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Farina BM, Godoy PL, Benson RBJ, Langer MC, Ferreira GS. Turtle body size evolution is determined by lineage-specific specializations rather than global trends. Ecol Evol 2023; 13:e10201. [PMID: 37384241 PMCID: PMC10293707 DOI: 10.1002/ece3.10201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/30/2023] Open
Abstract
Organisms display a considerable variety of body sizes and shapes, and macroevolutionary investigations help to understand the evolutionary dynamics behind such variations. Turtles (Testudinata) show great body size disparity, especially when their rich fossil record is accounted for. We explored body size evolution in turtles, testing which factors might influence the observed patterns and evaluating the existence of long-term directional trends. We constructed the most comprehensive body size dataset for the group to date, tested for correlation with paleotemperature, estimated ancestral body sizes, and performed macroevolutionary model-fitting analyses. We found no evidence for directional body size evolution, even when using very flexible models, thereby rejecting the occurrence of Cope's rule. We also found no significant effect of paleotemperature on overall through-time body size patterns. In contrast, we found a significant influence of habitat preference on turtle body size. Freshwater turtles display a rather homogeneous body size distribution through time. In contrast, terrestrial and marine turtles show more pronounced variation, with terrestrial forms being restricted to larger body sizes, up to the origin of testudinids in the Cenozoic, and marine turtles undergoing a reduction in body size disparity after the extinctions of many groups in the mid-Cenozoic. Our results, therefore, suggest that long-term, generalized patterns are probably explained by factors specific to certain groups and related at least partly to habitat use.
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Affiliation(s)
- Bruna M. Farina
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
- Laboratório de Paleontologia de Ribeirão PretoUniversidade de São PauloRibeirão PretoBrazil
| | - Pedro L. Godoy
- Laboratório de Paleontologia de Ribeirão PretoUniversidade de São PauloRibeirão PretoBrazil
- Department of Anatomical SciencesStony Brook UniversityStony BrookNew YorkUSA
| | - Roger B. J. Benson
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Max C. Langer
- Laboratório de Paleontologia de Ribeirão PretoUniversidade de São PauloRibeirão PretoBrazil
| | - Gabriel S. Ferreira
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP)Eberhard Karls Universität TübingenTübingenGermany
- Fachbereich GeowissenschaftenEberhard Karls Universität TübingenTübingenGermany
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2
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Pedro Selvatti A, Romero Rebello Moreira F, Cardoso de Carvalho D, Prosdocimi F, Augusta de Moraes Russo C, Carolina Martins Junqueira A. Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles. Mol Phylogenet Evol 2023; 183:107773. [PMID: 36977459 DOI: 10.1016/j.ympev.2023.107773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 02/07/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Although a consensus exists that all living turtles fall within either Pleurodira or Cryptodira clades, estimating when these lineages split is still under debate. Most molecular studies date the split in the Triassic Period, whereas a Jurassic age is unanimous among morphological studies. Each hypothesis implies different paleobiogeographical scenarios to explain early turtle evolution. Here we explored the rich turtle fossil record with the Fossilized Birth-Death (FBD) and the traditional node dating (ND) methods using complete mitochondrial genomes (147 taxa) and a set of nuclear orthologs with over 10 million bp (25 taxa) to date the major splits in Testudines. Our results support an Early Jurassic split (191-182 Ma) for the crown Testudines with great consistency across different dating methods and datasets, with a narrow confidence interval. This result is independently supported by the oldest fossils of Testudines that postdate the Middle Jurassic (174 Ma), which were not used for calibration in this study. This age coincides with the Pangaea fragmentation and the formation of saltwater barriers such as the Atlantic Ocean and the Turgai Strait, supporting that diversification in Testudines was triggered by vicariance. Our ages of the splits in Pleurodira coincide with the geologic events of the Late Jurassic and Early Cretaceous. Conversely, the early Cryptodira radiation remained in Laurasia, and its diversification ensued as all its major lineages expanded their distribution into every continent during the Cenozoic. We provide the first detailed hypothesis of the evolution of Cryptodira in the Southern Hemisphere, in which our time estimates are correlated with each contact between landmasses derived from Gondwana and Laurasia. Although most South American Cryptodira arrived through the Great American Biotic Interchange, our results indicate that the Chelonoidis ancestor probably arrived from Africa through the chain islands of the South Atlantic during the Paleogene. Together, the presence of ancient turtle diversity and the vital role that turtles occupy in marine and terrestrial ecosystems underline South America as a chief area for conservation.
