Príncipe island hawksbills: Genetic isolation of an eastern Atlantic stock

The hawksbill turtle is a critically endangered species that has been extensively exploited for centuries. Príncipe Island off western Africa harbours one of the species' major nesting populations in the eastern Atlantic, as well as hosting year-round foraging aggregations of juveniles, subadults and adult males. To gain insight into the population's genetic structure and relationships with regional stocks, we analysed mitochondrial DNA (mtDNA) sequences of nesting females (N = 9), foraging adult females (N = 11), adult males (N = 32), subadults (N = 15) and juveniles (N = 80). The nesting population was found to be fixed for a single haplotype (EATL), which had been previously reported in both western and eastern Atlantic hawksbill foraging sites but had no known rookery source prior to this study. Thus it is now possible to confirm the westward transoceanic movement by hawksbills originating from Príncipe Island. Our analyses demonstrated that the Príncipe Island nesting colony is genetically distinct from breeding populations in the western Atlantic and is phylogenetically linked with Indo-Pacific hawksbill clades, suggesting that Príncipe Island was most likely colonised by migrants from the Indian Ocean via the Cape of Good Hope in southern Africa. Mixed stock analyses revealed that the eastern Atlantic appears to be the primary foraging area for Príncipe hawksbills (75%) while most of the foraging juveniles in Príncipe waters originate from the Príncipe rookery (84%). Furthermore, the presence of Caribbean haplotypes at low frequencies (< 5%) suggests that eastward transatlantic movements by juveniles to distant foraging and developmental habitats also take place. Depleted hawksbill populations in the eastern Atlantic combined with the low genetic variability and high genetic distinctiveness found in the Príncipe nesting and foraging aggregations with respect to the western Atlantic, underscore the high degree of isolation and vulnerability of this eastern Atlantic stock. These characteristics are highly relevant for the development of effective conservation programmes and highlight the urgent need to consolidate international cooperation across regional boundaries.     

The genetic structure of Australasian green turtles (Chelonia mydas): exploring the geographical scale of genetic exchange

Ecological and genetic studies of marine turtles generally support the hypothesis of natal homing, but leave open the question of the geographical scale of genetic exchange and the capacity of turtles to shift breeding sites. Here we combine analyses of mitochondrial DNA (mtDNA) variation and recapture data to assess the geographical scale of individual breeding populations and the distribution of such populations through Australasia. We conducted multiscale assessments of mtDNA variation among 714 samples from 27 green turtle rookeries and of adult female dispersal among nesting sites in eastern Australia. Many of these rookeries are on shelves that were flooded by rising sea levels less than 10 000 years (c. 450 generations) ago. Analyses of sequence variation among the mtDNA control region revealed 25 haplotypes, and their frequency distributions indicated 17 genetically distinct breeding stocks (Management Units) consisting either of individual rookeries or groups of rookeries in general that are separated by more than 500 km. The population structure inferred from mtDNA was consistent with the scale of movements observed in long-term mark-recapture studies of east Australian rookeries. Phylogenetic analysis of the haplotypes revealed five clades with significant partitioning of sequence diversity (Phi = 68.4) between Pacific Ocean and Southeast Asian/Indian Ocean rookeries. Isolation by distance was indicated for rookeries separated by up to 2000 km but explained only 12% of the genetic structure. The emerging general picture is one of dynamic population structure influenced by the capacity of females to relocate among proximal breeding sites, although this may be conditional on large population sizes as existed historically across this region.     

Mitochondrial DNA diversity and phylogeography of endangered green turtle (Chelonia mydas) populations in Africa

We analysed the genetic structure of seven nesting sites of the endangered green turtle (Chelonia mydas) in Africa using mitochondrial DNA control region sequences. Tissue samples were collected from 188 nesting females at six sites in West Africa and one in the Indian Ocean. A 488 bp fragment of the control region revealed 14 different haplotypes, 10 of which are previously undescribed. The most common haplotype (CM8) was observed in 157 individuals. All other haplotypes were closely related, except two divergent lineages: CM38, removed by four substitutions, and the three Indian Ocean haplotypes, distinguished by 31 substitutions. Significant differences in haplotype and nucleotide diversity were observed between Atlantic rookeries and among ocean basins. Analysis of molecular variance revealed high levels of differentiation between the Atlantic and the Indian Ocean populations but a much shallower Atlantic substructuring. Green turtle population genetic structure is thought to have been shaped by a dynamic succession of extinction and recolonisation of rookeries, by natal homing and occasional breakdown in nest-site fidelity. Mismatch distributions of pairwise differences between haplotypes at each rookery were found to be consistent with recent population expansion. We argue that demographic histories can be explained by scenarios at several temporal scales, including geological events, sea level fluctuations and more recent patterns of exploitation. We discuss management and conservation implications of our results for these threatened populations, identifying two ESUs (one in the Atlantic and one in the Indian ocean) and three MUs within the Atlantic.     

