Population structure and phylogeography reveal pathways of colonization by a migratory marine reptile (Chelonia mydas) in the central and eastern Pacific

Genetic structure and diversity of green turtle (Chelonia mydas) in the Gulf of Thailand

Background and Aim

The International Union for the Conservation of Nature and Natural Resources lists the green turtle as endangered. Green turtle nesting behavior in the Gulf of Thailand has decreased to <50% of the 1995 level. The population structure of green turtles in the Gulf of Thailand has not yet been studied. This study aimed to characterize the genetic diversity of green turtles in the Gulf of Thailand based on comparisons of mitochondrial DNA (mtDNA) control region with sequences of Indo-Pacific management units (MUs) and rookeries, to investigate population structures, and to explore phylogeographic relationships.

Materials and Methods

Blood samples (1 mL each) from 91 stranded green turtles were collected from four parts of the Gulf of Thailand (eastern, upper, central, and lower). The control mtDNA region was amplified by polymerase chain reaction using LCM15382 and H950 primer. The obtained 384-bp or 770-bp sequences were analyzed for haplotype, clade, and haplotype and nucleotide diversities and were used to construct a phylogenetic tree and haplotype network diagram, respectively. In addition, we analyzed genetic differentiation within and among populations of green turtles in the Gulf of Thailand and between green turtles in the Gulf of Thailand and other Indo-Pacific MUs and rookeries.

Results

In total, 12 (based on 384 bp) or 13 (based on 770 bp) haplotypes and two clades (clades VII and VIII) were identified, with nine or 10 haplotypes belonging to clade VIII and three haplotypes belonging to clade VII. Of the new haplotypes, four or five were identified and classified as clade VII (two haplotypes, for both fragment lengths) and clade VIII (two or three haplotypes, for 384 bp or 770 bp fragments, respectively). The overall haplotype and nucleotide diversity of green turtles in the Gulf of Thailand were high (0.755 ± 0.039 and 0.01146 ± 0.00248, respectively). Based on the analysis of molecular variance, green turtles in the Gulf of Thailand could be divided into two subpopulations (UC-Eastern Gulf of Thailand [UC-EGT] and lower Gulf of Thailand [LGT]). Comparisons with other MUs and rookeries in the Indo-Pacific showed that UC-EGT was not genetically different from the Peninsular Malaysia and Eastern Taiwan (Lanyu) MUs and the Terrangganu and Mersing rookeries, and LGT were not genetically different from Peninsular Malaysia, Sipadan, Brunei Bay, Eastern Taiwan (Lanyu), Scott Reef and Browse Island, and Gulf of Carpentaria MUs and the Perak, Perhentain Island, Redang, Pahang, and Vietnam rookeries.

Conclusion

To the best of our knowledge, this is the first report to identify the haplotypes and clades of green turtles in the Gulf of Thailand and to show that the populations in the Gulf of Thailand not only present high genetic diversity but also have haplotypic endemism. Longer mtDNA fragments (770 bp) increased the resolution of the stock structure. Clade VII is a unique clade not only for Japan but also for Thailand and Malaysia, and CmP82 is a unique haplotype for both the Gulf of Thailand and Malaysia. Conservation and management of these populations are important to preserve the genetic diversity, biological diversity, and evolutionary potential of green turtles in the Gulf of Thailand.

Blood analyte reference intervals and correlations with trace elements of immature and adult Eastern Pacific green turtles (Chelonia mydas) in coastal lagoons of Baja California Sur, México

Sea turtles can bioaccumulate high concentrations of potentially toxic contaminants. To better understand trace element effects on sea turtles' health, we established reference intervals for hematological and plasma biochemical analytes in 40 in-water, foraging immature and adult Eastern Pacific green turtles (Chelonia mydas) from two coastal lagoons in Baja California Sur, quantified whole blood concentrations of eight trace elements, and assessed their correlations. Rank-order trace element concentrations in both immature and adult turtles was zinc > selenium > nickel > arsenic > copper > cadmium > lead > manganese. Immature turtles had significantly higher copper and lower nickel and zinc concentrations. Additionally, a number of relationships between trace elements and blood analytes were identified. These data provide baseline information useful for future investigations into this population, or in other geographic regions and various life-stage classes.