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Adrian B, Smith HF, Hutchison JH, Townsend KEB. Geometric morphometrics and anatomical network analyses reveal ecospace partitioning among geoemydid turtles from the Uinta Formation, Utah. Anat Rec (Hoboken) 2021; 305:1359-1393. [PMID: 34605614 DOI: 10.1002/ar.24792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/19/2021] [Accepted: 09/03/2021] [Indexed: 01/13/2023]
Abstract
We present new fossil records of the geoemydid turtle Bridgeremys pusilla from the Uinta Formation of Utah. Turtles are abundant throughout the unit, and known taxa are similar to those from the older strata in the Upper Green River Basin in Wyoming from the Bridger and Washakie Formations. B. pusilla is known from Bridgerian deposits but was not previously known from after the Turtle Bluff Member of the Bridger Formation. The taxon was coveal with two species of the geoemydid Echmatemys (E. callopyge and E. wyomingensis), a common genus of extinct pond turtles known primarily from lacustrine and fluvial deposits in western North America, including the Uinta Basin. In addition to previously documented morphological differences, our geometric morphometric analyses revealed significant differences in epiplastral morphology between B. pusilla and the two coeval Echmatemys species. Bridgeremys pusilla shared several morphological characters with Testudinidae. However, our anatomical network analysis suggests that the carapace of B. pusilla distributed stress forces in a manner more similar to emydids (basal and derived) than to derived testudinoids (Testudinidae and Emydidae), including Echmatemys species. This finding changes our understanding of the ecology of the species and sheds light onto how geoemydid turtles of the Uinta Formation may have partitioned the available ecospace. These new Uintan records extend the geographic range of B. pusilla into the Uinta Basin and stratigraphically through the top of the Uinta Formation, extending the temporal range of the taxon by more than 4 million years through the Uintan North American Land Mammal Age to the base of the Duchesne River Formation.
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Affiliation(s)
- Brent Adrian
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA
| | - Heather F Smith
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - J Howard Hutchison
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, California, USA
| | - K E Beth Townsend
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA
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4
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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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5
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Chatterji RM, Hutchinson MN, Jones MEH. Redescription of the skull of the Australian flatback sea turtle, Natator depressus, provides new morphological evidence for phylogenetic relationships among sea turtles (Chelonioidea). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Chelonioidea (sea turtles) are a group where available morphological evidence for crown-group relationships are incongruent with those established using molecular data. However, morphological surveys of crown-group taxa tend to focus on a recurring subset of the extant species. The Australian flatback sea turtle, Natator depressus, is often excluded from comparisons and it is the most poorly known of the seven extant species of Chelonioidea. Previous descriptions of its skull morphology are limited and conflict. Here we describe three skulls of adult N. depressus and re-examine the phylogenetic relationships according to morphological character data. Using X-ray micro Computed Tomography we describe internal structures of the braincase and identify new phylogenetically informative characters not previously reported. Phylogenetic analysis using a Bayesian approach strongly supports a sister-group relationship between Chelonia mydas and N. depressus, a topology that was not supported by previous analyses of morphological data but one that matches the topology supported by analysis of molecular data. Our results highlight the general need to sample the morphological anatomy of crown-group taxa more thoroughly before concluding that morphological and molecular evidence are incongruous.
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Affiliation(s)
- Ray M Chatterji
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, SA, Australia
- South Australian Museum, Adelaide, Adelaide, South Australia, SA, Australia
| | - Mark N Hutchinson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, SA, Australia
- South Australian Museum, Adelaide, Adelaide, South Australia, SA, Australia
| | - Marc E H Jones
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, SA, Australia
- South Australian Museum, Adelaide, Adelaide, South Australia, SA, Australia
- Earth Sciences, Natural History Museum, London, UK
- Cell and Developmental Biology, UCL, University College London, London, UK
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6
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Zhao Z, Heideman N, Bester P, Jordaan A, Hofmeyr MD. Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa. BMC Evol Biol 2020; 20:153. [PMID: 33187474 PMCID: PMC7666511 DOI: 10.1186/s12862-020-01717-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world's tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. RESULTS We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63-5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. CONCLUSION Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B-Ptr, Ptt-A and Pv-A.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa.
