Mixed-stock analysis reveals the migrations of juvenile hawksbill turtles (Eretmochelys imbricata) in the Caribbean Sea

Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale

Hawksbill sea turtles (Eretmochelys imbricata) from the Hawaiian archipelago form a small and genetically isolated population, consisting of only a few tens of individuals breeding annually. Most females nest on the island of Hawai'i, but little is known about the demographics of this rookery. This study used genetic relatedness, inferred from 135 microhaplotype markers, to determine breeding sex-ratios, estimate female nesting frequency and assess relationships between individuals nesting on different beaches. Samples were collected during the 2017 nesting season and final data included 13 nesting females and 1002 unhatched embryos, salvaged from 41 nests, of which 13 had no observed mother. Results show that most females used a single nesting beach laying 1-5 nests each. From female and offspring alleles, the paternal genotypes of 12 breeding males were reconstructed and many showed high relatedness to their mates. Pairwise relatedness of offspring revealed one instance of polygyny but otherwise suggested a 1 : 1 breeding-sex ratio. Relatedness analysis and spatial-autocorrelation of genotypes indicate that turtles from different nesting areas do not regularly interbreed, suggesting that strong natal homing tendencies in both sexes result in non-random mating across the study area. Complexes of nearby nesting beaches also showed unique patterns of inbreeding across loci, further indicating that Hawaiian hawksbill turtles have demographically discontinuous nesting populations separated by only tens of km.

Dietary plasticity linked to divergent growth trajectories in a critically endangered sea turtle

Foraging habitat selection and diet quality are key factors that influence individual fitness and meta-population dynamics through effects on demographic rates. There is growing evidence that sea turtles exhibit regional differences in somatic growth linked to alternative dispersal patterns during the oceanic life stage. Yet, the role of habitat quality and diet in shaping somatic growth rates is poorly understood. Here, we evaluate whether diet variation is linked to regional growth variation in hawksbill sea turtles (Eretmochelys imbricata), which grow significantly slower in Texas, United States versus Florida, United States, through novel integrations of skeletal growth, gastrointestinal content (GI), and bulk tissue and amino acid (AA)-specific stable nitrogen (δ15N) and carbon (δ13C) isotope analyses. We also used AA δ15N ΣV values (heterotrophic bacterial re-synthesis index) and δ13C essential AA (δ13CEAA) fingerprinting to test assumptions about the energy sources fueling hawksbill food webs regionally. GI content analyses, framed within a global synthesis of hawksbill dietary plasticity, revealed that relatively fast-growing hawksbills stranded in Florida conformed with assumptions of extensive spongivory for this species. In contrast, relatively slow-growing hawksbills stranded in Texas consumed considerable amounts of non-sponge invertebrate prey and appear to forage higher in the food web as indicated by isotopic niche metrics and higher AA δ15N-based trophic position estimates internally indexed to baseline nitrogen isotope variation. However, regional differences in estimated trophic position may also be driven by unique isotope dynamics of sponge food webs. AA δ15N ΣV values and δ13CEAA fingerprinting indicated minimal bacterial re-synthesis of organic matter (ΣV < 2) and that eukaryotic microalgae were the primary energy source supporting hawksbill food webs. These findings run contrary to assumptions that hawksbill diets predominantly comprise high microbial abundance sponges expected to primarily derive energy from bacterial symbionts. Our findings suggest alternative foraging patterns could underlie regional variation in hawksbill growth rates, as divergence from typical sponge prey might correspond with increased energy expenditure and reduced foraging success or diet quality. As a result, differential dispersal patterns may infer substantial individual and population fitness costs and represent a previously unrecognized challenge to the persistence and recovery of this critically endangered species.

Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability

Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120–14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome‐wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to ~1/4th of present‐day levels during the Last Glacial Maximum (LGM; 26–19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species’ demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species’ demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated.

Critical In-Water Habitats for Post-Nesting Sea Turtles from the Southern Gulf of Mexico

Marine turtles are globally endangered species that spend more than 95% of their life cycle in in-water habitats. Nevertheless, most of the conservation, recovery and research efforts have targeted the on-land habitats, due to their easier access, where adult females lay their eggs. Targeting the large knowledge gaps on the in-water critical habitats of turtles, particularly in the Large Marine Ecosystem Gulf of Mexico, is crucial for their conservation and recovery in the long term. We used satellite telemetry to track 85 nesting females from their beaches after they nested to identify their feeding and residency habitats, their migratory corridors and to describe the context for those areas. We delimited major migratory corridors in the southern Gulf of Mexico and West Caribbean and described physical features of internesting and feeding home ranges located mainly around the Yucatan Peninsula and Veracruz, Mexico. We also contributed by describing general aggregation and movement patterns for the four marine turtle species in the Atlantic, expanding the knowledge of the studied species. Several tracked individuals emigrated from the Gulf of Mexico to as far as Nicaragua, Honduras, and the Bahamas. This information is critical for identifying gaps in marine protection and for deciphering the spatial connectivity in large ocean basins, and it provides an opportunity to assess potential impacts on marine turtle populations and their habitats.

