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Article

Genetic Diversity of the Critically Endangered Big-Headed Turtle (Platysternon megacephalum) Based on Wild and Traded Samples: Implications for Conservation

by
Hanh Thi Ngo
1,2,3,
Timothy E. M. McCormack
4,
Ha Van Hoang
4,
Thuy Thu Nguyen
4,
Benjamin Tapley
5,
Mai Huyen Le
6,
Dat Trong Le
7,
Tham Thi Nguyen
1,8,
Ha Le Thi Trinh
9,
Thomas Ziegler
2,3,
Truong Quang Nguyen
10,11 and
Minh Duc Le
1,8,12,*
1
Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hoan Kiem District, Hanoi 11000, Vietnam
2
Institute of Zoology, University of Cologne, Zülpicher Strasse 47B, 50674 Cologne, Germany
3
Cologne Zoo, Riehler Straße 173, 50735 Cologne, Germany
4
Asian Turtle Program—Indo-Myanmar Conservation, Room 1806, C14 Bac Ha Building, To Huu Road, Nam Tu Liem District, Hanoi 12011, Vietnam
5
Zoological Society of London, Regent’s Park, London NW1 4RY, UK
6
Department of Genetics, Faculty of Biology, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Road, Thanh Xuan District, Hanoi 11416, Vietnam
7
Cuc Phuong National Park, Nho Quan District, Ninh Binh 08400, Vietnam
8
Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Road, Thanh Xuan District, Hanoi 11416, Vietnam
9
Department of Oceanic Science and Technology, Faculty of Hydrology, Meteorology, and Oceanography, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Road, Thanh Xuan District, Hanoi 11416, Vietnam
10
Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10072, Vietnam
11
Vietnam Academy of Science and Technology, Graduate University of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10072, Vietnam
12
Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
 
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*
Author to whom correspondence should be addressed.
Diversity 2023, 15(9), 958; https://doi.org/10.3390/d15090958
Submission received: 30 June 2023 / Revised: 8 August 2023 / Accepted: 14 August 2023 / Published: 24 August 2023
(This article belongs to the Collection Genetic Diversity)
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Abstract

:
Overexploitation has driven catastrophic declines in most turtle species in Asia. Many turtles are seized annually by law enforcement officers; unfortunately, seized turtles often lack associated information on their provenance. There is also taxonomic confusion regarding the clear delineation of turtle species and subspecies in Asia. This lack of provenance data and taxonomic uncertainty is problematic as it may preclude release, make appropriate release sites hard to select, or result in genetic pollution when animals are released. In this study, we amassed and analyzed the largest number of genetic samples of the critically endangered big-headed turtle (Platysternon megacephalum) to date. Our phylogenetic and network results based on nearly 500 sequences of a mitochondrial ND4 fragment corroborate the earlier hypothesis that only two of the three currently recognized subspecies have strong molecular support and that there is greater genetic structuring within one subspecies than has been previously reported. The vast majority of P. megacephalum confiscated from the trade in Vietnam belong to Subclade 3 of P. m. peguense, and this subclade is the most broadly distributed taxon of the big-headed turtle in Vietnam based on samples with known localities. Nonetheless, for the other two subclades, all their samples originate from the trade and could not be assigned to any geographic provenance because of the lack of wild-caught samples. In addition, our results reveal two trade centers of the species, Quang Ninh Province on the border between China and Vietnam and Kon Tum Province in the Central Highlands. However, smaller animal seizures occur across the range of the species in Vietnam. While the data presented here have facilitated the selection of appropriate release sites for confiscated P. megacephalum, the significant costs of genetic screening and the shortage of samples from wild animals with good localities hinder the rewilding efforts, especially for conservation practitioners working in countries where conservation activities are not well funded and research on poorly studied species is still limited. Nevertheless, we urge that wildlife translocations include robust pre-translocation genetic screening to ensure that all individual animals are reintroduced at appropriate sites.

