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Jorgewich-Cohen G, Werneburg I, Jobbins M, Ferreira GS, Taylor MD, Bastiaans D, Sánchez-Villagra MR. Morphological Diversity of Turtle Hyoid Apparatus is Linked to Feeding Behavior. Integr Org Biol 2024; 6:obae014. [PMID: 38741667 PMCID: PMC11090499 DOI: 10.1093/iob/obae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/03/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
The hyoid apparatus of tetrapods is highly diverse in its morphology. It plays an important role in feeding, breathing, sound production, and various other behaviors. Among turtles, the diversity of the hyoid apparatus has been recurrently linked to their habitat. The ossification of the hyoid corpus is often the main trait used in correlations with "niche" occupancy, an ossified corpus being associated with aquatic environments and a cartilaginous corpus with terrestrial life. Most studies conducted so far have focused on species belonging to Testudinoidea, the clade that occupies the biggest diversity of habitats (i.e., terrestrial, semi-terrestrial, and aquatic animals), while other turtle lineages have been largely understudied. We assessed the adult anatomy of the hyoid apparatus of 92 turtle species from all "families", together with ossification sequences from embryological series of 11 species, some described for the first time here. Using nearly 40 different discrete anatomical characters, we discuss the evolutionary patterns and the biological significance of morphological transformations in the turtle hyoid elements. Morphological changes are strongly associated to feeding modes, with several instances of convergent evolution within and outside the Testudines clade, and are not as strongly connected to habitat as previously thought. Some of the hyoid character states we describe are diagnostic of specific turtle clades, thus providing phylogenetically relevant information.
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Affiliation(s)
- G Jorgewich-Cohen
- Department of Paleontology, University of Zurich, 8006 Zurich, Switzerland
| | - I Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment an der Universität Tübingen, Tübingen, Germany
- Fachbereich Geowissenshcaten dr Universität Tübingen, 72074 Tübingen, Germany
| | - M Jobbins
- Department of Paleontology, University of Zurich, 8006 Zurich, Switzerland
| | - G S Ferreira
- Senckenberg Centre for Human Evolution and Palaeoenvironment an der Universität Tübingen, Tübingen, Germany
- Fachbereich Geowissenshcaten dr Universität Tübingen, 72074 Tübingen, Germany
| | - M D Taylor
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
- The UWA Oceans Institute, The University of Western Australia, Perth, WA 6009, Australia
| | - D Bastiaans
- Department of Paleontology, University of Zurich, 8006 Zurich, Switzerland
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Chroust M, Mazuch M, Ivanov M, Alba DM, Luján ÀH. Redescription of the soft-shell turtle Rafetus bohemicus (Testudines, Trionychidae) from the Early Miocene of Czechia. PeerJ 2023; 11:e15658. [PMID: 37525660 PMCID: PMC10387236 DOI: 10.7717/peerj.15658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 06/07/2023] [Indexed: 08/02/2023] Open
Abstract
The taxonomy of the soft-shell turtle Rafetus bohemicus (Liebus, 1930), family Trionychidae, subfamily Trionychinae, is revised based on new and previously mentioned material (including the type material) from the Early Miocene (Burdigalian, MN 3) sites of the Most Basin, Czechia. Given that the diagnosis was so far based only on plastral elements, here we focused on the cranial material and combined our study with previously published data on postcranial elements. 3D models of the skulls derived from CT scans allow us to provide the first complete skull description of R. bohemicus, including several new cranial diagnostic characters of the species. Our results not only enable the distinction of the trionychid genera Trionyx and Rafetus, both recorded from Central Europe during the Early Miocene, but further allow us to provide an emended diagnosis for R. bohemicus. We confirm the conclusions of a previous study according to which Trionyx pontanus, T. preschenensis, T. aspidiformis, and T. elongatus are nomina dubia. R. bohemicus from Břešt'any (MN 3) represents the oldest record of this genus in Europe as well as the oldest occurrence of the genus.
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Affiliation(s)
- Milan Chroust
- Charles University, Institute of Geology and Palaeontology, Prague, Czech Republic
- Institute of Geology of the Czech Academy of Sciences, Department of Paleobiology and Paleoecology, Prague, Czech Republic
| | - Martin Mazuch
- Charles University, Institute of Geology and Palaeontology, Prague, Czech Republic
| | - Martin Ivanov
- Masaryk University, Department of Geological Sciences, Brno, Czech Republic
| | - David M. Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Àngel H. Luján
- Masaryk University, Department of Geological Sciences, Brno, Czech Republic
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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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: 62] [Impact Index Per Article: 20.7] [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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Abdala CS, Quinteros AS, Semhan RV, Bulacios Arroyo AL, Schulte J, Paz MM, Ruiz-Monachesi MR, Laspiur A, Aguilar-Kirigin AJ, Gutiérrez Poblete R, Valladares Faundez P, Valdés J, Portelli S, Santa Cruz R, Aparicio J, Garcia N, Langstroth R. Unravelling interspecific relationships among highland lizards: first phylogenetic hypothesis using total evidence of the Liolaemus montanus group (Iguania: Liolaemidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The South American lizard genus Liolaemus comprises > 260 species, of which > 60 are recognized as members of the Liolaemus montanus group, distributed throughout the Andes in central Peru, Bolivia, Chile and central Argentina. Despite its great morphological diversity and complex taxonomic history, a robust phylogenetic estimate is still lacking for this group. Here, we study the morphological and molecular diversity of the L. montanus group and present the most complete quantitative phylogenetic hypothesis for the group to date. Our phylogeny includes 103 terminal taxa, of which 91 are members of the L. montanus group (58 are assigned to available species and 33 are of uncertain taxonomic status). Our matrix includes 306 morphological and ecological characters and 3057 molecular characters. Morphological characters include 48 continuous and 258 discrete characters, of which 70% (216) are new to the literature. The molecular characters represent five mitochondrial markers. We performed three analyses: a morphology-only matrix, a molecular-only matrix and a matrix including both morphological and molecular characters (total evidence hypothesis). Our total evidence hypothesis recovered the L. montanus group as monophyletic and included ≥ 12 major clades, revealing an unexpectedly complex phylogeny.
