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Kundu S, Mukherjee T, Kamalakannan M, Barhadiya G, Ghosh C, Kim HW. Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle ( Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences. PeerJ 2023; 11:e15975. [PMID: 37692114 PMCID: PMC10492536 DOI: 10.7717/peerj.15975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021-2040 and 2061-2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan, South Korea
| | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata, West Bengal, India
| | | | - Gaurav Barhadiya
- Department of Environmental Studies, University of Delhi, New Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, New Delhi, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan, South Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, South Korea
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Ascarrunz E, Claude J, Joyce WG. The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters. PeerJ 2021; 9:e11805. [PMID: 34430073 PMCID: PMC8349520 DOI: 10.7717/peerj.11805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/27/2021] [Indexed: 11/30/2022] Open
Abstract
The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as "Ocadia" kehreri and "Ocadia" messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.
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Affiliation(s)
- Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Julien Claude
- Institut des Sciences de l’Évolution de Montpellier, UMR UM/CNRS/IRD/EPHE, Montpellier, France
| | - Walter G. Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc Natl Acad Sci U S A 2021; 118:2012215118. [PMID: 33558231 DOI: 10.1073/pnas.2012215118] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.
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Kundu S, Kumar V, Tyagi K, Chandra K. The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny. PLoS One 2020; 15:e0225233. [PMID: 32324729 PMCID: PMC7179895 DOI: 10.1371/journal.pone.0225233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/08/2020] [Indexed: 12/02/2022] Open
Abstract
The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
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Kundu S, Kumar V, Tyagi K, Chakraborty R, Chandra K. The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis. Ecol Evol 2019; 9:10854-10868. [PMID: 31624586 PMCID: PMC6787814 DOI: 10.1002/ece3.5606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/24/2019] [Accepted: 08/07/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with "GTG" and NADH dehydrogenase subunit 5 with "ATA." The termination codons, "TAA" and "AGA" were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3' end of CR. Further, two copies of a unique tandem repeat "TTCTCTTT" were identified in P. tentoria. The Bayesian and maximum-likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in-depth phylogenetic and evolutionary relationships.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Vikas Kumar
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kaomud Tyagi
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Rajasree Chakraborty
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kailash Chandra
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
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Ascarrunz E, Claude J, Joyce WG. Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods. PeerJ 2019; 7:e7476. [PMID: 31497387 PMCID: PMC6708579 DOI: 10.7717/peerj.7476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. METHODS We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. RESULTS Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.
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Affiliation(s)
- Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Julien Claude
- Institut des Sciences de l’Évolution de Montpellier, UMR UM/CNRS/IRD/EPHE, Montpellier, France
| | - Walter G. Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Garbin RC, Ascarrunz E, Joyce WG. Polymorphic characters in the reconstruction of the phylogeny of geoemydid turtles. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Rafaella C Garbin
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling. Mol Phylogenet Evol 2018; 120:1-15. [DOI: 10.1016/j.ympev.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 01/25/2023]
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Takahashi A, Otsuka H, Ota H. A New Species of the GenusMauremys(Testudines: Geoemydidae) from the Upper Pleistocene of Miyakojima Island, Ryukyus Archipelago, Japan. CURRENT HERPETOLOGY 2015. [DOI: 10.5358/hsj.34.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Le M, Duong HT, Dinh LD, Nguyen TQ, Pritchard PCH, McCormack T. A phylogeny of softshell turtles (Testudines: Trionychidae) with reference to the taxonomic status of the critically endangered, giant softshell turtle, Rafetus swinhoei. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0169-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Le M, Nguyen TV, Duong HT, Nguyen HM, Dinh LD, Do T, Nguyen HD, Amato G. Discovery of the Roosevelt’s Barking Deer (Muntiacus rooseveltorum) in Vietnam. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0581-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Iverson JB, Le M, Ingram C. Molecular phylogenetics of the mud and musk turtle family Kinosternidae. Mol Phylogenet Evol 2013; 69:929-39. [DOI: 10.1016/j.ympev.2013.06.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 05/15/2013] [Accepted: 06/18/2013] [Indexed: 11/24/2022]
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Fritz U, Stuckas H, Vargas‐Ramírez M, Hundsdörfer AK, Maran J, Päckert M. Molecular phylogeny of Central and South American slider turtles: implications for biogeography and systematics (Testudines: Emydidae:Trachemys). J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00647.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Germany
| | - Heiko Stuckas
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Germany
| | | | | | - Jérôme Maran
- L’Association du Refuge des Tortues, Bessières, France
| | - Martin Päckert
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Germany
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Vargas-Ramírez M, Vences M, Branch WR, Daniels SR, Glaw F, Hofmeyr MD, Kuchling G, Maran J, Papenfuss TJ, Široký P, Vieites DR, Fritz U. Deep genealogical lineages in the widely distributed African helmeted terrapin: Evidence from mitochondrial and nuclear DNA (Testudines: Pelomedusidae: Pelomedusa subrufa). Mol Phylogenet Evol 2010; 56:428-40. [DOI: 10.1016/j.ympev.2010.03.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/11/2010] [Accepted: 03/12/2010] [Indexed: 10/19/2022]
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LE MINH, MCCORD WILLIAMP. Phylogenetic relationships and biogeographical history of the genusRhinoclemmysFitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea). Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.2008.00413.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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