Population recovery changes population composition at a major southern Caribbean juvenile developmental habitat for the green turtle, Chelonia mydas

Understanding the population composition and dynamics of migratory megafauna at key developmental habitats is critical for conservation and management. The present study investigated whether differential recovery of Caribbean green turtle (Chelonia mydas) rookeries influenced population composition at a major juvenile feeding ground in the southern Caribbean (Lac Bay, Bonaire, Caribbean Netherlands) using genetic and demographic analyses. Genetic divergence indicated a strong temporal shift in population composition between 2006-2007 and 2015-2016 (ϕ_ST = 0.101, P < 0.001). Juvenile recruitment (<75.0 cm straight carapace length; SCL) from the north-western Caribbean increased from 12% to 38% while recruitment from the eastern Caribbean region decreased from 46% to 20% between 2006-2007 and 2015-2016. Furthermore, the product of the population growth rate and adult female abundance was a significant predictor for population composition in 2015-2016. Our results may reflect early warning signals of declining reproductive output at eastern Caribbean rookeries, potential displacement effects of smaller rookeries by larger rookeries, and advocate for genetic monitoring as a useful method for monitoring trends in juvenile megafauna. Furthermore, these findings underline the need for adequate conservation of juvenile developmental habitats and a deeper understanding of the interactions between megafaunal population dynamics in different habitats.

Connecting paths between juvenile and adult habitats in the Atlantic green turtle using genetics and satellite tracking

Although it is commonly assumed that female sea turtles always return to the beach they hatched, the pathways they use during the years preceding their first reproduction and their natal origins are most often unknown, as it is the case for juvenile green turtles found in Martinique waters in the Caribbean. Given the oceanic circulation of the Guiana current flowing toward Martinique and the presence of important nesting sites for this species in Suriname and French Guiana, we may assume that a large proportion of the juvenile green turtles found in Martinique are originating from the Suriname-French Guiana beaches. To confirm this hypothesis, we performed mixed stock analysis (MSA) on 40 green turtles sampled in Martinique Island and satellite tracked 31 juvenile green turtles tagged in Martinique to (a) assess their natal origin and (b) identify their destination. Our results from MSA confirm that these juveniles are descendant from females laying on several Caribbean and Atlantic beaches, mostly from Suriname and French Guiana, but also from more southern Brazilian beaches. These results were confirmed by the tracking data as the 10 turtles leaving Martinique headed across the Caribbean-Atlantic region in six different directions and 50% of these turtles reached the Brazilian foraging grounds used by the adult green turtles coming from French Guiana. One turtle left the French Guianan coast to perform the first transatlantic migration ever recorded in juvenile green turtles, swimming toward Guinea-Bissau, which is the most important nesting site for green turtles along the African coast. The extensive movements of the migrant turtles evidenced the crossing of international waters and more than 25 exclusive economic zones, reinforcing the need for an international cooperative network to ensure the conservation of future breeders in this endangered species.

Multinational genetic connectivity identified in western Pacific hawksbill turtles, Eretmochelys imbricata

Context An understanding of the genetic stock structure of wide-ranging marine species is necessary for sound conservation management. Eretmochelys imbricata is Critically Endangered globally, but is among the least studied marine turtles. Reduced population sizes, its long-distance migratory nature between feeding and nesting habitats and poor understanding of its stock structure, biology and anthropogenic impact(s) pose challenges to developing effective conservation strategies for regional conspecifics. Aims Quantification of the population connectivity between specific feeding areas and regional nesting populations is needed for threat assessment and development of mitigation actions. Methods Here, we sequenced the mitochondrial DNA (mtDNA) of 91 immature and adult foraging E. imbricata individuals captured at the Howick Group of islands in the far-northern section of the Great Barrier Reef (nGBR), Queensland, Australia. We used a Bayesian mixed-stock analysis (MSA) approach to determine the contribution of nine regional genetically characterised breeding populations to this feeding aggregation. Key results The MSA estimated that a majority (83%; 95% CI = 70–92%) of feeding E. imbricata had originated from nesting beaches in the Bismarck–Solomon Sea region, whereas only 15% (95% CI = 6–25%) had originated from nGBR rookeries. International reproductive migrations were also corroborated by the return of 18 uniquely numbered titanium flipper tags that had been applied to E. imbricata found foraging in the Howick Group and had swum to rookeries within the Bismarck–Solomon Sea region. These 18 turtles represent 86% of all migration tag–recaptures from the Howick Group. Conclusions We postulate that recent increases in nesting populations within the Solomon Islands may be due to the high level of protection afforded to foraging turtles within the Great Barrier Reef. Implications An understanding of the connectivity between specific feeding areas and nesting populations is necessary to determine threats to animals over their entire life history and, therefore, allow the development of sound conservation management actions.