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Affiliation(s)
- Cristian Simón Abdala
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET) – Unidad ejecutora Lillo (UEL), Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo (IML), Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Andrés Sebastián Quinteros
- Instituto de Bio y Geociencias del NOA, Consejo Nacional de Investigación Científicas y Técnicas, Universidad Nacional de Salta, Salta, Argentina
| | - Romina Valeria Semhan
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET) – Unidad ejecutora Lillo (UEL), Tucumán, Argentina
| | - Ana Lucia Bulacios Arroyo
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET) – Unidad ejecutora Lillo (UEL), Tucumán, Argentina
| | - James Schulte
- Department of Biology, Center for the Sciences, Beloit College, Beloit, WI, USA
| | - Marcos Maximiliano Paz
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET) – Unidad ejecutora Lillo (UEL), Tucumán, Argentina
| | - Mario Ricardo Ruiz-Monachesi
- Instituto de Bio y Geociencias del NOA, Consejo Nacional de Investigación Científicas y Técnicas, Universidad Nacional de Salta, Salta, Argentina
| | - Alejandro Laspiur
- Departamento de Biología, Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN) – Escuela Universitaria de Ciencias de la Salud (EUCS) – Universidad Nacional de San Juan, Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia, San Juan, Argentina
| | - Alvaro Juan Aguilar-Kirigin
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Estado Plurinacional de Bolivia
| | | | - Pablo Valladares Faundez
- Laboratorio de Zoología Integrativa, Departamento de Biología, Facultad de Ciencias, Universidad de Tarapacá, Arica, Chile
| | - Julián Valdés
- Cátedra Genética Evolutiva, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Sabrina Portelli
- Instituto de Bio y Geociencias del NOA, Consejo Nacional de Investigación Científicas y Técnicas, Universidad Nacional de Salta, Salta, Argentina
| | - Roy Santa Cruz
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Estado Plurinacional de Bolivia
| | - James Aparicio
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Estado Plurinacional de Bolivia
- Museo Nacional de Historia Natural (MNHN), Cota Cota (Ovidio Suárez), La Paz, Bolivia
| | - Noelia Garcia
- Consejo Nacional de Investigación Científicas y Técnicas (CONICET) – Unidad ejecutora Lillo (UEL), Tucumán, Argentina
| | - Robert Langstroth
- Área de Herpetología, Colección Boliviana de Fauna, Campus Universitario de Cota Cota, Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Estado Plurinacional de Bolivia
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Kundu S, Kumar V, Tyagi K, Chakraborty R, Singha D, Rahaman I, Pakrashi A, Chandra K. Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae. Sci Rep 2018; 8:17378. [PMID: 30478342 PMCID: PMC6255766 DOI: 10.1038/s41598-018-35822-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/09/2018] [Indexed: 11/08/2022] Open
Abstract
The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5'-GACATA-3' and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India.
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Iftikar Rahaman
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
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7
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Portelli SN, Quinteros AS. Phylogeny, time divergence, and historical biogeography of the South American Liolaemus alticolor-bibronii group (Iguania: Liolaemidae). PeerJ 2018; 6:e4404. [PMID: 29479502 PMCID: PMC5824678 DOI: 10.7717/peerj.4404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/02/2018] [Indexed: 11/20/2022] Open
Abstract
The genus Liolaemus comprises more than 260 species and can be divided in two subgenera: Eulaemus and Liolaemus sensu stricto. In this paper, we present a phylogenetic analysis, divergence times, and ancestral distribution ranges of the Liolaemus alticolor-bibronii group (Liolaemus sensu stricto subgenus). We inferred a total evidence phylogeny combining molecular (Cytb and 12S genes) and morphological characters using Maximum Parsimony and Bayesian Inference. Divergence times were calculated using Bayesian MCMC with an uncorrelated lognormal distributed relaxed clock, calibrated with a fossil record. Ancestral ranges were estimated using the Dispersal-Extinction-Cladogenesis (DEC-Lagrange). Effects of some a priori parameters of DEC were also tested. Distribution ranged from central Perú to southern Argentina, including areas at sea level up to the high Andes. The L. alticolor-bibronii group was recovered as monophyletic, formed by two clades: L. walkeri and L. gracilis, the latter can be split in two groups. Additionally, many species candidates were recognized. We estimate that the L. alticolor-bibronii group diversified 14.5 Myr ago, during the Middle Miocene. Our results suggest that the ancestor of the Liolaemus alticolor-bibronii group was distributed in a wide area including Patagonia and Puna highlands. The speciation pattern follows the South-North Diversification Hypothesis, following the Andean uplift.