Revisiting the genetic diversity and population structure of the endangered Green Sea Turtle (Chelonia mydas) breeding populations in the Xisha (Paracel) Islands, South China Sea

The Green Sea Turtle (Chelonia mydas) is an umbrella species in the South China Sea, a Chinese national first-level protected wild animal, and the only sea turtle that nests in waters around China. The largest C. mydas nesting ground is distributed in the Xisha (Paracel) Islands, which plays a vital role in the survival of sea turtle populations in the region. This study reveals the genetic diversity and population structure of the breeding population of C. mydas in the Xisha (Paracel) Islands using three mitochondrial markers. A total of 15 D-loop, five Cytochrome b (Cyt b), and seven Cytochrome C Oxidase subunit I (COI) haplotypes were identified in the breeding population of C. mydas in the Xisha (Paracel) Islands. D-loop haplotypes are distributed in clades III, IV, and VIII of the C. mydas mitochondrial control region. It is the first time that one haplotype from Clade IV was found in this C. mydas population, and five new D-loop haplotypes were also identified. The haplotype and nucleotide diversity were calculated for each marker: D-loop (0.415 haplotype diversity, 0.00204 nucleotide diversity), Cyt b (0.140, 0.00038) and COI (0.308, 0.00083). The average genetic distance (p) of each molecular marker was less than 0.01. Neutral detection and nucleotide mismatch analysis suggested that the breeding population of C. mydas in the Xisha (Paracel) Islands did not experience a population expansion event in recent history. It is recommended that a sea turtle protection area be established in the Xisha (Paracel) Islands area to strengthen protection and effectively protect the uniqueness and sustainability of the breeding population of C. mydas in the South China Sea.

Genetics, Morphometrics and Health Characterization of Green Turtle Foraging Grounds in Mainland and Insular Chile

Simple Summary

Chilean waters constitute a foraging habitat for the endangered green turtle. Information about this species in the country has increased in recent years; nevertheless, little is known of its ecology and health status. Additionally, some populations have drastically decreased, probably due to human factors. Here, we studied the proportion of sex, age, morphological variation, genetic characteristics, origin, and health status of green turtles in mainland and insular Chile. We found that turtles from both regions are morphologically and genetically different. Individuals from the mainland territory are juveniles and probably originated from Galapagos. In contrast, the insular territory hosts juveniles and adults that probably originated from Galapagos and French Polynesia. We also found that turtles from both regions are facing numerous anthropic threats that must be controlled. We suggest the creation of protected areas for mainland foraging grounds, and strengthen the administrative plan of the insular region to ensure sea turtle population health.

Abstract

Two divergent genetic lineages have been described for the endangered green turtle in the Pacific Ocean, occurring sympatrically in some foraging grounds. Chile has seven known green turtle foraging grounds, hosting mainly juveniles of different lineages. Unfortunately, anthropic factors have led to the decline or disappearance of most foraging aggregations. We investigated age-class/sex structure, morphological variation, genetic diversity and structure, and health status of turtles from two mainland (Bahia Salado and Playa Chinchorro) and one insular (Easter Island) Chilean foraging grounds. Bahia Salado is composed of juveniles, and with Playa Chinchorro, exclusively harbors individuals of the north-central/eastern Pacific lineage, with Galapagos as the major genetic contributor. Conversely, Easter Island hosts juveniles and adults from both the eastern Pacific and French Polynesia. Morphological variation was found between lineages and foraging grounds, suggesting an underlying genetic component but also an environmental influence. Turtles from Easter Island, unlike Bahia Salado, exhibited injuries/alterations probably related to anthropic threats. Our findings point to establishing legal protection for mainland Chile’s foraging grounds, and to ensure that the administrative plan for Easter Island’s marine protected area maintains ecosystem health, turtle population viability, and related cultural and touristic activities.

Population Genetics and Phylogeography of Galapagos Fur Seals

Pinnipeds found across islands provide an ideal opportunity to examine the evolutionary process of population subdivision affected by several mechanisms. Here, we report the genetic consequences of the geographic distribution of rookeries in Galapagos fur seals (GFS: Arctocephalus galapagoensis) in creating population structure. We show that rookeries across four islands (nine rookeries) are genetically structured into the following major groups: 1) a western cluster of individuals from Fernandina; 2) a central group from north and east Isabela, Santiago, and Pinta; and possibly, 3) a third cluster in the northeast from Pinta. Furthermore, asymmetric levels of gene flow obtained from eight microsatellites found migration from west Isabela to Fernandina islands (number of migrants Nm = 1), with imperceptible Nm in any other direction. Our findings suggest that the marked structuring of populations recovered in GFS is likely related to an interplay between long-term site fidelity and long-distance migration in both male and female individuals, probably influenced by varying degrees of marine productivity.

Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle

Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle (Chelonia mydas) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq; 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds (n = 158). Our results support genetic divergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation of C. mydas to the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.