Natal foraging philopatry in eastern Pacific hawksbill turtles

The complex processes involved with animal migration have long been a subject of biological interest, and broad-scale movement patterns of many marine turtle populations still remain unresolved. While it is widely accepted that once marine turtles reach sexual maturity they home to natal areas for nesting or reproduction, the role of philopatry to natal areas during other life stages has received less scrutiny, despite widespread evidence across the taxa. Here we report on genetic research that indicates that juvenile hawksbill turtles (Eretmochelys imbricata) in the eastern Pacific Ocean use foraging grounds in the region of their natal beaches, a pattern we term natal foraging philopatry. Our findings confirm that traditional views of natal homing solely for reproduction are incomplete and that many marine turtle species exhibit philopatry to natal areas to forage. Our results have important implications for life-history research and conservation of marine turtles and may extend to other wide-ranging marine vertebrates that demonstrate natal philopatry.

Linking loggerhead locations: using multiple methods to determine the origin of sea turtles in feeding grounds

Many marine megavertebrate taxa, including sea turtles, disperse widely from their hatching or birthing locations but display natal homing as adults. We used flipper tagging, satellite tracking and genetics to identify the origin of loggerhead turtles living in Amvrakikos Gulf, Greece. This location has been identified as hosting regionally important numbers of large-juvenile to adult sized turtles that display long-term residency and/or association to the area, and also presents a male biased sex ratio for adults. A total of 20 individuals were linked to nesting areas in Greece through flipper tagging and satellite telemetry, with the majority (16) associated with Zakynthos Island. One additional female was tracked from Amvrakikos Gulf to Turkey where she likely nested. Mitochondrial DNA mixed stock analyses of turtles captured in Amvrakikos Gulf (n = 95) indicated 82% of individuals originated from Greek nesting stocks, mainly from Zakynthos Island (63%), with lesser contributions from central Turkey, Cyprus and Libya. These results suggest that the male-biased sex ratio found in Amvrakikos Gulf may be driven by the fact that males breed twice as frequently on Zakynthos, resulting in their using foraging grounds of greater proximity to the breeding site. Conservation measures in localised foraging habitats for the protection of marine vertebrates, such as sea turtles, may have positive impacts on several disparate breeding stocks and the use of multiple methods to determine source populations can indicate the relative effectiveness of these measures.

Mitochondrial DNA Profiling of Illegal Tortoiseshell Products Derived from Hawksbill Sea Turtles

The hawksbill sea turtle (Eretmochelys imbricata) is a highly endangered species, commonly poached for its ornate shell. "Tortoiseshell" products made from the shell are widely, although illegally, available in many countries. Hawksbills have a circumglobal distribution; thus, determining their origin is difficult, although genetic differences exist geographically. In the research presented, a procedure was developed to extract and amplify mitochondrial DNA from tortoiseshell items, in an effort to better understand where the species is being poached. Confiscated tortoiseshell items were obtained from the U.S. Fish and Wildlife Service, and DNA from 56 of them was analyzed. Multiple mitochondrial haplotypes were identified, including five not previously reported. Only one tortoiseshell item proved to be of Atlantic origin, while all others corresponded to genetic stocks in the Indo-Pacific region. The developed methodology allows for unique, and previously unattainable, genetic information on the illegal poaching of sea turtles for the decorative tortoiseshell trade.