1. Introduction

In Asia, many turtle population declines have been driven by unsustainable harvesting to supply Chinese markets [1,2,3]. A substantial proportion of the trade in turtles is illegal, and animals are often confiscated and housed in rescue centers and some may be rehabilitated or bred for release to supplement depleted populations [4,5,6]. Wildlife translocations should follow IUCN guidelines for reintroductions and other conservation translocations [7], particularly regarding genetic provenance as wildlife translocations that are not informed by genetics may inadvertently result in outbreeding and introgression [8,9,10], which may have dire consequences for species [11,12,13]. Following the IUCN guidelines is often difficult for animals seized from the illegal wildlife trade as their origin is often unknown [14] and animals are often brought together from a large geographic area and shipped through centralized illegal trade routes [15,16]. This is compounded by taxonomic confusion regarding the clear delineation of turtle species and subspecies in Southeast Asia [12,17]. Taxonomic uncertainty has already undermined existing turtle translocation programs [4,18].
A relevant case study involves the big-headed turtle (Platysternon megacephalum) in Vietnam. This critically endangered species [19] is the sole representative of the monotypic family Platysternidae. As such, it is recognized as a global priority for conservation due to its global endangerment and evolutionary distinctiveness [20]. This territorial species exhibits site fidelity and is thought to only move short distances, making it a good candidate for translocation [21]. However, its restriction to linear habitats makes the species inherently vulnerable to overexploitation, and it is collected in enormous volumes for consumption and traditional medicine [22,23,24,25,26,27,28,29]. Populations of the turtle have severely declined across their ranges due to overhunting to supply the high demand in China [29,30,31,32]. To reduce the market pressure on the species, it has been listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).
Morphologically, there are three recognized P. megacephalum subspecies, including P. m. megacephalum, P. m. peguense, and P. m. shiui [33], all of which occur in Vietnam [18]. The different subspecies of P. megacephalum cannot be reliably differentiated from one another based on morphology alone due to geographic variation in both morphology and color pattern [33]. Genetic analyses have also provided support for the existence of the three taxonomic units [34,35,36]. Nonetheless, previous studies only employed a limited number of samples, especially from Vietnam. As a result, it is still unclear if any other genetically distinct populations have gone unnoticed by the previous molecular analyses. Other turtle species in Southeast Asia with broad distributions, such as P. megacephalum, have shown a great deal of genetic differentiation between populations occurring in specific geographic regions, e.g., species in genera Cuora, Pelodiscus, and Sacalia [37,38,39,40,41,42].
Detailed knowledge of phylogeographic patterns of threatened species is essential when developing ex situ conservation programs in order to maintain the genetic integrity of captive populations and to minimize the risks of genetic pollution to wild populations when the animals are released [12,43]. Between 2015 and 2021, the Turtle Conservation Centre (TCC) of Cuc Phuong National Park received nearly 600 confiscated P. megacephalum, which might have been collected from Vietnam’s protected areas (Table 1). The aim of this study was to assess the genetic diversity of P. megacephalum in Vietnam using both traded samples and those with reliable locality data in order to ensure the appropriate selection of release sites for seized animals. We also recommend measures to better manage confiscated animals in the face of uncertain origin and lack of resources to perform genetic screening and other necessary tests.

2. Material and Methods

2.1. Taxonomic Sampling

In total, 465 new samples of Platysternon megacephalum were incorporated into the analysis. Of these, 15 were collected from the wild, four were from within the distribution range of Platysternon megacephalum shiui, and 11 were from that of P. megacephalum peguense based on Rhodin et al. [18]. The rest of the samples were from individuals confiscated from the trade (N = 450) (Figure 1). In addition, we obtained two sequences of the mitochondrial ND4 from GenBank for P. m. megacephalum and P. megacephalum shiui based on Luo et al. [35] and Rhodin et al. [18] (DQ256377 and DQ016387 instead of P. megacephlum as labeled on GenBank), one for P. megacephalum peguense (MH822616), and one for the closely related taxon, Chrysemys picta (NC002073), to be used as an outgroup species [18,35,44] (Supplementary Materials, Table S1).