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.     

Geographic Patterns of Genetic Variation in a Broadly Distributed Marine Vertebrate: New Insights into Loggerhead Turtle Stock Structure from Expanded Mitochondrial DNA Sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.     

Phylogeography and population structure of the Atlantic and Mediterranean green turtle Chelonia mydas: a mitochondrial DNA control region sequence assessment

Mitochondrial (mt) DNA sequences were analysed to resolve the phylogeography and population genetic structure of Atlantic and Mediterranean populations of green turtles ( Chelonia mydas ). Analysis of sequence variation over 487 base pairs of the control (D-loop) region identified 18 haplotypes among 147 individuals from nine nesting populations. Pairwise comparisons of haplotype frequencies distinguished most nesting colonies, indicating significant genetic differentiation among rookeries and a strong propensity for natal homing behaviour by nesting females. Comparison of control region sequence data to earlier restriction fragment length polymorphism (RFLP) data for the same individuals demonstrates approximately a sixfold higher substitution rate in the 5' end of the control region. The sequence data provide higher resolution both in terms of the number of mtDNA genotype variants and the phylogeographic relationships detected within the Atlantic region, and reveal a gene genealogy that distinguishes two groups of haplotypes corresponding to (i) the western Caribbean and Mediterranean, and (ii) eastern Caribbean, South Atlantic and West Africa. The data suggest that phylogeographic patterns in the Atlantic Ocean may be interpreted in terms of female nest site fidelity and episodic dispersal events. The distribution of mtDNA haplotypes within the region is thus explained by the geological and climatic alternations (glacial and interglacial) over the last million years.     

Geographical variation in the White-tailed Tropicbird Phaethon lepturus, with the description of a new subspecies endemic to Europa Island, southern Mozambique Channel

Geographical variation in measurements and colouration among populations and subspecies of White-tailed Tropicbirds Phaethon lepturus , including birds from Europa Island (southern Mozambique Channel] was examined worldwide. Two groups were distinguished: the 'large subspecies' (lepturus and fulvus from the Indian Ocean, catesbyi from the western Atlantic Ocean) and the 'small subspecies' (ascensionis from the central and eastern Atlantic Ocean, dorotheae from the Pacific Ocean, and the birds from Europa Island). No clinal variation was found in the Indian Ocean, the birds from Europa Island being the only 'small' ones. This population also had a high frequency of golden morphs, a feature that does not exist elsewhere in the western Indian Ocean. These results indicate that Europa's population is isolated from all nearby colonies in the Indian Ocean, and does not belong to any of the two previously known subspecies of the area. It also differs from the birds of the two small subspecies by the frequency of the colour morphs and the distribution. Consequently, we propose to treat this population as a previously undescribed subspecies, endemic to Europa Island, for which we propose the name Phaethon lepturus europae. Geographical isolation of Europa Island and oceanic conditions in the Mozambique Channel are discussed to explain the isolation of this population.     

Global phylogeography of the ridley sea turtles (Lepidochelys spp.) as inferred from mitochondrial DNA sequences