Phylogeography, Genetic Diversity, and Management Units of Hawksbill Turtles in the Indo-Pacific

Hawksbill turtle (Eretmochelys imbricata) populations have experienced global decline because of a history of intense commercial exploitation for shell and stuffed taxidermied whole animals, and harvest for eggs and meat. Improved understanding of genetic diversity and phylogeography is needed to aid conservation. In this study, we analyzed the most geographically comprehensive sample of hawksbill turtles from the Indo-Pacific Ocean, sequencing 766 bp of the mitochondrial control region from 13 locations (plus Aldabra, n = 4) spanning over 13500 km. Our analysis of 492 samples revealed 52 haplotypes distributed in 5 divergent clades. Diversification times differed between the Indo-Pacific and Atlantic lineages and appear to be related to the sea-level changes that occurred during the Last Glacial Maximum. We found signals of demographic expansion only for turtles from the Persian Gulf region, which can be tied to a more recent colonization event. Our analyses revealed evidence of transoceanic migration, including connections between feeding grounds from the Atlantic Ocean and Indo-Pacific rookeries. Hawksbill turtles appear to have a complex pattern of phylogeography, showing a weak isolation by distance and evidence of multiple colonization events. Our novel dataset will allow mixed-stock analyses of hawksbill turtle feeding grounds in the Indo-Pacific by providing baseline data needed for conservation efforts in the region. Eight management units are proposed in our study for the Indo-Pacific region that can be incorporated in conservation plans of this critically endangered species.

Artisanal Green Turtle, Chelonia mydas, fishery of Caribbean Nicaragua: I. Catch rates and trends, 1991-2011

This is the first assessment of catch rates for the legal, artisanal green turtle, Chelonia mydas, fishery in Caribbean Nicaragua. Data were collected by community members, monitoring up to 14 landing sites from 1991 to 2011. We examined take levels, and temporal and spatial variability in catch rates for the overall fishery, by region, and community using General Additive Mixed Models (GAMMs). More than 171,556 green turtles were killed during the period, with a mean estimated minimum 8,169±2,182 annually. There was a statistically significant decline in catch rates overall. Catch rates peaked in 1997 and 2002, followed by a downward trend, particularly from mid-2008 to the end of the study period. Similar downward trends were evident in both study regions. Community specific catch rate trends also indicated declines with decreases ranging from 21% to 90%. Decrease in catch rates in Nicaragua is cause for concern even though the principal source rookery at Tortuguero, Costa Rica, shows an increase in nesting activity. Explanations for the apparent discrepancy between the increasing trend at Tortuguero and decreasing catch rate trends in Nicaragua include: i) an increase in reproductive output, ii) insufficient time has passed to observe the impact of the fishery on the rookery due to a time lag, iii) changes in other segments of the population have not been detected since only nesting activity is monitored, iv) the expansive northern Nicaragua foraging ground may provide a refuge for a sufficient portion of the Tortuguero rookery, and/or v) a larger than expected contribution of non-Tortuguero rookeries occurring in Nicaragua turtle fishing areas. Our results highlight the need for close monitoring of rookeries and in-water aggregations in the Caribbean. Where consumptive use still occurs, nations sharing this resource should implement scientifically based limits on exploitation to ensure sustainability and mitigate impacts to regional population diversity.

Genetic structure and natal origins of immature hawksbill turtles (Eretmochelys imbricata) in Brazilian waters

Understanding the connections between sea turtle populations is fundamental for their effective conservation. Brazil hosts important hawksbill feeding areas, but few studies have focused on how they connect with nesting populations in the Atlantic. Here, we (1) characterized mitochondrial DNA control region haplotypes of immature hawksbills feeding along the coast of Brazil (five areas ranging from equatorial to temperate latitudes, 157 skin samples), (2) analyzed genetic structure among Atlantic hawksbill feeding populations, and (3) inferred natal origins of hawksbills in Brazilian waters using genetic, oceanographic, and population size information. We report ten haplotypes for the sampled Brazilian sites, most of which were previously observed at other Atlantic feeding grounds and rookeries. Genetic profiles of Brazilian feeding areas were significantly different from those in other regions (Caribbean and Africa), and a significant structure was observed between Brazilian feeding grounds grouped into areas influenced by the South Equatorial/North Brazil Current and those influenced by the Brazil Current. Our genetic analysis estimates that the studied Brazilian feeding aggregations are mostly composed of animals originating from the domestic rookeries Bahia and Pipa, but some contributions from African and Caribbean rookeries were also observed. Oceanographic data corroborated the local origins, but showed higher connection with West Africa and none with the Caribbean. High correlation was observed between origins estimated through genetics/rookery size and oceanographic/rookery size data, demonstrating that ocean currents and population sizes influence haplotype distribution of Brazil's hawksbill populations. The information presented here highlights the importance of national conservation strategies and international cooperation for the recovery of endangered hawksbill turtle populations.