Multi-tissue stable isotope analyses reveal temporal changes in the feeding patterns of green turtles in the Galapagos Marine Reserve

Knowledge of feeding patterns of highly migratory species is critical for understanding their habitat use and informing the management of their populations. The Galapagos Islands are one of the most important nesting and feeding areas for green turtles (Chelonia mydas) across the tropical eastern Pacific, yet little is known about the feeding patterns of this species. The isotopic composition of different tissues has been used to gain insight into the trophic dynamics of mobile aquatic consumers whose trophic behavior is difficult to directly measure. To elucidate the temporal feeding patterns and isotopic niche sizes of Galapagos green turtles, stable isotope analyses were performed on multiple tissues (skin and carapace) collected at the two most important nesting areas in the archipelago: Bachas and Quinta Playa. The δ¹³ C and δ¹⁵ N signatures on the skin and carapace samples from 56 adult females revealed significant differences between tissues (p = .001 and p = .021, respectively) and nesting areas (p = .011 and p = .003, respectively). These differences suggest a shift from oceanic feeding grounds to neritic habitats before nesting. The carapace isotope values indicated an offshore feeding strategy and a greater isotopic niche (SEAc = 1.91‰² ), whereas the skin isotope values represented an inshore feeding strategy with a narrower niche (SEAc = 1.37‰² ), likely related to the consumption of specific coastal prey. Our results suggest that Galapagos green turtles feed across different habitats, and this information can be applied to improve the management of this endangered species.

First detection of an ocellate octopus in the Revillagigedos ecoregion, a biodiversity hotspot located in the Tropical East Pacific Province

The biodiversity of mollusks, particularly cephalopods, has not been exhaustively determined in the Revillagigedos ecoregion, which is a biodiversity hotspot for several marine groups located in the Tropical East Pacific Province. In our study, we detected and examined ocellate octopuses from Socorro and Clarion Islands, and determined their identity using morphological criteria and molecular data from two mitochondrial genes (COIII and COI). The taxon identified was Octopus oculifer, a species considered endemic to the Galapagos Archipelago. In addition, according to our analyses, O. mimus, O. hubbsorum and O. oculifer are very closely related and may represent a species complex comprised of three morphotypes. We found that the evolutionary relationships among octopuses are not determined by the presence of ocelli. This study is the first to report a clade represented by ocellate and non-ocellate species, in addition, the identity of cephalopods in the Revillagigedos was determined with analytical support.

Integrating morphological and genetic data at different spatial scales in a cosmopolitan marine turtle species: challenges for management and conservation

Patterns of genetic structure in highly mobile marine vertebrates may be accompanied by phenotypic variation. Most studies in marine turtles focused on population genetic structure have been performed at rookeries. We studied whether genetic and morphological variation of the endangered green turtle (Chelonia mydas) is consistent geographically, focusing on foraging grounds. An association between population genetic structure and body shape variation at broad (inter-lineage) and fine (foraging grounds) scales was predicted and analysed using mitochondrial DNA and geometric morphometrics. Although genetic and phenotypic differentiation patterns were congruent between lineages, no fine-scale association was found, suggesting adaptive divergence. Connectivity among Pacific foraging grounds found here suggests that temperatures of ocean surface currents may influence the genetic structure of C. mydas on a broad scale. Our results suggest that vicariance, dispersal, life-history traits and ecological conditions operating in foraging grounds have shaped the intraspecific morphology and genetic diversity of this species. Considering a range of geographic and temporal scales is useful when management strategies are required for cosmopolitan species. Integrating morphological and genetic tools at different spatial scales, conservation management is proposed based on protection of neutral and adaptive diversity. This approach opens new questions and challenges, especially regarding conservation genetics in cosmopolitan species.

Identifying genetic lineages through shape: An example in a cosmopolitan marine turtle species using geometric morphometrics

The green turtle (Chelonia mydas) is a globally distributed marine species whose evolutionary history has been molded by geological events and oceanographic and climate changes. Divergence between Atlantic and Pacific clades has been associated with the uplift of the Panama Isthmus, and inside the Pacific region, a biogeographic barrier located west of Hawaii has restricted the gene flow between Central/Eastern and Western Pacific populations. We investigated the carapace shape of C. mydas from individuals of Atlantic, Eastern Pacific, and Western Pacific genetic lineages using geometric morphometrics to evaluate congruence between external morphology and species' phylogeography. Furthermore, we assessed the variation of carapace shape according to foraging grounds. Three morphologically distinctive groups were observed which aligned with predictions based on the species' lineages, suggesting a substantial genetic influence on carapace shape. Based on the relationship between this trait and genetic lineages, we propose the existence of at least three distinct morphotypes of C. mydas. Well-defined groups in some foraging grounds (Galapagos, Costa Rica and New Zealand) may suggest that ecological or environmental conditions in these sites could also be influencing carapace shape in C. mydas. Geometric morphometrics is a suitable tool to differentiate genetic lineages in this cosmopolitan marine species. Consequently, this study opens new possibilities to explore and test ecological and evolutionary hypotheses in species with wide morphological variation and broad geographic distribution range.

