongly supported clades that included all western Atlantic lutjanines: one included six species of Lutjanus from the western Atlantic, two species of Lutjanus from the eastern Pacific, and the monotypic genera Rhomboplites and Ocyurus (western Atlantic); one that included three, probably four, species of Lutjanus in the western Atlantic; and one that included Lutjanus cyanopterus (western Atlantic), an unknown species of Lutjanus from the eastern Pacific, and three species of Lutjanus from the Indo‐Pacific. Molecular‐clock calibrations supported an early Miocene diversification of an Indo‐Pacific lutjanine lineage that dispersed into the western Atlantic via the Panamanian Gateway. Divergent evolution among these lutjanines appears to have occurred both by vicariant and ecological speciation: the former following significant geographic or geological events, including both shoaling and closure of the Panamanian Gateway and tectonic upheavals, whereas the latter occurred via phenotypic diversification inferred to indicate adaptation to life in different habitats. Taxonomic revision of western Atlantic lutjanines appears warranted in that monotypic Ocyurus and Rhomboplites should be subsumed within the genus Lutjanus. Finally, it appears that retail mislabelling of ‘red snapper’ in commercial markets extends beyond the USA. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 915–929.     

Molecular data illuminate cryptic nudibranch species: the evolution of the Scyllaeidae (Nudibranchia: Dendronotina) with a revision of Notobryon

Scyllaeidae represents a small clade of dendronotoid nudibranchs. Notobryon wardi Odhner, 1936, has been reported to occur in tropical oceans from the Indo‐Pacific and eastern Pacific to temperate South Africa. The systematics of Notobryon has not been reviewed using modern systematic tools. Here, specimens of Notobryon were examined from the eastern Pacific, the Indo‐Pacific, and from temperate South Africa. Additionally, representatives of Scyllaea and Crosslandia were studied. Scyllaeidae was found to be monophyletic. Notobryon was also found to be monophyletic and is the sister group to Crosslandia plus Scyllaea. The molecular data also clearly indicate that within Notobryon, at least three distinct species are present, two of which are here described. Genetic distance data indicate that eastern Pacific and South African exemplars are 10–23% divergent from Indo‐Pacific exemplars of Notobryon wardi. Scyllaea pelagica has been regarded as a single, circumtropical species. Our molecular studies clearly indicate that the Atlantic and Indo‐Pacific populations are distinct and we resurrect Scyllaea fulva Quoy & Gaimard, 1824 for the Indo‐Pacific species. Our morphological studies clearly corroborate our molecular findings and differences in morphology distinguish closely related species. Different species clearly have distinct penial morphology. These studies clearly reinforce the view that eastern Pacific, Indo‐Pacific, and temperate biotas consist largely of distinct faunas, with only a minor degree of faunal overlap. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 311–336.     

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.     

Tethyan vicariance, relictualism and speciation: evidence from a global molecular phylogeny of the opisthobranch genus Bulla

Aim Our aims were: (1) to reconstruct a molecular phylogeny of the cephalaspidean opisthobranch genus Bulla, an inhabitant of shallow sedimentary environments; (2) to test if divergence times are consistent with Miocene and later vicariance among the four tropical marine biogeographical provinces; (3) to examine the phylogenetic status of possible Tethyan relict species; and (4) to infer the timing and causes of speciation events. Location Tropical and warm‐temperate regions of the Atlantic, Indo‐West Pacific, Australasia and eastern Pacific. Methods Ten of the 12 nominal species of Bulla were sampled, in a total sample of 65 individuals, together with cephalaspidean outgroups. Phylogenetic relationships were inferred by Bayesian analysis of partial sequences of the mitochondrial cytochrome c oxidase I (COI) and 16S rRNA and nuclear 28S rRNA genes. Divergence times and rates of evolution were estimated using uncorrelated relaxed‐clock Bayesian methods with fossil calibrations (based on literature review and examination of fossil specimens), implemented in beast . The geographical pattern of speciation was assessed by estimating the degree of overlap between sister lineages. Results Four clades were supported: Indo‐West Pacific (four species), Australasia (one species), Atlantic plus eastern Pacific (three species) and Atlantic (two species), with estimated mean ages of 35–46 Ma. Nominal species were monophyletic, but deep divergences were found within one Indo‐West Pacific and one West Atlantic species. Species‐level divergences occurred in the Miocene or earlier. The age of a sister relationship across the Isthmus of Panama was estimated at 7.9–32.1 Ma, and the divergence of a pair of sister species on either side of the Atlantic Ocean occurred 20.4–27.2 Ma. Main conclusions Fossils suggest that Bulla originated in the Tethys realm during the Middle Eocene. Average ages of the four main clades fall in the Eocene, and far pre‐date the 18–19 Ma closure of the Tethys Seaway. This discrepancy could indicate earlier vicariant events, selective extinction or errors of calibration. Similarly, the transisthmian divergence estimate far pre‐dates the uplift of the Panamanian Isthmus at about 3 Ma. Speciation events occurred in the Miocene, consistent with tectonic events in the central Indo‐West Pacific, isolation of the Arabian Sea by upwelling and westward trans‐Atlantic dispersal. Differences in habitat between sister species suggest that ecological speciation may also have played a role. The basal position of the Australasian species supports its interpretation as a Tethyan relict.     