Contextualising the Last Survivors: Population Structure of Marine Turtles in the Dominican Republic

Nesting by three species of marine turtles persists in the Dominican Republic, despite historic threats and long-term population decline. We conducted a genetic survey of marine turtles in the Dominican Republic in order to link them with other rookeries around the Caribbean. We sequenced a 740bp fragment of the control region of the mitochondrial DNA of 92 samples from three marine turtle species [hawksbill (n = 48), green (n = 2) and leatherback (n = 42)], and incorporated published data from other nesting populations and foraging grounds. The leatherback turtle (Dermochelys coriacea) in the Dominican Republic appeared to be isolated from Awala-Yalimapo, Cayenne, Trinidad and St. Croix but connected with other Caribbean populations. Two distinct nesting populations of hawksbill turtles (Eremochelys imbricata) were detected in the Dominican Republic and exhibited interesting patterns of connectivity with other nesting sites and juvenile and adult male foraging aggregations. The green sea turtle (Chelonia mydas) has almost been extirpated from the Dominican Republic and limited inference could be made from our samples. Finally, results were compared with Lagrangian drifting buoys and published Lagrangian virtual particles that travelled through the Dominican Republic and Caribbean waters. Conservation implications of sink-source effects or genetic isolation derived from these complex inter-connections are discussed for each species and population.

Re-examination of population structure and phylogeography of hawksbill turtles in the wider Caribbean using longer mtDNA sequences

Management of the critically endangered hawksbill turtle in the Wider Caribbean (WC) has been hampered by knowledge gaps regarding stock structure. We carried out a comprehensive stock structure re-assessment of 11 WC hawksbill rookeries using longer mtDNA sequences, larger sample sizes (N = 647), and additional rookeries compared to previous surveys. Additional variation detected by 740 bp sequences between populations allowed us to differentiate populations such as Barbados-Windward and Guadeloupe (F (st) = 0.683, P < 0.05) that appeared genetically indistinguishable based on shorter 380 bp sequences. POWSIM analysis showed that longer sequences improved power to detect population structure and that when N < 30, increasing the variation detected was as effective in increasing power as increasing sample size. Geographic patterns of genetic variation suggest a model of periodic long-distance colonization coupled with region-wide dispersal and subsequent secondary contact within the WC. Mismatch analysis results for individual clades suggest a general population expansion in the WC following a historic bottleneck about 100 000-300 000 years ago. We estimated an effective female population size (N (ef)) of 6000-9000 for the WC, similar to the current estimated numbers of breeding females, highlighting the importance of these regional rookeries to maintaining genetic diversity in hawksbills. Our results provide a basis for standardizing future work to 740 bp sequence reads and establish a more complete baseline for determining stock boundaries in this migratory marine species. Finally, our findings illustrate the value of maintaining an archive of specimens for re-analysis as new markers become available.

Protected areas host important remnants of marine turtle nesting stocks in the Dominican Republic

Nesting by marine turtles in the Caribbean has declined considerably, mainly because of human exploitation, but there has previously been no monitoring in the Dominican Republic. We present the first detailed assessment of the status of marine turtle nesting in the country, based on surveys during 2006–2010. Nesting populations of hawksbill Eretmochelys imbricata and leatherback turtle Dermochelys coriacea are of regional importance and the green turtle Chelonia mydas is still present, although nesting in low numbers. The two main nesting sites are within protected areas: the Jaragua National Park in the south-west, important for leatherback turtles (mean of 126 nests per season), and Del Este National Park on Saona Island in the south-east, principally for hawksbill turtles (mean of 100 nests per season). Comparison with historical data suggests all rookeries are profoundly reduced in size. Although the main nesting beaches are within protected areas, illegal egg-take and meat consumption continues there, and also elsewhere in the country.

Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast

Surprisingly, a high frequency of interspecific sea turtle hybrids has been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as Eretmochelys imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, because most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analysed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (E. imbricata), loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years.