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Phillip Bester
- Department of Virology, University of the Free State and National Health Laboratory Service (NHLS), Bloemfontein, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Margaretha D Hofmeyr
- Department of Biodiversity and Conservation Biology, Chelonian Biodiversity and Conservation, University of the Western Cape, Bellville, South Africa
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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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8
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Garcia G, Pinton A, Valentin X, Kostopoulos DS, Merceron G, de Bonis L, Koufos GD. The earliest known crown-Testudo tortoise from the late Miocene (Vallesian, 9 Ma) of Greece. PLoS One 2020; 15:e0224783. [PMID: 32267839 PMCID: PMC7141670 DOI: 10.1371/journal.pone.0224783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 10/21/2019] [Indexed: 11/19/2022] Open
Abstract
We here report on fossil remains of the earliest known crown-Testudo, an extant clade of Mediterranean testudinid tortoises from the late Miocene (Vallesian, MN 10) from the hominoid locality Ravin de la Pluie (RPl) in Greece. The material studied is a small, nearly complete carapace with a clearly distinct hypo-xiphiplastral hinge. This supports the sensu stricto generic assignment. This new terrestrial testudinid specimen is characterized by a possible tectiform, narrow, elongated shell with a pentagonal pygal and a long, posteriorly elevated, lenticular and rounded dorsal epiplastral lip. These unique features differ from those of other known Mediterranean hinged forms and allow the erection of the new species Testudo hellenica sp. nov. This taxon is phylogenetically close to two Greek species, the extant T. marginata and the fossil T. marmorum (Turolian, around 7.3 Ma). This record provides evidence for the first appearance of the genus Testudo sensu stricto at a minimum age of 9 Ma.
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Affiliation(s)
- Géraldine Garcia
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - Aurélie Pinton
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - Xavier Valentin
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | | | - Gildas Merceron
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - Louis de Bonis
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - George D. Koufos
- Department of Geology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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9
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Sex is determined by XX/XY sex chromosomes in Australasian side-necked turtles (Testudines: Chelidae). Sci Rep 2020; 10:4276. [PMID: 32152354 PMCID: PMC7062838 DOI: 10.1038/s41598-020-61116-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/21/2020] [Indexed: 12/22/2022] Open
Abstract
Turtles demonstrate variability in sex determination and, hence, constitute an excellent model for the evolution of sex chromosomes. Notably, the sex determination of the freshwater turtles from the family Chelidae, a species-rich group with wide geographical distribution in the southern hemisphere, is still poorly explored. Here we documented the presence of an XX/XY sex determination system in seven species of the Australasian chelid genera Chelodina, Emydura, and Elseya by conventional (karyogram reconstruction, C-banding) and molecular cytogenetic methods (comparative genome hybridization, in situ hybridization with probes specific for GATA microsatellite motif, the rDNA loci, and the telomeric repeats). The sex chromosomes are microchromosomes in all examined species of the genus Chelodina. In contrast, the sex chromosomes are the 4th largest pair of macrochromosomes in the genera Emydura and Elseya. Their X chromosomes are submetacentric, while their Y chromosomes are metacentric. The chelid Y chromosomes contain a substantial male-specific genomic region with an accumulation of the GATA microsatellite motif, and occasionally, of the rDNA loci and telomeric repeats. Despite morphological differences between sex chromosomes, we conclude that male heterogamety was likely already present in the common ancestor of Chelodina, Emydura and Elseya in the Mesozoic period.
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10
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Zhao Z, Heideman N, Grobler P, Jordaan A, Bester P, Hofmeyr MD. Unraveling the diversification and systematic puzzle of the highly polymorphic Psammobates tentorius(Bell, 1828) complex (Reptilia: Testudinidae) through phylogenetic analyses and species delimitation approaches. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Neil Heideman
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Paul Grobler
- Department of Genetics University of the Free State Bloemfontein South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology University of the Free State Bloemfontein South Africa
| | - Phillip Bester
- Department of Virology University of the Free State and National Health Laboratory Service (NHLS) Bloemfontein South Africa
| | - Margaretha D. Hofmeyr
- Chelonian Biodiversity and Conservation Department of Biodiversity and Conservation Biology University of the Western Cape Bellville South Africa
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11
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Foth C, Evers SW, Joyce WG, Volpato VS, Benson RBJ. Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology. J Anat 2019; 235:1078-1097. [PMID: 31373396 DOI: 10.1111/joa.13071] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 02/06/2023] Open
Abstract
The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air-filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance-matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing.