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Affiliation(s)
- Sabrina N. Portelli
- UNSa-CONICET, Instituto de Bio y Geociencias del NOA, Rosario de Lerma, Salta, Argentina
| | - Andrés S. Quinteros
- UNSa-CONICET, Instituto de Bio y Geociencias del NOA, Rosario de Lerma, Salta, Argentina
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Brinkman D, Rabi M, Zhao L. Lower Cretaceous fossils from China shed light on the ancestral body plan of crown softshell turtles (Trionychidae, Cryptodira). Sci Rep 2017; 7:6719. [PMID: 28751684 PMCID: PMC5532300 DOI: 10.1038/s41598-017-04101-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/08/2017] [Indexed: 12/04/2022] Open
Abstract
Pan-trionychids or softshell turtles are a highly specialized and widespread extant group of aquatic taxa with an evolutionary history that goes back to the Early Cretaceous. The earliest pan-trionychids had already fully developed the "classic" softshell turtle morphology and it has been impossible to resolve whether they are stem members of the family or are within the crown. This has hindered our understanding of the evolution of the two basic body plans of crown-trionychids. Thus it remains unclear whether the more heavily ossified shell of the cyclanorbines or the highly reduced trionychine morphotype is the ancestral condition for softshell turtles. A new pan-trionychid from the Early Cretaceous of Zhejiang, China, Perochelys hengshanensis sp. nov., allows a revision of softshell-turtle phylogeny. Equal character weighting resulted in a topology that is fundamentally inconsistent with molecular divergence date estimates of deeply nested extant species. In contrast, implied weighting retrieved Lower Cretaceous Perochelys spp. and Petrochelys kyrgyzensis as stem trionychids, which is fully consistent with their basal stratigraphic occurrence and an Aptian-Santonian molecular age estimate for crown-trionychids. These results indicate that the primitive morphology for soft-shell turtles is a poorly ossified shell like that of crown-trionychines and that shell re-ossification in cyclanorbines (including re-acquisition of peripheral elements) is secondary.
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Affiliation(s)
- Donald Brinkman
- Royal Tyrrell Museum of Palaeontology, Box 7500, Drumheller, Alberta, Canada, T0J 0Y0.
- Adjunct Professor, Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
| | - Márton Rabi
- Department of Earth Sciences, University of Torino, Via Valperga Caluso 35, 10125, Torino, Italy.
- Institute of Geosciences, University of Tübingen, Sigwartstr. 10, 72076, Tübingen, Germany.
| | - Lijun Zhao
- Zhejiang Museum of Natural History, No. 71 Jiaogong Road, Hangzhou, Zhejiang, China
- Zhejiang Museum of Natural History, 6 Westlake Culture Square, Hangzhou, Zhejiang Province, China
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Shaffer HB, McCartney-Melstad E, Near TJ, Mount GG, Spinks PQ. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Mol Phylogenet Evol 2017; 115:7-15. [PMID: 28711671 DOI: 10.1016/j.ympev.2017.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/30/2017] [Accepted: 07/10/2017] [Indexed: 10/19/2022]
Abstract
Accurate time-calibrated phylogenies are the centerpiece of many macroevolutionary studies, and the relationship between the size and scale of molecular data sets and the density and accuracy of fossil calibrations is a key element of time tree studies. Here, we develop a target capture array specifically for living turtles, compare its efficiency to an ultraconserved element (UCE) dataset, and present a time-calibrated molecular phylogeny based on 539 nuclear loci sequenced from 26 species representing the breadth of living turtle diversity plus outgroups. Our gene array, based on three fully sequenced turtle genomes, is 2.4 times more variable across turtles than a recently published UCE data set for an identical subset of 13 species, confirming that taxon-specific arrays return more informative data per sequencing effort than UCEs. We used our genomic data to estimate the ages of living turtle clades including a mid-late Triassic origin for crown turtles and a mid-Carboniferous split of turtles from their sister group, Archosauria. By specifically excluding several of the earliest potential crown turtle fossils and limiting the age of fossil calibration points to the unambiguous crown lineage Caribemys oxfordiensis from the Late Jurassic (Oxfordian, 163.5-157.3Ma) we corroborate a relatively ancient age for living turtles. We also provide novel age estimates for five of the ten testudine families containing more than a single species, as well as several intrafamilial clades. Most of the diversity of crown turtles appears to date to the Paleogene, well after the Cretaceous-Paleogene mass extinction 66mya.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.
| | - Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Genevieve G Mount
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences, Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, Hadrys H. The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches. PLoS One 2017; 12:e0174842. [PMID: 28406914 PMCID: PMC5390999 DOI: 10.1371/journal.pone.0174842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/16/2017] [Indexed: 01/13/2023] Open
Abstract
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.
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Affiliation(s)
- Jessica Rach
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Tjard Bergmann
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Omid Paknia
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Heike Hadrys
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
- * E-mail:
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Li H, Liu J, Xiong L, Zhang H, Zhou H, Yin H, Jing W, Li J, Shi Q, Wang Y, Liu J, Nie L. Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes. J Evol Biol 2017; 30:1011-1023. [PMID: 28294452 DOI: 10.1111/jeb.13070] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 11/30/2022]
Abstract
The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.