2.2. Molecular Data

Total genomic DNA was extracted from blood and tail tissue samples using the DNeasy Blood and Tissue Kit (Qiagen—Hilden, Germany) following the manufacturer’s instructions for blood and animal tissue. Samples were collected in a way to cause the least harm to the animals. The genomic extraction was checked by electrophoresis. A negative control was used for every extraction. We amplified a fragment of mitochondrial NADH dehydrogenase subunit 4 for all samples using HotStar Taq Mastermix (Qiagen—Hilden, Germany) and Dream Taq PCR Mastermix (ThermoFisher Scientific—Vilnius, Lithuania). The standard PCR conditions were 95 °C for 15 min with HotStar Taq Mastermix (Qiagen—Hilden, Germany) or 95 °C for 5 min with Dream Taq PCR Mastermix (ThermoFisher Scientific—Vilnius, Lithuania), 35 cycles at 95 °C for 30 s, 45 °C for 45 s, 72 °C for 60 s, and final elongation at 72 °C for 6 min. The PCR volume consisted of 2 μL of each primer at 10 pmol/μL, 5 μL water, 10 μL of Mastermix, and 1–4 μL DNA template depending on the quantity of DNA. Two new primers were designed to amplify a 689bp fragment of the mitochondrial NADH dehydrogenase 4 gene (ND4) (PlaND4F1—GCTAAAAATCATACTTCCAACCAT and PlaND4R1—GGATTATTGACCCTGCGATTGGAGCTT). ND4 was selected in this study because it has been shown to be an informative marker in resolving issues related to turtle population genetics and taxonomy [17,45,46,47]. A negative and positive control were used for every PCR reaction. To confirm if the correct size was amplified, 5 μL of PCR product was run on a 1% agarose gel with GeneRuler 100bp DNA ladder (SM0241, Thermo FishcerScientific—Vilnius, Lithuania), 1X TBE buffer, stained with 2 pg/μL bromide, and photographed under UV light. Successful PCR products were cleaned using GeneJet PCR Purification Kit (Thermo FisherScientific—Vilnius, Lithuania) following the manufacturer’s instructions. Cleaned PCR products were sent to 1st Base (Malaysia) for sequencing.

2.3. Genetic, Phylogenetic, and Network Analyses

The sequences were edited using Sequencher v4.1.4 (Gene Codes Corp, Ann Arbor, MI, USA) by eye and then aligned using Bioedit v7.1.3 with default settings [48]. Data were first evaluated by DnaSP v6.12.03 to determine sequence variation and haplotype diversity [49]. Sequences were then analyzed using two phylogenetic methods, Bayesian inference (BI) in MrBayes v3.2.7 and maximum likelihood (ML) in IQ-TREE v1.6.8 [50,51]. Intraspecific relationships among populations of the P. megacephalum were also inferred using the NeighborNet algorithm in SplitsTree v4.14.2 [52,53]. For BI, we performed both single and multiple models by codon partitions to examine the robustness of the tree topology [54,55]. Analyses were conducted with a random starting tree and run for 1 × 107 generations, four Markov chains (one cold, three heated) with default settings. Values of sample points were plotted against the number of generations to detect the stationarity of the Markov chains. Trees generated prior to stationarity were removed from the final analyses using the burn-in function. Two independent analyses were performed simultaneously. The cutoff point for the burn-in function was set to 60 as −lnL scores reached stationarity after 60,000 generations. The posterior probability (PP) values for all clades in the final majority rule consensus tree were provided. Nodal support was also evaluated using bootstrap replication (BP) as calculated in SplitsTree (1000 replications) and employing ultrafast BP (10,000 replications) in IQ-TREE.
We regarded UBP or PP value ≥ 95% as strong support for a clade [48,56]. For ML and BI analyses, we used the optimal model calculated by jModelTest v.2.1.10 [57]. The optimal model for nucleotide evolution was set to GTR + G or TVM + G for BI and ML analyses. The network analysis was performed in SplitsTree with the following settings: edge fitting as ordinary least squares, equal angle as chosen splits transformation, least squares to modify weights, and four maximum dimensions as the filtering option. The generated split graph showed a visual representation of conflicting signals in the data by presenting them as a series of parallel edges. The program computed the least squares fit (LSfit) between the pairwise distances from the graph and the distances from the matrix to produce a distance-based unrooted tree diagram using the neighbor-joining algorithm [58]. Uncorrected pairwise genetic distance was calculated in PAUP 4.0 because it has been a preferable way to present data in previous taxonomic studies [59].