Mixed stock analysis of juvenile green turtles aggregating at two foraging grounds in Fiji reveals major contribution from the American Samoa Management Unit

In this study we assessed the breeding population, or Management Unit (MU), origin of green turtles (Chelonia mydas) present at Yadua Island and Makogai Island foraging grounds in Fiji, central South Pacific. Based on analysis of mitochondrial (mt) DNA sequences from 150 immature green turtles caught during surveys carried out in 2015–2016, we identified a total of 18 haplotypes, the most common being CmP22.1 (44%) which is a primary haplotype characterizing the American Samoa breeding population. Results of a Bayesian mixed-stock analysis reveals that the two foraging grounds are used by green turtles from the American Samoa MU (72%, Credible Interval (CI): 56–87%), New Caledonia MU (17%, CI: 6–26%) and French Polynesia MU (7%, CI: 0–23%). The prominence of the contribution we found from the American Samoa MU compared to that of French Polynesia, both which have historic telemetry and tagging data showing connectivity with Fijian foraging areas, may reflect the current relative abundance of these two nesting populations and draws attention to a need to update population surveys and identify any significant nesting in Fiji that may have been overlooked.

Shared Epizoic Taxa and Differences in Diatom Community Structure Between Green Turtles (Chelonia mydas) from Distant Habitats

The first reports of diatoms growing on marine mammals date back to the early 1900s. However, only recently has direct evidence been provided for similar associations between diatoms and sea turtles. We present a comparison of diatom communities inhabiting carapaces of green turtles Chelonia mydas sampled at two remote sites located within the Indian (Iran) and Atlantic (Costa Rica) Ocean basins. Diatom observations and counts were carried out using scanning electron microscopy. Techniques involving critical point drying enabled observations of diatoms and other microepibionts still attached to sea turtle carapace and revealed specific aspects of the epizoic community structure. Species-poor, well-developed diatom communities were found on all examined sea turtles. Significant differences between the two host sea turtle populations were observed in terms of diatom abundance and their community structure (including growth form structure). A total of 12 and 22 diatom taxa were found from sea turtles in Iran and Costa Rica, respectively, and eight of these species belonging to Amphora, Chelonicola, Cocconeis, Navicula, Nitzschia and Poulinea genera were observed in samples from both locations. Potential mechanisms of diatom dispersal and the influence of the external environment, sea turtle behaviour, its life stage, and foraging and breeding habitats, as well as epibiotic bacterial flora on epizoic communities, are discussed.

Assessing Fukushima-Derived Radiocesium in Migratory Pacific Predators

The 2011 release of Fukushima-derived radionuclides into the Pacific Ocean made migratory sharks, teleosts, and marine mammals a source of speculation and anxiety regarding radiocesium (^134+137Cs) contamination, despite a lack of actual radiocesium measurements for these taxa. We measured radiocesium in a diverse suite of large predators from the North Pacific Ocean and report no detectable (i.e., ≥ 0.1 Bq kg^-1 dry wt) Fukushima-derived ¹³⁴Cs in all samples, except in one olive ridley sea turtle (Lepidochelys olivacea) with trace levels (0.1 Bq kg^-1). Levels of ¹³⁷Cs varied within and across taxa, but were generally consistent with pre-Fukushima levels and were lower than naturally occurring ⁴⁰K by one to one to two orders of magnitude. Predator size had a weaker effect on ¹³⁷Cs and ⁴⁰K levels than tissue lipid content. Predator stable isotope values (δ¹³C and δ¹⁵N) were used to infer recent migration patterns, and showed that predators in the central, eastern, and western Pacific should not be assumed to accumulate detectable levels of radiocesium a priori. Nondetection of ¹³⁴Cs and low levels of ¹³⁷Cs in diverse marine megafauna far from Fukushima confirms negligible increases in radiocesium, with levels comparable to those prior to the release from Fukushima. Reported levels can inform recently developed models of cesium transport and bioaccumulation in marine species.