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Affiliation(s)
- H Li
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Liu
- The College of Life Sciences, Beijing Normal University, Beijing, China
| | - L Xiong
- Wannan medical college, Wuhu, Anhui, China
| | - H Zhang
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - H Zhou
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - H Yin
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - W Jing
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Li
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - Q Shi
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - Y Wang
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Liu
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - L Nie
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
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12
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Rovatsos M, Praschag P, Fritz U, Kratochvšl L. Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae). Sci Rep 2017; 7:42150. [PMID: 28186115 PMCID: PMC5301483 DOI: 10.1038/srep42150] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/05/2017] [Indexed: 01/18/2023] Open
Abstract
Turtles demonstrate variability in sex determination ranging from environmental sex determination (ESD) to highly differentiated sex chromosomes. However, the evolutionary dynamics of sex determining systems in this group is not well known. Differentiated ZZ/ZW sex chromosomes were identified in two species of the softshell turtles (Trionychidae) from the subfamily Trionychinae and Z-specific genes were identified in a single species. We tested Z-specificity of a subset of these genes by quantitative PCR comparing copy gene numbers in male and female genomes in 10 species covering the phylogenetic diversity of trionychids. We demonstrated that differentiated ZZ/ZW sex chromosomes are conserved across the whole family and that they were already present in the common ancestor of the extant trionychids. As the sister lineage, Carettochelys insculpta, possess ESD, we can date the origin of the sex chromosomes in trionychids between 200 Mya (split of Trionychidae and Carettochelyidae) and 120 Mya (basal splitting of the recent trionychids). The results support the evolutionary stability of differentiated sex chromosomes in some lineages of ectothermic vertebrates. Moreover, our approach determining sex-linkage of protein coding genes can be used as a reliable technique of molecular sexing across trionychids useful for effective breeding strategy in conservation projects of endangered species.
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Affiliation(s)
- Michail Rovatsos
- Faculty of Science, Charles University, Department of Ecology, Viničná 7, 12844 Praha 2, Czech Republic
| | - Peter Praschag
- Turtle Island, Turtle Conservation Center, Am Katzelbach 98, 8054 Graz, Austria
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Lukáš Kratochvšl
- Faculty of Science, Charles University, Department of Ecology, Viničná 7, 12844 Praha 2, Czech Republic
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Cadena E. Palaeoamyda messeliana nov. comb. (Testudines, Pan-Trionychidae) from the Eocene Messel Pit and Geiseltal localities, Germany, taxonomic and phylogenetic insights. PeerJ 2016; 4:e2647. [PMID: 27812431 PMCID: PMC5088588 DOI: 10.7717/peerj.2647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/03/2016] [Indexed: 11/20/2022] Open
Abstract
Background Abundant pan-trionychid (soft-shell) turtles specimens have been found in Eocene sequences of central Europe, particularly from two localities in Germany, the Messel Pit (a UNESCO World Natural Heritage Site) and Geiseltal, traditionally attributed to Trionyx messelianus or Rafetoides austriacus. Over the last two decades new specimens of this taxon from these two localities have been discovered and fully prepared. However, they have remained unstudied, as well as their phylogenetic position inside Pan-Trionychidae is unknown. Results Five new specimens of Palaeoamyda messeliana nov. comb. from Messel Pit and Geiseltal localities are fully described here. A revised diagnosis for the species is also presented here, together with its inclusion in a phylogenetic analysis of Pan-Trionychidae that shows that this species is sister to the extant Amyda cartilaginea, one of the most abundant pan-trionychid (soft-shell) turtles from Asia, both members of the clade Chitrini. The specimens described in here are among the best and most complete fossil pan-trionychid skeletons so far known.
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Affiliation(s)
- Edwin Cadena
- School of Geological Sciences and Engineering, Yachay Tech , San Miguel de Urcuquí , Imbabura , Ecuador
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Kundu S, Kumar V, Laskar BA, Chandra K, Tyagi K. Mitochondrial DNA effectively detects non-native Testudines: Invisible wildlife trade in northeast India. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Vitek NS, Joyce WG. A Review of the Fossil Record of New World Turtles of the CladePan-Trionychidae. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2015. [DOI: 10.3374/014.056.0204] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Origins of softshell turtles in Hawaii with implications for conservation. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0772-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Kundu S, Laskar BA, Venkataraman K, Banerjee D, Kumar V. DNA barcoding of Nilssonia congeners corroborates existence of wild N. nigricans in northeast India. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2753-6. [PMID: 26057013 DOI: 10.3109/19401736.2015.1046176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA barcode data of soft-shell turtles is limited in global DNA database while it is completely lacking for the highly debated species Nilssonia nigricans. We employed DNA barcoding technique to discriminate the species cluster for Nilssonia congeners, especially for the highly debated N. nigricans from different localities of northeast India. Sampling across the region included a few live specimens from wild, market sold carcass specimens, and a few dry carapaces meant for home decoration purpose. The generated sequences (621 bp of mtCOI) of dry carapaces showed 99-100% homology with the generated sequences of morphologically identified N. nigricans. The COI barcode sequences of N. nigricans (n = 12) showed 3.8% mean genetic divergence with N. hurum (n = 3), 10% with N. gangetica (n = 4), and 9.2% with N. formosa (GenBank sequences). Similarly, the mtCytb sequences of the dry carapace and live specimens of N. nigricans were 99-100% homologous with the conspecific database sequences and formed specific clusters. The inferred Neighbor-Joining (NJ), Maximum Likelihood (ML), and Bayesian (BA) phylogeny based on partial mtCOI gene efficiently discriminated all the congeners of Nilssonia into specific clusters and, therefore, it was helpful to detect the existence of N. nigricans.
