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Population-wide distribution of nucleotide diversity region demonstrating the presence of polymorphic sites extending outside the 384 bp segment traditionally used. The distribution of the variation along the set of sequences was estimated using the sliding window option, with a window length of 50 sites and a step size of 25 sites.
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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 surve...
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We conducted a study on foraging green sea turtles (Chelonia mydas) in the Northern Persian Gulf and Oman Sea to describe population structure, distribution, habitat preferences, and genetic structure. In total, 139 sea turtles from different size classes were examined from eight sites. Minimum and maximum curved carapace length and weight recorded...
Citations
... Acoustic data from the western Antarctic Peninsula is indicative of a single, stable fin whale population with limited evidence of acoustic vagrants [22]. Common acoustic 20 Hz pulses (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30) are relatively uniform in fin whales for the regions where recordings are available. However, some differences have been observed with the frequency of call overtones differing between the Antarctic Peninsula and Eastern Antarctica, with an increased variation in the groups of individuals east of 115 • (99 Hz, 94 Hz and 82 Hz overtones recorded in this region relative to the consistent 84 Hz in the WAP) [22]. ...
... Given the strong philopatry of female baleen whales to breeding grounds [23], short fragments of the mitochondrial DNA control region (mtDNA CR) have been the standard locus used to resolve the population structure in whale species (e.g., [23][24][25]). While historically more accessible, short gene fragments have a lower statistical power to resolve the population structure, especially in species with low mtDNA CR diversity (e.g., [26,27]). In recent years, technical advancements in nextgeneration sequencing have increased the speed and affordability of sequencing multiple samples at the genomic scale, thereby enhancing the power to resolve the population structure [28,29]. ...
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.
... Therefore, accurately and comprehensively understanding sea turtle genetic diversity will help develop effective conservation strategies. Due to its simple structure and relatively rapid evolution rate, mitochondrial DNA (mtDNA) molecular markers are the commonly used genetic markers for assessing sea turtle population structure, genetic diversity, and phylogeography (Naro-Maciel et al., 2008;Guo, Wang & Liu, 2009;Leroux et al., 2012;Vargas et al., 2016;Yang, 2015). Yang (2015) and Wei (2016) both used mitochondrial genes to do a preliminary study of the genetic diversity of C. mydas in the South China Sea, but their samples were mainly juvenile sea turtles from eggs that were incubated artificially or from C. mydas confiscated by the coast guard. ...
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.
... The 2 hawksbill index nesting beaches in the USA occur exclusively in the Caribbean, on Mona Island, Puerto Rico, and on Buck Island in St. Croix, US Virgin Islands (Spotila 2004). Although historical population data are lacking for hawksbills, it is estimated that populations in the Caribbean have seen reductions of up to 75 %; also, population estimates suggest that approximately 13 000 nesting females remain in the wider Caribbean (Beggs et al. 2007, Mortimer & Donnelly 2008, Leroux et al. 2012. Although hawksbill sea turtle management units in the Western Atlantic have been identified as more resilient to climate change compared to other management units (East Pacific, Southwest Atlantic, and East Atlantic), this population is still vulnerable to future anthropogenic stressors . ...
... This thermal stress has the potential to impact future population success by increasing feminization and mortality of hatchlings, causing overall population decline. Decreases in hawksbill populations may eventually lead to losses in genetic diversity, genetic bottlenecks, and losses in individual fitness due to low population densities and in creased difficulty in finding mates, eventually leading to population collapse and extinction, making conservation of this species ecologically paramount (Courchamp et al. 2008, Leroux et al. 2012. Continued loss of hawksbill populations could be detrimental to coral reef ecosystems because of the role hawksbills play by feeding on sponges (Meylan 1988, León & Bjorndal 2002, Spotila 2004, Carrión-Cortez et al. 2013). ...
The hawksbill sea turtle is listed as Critically Endangered under the IUCN Red List and has been slow to recover in the Caribbean due to historical exploitation and ongoing anthropogenic threats. In turtles, sex and reproductive success are determined by incubation temperatures, whereby lower temperatures produce male hatchlings and higher temperatures produce female hatchlings. As incubation temperatures increase due to climate change, nests are predicted to produce predominantly female hatchlings, threatening sex ratios, reproductive success, and species persistence. One of the largest remaining nesting hawksbill populations within the USA nests on Buck Island. This study aimed to (1) assess the factors driving incubation temperatures and (2) identify the relationship between hatch success and the proportion of time exposed to increasing incubation temperatures. Nest incubation temperatures, beach sector, habitat type, deposition month, percent soil composition, hatch success, and emergence success data were collected from 2019 to 2021. Differences in incubation temperatures across these factors confirmed that the absence of vegetative cover is increasing incubation temperatures on Buck Island, leading to reduced hatchling survival. Results from this study indicate that declines in hatch success may be driven by long-term exposure to temperatures that were previously considered in the literature to be non-lethal to embryos. These findings emphasize the continued need for conservation interventions to protect the future of hawksbills.