A phylogeny of Southern Hemisphere whelks (Gastropoda: Buccinulidae) and concordance with the fossil record

Under current marine snail taxonomy, the majority of whelks from the Southern Hemisphere (Buccinulidae) are hypothesised to represent a monophyletic clade that has evolved independently from Northern Hemisphere taxa (Buccinidae). Phylogenetic analysis of mitochondrial genomic and nuclear ribosomal DNA sequence data indicates that Southern Hemisphere taxa are not monophyletic, and results suggest that dispersal across the equator has occurred in both directions. New Zealand buccinulid whelks, noted for their high endemic diversity, are also found to not be monophyletic. Using independent fossil calibrations, estimated genetic divergence dates show remarkable concordance with the fossil record of the Penion and Kelletia. The divergence dates and the geographic distribution of the genera through time implies that some benthic marine snails are capable of dispersal over long distances, despite varied developmental strategies. Phylogenetic results also indicate that one species, P. benthicolus belongs in Antarctoneptunea.

Hawksbill turtle terra incognita: conservation genetics of eastern Pacific rookeries

Prior to 2008 and the discovery of several important hawksbill turtle (Eretmochelys imbricata) nesting colonies in the EP (Eastern Pacific), the species was considered virtually absent from the region. Research since that time has yielded new insights into EP hawksbills, salient among them being the use of mangrove estuaries for nesting. These recent revelations have raised interest in the genetic characterization of hawksbills in the EP, studies of which have remained lacking to date. Between 2008 and 2014, we collected tissue samples from 269 nesting hawksbills at nine rookeries across the EP and used mitochondrial DNA sequences (766 bp) to generate the first genetic characterization of rookeries in the region. Our results inform genetic diversity, population differentiation, and phylogeography of the species. Hawksbills in the EP demonstrate low genetic diversity: We identified a total of only seven haplotypes across the region, including five new and two previously identified nesting haplotypes (pooled frequencies of 58.4% and 41.6%, respectively), the former only evident in Central American rookeries. Despite low genetic diversity, we found strong stock structure between the four principal rookeries, suggesting the existence of multiple populations and warranting their recognition as distinct management units. Furthermore, haplotypes EiIP106 and EiIP108 are unique to hawksbills that nest in mangrove estuaries, a behavior found only in hawksbills along Pacific Central America. The detected genetic differentiation supports the existence of a novel mangrove estuary "reproductive ecotype" that may warrant additional conservation attention. From a phylogeographic perspective, our research indicates hawksbills colonized the EP via the Indo-Pacific, and do not represent relict populations isolated from the Atlantic by the rising of the Panama Isthmus. Low overall genetic diversity in the EP is likely the combined result of few rookeries, extremely small reproductive populations and evolutionarily recent colonization events. Additional research with larger sample sizes and variable markers will help further genetic understanding of hawksbill turtles in the EP.

Multinational tagging efforts illustrate regional scale of distribution and threats for east pacific green turtles (Chelonia mydas agassizii)

To further describe movement patterns and distribution of East Pacific green turtles (Chelonia mydas agassizii) and to determine threat levels for this species within the Eastern Pacific. In order to do this we combined published data from existing flipper tagging and early satellite tracking studies with data from an additional 12 satellite tracked green turtles (1996-2006). Three of these were tracked from their foraging grounds in the Gulf of California along the east coast of the Baja California peninsula to their breeding grounds in Michoacán (1337-2928 km). In addition, three post-nesting females were satellite tracked from Colola beach, Michoacán to their foraging grounds in southern Mexico and Central America (941.3-3020 km). A further six turtles were tracked in the Gulf of California within their foraging grounds giving insights into the scale of ranging behaviour. Turtles undertaking long-distance migrations showed a tendency to follow the coastline. Turtles tracked within foraging grounds showed that foraging individuals typically ranged up to 691.6 km (maximum) from release site location. Additionally, we carried out threat analysis (using the cumulative global human impact in the Eastern Pacific) clustering pre-existing satellite tracking studies from Galapagos, Costa Rica, and data obtained from this study; this indicated that turtles foraging and nesting in Central American waters are subject to the highest anthropogenic impact. Considering that turtles from all three rookeries were found to migrate towards Central America, it is highly important to implement conservation plans in Central American coastal areas to ensure the survival of the remaining green turtles in the Eastern Pacific. Finally, by combining satellite tracking data from this and previous studies, and data of tag returns we created the best available distributional patterns for this particular sea turtle species, which emphasized that conservation measures in key areas may have positive consequences on a regional scale.