3. Results

The final matrix consisted of 470 terminals and 666 aligned characters without internal gaps. The haplotype diversity of Platysternon megacephalum peguense was 0.44 and of P. m. megacephalum/shiui 0.35, while the nucleotide diversity of P. m. peguense and P. m. megacephalum/shiui was 0.0019 and 0.0037, respectively. The number of unique haplotypes of P. m. peguense and P. m. megacephalum/shiui was 22 and 3, respectively. Within P. m. peguense, Subclade 1 has three unique haplotypes (20, 21, 22), Subclade 2 possesses two (18 and 19), and the remaining seventeen haplotypes belong to Subclade 3 (1–17) (Supplementary Materials, Matrix S1). All known-locality samples in Subclade 3 were divided into three unique haplotypes: haplotype 1 (337 samples), haplotype 4 (five samples), and haplotype 7 (24 samples). While haplotype 1 has the broadest distribution, each of the other two is restricted to a single location (Figure 1, Supplementary Materials, Matrix S1).
Both ML and BI analyses recovered similar topologies with two major clades with only significant nodal values coming from BI. The first one consisted of Platysternon m. megacephalum and P. megacephalum shiuii and the other comprised only P. megacephalum peguense (Figure 2). The sequences regarded as P. m. megacephalum from GenBank were paraphyletic with one being more closely related to P. megacephalum shiui than the other. The set of relationships received strong support from both ML and BI (Figure 2A). P. m. peguense was divided into at least three monophyletic subclades. In fact, Subclade 1 included two lineages, one comprising samples Pm327 and Pm547, and the other comprising samples Pm449, Pm450, Pm453, Pm456, Pm463, Pm465, and Pm466; both lineages were strongly or reasonably corroborated by BI and ML (UFB and PP ≥ 94%) (Supplementary Materials, Figure S1). The network analysis produced the same results as those supported by phylogenetic assignments in recovering three subclades within P. megacephalum. peguense and two more distantly related clades consisting of P. megacephalum peguense and P. megacephalum shiui + P. m. megacephalum (Figure 2B).
In terms of genetic distance, P. megacephalum shiui was separated from P. m. megacephalum by approximately 1%, comparable to the level of variation within Subclade 1 and 2 of P. megacephalum peguense. Similarly, two samples of P. m. megacephalum were also differentiated by only 1%. The divergence between P. megacephalum shiui + P. m. megacephalum and P. megacephalum peguenese is significant, ranging around 5–6.73 %, while the divergence between the three subclades of P. megacephalum peguenese is about 0.6–1.8% (Table 2).
Only a few of the confiscated samples (N = 5) are clustered with the Platysternon megacephalum shiui reference. Most of them (approximately 96%) are clustered in Subclade 3 of P. megacephalum peguense. As expected, the distribution of the origin for samples identified as P. megacephalum shiui in the cladogram is limited to a small area of northeastern Vietnam. However, the distribution of Subclade 3 (N = 11 samples from the wild and N = 432 samples confiscated from trade) covers a broad geographic region extending from the northwestern part of the country to the Central Highlands (Figure 1). Locations for samples in Subclades 1 (N = 9) and 2 (N = 5) are currently unknown because none had reliable localities information.