... During the second half of the last century, estimated numbers dropped by 95% in the region, including at the well-monitored nesting population at Tortuguero (Carr and Stancyk, 1975;Bjorndal et al., 1993;Meylan, 1999;Bjorndal and Jackson, 2003). Nevertheless, the Tortuguero rookery presents a predominant genetic stock for E. imbricata that can be traced throughout several foraging areas and other nesting beaches around the Caribbean (Troëng et al., 2005; Leroux et al., 2012). Similarly, Green Sea Turtles (Chelonia mydas) at Tortuguero possess a predominant haplotype present in roughly 90% of the nesting population that is distinct from others found around the Greater Caribbean (Peare and Parker, 1996;Bjorndal et al., 2005). ...
Although hybridization processes in the Cheloniidae family have been documented since the 19th century, detailed reports of these occurrences are scarce. Therefore, the record of a hybridization between Green Sea Turtles (Chelonia mydas) and Hawksbill Sea Turtles (Eretmochelys imbricata) signifies an important event. In this study, we report the third known record of hybridization between C. mydas and E. imbricata in the Caribbean Sea. In Tortuguero, Costa Rica, we marked and monitored several nests from both species during the 2020 nesting season. Offspring from two E. imbricata clutches showed morphological characteristics corresponding to both species. We compared 20 individuals from each of these nests to large groups of pure C. mydas and E. imbricata individuals. We measured carapace length and mass of each hatchling and documented other morphological properties such as scale patterns on the head to better identify the species. Because these hatchlings presented different combinations of representative characteristics of each species, we concluded that they are hybrid individuals. Our findings provide a new record of a C. mydas · E. imbricata hybridization event.
... (Gorham et al., 2014) and southeastern Florida (Wood et al., 2013); however, additional sampling of dispersal-stage individuals in the Gulf is needed to confirm. If only using a short fragment, the long-fragment haplotype EiA23 is indistinguishable from EiA24, EiA39, EiA41, EiA42, EiA43, and EiA83, found in Mexican rookeries but also in the Dominican Republic, Trinidad and Tobago, Antigua and Barbuda, Nicaragua, and Puerto Rico, USA (Carreras et al., 2013;Cazabon-Mannette et al., 2016;Labastida-Estrada et al., 2019;Leroux et al., 2012;Levasseur et al., 2019;Velez-Zuazo et al., 2008), illustrating that the longer mtDNA fragment is key for higher genetic resolution among rookeries. ...
Regional genetic differentiation of mitochondrial lineages occurs in migratory species with natal philopatry such as sea turtles. However, early juvenile dispersal represents a key opportunity for gene flow and colonization of new regions through founder events, making it an important yet under-studied life stage. To assess connectivity among sea turtle life stages and ocean basins, we sequenced mitochondrial DNA (mtDNA) fragments from 35 juveniles sampled in the Gulf of Mexico from the rarely observed dispersal stage across three species: green turtles (Chelonia mydas; n = 30), hawksbills (Eretmochelys imbricata; n = 3), and loggerheads (Caretta caretta; n = 2). We estimated green turtle rookery contributions using a many-to-many Bayesian mixed stock analysis that incorporated dispersal probabilities based on rookery size and transport via ocean currents. We assembled a gene tree including 709 distinct mtDNA control region haplotypes from the literature for all seven extant sea turtle species to assess gaps in life-stage data across ocean basins, as well as contextualize the lineages we sampled from dispersing juveniles. Our results indicate a high likelihood that green turtles sampled in the Gulf of Mexico originated from rookeries along the coast of Mexico, with smaller contributions from Costa Rica and Suriname. The gene tree analysis yielded species-level relationships consistent with those presented previously, while intra-species relationships between lineages and ocean basins differed, particularly within loggerhead and green turtle clades. Our results highlight the lack of genetic data from juvenile sea turtles, especially the early dispersal stage, and the potential for these data to answer broader questions of connectivity and diversification across species and lineages.