Multiple distant origins for green sea turtles aggregating off Gorgona Island in the Colombian eastern Pacific

Mitochondrial DNA analyses have been useful for resolving maternal lineages and migratory behavior to foraging grounds (FG) in sea turtles. However, little is known about source rookeries and haplotype composition of foraging green turtle aggregations in the southeastern Pacific. We used mitochondrial DNA control region sequences to identify the haplotype composition of 55 green turtles, Chelonia mydas, captured in foraging grounds of Gorgona National Park in the Colombian Pacific. Amplified fragments of the control region (457 bp) revealed the presence of seven haplotypes, with haplotype (h) and nucleotide (π) diversities of h = 0.300±0.080 and π = 0.009±0.005 respectively. The most common haplotype was CMP4 observed in 83% of individuals, followed by CMP22 (5%). The genetic composition of the Gorgona foraging population primarily comprised haplotypes that have been found at eastern Pacific rookeries including Mexico and the Galapagos, as well as haplotypes of unknown stock origin that likely originated from more distant western Pacific rookeries. Mixed stock analysis suggests that the Gorgona FG population is comprised mostly of animals from the Galapagos rookery (80%). Lagrangian drifter data showed that movement of turtles along the eastern Pacific coast and eastward from distant western and central Pacific sites was possible through passive drift. Our results highlight the importance of this protected area for conservation management of green turtles recruited from distant sites along the eastern Pacific Ocean.

Global phylogeography and evolution of chelonid fibropapilloma-associated herpesvirus

A global phylogeny for chelonid fibropapilloma-associated herpesvirus (CFPHV), the most likely aetiological agent of fibropapillomatosis (FP) in sea turtles, was inferred, using dated sequences, through Bayesian Markov chain Monte Carlo analysis and used to estimate the virus evolutionary rate independent of the evolution of the host, and to resolve the phylogenetic positions of new haplotypes from Puerto Rico and the Gulf of Guinea. Four phylogeographical groups were identified: eastern Pacific, western Atlantic/eastern Caribbean, mid-west Pacific and Atlantic. The latter comprises the Gulf of Guinea and Puerto Rico, suggesting recent virus gene flow between these two regions. One virus haplotype from Florida remained elusive, representing either an independent lineage sharing a common ancestor with all other identified virus variants or an Atlantic representative of the lineage giving rise to the eastern Pacific group. The virus evolutionary rate ranged from 1.62×10(-4) to 2.22×10(-4) substitutions per site per year, which is much faster than what is expected for a herpesvirus. The mean time for the most recent common ancestor of the modern virus variants was estimated at 192.90-429.71 years ago, which, although more recent than previous estimates, still supports an interpretation that the global FP pandemic is not the result of a recent acquisition of a virulence mutation(s). The phylogeographical pattern obtained seems partially to reflect sea turtle movements, whereas altered environments appear to be implicated in current FP outbreaks and in the modern evolutionary history of CFPHV.

Comparative phylogeny and historical perspectives on population genetics of the Pacific hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas), inferred from feeding populations in the Yaeyama Islands, Japan

Mitochondrial DNA sequence polymorphisms and patterns of genetic diversity represent the genealogy and relative impacts of historical, geographic, and demographic events on populations. In this study, historical patterns of population dynamics and differentiation in hawksbill (Eretmochelys imbricata) and green turtles (Chelonia mydas) in the Pacific were estimated from feeding populations in the Yaeyama Islands, Japan. Phylogenetic relationships of the haplotypes indicated that hawksbill and green turtles in the Pacific probably underwent very similar patterns and processes of population dynamics over the last million years, with population subdivision during the early Pleistocene and population expansion after the last glacial maximum. These significant contemporary historical events were suggested to have been caused by climatic and sea-level fluctuations. On the other hand, comparing our results to long-term population dynamics in the Atlantic, population subdivisions during the early Pleistocene were specific to Pacific hawksbill and green turtles. Therefore, regional differences in historical population dynamics are suggested. Despite limited sampling locations, these results are the first step in estimating the historical trends in Pacific sea turtles by using phylogenetics and population genetics.

Genomic approaches with natural fish populations

Natural populations v. inbred stocks provide a much richer resource for identifying the effects of nucleotide substitutions because natural populations have greater polymorphism. Additionally, natural populations offer an advantage over most common research organisms because they are subject to natural selection, and analyses of these adaptations can be used to identify biologically important changes. Among fishes, these analyses are enhanced by having a wide diversity of species (>28 000 species, more than any other group of vertebrates) living in a huge range of environments (from below freezing to > 46 degrees C, in fresh water to salinities >40 ppt.). Moreover, fishes exhibit many different life-history and reproductive strategies and have many different phenotypes and social structures. Although fishes provide numerous advantages over other vertebrate models, there is still a dearth of available genomic tools for fishes. Fishes make up approximately half of all known vertebrate species, yet <0.2% of fish species have significant genomic resources. Nonetheless, genomic approaches with fishes have provided some of the first measures of individual variation in gene expression and insights into environmental and ecological adaptations. Thus, genomic approaches with natural fish populations have the potential to revolutionize fundamental studies of diverse fish species that offer myriad ecological and evolutionary questions.