4. Discussion

In this study, we amassed and analyzed the largest number of genetic samples of Platysternon megacephalum to date. Our phylogenetic results based on nearly 500 sequences corroborate the earlier hypothesis that Platysternon megacephalum megacephalum and P. megacephalum shiui are more closely related to each other than they are to P. megacephalum peguense [35]. However, Luo et al. [35] only included three samples, one collected from Huangshan Mountain, Anhui Province, China (GenBank accession number DQ016387), one from Yunnan Province (GenBank accession number MH822616), and the third without any information on its origin (GenBank accession number DQ256377) [35,60,61]. Luo et al. [35] considered DQ016387 P. megacephalum megacephalum, MH822616 P. megacephalum peguense, and DQ256377 P. megacephalum shiui. While the localities of the first two samples fall within the distributions of the respective subspecies [18], it is unclear why Luo et al. [35] regarded the last sample as P. megacephalum shiui as locality data were lacking. In contrast to their identification, this study shows that DQ016387 is more closely related to P. megacephalum shiui than DQ256377 (Figure 2).
The subspecies P. megacephalum shiui was described in 1987 based on two specimens, USNM 266160 and USNM 266161, acquired from the trade in the vicinity of Lang Son City, Lang Son Province, Vietnam. Its main morphological diagnostic characteristics were stated to be the presence of bright yellow, orange, or pink spots on the head, shell, limbs, sockets, and the ventral surface of the tail [62]. Our observations of P. megacephalum shiui contradict this diagnosis because its coloration varied substantially, and the speckles of some animals were brownish rather than bright orange-pink. The results supported by this study reveal that P. m. megacephalum is paraphyletic to P. megacephalum shiui, and the genetic distance between them is low and falls within the divergence range observed between the different subclades of P. megacephalum peguense. On the other hand, P. m. megacephalum and P. megacephalum peguense exhibit a level of genetic differentiation (5–6.7%) equivalent to independent species when compared with analogous estimates in other turtle species [42,63]. The same conclusion has been recommended by Gong et al. [36].
The genetic analyses presented in this study clearly show that the vast majority of individuals confiscated from the trade in Vietnam belong to Subclade 3 of P. megacephalum peguense. The subclade is broadly distributed from Anhui Province, China, to Kon Tum Province, Vietnam, based on samples included in this study. Most of the confiscations took place in Quang Ninh Province, a major export port between Vietnam and China (Figure 2, Supplementary Materials—Table S1). Wildlife and their products seized here often do not have any information about origins. It is, therefore, very challenging to determine the exact geographic provenance of confiscated turtles in Quang Ninh. Our haplotype analysis shows that many samples of haplotype 1 and all of haplotype 4 and haplotype 7, except one of haplotype 7 seized in Ha Nam Province, northern Vietnam, come from this port, although they are naturally distributed far from this location (Figure 1, Supplementary Materials, Matrix S1). Many samples assigned to Subclades 1 and 2 as well as to P. megacephalum shiui also originate from animals confiscated at this port (Supplementary Materials, Table S1).
The second most common confiscation site was in Kon Tum Province. As Kon Tum is in the Central Highlands, south-central Vietnam, and far away from the border region with China, it is reasonable to suggest that either the shipments originated from nearby localities or neighboring countries, such as Cambodia or Thailand. Unfortunately, genetic data from P. megacephalum populations from these countries are not currently available; therefore, we are unable to draw more conclusions about the origins of animals confiscated in Kon Tum Province. All animals confiscated at this location cluster in Subclade 3 and many in haplotype 1, except for one in Subclade 1 (Supplementary Materials, Table S1). It is intriguing that even though haplotype 4 naturally occurs nearby this confiscation site, all the confiscated samples belonging to this haplotype were found in Quang Ninh Province, northern Vietnam. Similarly, samples of haplotype 7 were all seized in northern Vietnam, probably on their way to China. On the other hand, many samples of haplotype 1 found their way to Kon Tum Province, although the location falls outside of its natural range (Figure 1). Since the major confiscation site in Kon Tum Province is located south of the species distribution, it is apparent that the turtle trade pattern in Vietnam is much more complicated than just the general south-north direction as proposed in previous studies [15,16].
Compared with P. megacephalum. peguense, P. megacephalum shiui has been recorded in the trade in a much smaller number in Vietnam. We suspect that as P. megacephalum shiui inhabit the area near the border between Vietnam and China, they can be conveniently transported to China without going through major highways; therefore, they are less likely to be intercepted by law enforcement officers. It is also possible that the population of P. megacephalum shiui has been severely depleted by long-term unsustainable hunting activities with very few individuals left in the wild. Further study is warranted to test these hypotheses and better understand the implications of the trade on different P. megacephalum turtle populations.
The inclusion of more samples with robust provenance data in this study confirms the hypothesis that the Red River, a well-known zoological border [64], is the natural barrier separating the two lineages, with P. megacephalum peguense occupying the western side (and P. megacephalum occurring on the eastern side of the river [36]. Other previous studies suggest that the P. megacephalum shiui is probably more broadly distributed with its range extending further west [18]. Nonetheless, our georeferenced samples are still very limited and could not be used to locate the natural ranges of Subclade 1 and 2 of P. megacephalum peguense. It is therefore essential to sample and analyze additional individuals from the species range as the uncertainty regarding the distribution ranges of the different P. megacephalum lineages has impeded our ability to release confiscated turtles back into the wild because doing so without any knowledge of their distribution can result in genetic pollution of local gene pools [12,65]. Keeping turtles in rescue centers in the long term incurs expense and considerable effort. Furthermore, the aggressive behavior of P. megacephalum makes it difficult to keep them for a long time, and the cost of maintaining them in captivity is relatively high because they need to be maintained in individual enclosures [66,67]. Finally, big-headed turtles require clean water and seasonality [66] if they are to thrive and breed, which makes catering for large numbers of them in rescue centers problematic.
Although genetic screening has been demonstrated to be a useful tool in assisting the appropriate release to the wild of vertebrates that lack provenance information and this approach has been strongly recommended by IUCN [7,12,66], it has rarely been used in practice. One of the barriers is the cost of screening and the number of turtles being seized, especially if more detailed genetic information based on nuclear markers, e.g., microsatellites or single nucleotide polymorphism, is needed to identify genetically distinct populations [39,68,69,70]. Unfortunately, as most seizures to date have occurred in developing countries and involved their native species, the access to funding sources is restricted or not timely enough to facilitate proper release, which is necessary if the considerable expense of managing a large number of individuals is to be avoided. Furthermore, if exit strategies do not exist for animals that have been confiscated, the resources required to manage animals in rescue centers may become increasingly stretched, and this may have implications for the welfare of individual animals. Sustainable funding solutions need to be developed if translocations in developing countries are to follow IUCN guidelines for reintroductions and other conservation translocations. Finally, expertise in molecular analysis is limited in many Southeast Asian countries, making it difficult to ensure that all wildlife translocations are informed by genetic data when provenance information is lacking. However, with the critical and long-term negative impacts of genetic admixture on native populations, genetic screening should be applied to all individuals whenever possible to prevent impending large-scale biodiversity catastrophes associated with wildlife trade and subsequent conservation translocations. This is also in line with the One Plan Approach to Conservation, developed by IUCN’s Conservation Planning Specialist Group (CPSG), which combines in situ and ex situ efforts and various expertise for the optimum and timely protection of species.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/d15090958/s1, Figure S1: Bayesian cladogram based on a fragment of the mitochondrial ND4 gene. The numbers above and below branches are Bayesian posterior probabilities and maximum likelihood ultrafast bootstrap values. Table S1: Samples of Platysternon used in this study. Colors match to those employed in Figure 2A,B.