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Affiliation(s)
- Shantanu Kundu
- a Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India , New Alipore, Kolkata , India
| | - Boni Amin Laskar
- a Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India , New Alipore, Kolkata , India
| | - Krishnamoorthy Venkataraman
- a Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India , New Alipore, Kolkata , India
| | - Dhriti Banerjee
- a Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India , New Alipore, Kolkata , India
| | - Vikas Kumar
- a Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India , New Alipore, Kolkata , India
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Rice R, Riccio P, Gilbert SF, Cebra-Thomas J. Emerging from the rib: resolving the turtle controversies. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:208-20. [PMID: 25675951 DOI: 10.1002/jez.b.22600] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 09/29/2014] [Indexed: 12/15/2022]
Abstract
Two of the major controversies in the present study of turtle shell development involve the mechanism by which the carapacial ridge initiates shell formation and the mechanism by which each rib forms the costal bones adjacent to it. This paper claims that both sides of each debate might be correct-but within the species examined. Mechanism is more properly "mechanisms," and there is more than one single way to initiate carapace formation and to form the costal bones. In the initiation of the shell, the rib precursors may be kept dorsal by either "axial displacement" (in the hard-shell turtles) or "axial arrest" (in the soft-shell turtle Pelodiscus), or by a combination of these. The former process would deflect the rib into the dorsal dermis and allow it to continue its growth there, while the latter process would truncate rib growth. In both instances, though, the result is to keep the ribs from extending into the ventral body wall. Our recent work has shown that the properties of the carapacial ridge, a key evolutionary innovation of turtles, differ greatly between these two groups. Similarly, the mechanism of costal bone formation may differ between soft-shell and hard-shell turtles, in that the hard-shell species may have both periosteal flattening as well as dermal bone induction, while the soft-shelled turtles may have only the first of these processes.
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Affiliation(s)
- Ritva Rice
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Angielczyk KD, Burroughs RW, Feldman CR. Do turtles follow the rules? Latitudinal gradients in species richness, body size, and geographic range area of the world's turtles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:270-94. [DOI: 10.1002/jez.b.22602] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/10/2014] [Accepted: 09/29/2014] [Indexed: 11/11/2022]
Affiliation(s)
| | - Robert W. Burroughs
- Jackson School of Geosciences; The University of Texas at Austin; Austin Texas
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20
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Suzuki D, Hikida T. Taxonomic Status of the Soft-Shell Turtle Populations in Japan: A Molecular Approach. CURRENT HERPETOLOGY 2014. [DOI: 10.5358/hsj.33.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Hodges K, Donnellan S, Georges A. Phylogeography of the Australian freshwater turtleChelodina expansareveals complex relationships among inland and coastal bioregions. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kate Hodges
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures; University of Canberra; Canberra ACT 2601 Australia
| | | | - Arthur Georges
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures; University of Canberra; Canberra ACT 2601 Australia
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22
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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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23
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Resolving the phylogenetic history of the short-necked turtles, genera Elseya and Myuchelys (Testudines: Chelidae) from Australia and New Guinea. Mol Phylogenet Evol 2013; 68:251-8. [PMID: 23563271 DOI: 10.1016/j.ympev.2013.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 03/14/2013] [Accepted: 03/24/2013] [Indexed: 11/22/2022]
Abstract
Phylogenetic relationships and taxonomy of the short-necked turtles of the genera Elseya, Myuchelys, and Emydura in Australia and New Guinea have long been debated as a result of conflicting hypotheses supported by different data sets and phylogenetic analyses. To resolve this contentious issue, we analyzed sequences from two mitochondrial genes (cytochrome b and ND4) and one nuclear intron gene (R35) from all species of the genera Elseya, Myuchelys, Emydura, and their relatives. Phylogenetic analyses using three methods (maximum parsimony, maximum likelihood, and Bayesian inference) produce a single, well resolved, and strongly corroborated hypothesis, which provides support for the three genera, with the exception that the genus Myuchelys is paraphyletic - Myuchelys purvisi is the sister taxon to the remaining Elseya, Myuchelys and Emydura. A new genus is proposed for the species Myuchelys purvisi to address this paraphyletic relationship. Time-calibration analysis suggests that diversification of the group in Australia coincides with periods of aridification in the late Eocene and between the mid-Miocene and early Pliocene. Other speciation events occurred during the faunal exchange between Australia and the island of New Guinea during the late Miocene and early Pliocene. Lineages distributed in New Guinea are likely influenced by the complex geologic history of the island, and include cryptic species diversity.