... The highly significant olive ridley mtDNA structure between ocean regions (Figs. 1 and 2, Table S5) corroborates previous results from a limited dataset of 80 shorter sequences, and suggests high female philopatry at this level (Bowen et al. 1997). In contrast to findings in loggerheads (Shamblin et al. 2014) and hawksbills (Leroux et al. 2012), the longer mtDNA control region sequences (~ 653 vs. ~400 bp) did not provide substantially higher resolution in detecting new population structure; instead, the results were similar to those reported previously (Bowen et al. 1997;Shanker et al. 2004). We found that only one of the 732 olive ridley mtDNA rookery sequences corresponded to haplotypes from a different ocean region (an EP haplotype found in Australia), showing that female single-generation dispersal between ocean regions is rare, a pattern observed in most sea turtles (Reid et al. 2019). ...
Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and 'Critically Endangered' Kemp's ridley (L. kempii). To investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp's (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (< 1 Mya) with low within- clade diversity, supporting a recurrent extinction-recolonization model for these ocean regions. All data showed that ATL and IWP groups were more closely related than those in the EP, with mtDNA data supporting recent recolonization of the ATL from the IWP. Individual olive ridley dispersal between the ATL, EP, and IN/IWP could be interpreted as more male- than female-biased, and genetic diversity was lowest in the Atlantic Ocean. All populations showed signs of recent expansion, and estimated time frames were concordant with their recent colonization history. Investigating species abundance and distribution changes over time is central to evolutionary biology, and this study provides a historical biogeographic context for marine vertebrate conservation and management.
Supplementary information:
The online version contains supplementary material available at 10.1007/s10592-022-01465-3.
... Previous phylogenetic studies have determined that sea turtles show evidence of connectivity resulting from episodic single colonization or long-distance dispersal events followed by secondary or multiple contact over evolutionary timescales (Leroux et al. 2012). Jensen et al. (2019) noted that the Indo-West Pacific was a source for green turtles, or center of origin for the present-day global mtDNA lineage diversity. ...
The Qilianyu cluster of the Xisha (Paracel) Islands has one of the few remaining
green turtle Chelonia mydas rookeries in the China region. Genetic samples were obtained from
dead green turtle embryos and hatchlings salvaged from post-hatched nests at Middle Island (n =
3), North Island (n = 9) and South Sand (n = 1) of the Qilianyu cluster in 2017−2019. The ~800 bp
mitochondrial DNA control region was sequenced from the samples, and 5 haplotypes were identified
belonging to 2 documented clades (clades III and VIII), including 2 new haplotypes
(CmP243.1 and CmP244.1) and 3 previously reported haplotypes (CmP18.1, CmP19.1, CmP20.1).
These results were combined with previously published mtDNA data for the Qilianyu cluster and
nearby (~93 km) Yongle Islands indicating a lack of differentiation based on truncated 384 bp control
region sequences (exact test, p = 0.0997; FST = 0.015, p = 0.2760), to represent a single Xisha
Islands rookery. The rookery at the Xisha Islands was significantly differentiated (p < 0.01) from
all 19 management units (MUs) documented in the Indo-Pacific and Japan regions, supporting
recognition of the Xisha Islands rookery as a new independent MU. The results will help inform
national and international conservation action plans by China and the countries around the South
China Sea to protect green turtles in the West Pacific Ocean.
... Previous studies suggested the occurrence of a population decline followed by an expansion in wider Caribbean hawksbill turtles around 900 kya (Reece et al., 2005) and 100-300 kya (Leroux et al., 2012) based upon mitochondrial DNA. The difference between these estimates was attributed to the analysis being performed on individual clades (Leroux et al., 2012) rather than on the pooled sample (Reece et al., 2005) by Leroux and colleagues (2012). ...
... Previous studies suggested the occurrence of a population decline followed by an expansion in wider Caribbean hawksbill turtles around 900 kya (Reece et al., 2005) and 100-300 kya (Leroux et al., 2012) based upon mitochondrial DNA. The difference between these estimates was attributed to the analysis being performed on individual clades (Leroux et al., 2012) rather than on the pooled sample (Reece et al., 2005) by Leroux and colleagues (2012). By contrast, our results suggested a more recent population decline and expansion associated with the timing of the last glacial cycle, consistent with post-LGM population expansions reported for Indo-Pacific hawksbill turtles (Vargas et al., 2016) and green turtles (Reid et al., 2019). ...