Present and past genetic connectivity of the Indo‐Pacific tropical eel Anguilla bicolor

Aim The objective of this study was to reveal the present population structure and infer the gene‐flow history of the Indo‐Pacific tropical eel Anguilla bicolor. Location The Indo‐Pacific region. Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight representative localities where two subspecies have been historically designated. In order to infer the population structure, genetic differentiation estimates, analysis of molecular variance and gene‐tree reconstruction were performed. The history of migration events and population growth was assessed using neutrality tests based on allelic frequency spectrum, coalescent‐based estimation of gene flow and Bayesian demographic analysis using control region sequences. Results Population structure analysis showed genetic divergence between eels from the Indian and Pacific oceans (F_ST = 0.0174–0.0251, P < 0.05 for microsatellites; Φ_ST = 0.706, P < 0.001 for control region), while no significant variation was observed within each ocean. Two mitochondrial sublineages that do not coincide with geographical regions were found in the Indian Ocean clade of a gene tree. However, these two sublineages were not differentiated at the microsatellite markers. The estimation of mitochondrial gene‐flow history suggested allopatric isolation between the Indian and Pacific oceans, and a possible secondary contact within the Indian Ocean after an initial population splitting. Bayesian demographic history reconstruction and neutrality tests indicated population growth in each ocean after the Indo‐Pacific divergence. Main conclusions Anguilla bicolor has diverged between the Indian and Pacific oceans, which is consistent with the classical subspecies designation, but is apparently genetically homogeneous in the Indian Ocean. The analysis of gene‐flow and demographic history indicated that the two mitochondrial sublineages observed in the Indian Ocean probably represent the haplotype groups of relict ancestral populations. A comparison with a sympatric congener suggested that absolute physical barriers to gene flow may not be necessary for population divergence in eels.     

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.     

Nuclear and mitochondrial DNA analyses reveal four genetically separated breeding units of the swordfish

Variants in the calmodulin gene intron 4 ( CaM ) and the mtDNA D-loop region ( D-loop ) detected by RFLP and nucleotide sequence analyses were used to investigate the global stock structure of the swordfish Xiphias gladius . Two alleles ( A and B ) were observed at the CaM locus among 8 samples (Mediterranean, Tarifa, four Atlantic areas, Indian and Pacific oceans) comprising 567 individuals. Genotype distributions at this locus within samples were in accordance with Hardy-Weinberg equilibrium. Significant differences in allele frequencies were observed between Mediterranean-Northwest Atlantic samples ( A =0·347–0·493) and those from tropical Atlantic and Indo-Pacific ( A =0·81–1). In the D-loop region, Alu I and Rsa I digestions detected 4 ( A - D ) and 8 ( A - H ) genotypes, respectively. The frequency of type C for Alu I was lower in Indo-Pacific samples (0·2) than Atlantic and Mediterranean samples (0·365–0·643). Frequency of type C for Rsa I increased from the Pacific (0·398) to the Northwest Atlantic (0·698) and Tarifa (0·949) samples, and the Mediterranean sample was fixed for type C . These samples were classified into three groups (Mediterranean-Tarifa, Atlantic and Indo-Pacific) using a heterogeneity test of mtDNA genotype distributions. Combined analysis of the CaM and D-loop loci indicated that there are at least four breeding units: Mediterranean, northwestern Atlantic, tropical to South Atlantic, and Indo-Pacific.     

MITOCHONDRIAL DNA DIVERSITY IN THE SEA URCHINS STRONGYLOCENTROTUS PURPURATUS AND S. DROEBACHIENSIS

Restriction-fragment analysis was used to measure mitochondrial DNA (mtDNA) variability in 79 individuals of two species of temperate sea urchins. For the purple urchin Strongylocentrotus purpuratus, individuals were collected 1,500 km apart in 1985 and again from the same localities in 1988 (about one urchin generation). Twenty mtDNA genotypes belonging to four clades were found among 38 individuals. All four clades were found in both localities and in both years. Genetic structure was further tested by calculating the degree of interdeme genetic variation (G_ST) and comparing this value to the G_ST's from randomly shuffled data. No geographic structure was found. For S. droebachiensis, only six mtDNA genotypes were found among 41 individuals collected from the Pacific and Atlantic oceans. More than 80% of the individuals belonged to two genotypes. The genotype that dominated collections in the Pacific also occurred in the Atlantic; however, a common Atlantic genotype was never found in the Pacific. These two genotypes were identical at 64 of 65 restriction sites, and were only 0.2% divergent from each other. G_ST analysis confirmed that there were significant genetic differences between Atlantic and Pacific populations. The small divergence between genotypes suggests recent, but not continuous, migration. These marine species show smaller genotypic differences than terrestrial species over similar spatial and temporal scales. Both recruitment of adults from planktonic larval pools and the spread of sibling larvae over large distances from parents probably act as buffers to genetic differences in species with planktonic life-history phases.     