The Kemp's ridley sea turtle (Lepidochelys kempi) is restricted to the warm temperate zone of the North Atlantic Ocean, whereas the olive ridley turtle (L. olivacea) is globally distributed in warm-temperate and tropical seas, including nesting colonies in the North Atlantic that nearly overlap the range of L. kempi. To explain this lopsided distribution, Pritchard (1969) proposed a scenario in which an ancestral taxon was divided into Atlantic and Pacific forms (L. kempi and L. olivacea, respectively) by the Central American land bridge. According to this model, the olive ridley subsequently occupied the Pacific and Indian Oceans and recently colonized the Atlantic Ocean via southern Africa. To assess this biogeographic model, a 470 bp sequence of the mtDNA control region was compared among 89 ridley turtles, including the sole L. kempi nesting population and 7 nesting locations across the range of L. olivacea. These data confirm a fundamental partition between L. olivacea and L. kempi (p=0.052-0.069), shallow separations within L. olivacea (p=0.002-0.031), and strong geographic partitioning of mtDNA lineages. The most divergent L. olivacea haplotype is observed in the Indo-West Pacific region, as are the central haplotypes in a parsimony network, implicating this region as the source of the most recent radiation of olive ridley lineages. The most common olive ridley haplotype in Atlantic samples is distinguished from an Indo-West Pacific haplotype by a single nucleotide substitution, and East Pacific samples are distingushed from the same haplotype by two nucleotide substitutions. These shallow separations are consistent with the recent invasion of the Atlantic postulated by Pritchard (1969), and indicate that the East Pacific nesting colonies were also recently colonized from the Indo-West Pacific region. Molecular clock estimates place these invasions within the last 300,000 years. This revised version was published online in July 2006 with corrections to the Cover Date.     

Population stock structure of leatherback turtles (Dermochelys coriacea) in the Atlantic revealed using mtDNA and microsatellite markers

This study presents a comprehensive genetic analysis of stock structure for leatherback turtles (Dermochelys coriacea), combining 17 microsatellite loci and 763 bp of the mtDNA control region. Recently discovered eastern Atlantic nesting populations of this critically endangered species were absent in a previous survey that found little ocean-wide mtDNA variation. We added rookeries in West Africa and Brazil and generated longer sequences for previously analyzed samples. A total of 1,417 individuals were sampled from nine nesting sites in the Atlantic and SW Indian Ocean. We detected additional mtDNA variation with the longer sequences, identifying ten polymorphic sites that resolved a total of ten haplotypes, including three new variants of haplotypes previously described by shorter sequences. Population differentiation was substantial between all but two adjacent rookery pairs, and F _ST values ranged from 0.034 to 0.676 and 0.004 to 0.205 for mtDNA and microsatellite data respectively, suggesting that male-mediated gene flow is not as widespread as previously assumed. We detected weak (F _ST = 0.008 and 0.006) but significant differentiation with microsatellites between the two population pairs that were indistinguishable with mtDNA data. POWSIM analysis showed that our mtDNA marker had very low statistical power to detect weak structure (F _ST < 0.005), while our microsatellite marker array had high power. We conclude that the weak differentiation detected with microsatellites reflects a fine scale level of demographic independence that warrants recognition, and that all nine of the nesting colonies should be considered as demographically independent populations for conservation. Our findings illustrate the importance of evaluating the power of specific genetic markers to detect structure in order to correctly identify the appropriate population units to conserve.     

DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity

DNA barcoding is a global initiative that provides a standardized and efficient tool to catalogue and inventory biodiversity, with significant conservation applications. Despite progress across taxonomic realms, globally threatened marine turtles remain underrepresented in this effort. To obtain DNA barcodes of marine turtles, we sequenced a segment of the cytochrome c oxidase subunit I (COI) gene from all seven species in the Atlantic and Pacific Ocean basins (815 bp; n = 80). To further investigate intraspecific variation, we sequenced green turtles (Chelonia mydas) from nine additional Atlantic/Mediterranean nesting areas (n = 164) and from the Eastern Pacific (n = 5). We established character-based DNA barcodes for each species using unique combinations of character states at 76 nucleotide positions. We found that no haplotypes were shared among species and the mean of interspecific variation ranged from 1.68% to 13.0%, and the mean of intraspecific variability was relatively low (0–0.90%). The Eastern Pacific green turtle sequence was identical to an Australian haplotype, suggesting that this marker is not appropriate for identifying these phenotypically distinguishable populations. Analysis of COI revealed a north–south gradient in green turtles of Western Atlantic/Mediterranean nesting areas, supporting a hypothesis of recent dispersal from near equatorial glacial refugia. DNA barcoding of marine turtles is a powerful tool for species identification and wildlife forensics, which also provides complementary data for conservation genetic research.     