Author Contributions

Conceptualization, M.D.L., T.E.M.M. and B.T.; methodology, M.D.L., H.T.N. and M.H.L.; validation, H.T.N., M.D.L., T.T.N. (Tham Thi Nguyen), M.H.L. and H.V.H.; formal analysis, H.T.N. and M.D.L.; investigation, H.T.N., T.T.N. (Tham Thi Nguyen) and M.H.L.; resources, T.E.M.M., B.T., M.D.L., H.L.T.T., H.V.H., T.Q.N., D.T.L. and T.T.N. (Thuy Thu Nguyen); data curation, T.T.N. (Thuy Thu Nguyen), H.V.H., M.D.L., H.T.N., D.T.L., T.Z., T.Q.N. and M.H.L.; writing—original draft preparation, M.D.L., B.T. and H.T.N.; writing—review and editing, all authors; visualization, H.T.N. and M.D.L.; supervision, M.D.L., T.E.M.M. and B.T.; project administration, B.T., T.E.M.M. and M.D.L.; funding acquisition, T.E.M.M., B.T., T.Q.N., T.Z. and H.V.H. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Fondation Segré Conservation Fund, Cleveland Metroparks Zoo, US Fish and Wildlife Service, Institute of Ecology and Biological Resources—VAST (Project code IEBR NV.01-23) and by the ZSL EDGE Fellowship for Ha Hoang Van. Research of H.T. Ngo in Germany is funded by the German Academic Exchange Service (DAAD).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Sequences of all samples were uploaded to NCBI GenBank with accession numbers OR477227-OR477264. Accession numbers of the ND4 sequences taken from GenBank are provided in Table S1 (data retrieved from the NCBI in February 2023).