Turtle groups or turtle soup: dispersal patterns of hawksbill turtles in the Caribbean

Despite intense interest in conservation of marine turtles, spatial ecology during the oceanic juvenile phase remains relatively unknown. Here, we used mixed stock analysis and examination of oceanic drift to elucidate movements of hawksbill turtles (Eretmochelys imbricata) and address management implications within the Caribbean. Among samples collected from 92 neritic juvenile hawksbills in the Cayman Islands we detected 11 mtDNA control region haplotypes. To estimate contributions to the aggregation, we performed 'many-to-many' mixed stock analysis, incorporating published hawksbill genetic and population data. The Cayman Islands aggregation represents a diverse mixed stock: potentially contributing source rookeries spanned the Caribbean basin, delineating a scale of recruitment of 200-2500 km. As hawksbills undergo an extended phase of oceanic dispersal, ocean currents may drive patterns of genetic diversity observed on foraging aggregations. Therefore, using high-resolution Aviso ocean current data, we modelled movement of particles representing passively drifting oceanic juvenile hawksbills. Putative distribution patterns varied markedly by origin: particles from many rookeries were broadly distributed across the region, while others would appear to become entrained in local gyres. Overall, we detected a significant correlation between genetic profiles of foraging aggregations and patterns of particle distribution produced by a hatchling drift model (Mantel test, r = 0.77, P < 0.001; linear regression, r = 0.83, P < 0.001). Our results indicate that although there is a high degree of mixing across the Caribbean (a 'turtle soup'), current patterns play a substantial role in determining genetic structure of foraging aggregations (forming turtle groups). Thus, for marine turtles and other widely distributed marine species, integration of genetic and oceanographic data may enhance understanding of population connectivity and management requirements.

Chapter 2. Vulnerability of marine turtles to climate change

Marine turtles are generally viewed as vulnerable to climate change because of the role that temperature plays in the sex determination of embryos, their long life history, long age-to-maturity and their highly migratory nature. Extant species of marine turtles probably arose during the mid-late Jurassic period (180-150 Mya) so have survived past shifts in climate, including glacial periods and warm events and therefore have some capacity for adaptation. The present-day rates of increase of atmospheric greenhouse gas concentrations, and associated temperature changes, are very rapid; the capacity of marine turtles to adapt to this rapid change may be compromised by their relatively long generation times. We consider the evidence and likely consequences of present-day trends of climate change on marine turtles. Impacts are likely to be complex and may be positive as well as negative. For example, rising sea levels and increased storm intensity will negatively impact turtle nesting beaches; however, extreme storms can also lead to coastal accretion. Alteration of wind patterns and ocean currents will have implications for juveniles and adults in the open ocean. Warming temperatures are likely to impact directly all turtle life stages, such as the sex determination of embryos in the nest and growth rates. Warming of 2 degrees C could potentially result in a large shift in sex ratios towards females at many rookeries, although some populations may be resilient to warming if female biases remain within levels where population success is not impaired. Indirectly, climate change is likely to impact turtles through changes in food availability. The highly migratory nature of turtles and their ability to move considerable distances in short periods of time should increase their resilience to climate change. However, any such resilience of marine turtles to climate change is likely to be severely compromised by other anthropogenic influences. Development of coastlines may threaten nesting beaches and reproductive success, and pollution and eutrophication is threatening important coastal foraging habitats for turtles worldwide. Exploitation and bycatch in other fisheries has seriously reduced marine turtle populations. The synergistic effects of other human-induced stressors may seriously reduce the capacity of some turtle populations to adapt to the current rates of climate change. Conservation recommendations to increase the capacity of marine turtle populations to adapt to climate change include increasing population resilience, for example by the use of turtle exclusion devices in fisheries, protection of nesting beaches from the viewpoints of both conservation and coastal management, and increased international conservation efforts to protect turtles in regions where there is high unregulated or illegal fisheries (including turtle harvesting). Increasing research efforts on the critical knowledge gaps of processes influencing population numbers, such as identifying ocean foraging hotspots or the processes that underlie the initiation of nesting migrations and selection of breeding areas, will inform adaptive management in a changing climate.