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McCranie JR, Köhler F, Gutsche A, Orellana LV. Trachemys grayi emolli(Testudines, Emydidae) in Honduras and its systematic relationships based on mitochondrial DNA. ZOOSYST EVOL 2013. [DOI: 10.1002/zoos.201300003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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25
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Grechko VV. The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers. Mol Biol 2013. [DOI: 10.1134/s0026893313010056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Rivera ARV, Rivera G, Blob RW. Forelimb kinematics during swimming in the pig-nosed turtle, Carettochelys insculpta, compared with other turtle taxa: rowing versus flapping, convergence versus intermediacy. ACTA ACUST UNITED AC 2012; 216:668-80. [PMID: 23125335 DOI: 10.1242/jeb.079715] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Animals that swim using appendages do so by way of rowing and/or flapping motions. Often considered discrete categories, rowing and flapping are more appropriately regarded as points along a continuum. The pig-nosed turtle, Carettochelys insculpta, is unusual in that it is the only freshwater turtle to have limbs modified into flippers and swim via synchronous forelimb motions that resemble dorsoventral flapping, traits that evolved independently from their presence in sea turtles. We used high-speed videography to quantify forelimb kinematics in C. insculpta and a closely related, highly aquatic rower (Apalone ferox). Comparisons of our new data with those previously collected for a generalized freshwater rower (Trachemys scripta) and a flapping sea turtle (Caretta caretta) allow us to: (1) more precisely quantify and characterize the range of limb motions used by flappers versus rowers, and (2) assess whether the synchronous forelimb motions of C. insculpta can be classified as flapping (i.e. whether they exhibit forelimb kinematics and angles of attack more similar to closely related rowing species or more distantly related flapping sea turtles). We found that the forelimb kinematics of previously recognized rowers (T. scripta and A. ferox) were most similar to each other, but that those of C. insculpta were more similar to rowers than to flapping C. caretta. Nevertheless, of the three freshwater species, C. insculpta was most similar to flapping C. caretta. 'Flapping' in C. insculpta is achieved through humeral kinematics very different from those in C. caretta, with C. insculpta exhibiting significantly more anteroposterior humeral motion and protraction, and significantly less dorsoventral humeral motion and depression. Based on several intermediate kinematic parameters and angle of attack data, C. insculpta may in fact represent a synchronous rower or hybrid rower-flapper, suggesting that traditional views of C. insculpta as a flapper should be revised.
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Affiliation(s)
- Angela R V Rivera
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA.
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27
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Campione NE, Evans DC. A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biol 2012; 10:60. [PMID: 22781121 PMCID: PMC3403949 DOI: 10.1186/1741-7007-10-60] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Body size is intimately related to the physiology and ecology of an organism. Therefore, accurate and consistent body mass estimates are essential for inferring numerous aspects of paleobiology in extinct taxa, and investigating large-scale evolutionary and ecological patterns in the history of life. Scaling relationships between skeletal measurements and body mass in birds and mammals are commonly used to predict body mass in extinct members of these crown clades, but the applicability of these models for predicting mass in more distantly related stem taxa, such as non-avian dinosaurs and non-mammalian synapsids, has been criticized on biomechanical grounds. Here we test the major criticisms of scaling methods for estimating body mass using an extensive dataset of mammalian and non-avian reptilian species derived from individual skeletons with live weights. RESULTS Significant differences in the limb scaling of mammals and reptiles are noted in comparisons of limb proportions and limb length to body mass. Remarkably, however, the relationship between proximal (stylopodial) limb bone circumference and body mass is highly conserved in extant terrestrial mammals and reptiles, in spite of their disparate limb postures, gaits, and phylogenetic histories. As a result, we are able to conclusively reject the main criticisms of scaling methods that question the applicability of a universal scaling equation for estimating body mass in distantly related taxa. CONCLUSIONS The conserved nature of the relationship between stylopodial circumference and body mass suggests that the minimum diaphyseal circumference of the major weight-bearing bones is only weakly influenced by the varied forces exerted on the limbs (that is, compression or torsion) and most strongly related to the mass of the animal. Our results, therefore, provide a much-needed, robust, phylogenetically corrected framework for accurate and consistent estimation of body mass in extinct terrestrial quadrupeds, which is important for a wide range of paleobiological studies (including growth rates, metabolism, and energetics) and meta-analyses of body size evolution.
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Affiliation(s)
- Nicolás E Campione
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
| | - David C Evans
- Department of Palaeobiology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
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Phylogeography of the Phrynocephalus vlangalii Species Complex in the Upper Reaches of the Yellow River Inferred from mtDNA ND4-tRNALEU Segments. ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Fielder D, Vernes K, Alacs E, Georges A. Mitochondrial variation among Australian freshwater turtles (genus Myuchelys), with special reference to the Endangered M. bellii. ENDANGER SPECIES RES 2012. [DOI: 10.3354/esr00417] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Book Reviews. COPEIA 2011. [DOI: 10.1643/ot-11-084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Du WG, Ye H, Zhao B, Pizzatto L, Ji X, Shine R. Patterns of interspecific variation in the heart rates of embryonic reptiles. PLoS One 2011; 6:e29027. [PMID: 22174948 PMCID: PMC3236780 DOI: 10.1371/journal.pone.0029027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/18/2011] [Indexed: 11/18/2022] Open
Abstract
New non-invasive technologies allow direct measurement of heart rates (and thus, developmental rates) of embryos. We applied these methods to a diverse array of oviparous reptiles (24 species of lizards, 18 snakes, 11 turtles, 1 crocodilian), to identify general influences on cardiac rates during embryogenesis. Heart rates increased with ambient temperature in all lineages, but (at the same temperature) were faster in lizards and turtles than in snakes and crocodilians. We analysed these data within a phylogenetic framework. Embryonic heart rates were faster in species with smaller adult sizes, smaller egg sizes, and shorter incubation periods. Phylogenetic changes in heart rates were negatively correlated with concurrent changes in adult body mass and residual incubation period among the lizards, snakes (especially within pythons) and crocodilians. The total number of embryonic heart beats between oviposition and hatching was lower in squamates than in turtles or the crocodilian. Within squamates, embryonic iguanians and gekkonids required more heartbeats to complete development than did embryos of the other squamate families that we tested. These differences plausibly reflect phylogenetic divergence in the proportion of embryogenesis completed before versus after laying.