... By contrast, our results suggested a more recent population decline and expansion associated with the timing of the last glacial cycle, consistent with post-LGM population expansions reported for Indo-Pacific hawksbill turtles (Vargas et al., 2016) and green turtles (Reid et al., 2019). The differences between our findings and the studies of Reece et al. (2005) and Leroux et al. (2012) might be attributed to two causes. First, the large number of SNP markers employed in our study provides enhanced resolution compared to single-markerbased approaches, allowing for detailed reconstruction of past demographic histories (Edwards & Beerli, 2000). ...
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.
... Among them, the hawksbill sea turtle Eretmochelys imbricata (Linnaeus, 1766) is classified as Critically Endangered (IUCN, 2008). The species E. imbricata has a circumglobally distribution in tropical and subtropical waters in the Atlantic, Indian and Pacific Oceans (Pritchard and Mortimer, 1999;LeRoux et al., 2012). Previous research revealed that the populations of E. imbricata are concentrated mainly in the Eastern Atlantic Ocean and the Caribbean (Marcovaldi et al., 2007;Vilaça et al., 2013). ...
... In this context, the use of molecular markers such as mtDNA (control/D-loop region) stands out for being efficient in assessing the genetic structure among reproductive areas (Jensen et al., 2013;López-Barrera et al., 2016;Reis and Goldberg, 2017). Most studies on mtDNA used few bases for sequencing (∼300 bp), but in view of the need to obtain more detailed information about the detection of variation and population structure, longer sequences are being applied for this species (Troëng et al., 2005;LeRoux et al., 2012;Nishizawa et al., 2016;Arantes et al., 2020). ...
Marine turtle nesting areas are characterized by receiving several females every year. The species Eretmochelys imbricata, known as hawksbill turtle is listed as Critically Endangered by the IUCN, and has been the target of studies on genetic structure and population diversity in nesting areas. Therefore, this study aimed to analyze the genetic diversity and haplotype composition of populations sampled in nesting areas from the coast of northeastern Brazil based on the mtDNA D-loop region. We used genetic information and compared it with data from feeding areas available in public databases. We recorded a total of six exclusive haplotypes in the nesting areas and 27 exclusive haplotypes for the feeding areas. The H_1 haplotype was shared in all nesting areas. The turtles of these regions had a low diversity and a genetic structure composed of five divergent groups separating the reproductive areas from the ones of feeding areas. Positive and significant geographical distance relationships were also recorded with FST values (r = 0.2302, p = 0.007). Our results revealed that hawksbill turtles from reproductive areas comprise a single population that needs management strategies to protect the threatened species, in addition to providing information that contributes to future actions for the species conservation.
... Estimating N e is challenging for sea turtle populations that exhibit complex genetic structure with highly differentiated maternal lineages at rookeries, male-mediated gene flow, and overlapping generations Karl 2007, Hare et al. 2011). Most studies characterize a static N e value or back-cast changes to assess bottlenecks (e.g., LeRoux et al. 2012), and few investigate contemporary change-a reality that may be related to the difficulty of observing change given long generation times. Phillips and colleagues (2014) estimated N e for a hawksbill population in Seychelles and concluded that mating behavior and population connectivity maintained elevated N e , which may confer adaptive resilience. ...
Sea turtles present a model for the potential impacts of climate change on imperiled species, with projected warming generating concern about their persistence. Various sea turtle life-history traits are affected by temperature; most strikingly, warmer egg incubation temperatures cause female-biased sex ratios and higher embryo mortality. Predictions of sea turtle resilience to climate change are often focused on how resulting male limitation or reduced offspring production may affect populations. In the present article, by reviewing research on sea turtles, we provide an overview of how temperature impacts on incubating eggs may cascade through life history to ultimately affect population viability. We explore how sex-specific patterns in survival and breeding periodicity determine the differences among offspring, adult, and operational sex ratios. We then discuss the implications of skewed sex ratios for male-limited reproduction, consider the negative correlation between sex ratio skew and genetic diversity, and examine consequences for adaptive potential. Our synthesis underscores the importance of considering the effects of climate throughout the life history of any species. Lethal effects (e.g., embryo mortality) are relatively direct impacts, but sublethal effects at immature life-history stages may not alter population growth rates until cohorts reach reproductive maturity. This leaves a lag during which some species transition through several stages subject to distinct biological circumstances and climate impacts. These perspectives will help managers conceptualize the drivers of emergent population dynamics and identify existing knowledge gaps under different scenarios of predicted environmental change.