Population genetic structure of Earth's largest fish, the whale shark (Rhincodon typus)

Large pelagic vertebrates pose special conservation challenges because their movements generally exceed the boundaries of any single jurisdiction. To assess the population structure of whale sharks (Rhincodon typus), we sequenced complete mitochondrial DNA control regions from individuals collected across a global distribution. We observed 51 single site polymorphisms and 8 regions with indels comprising 44 haplotypes in 70 individuals, with high haplotype (h = 0.974 +/- 0.008) and nucleotide diversity (pi = 0.011 +/- 0.006). The control region has the largest length variation yet reported for an elasmobranch (1143-1332 bp). Phylogenetic analyses reveal no geographical clustering of lineages and the most common haplotype was distributed globally. The absence of population structure across the Indian and Pacific basins indicates that oceanic expanses and land barriers in Southeast Asia are not impediments to whale shark dispersal. We did, however, find significant haplotype frequency differences (AMOVA, Phi(ST) = 0.107, P < 0.001) principally between the Atlantic and Indo-Pacific populations. In contrast to other recent surveys of globally distributed sharks, we find much less population subdivision and no evidence for cryptic evolutionary partitions. Discovery of the mating and pupping areas of whale sharks is key to further population genetic studies. The global pattern of shared haplotypes in whale sharks provides a compelling argument for development of broad international approaches for management and conservation of Earth's largest fish.

Dispersal, recruitment and migratory behaviour in a hawksbill sea turtle aggregation

We investigated the dispersal, recruitment and migratory behaviour of the hawksbill sea turtle (Eretmochelys imbricata), among different life-history stages and demographic segments of the large hawksbill turtle aggregation at Mona Island, Puerto Rico. There were significant differences in both mitochondrial DNA (mtDNA) haplotype diversity and haplotype frequencies among the adult males, females and juveniles examined, but little evidence for temporal heterogeneity within these same groups sampled across years. Consistent with previous studies and the hypothesis of strong natal homing, there were striking mtDNA haplotype differences between nesting females on Mona Island and nesting females in other major Caribbean rookeries. Breeding males also showed strong, albeit weaker, genetic evidence of natal homing. Overall, Bayesian mixed-stock analysis suggests that Mona Island was the natal rookery for 79% (65-94%) of males in the aggregation. In contrast, the Mona Island rookery accounted for only a small subset of the new juvenile recruits to the foraging grounds or in the population of older juvenile hawksbills turtles on Mona. Instead, both new recruits and the older juvenile hawksbill turtles on Mona more likely recruited from other Caribbean rookeries, suggesting that a mechanism besides natal homing must be influencing recruitment to feeding habitats. The difference in the apparent degree of natal homing behaviour among the different life-history stages of hawksbill turtles at Mona Island underscores the complexity of the species' life-history dynamics and highlights the need for both local and regional conservation efforts.

Population genetics and phylogeography of sea turtles

The seven species of sea turtles occupy a diversity of niches, and have a history tracing back over 100 million years, yet all share basic life-history features, including exceptional navigation skills and periodic migrations from feeding to breeding habitats. Here, we review the biogeographic, behavioural, and ecological factors that shape the distribution of genetic diversity in sea turtles. Natal homing, wherein turtles return to their region of origin for mating and nesting, has been demonstrated with mtDNA sequences. These maternally inherited markers show strong population structure among nesting colonies while nuclear loci reveal a contrasting pattern of male-mediated gene flow, a phenomenon termed 'complex population structure'. Mixed-stock analyses indicate that multiple nesting colonies can contribute to feeding aggregates, such that exploitation of turtles in these habitats can reduce breeding populations across the region. The mtDNA data also demonstrate migrations across entire ocean basins, some of the longest movements of marine vertebrates. Multiple paternity occurs at reported rates of 0-100%, and can vary by as much as 9-100% within species. Hybridization in almost every combination among members of the Cheloniidae has been documented but the frequency and ultimate ramifications of hybridization are not clear. The global phylogeography of sea turtles reveals a gradient based on habitat preference and thermal regime. The cold-tolerant leatherback turtle (Dermochelys coriacea) shows no evolutionary partitions between Indo-Pacific and Atlantic populations, while the tropical green (Chelonia mydas), hawksbill (Eretmochelys imbricata), and ridleys (Lepidochelys olivacea vs. L. kempi) have ancient separations between oceans. Ridleys and loggerhead (Caretta caretta) also show more recent colonization between ocean basins, probably mediated by warm-water gyres that occasionally traverse the frigid upwelling zone in southern Africa. These rare events may be sufficient to prevent allopatric speciation under contemporary geographic and climatic conditions. Genetic studies have advanced our understanding of marine turtle biology and evolution, but significant gaps persist and provide challenges for the next generation of sea turtle geneticists.