Acknowledgments

We thank Hanoi Rescue Center for facilitating sample collection.

Conflicts of Interest

The authors declare no conflict of interest.

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Diversity 15 00958 g001
Figure 1. Origin of Platysternon megacephalum samples used in this study. Blue and green colors denote samples collected from the wild. Red and black represent confiscation sites.
Figure 1. Origin of Platysternon megacephalum samples used in this study. Blue and green colors denote samples collected from the wild. Red and black represent confiscation sites.
Diversity 15 00958 g001
Diversity 15 00958 g002
Figure 2. (A). Bayesian cladogram based on a fragment of the mitochondrial ND4 gene. The numbers above and below branches are Bayesian posterior probabilities and maximum likelihood ultrafast bootstrap values. (B). Split tree network based on a fragment of the ND4 gene. Samples presented in each clade are representatives of distinct haplotypes as identified by DnaSP. Red numbers at nodes are representative bootstrap values. Note: Sample with GenBank accession number MH822616 clusters in Subclade 3 in both analyses. A full cladogram of Figure 2A is available in the Supplementary Materials (Figure S1).
Figure 2. (A). Bayesian cladogram based on a fragment of the mitochondrial ND4 gene. The numbers above and below branches are Bayesian posterior probabilities and maximum likelihood ultrafast bootstrap values. (B). Split tree network based on a fragment of the ND4 gene. Samples presented in each clade are representatives of distinct haplotypes as identified by DnaSP. Red numbers at nodes are representative bootstrap values. Note: Sample with GenBank accession number MH822616 clusters in Subclade 3 in both analyses. A full cladogram of Figure 2A is available in the Supplementary Materials (Figure S1).
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Table 1. Summary of the big-headed turtle confiscations from different sites in Vietnam. FPD: Forest Protection Department.
Table 1. Summary of the big-headed turtle confiscations from different sites in Vietnam. FPD: Forest Protection Department.
DateCase#Number of Confiscated BHT IndividualsAge ClassSex Ratio (Female: Male:Unknown)
AdultSubadultJuvenile
10 June 2015Ninh Binh FPD, Ninh Binh Province2715486:8:13
24 August 2015Ninh Binh FPD, Ninh Binh Province71151:2:4
29 September 2015Hanoi Wildlife Rescue Centre (transferred from Ha Tinh Province)23135518:5:0
18 May 2016Ky Son Police, Nghe An Province103436:4:0
24 May 2016Ha Nam FPD, Ha Nam Province73132:3:2
7 September 2016Hanoi Pet Owner10010:0:1
4 October 2016Thai Binh Police, Thai Binh Province3915150916:14:9
9 November 2016Quang Ninh Province7735291314:27:36
4 April 2017Bac Giang FPD, Bac Giang Province41210:3:1
19 October 2017Gia Vien FPD, Ninh Binh Province684118924:36:8
24 May 2018Tien Yen FPD, Quang Ninh Province33001:1:1
17 August 2018Quang Nam Police10100:0:1
6 October 2018Quang Xuong, Thanh Hoa Province462821616:15:15
18 November 2018Pu Mat National Park, Nghe An Province94415:4:0
24 April 2019Pu Mat National Park, Nghe An Province146535:4:5
24 April 2019Huong Son Police, Ha Tinh Province41121:1:2
10 June 2019Quan Son, Thanh Hoa Province51130:1:4
16 July 2019Huong Son, Ha Tinh Province10100:0:1
6 August 2019Quy Chau, Nghe An Province2500250:0:25
12 September 2019Hanoi Wildlife Rescue Centre (transferred from Quang Ninh Province)43100:4:0
16 October 2020Que Phong Police, Nghe An Province60600:0:6
20 March 2021Hanoi Wildlife Rescue Centre20110:1:1
8 April 2021Sop Cop Police, Son La Province204797:1:12
22 April 2021Sop Cop Police, Son La Province20201:0:1
10 May 2021Hoa Binh Police71242:1:4
29 June 2021Quang Ninh Province7435261322:22:30
16 Jul 2021Dak Glei Police, Chu Mom Ray Rescue Centre, Kon Tum Province5214132519:6:27
10 September 2021Quang Ninh Province333015115:17:14
16 September 2021Quang Ninh Province13
18 October 2021Quang Nam Province20110:0:2
Total586257168161181:180:225
Table 2. Percentage of uncorrected pairwise distances between and within three clades of Platysternon megacephalum peguense and P. megacephalum. shiui. The highest pairwise distance within each clade is shown in parenthesis. Numbers in parentheses next to clade names correspond to the number of samples assigned to the clades.
Table 2. Percentage of uncorrected pairwise distances between and within three clades of Platysternon megacephalum peguense and P. megacephalum. shiui. The highest pairwise distance within each clade is shown in parenthesis. Numbers in parentheses next to clade names correspond to the number of samples assigned to the clades.
Big-Headed Turtle Clades123456
1DQ256377 P. m. shiui (1)(−)
2DQ016387 P. m. megacephalum (1)1.18(−)
3P. m. shiui (9)0.901.19(0.00)
4P. m. peguense (Subclade 1) (9)5.43–5.586.34–6.496.35–6.50(1.51)
5P. m. peguense (Subclade 2) (5)5.02–5.545.97–6.485.98–6.490.91–1.10(0.17)
6P. m. peguense (Subclade 3) (443)5.24–5.826.14–6.726.11–6.731.36–1.820.61–1.26(1.18)
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Ngo, H.T.; McCormack, T.E.M.; Hoang, H.V.; Nguyen, T.T.; Tapley, B.; Le, M.H.; Le, D.T.; Nguyen, T.T.; Trinh, H.L.T.; Ziegler, T.; et al. Genetic Diversity of the Critically Endangered Big-Headed Turtle (Platysternon megacephalum) Based on Wild and Traded Samples: Implications for Conservation. Diversity 2023, 15, 958. https://doi.org/10.3390/d15090958