Two deep evolutionary lineages in the circumtropical glasseye Heteropriacanthus cruentatus (Teleostei,Priacanthidae) with admixture in the south‐western Indian Ocean

A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo‐Pacific. A fixed single nucleotide polymorphism (SNP) was detected at a nuclear locus (S7 ribosomal protein) and is consistent with this finding. There is evidence of recent dispersal from the Atlantic to the Indian Ocean with individuals of mixed lineages detected in South Africa and the Mozambique Channel. Using coalescent analyses of the mitochondrial dataset, time of divergence between lineages was estimated to be c. 15·3 million years. The deep divergence between these two lineages indicates distinct evolutionary units, however, due to the lack of morphological differences and evidence of hybridization between lineages, taxonomic revision is not suggested at this time.     

Phylogeography of the humbug damselfish,Dascyllus aruanus (Linnaeus, 1758): evidence of Indo‐Pacific vicariance and genetic differentiation of peripheral populations

The phylogeographical structure of coral‐associated reef fishes may have been severely affected, more than species from deeper habitats, by habitat loss during periods of low sea level. The humbug damselfish, Dascyllus aruanus, is widely distributed across the Indo‐West Pacific, and exclusively inhabits branching corals. We used mitochondrial cytochrome b sequence and seven microsatellite loci on D. aruanus samples (260 individuals) from 13 locations across the Indo‐West Pacific to investigate its phylogeographical structure distribution‐wide. A major genetic partition was found between the Indian and Pacific Ocean populations, which we interpret as the result of geographical isolation on either side of the Indo‐Pacific barrier during glacial periods. The peripheral populations of the Red Sea and the Society Islands exhibited lower genetic diversity, and substantial genetic differences with the other populations, suggesting relative isolation. Thus, vicariance on either side of the Indo‐Pacific barrier and peripheral differentiation are considered to be the main drivers that have shaped the phylogeographical patterns presently observed in D. aruanus. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 931–942.     

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.     

Oceanic dispersal in a sedentary reef shark (Triaenodon obesus): genetic evidence for extensive connectivity without a pelagic larval stage

Aim Most reef fishes are site‐attached, but can maintain a broad distribution through their highly dispersive larval stage. The whitetip reef shark (Triaenodon obesus) is site‐attached, yet maintains the largest Indo‐Pacific distribution of any reef shark while lacking the larval stage of bony (teleost) fishes. Here we use mitochondrial DNA (mtDNA) sequence data to evaluate the enigma of the sedentary reef shark that maintains a distribution across two‐thirds of the planet. Location Tropical Pacific and Indian Oceans. Methods We analysed 1025 base pairs of the mtDNA control region in 310 individuals from 25 locations across the Indian and Pacific Oceans. Phylogeographic and population genetic analyses were used to reveal the dispersal and recent evolutionary history of the species. Results We resolved 15 mtDNA control region haplotypes, but two comprised 87% of the specimens and were detected at nearly every location. Similar to other sharks, genetic diversity was low (h = 0.550 ± 0.0254 and π = 0.00213 ± 0.00131). Spatial analyses of genetic variation demonstrated strong isolation across the Indo‐Pacific Barrier and between western and central Pacific locations. Pairwise Φ_ST comparisons indicated high connectivity among archipelagos of the central Pacific but isolation across short distances of contiguous habitat (Great Barrier Reef) and intermittent habitat (Hawaiian Archipelago). In the eastern Pacific only a single haplotype (the most common one in the central Pacific) was observed, indicating recent dispersal (or colonization) across the East Pacific Barrier. Main conclusions The shallow haplotype network indicates recent expansion of modern populations within the last half million years from a common ancestor. Based on the distribution of mtDNA diversity, this began with an Indo‐West Pacific centre of origin, with subsequent dispersal to the Central Pacific and East Pacific. Genetic differences between Indian and Pacific Ocean populations are consistent with Pleistocene closures of the Indo‐Pacific Barrier associated with glacial cycles. Pairwise population comparisons reveal weak but significant isolation by distance, and notably do not indicate the high coastal connectivity observed in other shark species. The finding of population structure among semi‐contiguous habitats, but population connectivity among archipelagos, may indicate a previously unsuspected oceanic dispersal behaviour in whitetip reef sharks.     