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Affiliation(s)
- Wei-Guo Du
- Key Laboratory of Animal Ecology and Conservational Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Mol Phylogenet Evol 2011; 62:496-507. [PMID: 22100825 DOI: 10.1016/j.ympev.2011.10.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 10/19/2011] [Accepted: 10/25/2011] [Indexed: 11/20/2022]
Abstract
The superfamily Testudinoidea is the most diverse and widely distributed clade of extant turtles. Surprisingly, despite an extensive fossil record, and increasing amount of molecular data available, the temporal origin of this group is still largely unknown. To address this issue, we used a comprehensive molecular dataset to perform phylogenetic and molecular dating analyses, as well as seven fossil constraints to calibrate the ages of the nodes in the phylogeny. The molecular dataset includes the complete mitochondrial genomes of 37 turtle species, including newly sequenced mitochondrial genomes of Phrynops hilarii, Emys orbicularis, Rhinoclemmys punctularia, and Chelonoidis nigra, and four nuclear markers. Our results revealed that the earliest divergences within crown testudinoids occurred around 95.0 Mya, in the early Late Cretaceous, earlier than previously reported, raising new questions about the historical biogeography of this group.
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Genetic variation of the Nile soft-shelled turtle (Trionyx triunguis). Int J Mol Sci 2011; 12:6418-31. [PMID: 22072896 PMCID: PMC3210987 DOI: 10.3390/ijms12106418] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/05/2011] [Accepted: 09/20/2011] [Indexed: 11/24/2022] Open
Abstract
We studied the genetic structure of Trionyx triunguis populations from the Mediterranean and African continent based on mtDNA D-loop (776 bp) and nine microsatellite loci. A total of 102 polymorphic sites and 13 mtDNA haplotypes were described. Nucleotide diversity and haplotypes diversity were 0.047 and 0.974 respectively. Both mtDNA and nDNA supported the existence of two main management units as the Mediterranean and Africa. Based on the mtDNA results, the Mediterranean can be divided into two subunits; western Turkey and the eastern Mediterranean.
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Vitek N. Insights into the Taxonomy and Systematics of North American Eocene Soft-Shelled Turtles from a Well-Preserved Specimen. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2011. [DOI: 10.3374/014.052.0201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Natasha Vitek
- Division of Vertebrate Paleontology, Peabody Museum of Natural History, Yale University, New Haven CT 06520-8118 USA
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Shallow genetic divergence indicates a Congo–Nile riverine connection for the softshell turtle Trionyx triunguis. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0160-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Comparison research and phylogenetic implications of mitochondrial control regions in four soft-shelled turtles of Trionychia (Reptilia, Testudinata). Genes Genomics 2010. [DOI: 10.1007/s13258-010-0015-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Fritz U, Gong S, Auer M, Kuchling G, Schneeweiß N, Hundsdörfer AK. The world’s economically most important chelonians represent a diverse species complex (Testudines: Trionychidae: Pelodiscus). ORG DIVERS EVOL 2010. [DOI: 10.1007/s13127-010-0007-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Evolutionary and developmental aspects of phalangeal formula variation in pig-nose and soft-shelled turtles (Carettochelyidae and Trionychidae). ORG DIVERS EVOL 2010. [DOI: 10.1007/s13127-010-0019-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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39
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WIENS JOHNJ, KUCZYNSKI CAITLINA, STEPHENS PATRICKR. Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01342.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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DELFINO MASSIMO, SCHEYER TORSTENM, FRITZ UWE, SÁNCHEZ-VILLAGRA MARCELOR. An integrative approach to examining a homology question: shell structures in soft-shell turtles. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01356.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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41
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Güçlü Ö, Ulger C, Türkozan O, Gemel R, Reimann M, Levy Y, Ergene S, Uçar AH, Aymak C. First Assessment of Mitochondrial DNA Diversity in the Endangered Nile Softshell Turtle, Trionyx triunguis, in the Mediterranean. CHELONIAN CONSERVATION AND BIOLOGY 2009. [DOI: 10.2744/ccb-0792.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Sánchez-Villagra MR, Müller H, Sheil CA, Scheyer TM, Nagashima H, Kuratani S. Skeletal development in the Chinese soft-shelled turtlePelodiscus sinensis(Testudines: Trionychidae). J Morphol 2009; 270:1381-99. [DOI: 10.1002/jmor.10766] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Joyce WG, Revan A, Lyson TR, Danilov IG. Two New Plastomenine Softshell Turtles from the Paleocene of Montana and Wyoming. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2009. [DOI: 10.3374/014.050.0202] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Spinks PQ, Shaffer HB. Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization. Syst Biol 2009; 58:1-20. [PMID: 20525565 DOI: 10.1093/sysbio/syp005] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the mechanisms by which widely disjunct members of a clade came to occupy their current distribution is one of the fundamental challenges of biogeography. Here, we used data from 7 nuclear and 1 mitochondrial gene to examine the phylogenetic and biogeographic history of Emys, a clade of turtles that is broadly disjunct in western and eastern North America and Europe. We found strong disagreement between mitochondrial and nuclear gene trees, with mitochondrial DNA supporting the monophyly of the North American taxa (marmorata + blandingii) to the exclusion of the European orbicularis, and nuclear genes supporting the monophyly of (blandingii + orbicularis) to the exclusion of marmorata. We used fossil-calibrated molecular chronograms, in combination with supporting evidence from the fossil record and paleoclimatology, to identify a potential example of ancient hybridization and mitochondrial gene capture 12 million years ago, which explains this discrepancy. Based on the weight of evidence, we argue that the invasion of Eurasia by Emys orbicularis occurred about 16 Ma via a trans-Beringian land bridge. The case of Emys emphasizes how single-gene trees can be strongly affected by population processes, including hybridization, and that the effects of these processes can persist through long periods of evolutionary history. Given the chaotic state of the current taxonomy of these turtles, our work also emphasizes the care that should be used in implementing taxonomic changes based on 1 or a few gene trees and the importance of taking a conservative approach in renaming or splitting higher taxa based on apparent nonmonophyly.