AMA Style

Ngo HT, McCormack TEM, Hoang HV, Nguyen TT, Tapley B, Le MH, Le DT, Nguyen TT, Trinh HLT, Ziegler T, et al. Genetic Diversity of the Critically Endangered Big-Headed Turtle (Platysternon megacephalum) Based on Wild and Traded Samples: Implications for Conservation. Diversity. 2023; 15(9):958. https://doi.org/10.3390/d15090958

Chicago/Turabian Style

Ngo, Hanh Thi, Timothy E. M. McCormack, Ha Van Hoang, Thuy Thu Nguyen, Benjamin Tapley, Mai Huyen Le, Dat Trong Le, Tham Thi Nguyen, Ha Le Thi Trinh, Thomas Ziegler, and et al. 2023. "Genetic Diversity of the Critically Endangered Big-Headed Turtle (Platysternon megacephalum) Based on Wild and Traded Samples: Implications for Conservation" Diversity 15, no. 9: 958. https://doi.org/10.3390/d15090958

APA Style

Ngo, H. T., McCormack, T. E. M., Hoang, H. V., Nguyen, T. T., Tapley, B., Le, M. H., Le, D. T., Nguyen, T. T., Trinh, H. L. T., Ziegler, T., Nguyen, T. Q., & Le, M. D. (2023). Genetic Diversity of the Critically Endangered Big-Headed Turtle (Platysternon megacephalum) Based on Wild and Traded Samples: Implications for Conservation. Diversity, 15(9), 958. https://doi.org/10.3390/d15090958

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