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.     

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over‐exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded F_ST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between‐ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17‐SNP panel was developed in Atlantic BFT by cross‐species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (F_ST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.     

GLOBAL PHYLOGEOGRAPHY OF THE LOGGERHEAD TURTLE (CARETTA CARETTA) AS INDICATED BY MITOCHONDRIAL DNA HAPLOTYPES

Restriction-site analyses of mitochondrial DNA (mtDNA) from the loggerhead sea turtle (Caretta caretta) reveal substantial phylogeographic structure among major nesting populations in the Atlantic, Indian, and Pacific oceans and the Mediterranean sea. Based on 176 samples from eight nesting populations, most breeding colonies were distinguished from other assayed nesting locations by diagnostic and often fixed restriction-site differences, indicating a strong propensity for natal homing by nesting females. Phylogenetic analyses revealed two distinctive matrilines in the loggerhead turtle that differ by a mean estimated sequence divergence p = 0.009, a value similar in magnitude to the deepest intraspecific mtDNA node (p = 0.007) reported in a global survey of the green sea turtle Chelonia mydas. In contrast to the green turtle, where a fundamental phylogenetic split distinguished turtles in the Atlantic Ocean and the Mediterranean Sea from those in the Indian and Pacific oceans, genotypes representing the two primary loggerhead mtDNA lineages were observed in both Atlantic–Mediterranean and Indian-Pacific samples. We attribute this aspect of phylogeographic structure in Caretta caretta to recent interoceanic gene flow, probably mediated by the ability of this temperate-adapted species to utilize habitats around southern Africa. These results demonstrate how differences in the ecology and geographic ranges of marine turtle species can influence their comparative global population structures.     

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.     

Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo‐Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global metapopulation. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA. The expansion may have happened during the Holocene, when tropical species could expand their range due to sea‐level rise, eliminating dispersal barriers and increasing plankton productivity. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now in Australia may be due to commercial‐scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo‐Pacific. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales.     

Species delineation and global population structure of Critically Endangered sawfishes (Pristidae)

Sawfishes are among the most endangered of all elasmobranch species, a factor fostering considerable worldwide interest in the conservation of these animals. However, conservation efforts have been hampered by the confusing taxonomy of the group and the poor state of knowledge about the family's geographical population structure. Based on historical taxonomy, external morphology, and mitochondrial DNA sequences (NADH‐2), we show here that, globally, the sawfish comprise five species in two genera: Pristis pristis (circumtropical), Pristis clavata (east Indo‐West Pacific), Pristis pectinata (Atlantic), Pristis zijsron (Indo‐West Pacific), and Anoxypristis cuspidata (Indo‐West Pacific, except for East Africa and the Red Sea). This improved understanding will have implications for the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), International Union for Conservation of Nature (IUCN) Red List assessments, and endangered species laws and regulations in several countries. Furthermore, based on both or either of NADH‐2 and the number of rostral teeth per side, we show that populations of P. pristis, P. pectinata, P. zijsron, and A. cuspidata exhibit significant geographic structuring across their respective ranges, meaning that regional‐level conservation will be required. Finally, the NADH‐2 gene may serve as a marker for the identification of rostra and fins involved in illegal trade. © 2012 The Linnean Society of London     

A molecular evaluation of the Liagoraceae sensu lato (Nemaliales,Rhodophyta) in Bermuda including Liagora nesophila sp. nov. and Yamadaella grassyi sp. nov.

We have undertaken a comprehensive, molecular‐assisted alpha‐taxonomic examination of the rhodophyte family Liagoraceae sensu lato, a group that has not previously been targeted for molecular studies in the western Atlantic. Sequence data from three molecular markers indicate that in Bermuda alone there are 10 species in nine different genera. These include the addition of three genera to the flora — Hommersandiophycus, Trichogloeopsis, and Yamadaella. Liagora pectinata, a species with a type locality in Bermuda, is phylogenetically allied with Indo‐Pacific species of Hommersandiophycus, and the species historically reported as L. ceranoides for the islands is morphologically and genetically distinct from that taxon, and is herein described as L. nesophila sp. nov. Molecular sequence data have also uncovered the Indo‐Pacific L. mannarensis in Bermuda, a long‐distance new western Atlantic record. DNA sequences of Trichogloeopsis pedicellata from the type locality (Bahamas) match with local specimens demonstrating its presence in Bermuda. We described Yamadaella grassyi sp. nov. from Bermuda, a species phylogenetically and morphologically distinct from the generitype, Y. caenomyce of the Indo‐Pacific. Our data also indicated a single species each of Ganonema, Gloiocallis, Helminthocladia, Titanophycus, and Trichogloea in the flora.