Historical and contemporary population genetic connectivity of the European short-snouted seahorse Hippocampus hippocampus and implications for management

This first genetic study of Hippocampus hippocampus covers the species' entire geographic range and employs two mtDNA markers (control region and cytochrome b) to establish patterns of population structuring. A total of 255 specimens from 21 locations were used to obtain 89 concatenated haplotypes. The common haplotype was present in all but one population, however, most haplotypes were unique. The haplotype network had a star-like construction, suggesting expansion from a bottleneck event. F(ST) and AMOVA revealed population subdivision into three geographic regions (English Channel + Bay of Biscay, Mediterranean Sea + Atlantic Ocean Iberian coast + Macaronesian Islands, and West Africa) with barriers to gene flow indentified at Cape Finisterre and the Cape Verde frontal zone. Neutrality tests and nested clade analysis suggest a complex demographic history, with both historic events and contemporary processes shaping patterns of genetic differentiation. The genetic population subdivision detected in this study indicates that H. hippocampus should be managed as three separate units. This is especially pertinent as H. hippocampus populations within the West African region are the only ones known to be specifically targeted for exploitation.     

Population structure and conservation implications for the loggerhead sea turtle of the Cape Verde Islands

The Cape Verde Islands harbour the second largest nesting aggregation of the globally endangered loggerhead sea turtle in the Atlantic. To characterize the unknown genetic structure, connectivity, and demographic history of this population, we sequenced a segment of the mitochondrial (mt) DNA control region (380 bp, n = 186) and genotyped 12 microsatellite loci (n = 128) in females nesting at three islands of Cape Verde. No genetic differentiation in either haplotype or allele frequencies was found among the islands (mtDNA F _ST = 0.001, P > 0.02; nDNA F _ST = 0.001, P > 0.126). However, population pairwise comparisons of the mtDNA data revealed significant differences between Cape Verde and all previously sequenced Atlantic and Mediterranean rookeries (F _ST = 0.745; P < 0.000). Results of a mixed stock analysis of mtDNA data from 10 published oceanic feeding grounds showed that feeding grounds of the Madeira, Azores, and the Canary Islands, in the Atlantic Ocean, and Gimnesies, Pitiüses, and Andalusia, in the Mediterranean sea, are feeding grounds used by turtles born in Cape Verde, but that about 43% (±19%) of Cape Verde juveniles disperse to unknown areas. In a subset of samples (n = 145) we evaluated the utility of a longer segment (~760 bp) amplified by recently designed mtDNA control region primers for assessing the genetic structure of Atlantic loggerhead turtles. The analysis of the longer fragment revealed more variants overall than in the shorter segments. The genetic data presented here are likely to improve assignment and population genetic analyses, with significant conservation and research applications.     

Genetic divergence between Atlantic and Indo-Pacific stocks of bigeye tuna (Thunnus obesus) and admixture around South Africa

Two mitochondrial DNA segments of the bigeye tuna (Thunnus obesus) were amplified by polymerase chain reaction (PCR), and restriction fragment length polymorphism (RFLP) analyses of these segments were used for the genetic stock study. The variation in a segment flanking the ATPase and COIII genes was low; only two genotypes (α and β) were detected by RsaI digestion. Yet a large difference in the genotype distribution was observed between ocean basin samples. The α type predominated in four Atlantic samples, where 178 of 244 individuals were the α type. In contrast, only one of 195 individuals collected in the Indo‐Pacific was the α type? The frequency of the α type varied considerably from 0 to 80% among seven samples collected off the Cape of Good Hope. The variation found in the other segment, containing the D‐loop region, was much higher; two endonucleases (DpnII and RsaI) detected five genotypes each and 15 composite genotypes. A highly significant difference in genotype frequencies was observed between the Atlantic and Indo‐Pacific samples, but no heterogeneity was observed among the four Atlantic or among four Indo‐Pacific samples. These results clearly indicate that not only gene flow, but also fish migration, between the Atlantic and Indian Oceans are severely restricted, and that fishes from these distinct stocks are intermingling around South Africa. The simple and diagnostic genetic marker found in this study can be used to estimate mixing ratios between Atlantic and Indian stocks around South Africa.     

Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal

Although many coastal shark species have widespread distributions, the genetic relatedness of worldwide populations has been examined for few species. The blacktip shark, (Carcharhinus limbatus), inhabits tropical and subtropical coastal waters throughout the world. In this study, we examined the genetic relationships of blacktip shark populations (n = 364 sharks) throughout the majority of the species' range using the entire mitochondrial control region (1067-1070 nucleotides). Two geographically distinct maternal lineages (western Atlantic, Gulf of Mexico, and Caribbean Sea clades, and eastern Atlantic, Indian, and Pacific Ocean clades) were identified and shallow population structure was detected throughout their geographic ranges. These findings indicate that a major population subdivision exists across the Atlantic Ocean, but not the Pacific Ocean. The historical dispersal of this widespread, coastal species may have been interrupted by the rise of the Isthmus of Panama. This scenario implies historical dispersal across the Pacific Ocean (supported by the recovery of the same common haplotype from the Philippines, Hawaii, and the Gulf of California reflecting recent/contemporary dispersal abilities) and an oceanic barrier to recent migration across the Atlantic. Genetic structure within the eastern Atlantic/Indo-Pacific (Phi(ST) = 0.612, P < 0.001) supports maternal philopatry throughout this area, expanding previous western Atlantic findings. Eastern Atlantic/Indo-Pacific C. limbatus control region haplotypes were paraphyletic to Carcharhinus tilstoni haplotypes in our maximum-parsimony analysis. The greater divergence of western Atlantic C. limbatus than C. tilstoni from eastern Atlantic/Indo-Pacific C. limbatus reflects the taxonomic uncertainty of western Atlantic C. limbatus.     

Genetic structure of loggerhead turtle (Caretta caretta) populations in Turkey

This study investigates genetic structure of loggerhead turtle (Caretta caretta) for conservation purposes using both mitochondrial and nuclear DNA markers. To evaluate overall genetic structure of C. caretta at the Turkish nesting beaches and to compare it with previously published data from other nesting sites of the Mediterranean Sea, we have studied 256 hatchlings from 18 different nesting beaches. Seven distinct haplotypes were detected, of which three have previously been reported from the Mediterranean and one from the Atlantic. The remaining three haplotypes are described for the first time for C. caretta in the present study. Distribution of these haplotypes among the nesting sites showed a significant genetic structuring, indicating that females are philopatric and that gene flow among populations is restricted. Both mtDNA and microsatellite analyses determined genetic structuring (mtDNA: γ_st = 0.214, p < 0.01; nDNA F_st = 0.0004 p < 0.05) among nesting aggregates of C. caretta throughout the study area and enabled the detection of the different haplotypes to inform conservation strategies.     

Evidence from genetic and Lagrangian drifter data for transatlantic transport of small juvenile green turtles

Aim A key life‐history component for many animals is the need for movement between different geographical locations at particular times. Green turtle (Chelonia mydas) hatchlings disperse from their natal location to spend an early pelagic stage in the ocean, followed by a neritic stage where small juveniles settle in coastal areas. In this study, we combined genetic and Lagrangian drifter data to investigate the connectivity between natal and foraging locations. In particular we focus on the evidence for transatlantic transport. Location Atlantic Ocean. Methods We used mitochondrial DNA (mtDNA) sequences (n = 1567) from foraging groups (n = 8) and nesting populations (n = 12) on both sides of the Atlantic. Genetic data were obtained for Cape Verde juvenile turtles, a foraging group not previously sampled for genetic study. Various statistical methods were used to explore spatial genetics and population genetic structure (e.g. exact tests of differentiation, Geneland and analysis of molecular variance). Many‐to‐many mixed stock analysis estimated the connectivity between nesting and foraging groups. Results Our key new finding is robust evidence for connectivity between a nesting population on the South American coast (25% of the Surinam nesting population are estimated to go to Cape Verde) and a foraging group off the coast of West Africa (38% of Cape Verde juveniles are estimated to originate from Surinam), thus extending the results of previous investigations by confirming that there is substantial transatlantic dispersal in both directions. Lagrangian drifter data demonstrated that transport by drift across the Atlantic within a few years is possible. Main conclusions Small juvenile green turtles seem capable of dispersing extensively, and can drop out of the pelagic phase on a transatlantic scale (the average distance between natal and foraging locations was 3048 km). Nevertheless, we also find support for the ‘closest‐to‐home’ hypothesis in that the degree of contribution from a nesting population to a foraging group is correlated with proximity. Larger‐sized turtles appear to feed closer to their natal breeding grounds (the average distance was 1133 km), indicating that those that have been initially transported to far‐flung foraging grounds may still be able to move nearer to home as they grow larger.     