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Affiliation(s)
- Phillip Q Spinks
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA.
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A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence. Parasitology 2009; 136:317-28. [DOI: 10.1017/s0031182008005453] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
SUMMARYThe taxonomic status of Echinococcus, an important zoonotic cestode genus, has remained controversial, despite numerous attempts to revise it. Although mitochondrial DNA (mtDNA) has been the source of markers of choice for reconstructing the phylogeny of the genus, results derived from mtDNA have led to significant inconsistencies with earlier species classifications based on phenotypic analysis. Here, we used nuclear DNA markers to test the phylogenic relationships of members of the genus Echinococcus. The analysis of sequence data for 5 nuclear genes revealed a significantly different phylogeny for Echinococcus from that proposed on the basis of mitochondrial DNA sequence data, but was in agreement with earlier species classifications. The most notable results from the nuclear phylogeny were (1) E. multilocularis was placed as basal taxon, (2) all genotypes of Echinococcus granulosus grouped as a monophyletic entity, and (3) genotypes G8 and G10 clustered together. We conclude that the analysis of nuclear DNA data provides a more reliable means of inferring phylogenetic relationships within Echinococcus than mtDNA and suggest that mtDNA should not be used as the sole source of markers in future studies where the goal is to reconstruct a phylogeny that does not only reflect a maternal lineage, but aims to describe the evolutionary history at species level or higher.
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Rohilla MS, Tiwari PK. Restriction fragment length polymorphism of mitochondrial DNA and phylogenetic relationships among five species of Indian freshwater turtles. J Appl Genet 2008; 49:167-82. [PMID: 18436991 DOI: 10.1007/bf03195610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA-based identification of species for phylogenetic analysis as well as forensic identification is widely being carried out with the help of polymerase chain reaction (PCR). In this study, a successful effort has been made to identify 5 species of Indian freshwater turtles, including 3 hard-shell turtles (Geoemydidae), i.e. Kachuga dhongoka, K. kachuga and Geoclemys hamiltoni, and 2 species of soft-shell turtles (Trionychidae), i.e. Aspideretes gangeticus and Lissemys punctata punctata, by using a well-optimized PCR-RFLP method. The analysis of nucleotide sequence variations in the PCR-amplified mitochondrial cyt-b genes (encoding cytochrome b) from the 5 species revealed its usefulness in the taxonomic differentiation of these species. On the basis of cyt-b sequence data and the PCR-RFLP pattern, a phylogeny was developed to resolve the genetic relationships between these species, living in the same habitat type. In comparison, the PCR-RFLP of mitochondrial 16S rDNA genes appeared less decisive in analysing phylogenetic relationships or even in species differentiation. Further, the molecular method (PCR-RFLP) developed here is simple, rapid, reliable and reproducible; hence it can be routinely applied for species identification, essential for conservation and management of endangered chelonian species.
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Affiliation(s)
- Manoj S Rohilla
- School of Studies in Zoology, Jiwaji University, Gwalior, India
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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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48
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McGaugh SE, Janzen FJ. The Status of Apalone atra Populations in Cuatro Ciénegas, Coahuila, México: Preliminary Data. CHELONIAN CONSERVATION AND BIOLOGY 2008. [DOI: 10.2744/ccb-0651.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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49
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McGaugh SE, Eckerman CM, Janzen FJ. Molecular phylogeography of Apalone spinifera (Reptilia, Trionychidae). ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00329.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Zou XH, Zhang FM, Zhang JG, Zang LL, Tang L, Wang J, Sang T, Ge S. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol 2008; 9:R49. [PMID: 18315873 PMCID: PMC2397501 DOI: 10.1186/gb-2008-9-3-r49] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 02/18/2008] [Accepted: 03/03/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genome resources for biological research and rice breeding, we will benefit from the availability of a robust phylogeny of the rice genus. RESULTS Through screening rice genome sequences, we sampled and sequenced 142 single-copy genes to clarify the relationships among all diploid genome types of the rice genus. The analysis identified two short internal branches around which most previous phylogenetic inconsistency emerged. These represent two episodes of rapid speciation that occurred approximately 5 and 10 million years ago (Mya) and gave rise to almost the entire diversity of the genus. The known chromosomal distribution of the sampled genes allowed the documentation of whole-genome sorting of ancestral alleles during the rapid speciation, which was responsible primarily for extensive incongruence between gene phylogenies and persisting phylogenetic ambiguity in the genus. Random sample analysis showed that 120 genes with an average length of 874 bp were needed to resolve both short branches with 95% confidence. CONCLUSION Our phylogenomic analysis successfully resolved the phylogeny of rice genome types, which lays a solid foundation for comparative and functional genomic studies of rice and its relatives. This study also highlights that organismal genomes might be mosaics of conflicting genealogies because of rapid speciation and demonstrates the power of phylogenomics in the reconstruction of rapid diversification.
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Affiliation(s)
- Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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