Genetic diversity and origin of leatherback turtles (Dermochelys coriacea) from the Brazilian coast

The leatherback sea turtle (Dermochelys coriacea) population that nests in Brazil is restricted to a few individuals, but high densities of pelagic individuals are observed along the southern and southeastern Brazilian coast. We investigated the diversity of the mitochondrial DNA (mtDNA) control region in order to understand the relationship between nesting and pelagic leatherbacks from Brazil and elsewhere. High-quality 711-bp sequences were generated, analyzed, and compared with published data from worldwide populations. We detected the presence of shared haplotypes between nesting and pelagic aggregates from Brazil, as well as haplotypes shared with other nesting areas from the Atlantic and Pacific. Furthermore, the use of longer control region sequences allowed the subdivision of the common Atlantic haplotype A into 3 different haplotypes (A1, A3, and A4), thus improving the resolution of mtDNA-based leatherback phylogeography. The use of longer sequences partially supported a closer association between nesting and pelagic individuals from Brazil and pointed to a complex origin for the pelagic individuals in the Brazilian coast.     

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.     

Molecular resolution of marine turtle stock composition in fishery bycatch: a case study in the Mediterranean

Based on an extensive sampling regime from both nesting populations and bycatch, frequency analyses of mitochondrial (mt) DNA control region haplotypes in the Mediterranean were used to assess the genetic structure and stock composition of the loggerhead sea turtle, Caretta caretta, in different marine fisheries. The analyses show the following. (i) In drifting longline fisheries working in Mediterranean pelagic habitats 53–55% of turtles caught originated from the Mediterranean stock; (ii) In bottom-trawl fisheries all turtle bycatch is derived from this regional stock; (iii) This regional stock contribution to fishery bycatch suggests that the population size of the Mediterranean loggerhead nesting population is significantly larger than previously thought. This is consistent with a recent holistic estimate based on the discovery of a large rookery in Libya. (iv) Present impact of fishery-related mortality on the Mediterranean nesting population is probably incompatible with its long-term conservation. Sea turtle conservation regulations are urgently needed for the Mediterranean fisheries. (v) The significant divergence of mtDNA haplotype frequencies of the Turkish loggerhead colonies define this nesting population as a particularly important management unit. Large immature and adult stages from this management unit seem to be harvested predominantly by Egyptian fisheries. (vi) Combined with other data, our findings suggest that all the nesting populations in the Mediterranean should be considered as management units sharing immature pelagic habitats throughout the Mediterranean (and possibly the eastern Atlantic), with distinct and more localized benthic feeding habitats in the eastern basin used by large immatures and adults. (vii) Between the strict oceanic pelagic and the benthic stages, immature turtles appear to live through an intermediate neritic stage, in which they switch between pelagic and benthic foods.     

PHYLOGEOGRAPHIC PATTERNS INDICATE TRANSATLANTIC MIGRATION FROM EUROPE TO NORTH AMERICA IN THE RED SEAWEED CHONDRUS CRISPUS (GIGARTINALES,RHODOPHYTA)1

Inferring how the Pleistocene climate oscillations have repopulated the extant population structure of Chondrus crispus Stackh. in the North Atlantic Ocean is important both for our understanding of the glacial episode promoting diversification and for the conservation and development of marine organisms. C. crispus is an ecologically and commercially important red seaweed with broad distributions in the North Atlantic. Here, we employed both partial mtDNA Cox1 and nrDNA internal transcribed spacer region 2 (ITS2) sequences to explore the genetic structure of 17 C. crispus populations from this area. Twenty‐eight and 30 haplotypes were inferred from these two markers, respectively. Analysis of molecular variance (AMOVA) and of the population statistic Φ_ST not only revealed significant genetic structure within C. crispus populations but also detected significant levels of genetic subdivision among and within populations in the North Atlantic. On the basis of high haplotype diversity and the presence of endemic haplotypes, we postulate that C. crispus had survived in Pleistocene glacial refugia in the northeast Atlantic, such as the English Channel and the northwestern Iberian Peninsula. We also hypothesize that C. crispus from the English Channel refugium repopulated most of northeastern Europe and recolonized northeastern North America in the Late Pleistocene. The observed phylogeographic pattern of C. crispus populations is in agreement with a scenario in which severe Quaternary glaciations influenced the genetic structure of North Atlantic marine organisms with contiguous population expansion and locally restricted gene flow coupled with a transatlantic dispersal in the Late Pleistocene.