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Affiliation(s)
- Christian Foth
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Serjoscha W Evers
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland.,Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Virginie S Volpato
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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12
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Luo H, Li H, Huang A, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Yu G, Zhang M. The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis. Genes (Basel) 2019; 10:E487. [PMID: 31252631 PMCID: PMC6678547 DOI: 10.3390/genes10070487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022] Open
Abstract
Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.
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Affiliation(s)
- Hongdi Luo
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Haijun Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - An Huang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qingyong Ni
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Bo Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ying Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, Hebei, China
| | - Guohua Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, Guangxi, China.
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Mingwang Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
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13
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Garbin RC, Böhme M, Joyce WG. A new testudinoid turtle from the middle to late Eocene of Vietnam. PeerJ 2019; 7:e6280. [PMID: 30805245 PMCID: PMC6383559 DOI: 10.7717/peerj.6280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/12/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Testudinoidea is a major clade of turtles that has colonized different ecological environments across the globe throughout the Tertiary. Aquatic testudinoids have a particularly rich fossil record in the Tertiary of the northern hemisphere, but little is known about the evolutionary history of the group, as the phylogenetic relationships of most fossils have not been established with confidence, in part due to high levels of homoplasy and polymorphism. METHODS We here focus on describing a sample of 30 testudinoid shells, belonging to a single population that was collected from lake sediments from the middle to late Eocene (35-39 Ma) Na Duong Formation in Vietnam. The phylogenetic placement of this new material is investigated by integrating it and 11 other species of putative geoemydids from the Eocene and Oligocene to a recently published matrix of geoemydid turtles, that embraces the use of polymorphic characters, and then running a total-evidence analysis. RESULTS The new material is highly polymorphic, but can be inferred with confidence to be a new taxon, Banhxeochelys trani gen. et sp. nov. It shares morphological similarities with other southeastern Asian testudinoids, Isometremys lacuna and Guangdongemys pingi, but is placed phylogenetically at the base of Pan-Testuguria when fossils are included in the analysis, or as a stem geoemydid when other fossils are deactivated from the matrix. The vast majority of other putative fossil geoemydids are placed at the base of Pan-Testuguria as well. DISCUSSION The phylogenetic placement of fossil testudinoids used in the analysis is discussed individually and each species compared to Banhxeochelys trani gen. et sp. nov. The high levels of polymorphism observed in the new taxon is discussed in terms of ontogenetic and random variability. This is the first time that a large sample of fossil testudinoids has its morphological variation described in detail.
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Affiliation(s)
- Rafaella C. Garbin
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Madelaine Böhme
- Department of Geosciences, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Palaeoecology, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
| | - Walter G. Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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14
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Xiong L, Wang J, Nie L. The complete mitochondrial genome of the Madagascan plowshare tortoise Astrochelys yniphora (Testudines, Testudinidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1605860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Lei Xiong
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, P.R. China
- Provincial Key Laboratory of Biological Macro-molecules Research, Biochemistry Department, Wannan Medical College, Wuhu, P.R. China
| | - Jue Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, P.R. China
| | - Liuwang Nie
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, P.R. China
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15
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Vlachos E, Rabi M. Total evidence analysis and body size evolution of extant and extinct tortoises (Testudines: Cryptodira: Pan-Testudinidae). Cladistics 2018; 34:652-683. [PMID: 34706483 DOI: 10.1111/cla.12227] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 01/18/2023] Open
Abstract
Testudinidae (tortoises) is an extant clade of terrestrial turtles of worldwide distribution and with a rich fossil record that provides an exceptional context for studying their evolutionary history. Because of the lack of global phylogenetic analyses integrating extinct taxa, our current knowledge of the relationships of the total clade of Testudinidae is rather poor. To resolve this issue, we performed the first total evidence analysis of Pan-Testudinidae. The total evidence trees are congruent with the molecular topology and agree on the dichotomy of derived Testudinidae (=Testudininae; Converted Clade Name) into two previously recognized major clades, Testudona and Geochelona (New Clade Name). The integration of extinct taxa into the analysis allowed the stratigraphic fit of the total evidence trees, indicating that crown Testudininae, Testudona and Geochelona all originated by the Late Eocene, in agreement with recent molecular estimates. Ghost lineage analysis indicates high diversification in the Late Eocene and in the Miocene. The age of crown Testudo is Late Miocene, again in accordance with some molecular dates. Phylogenetic placement of fossils demonstrates that giant body size independently evolved in multiple continental mainland taxa and confirms recent results deduced from living taxa-giantism in Testudinidae is not linked to the insular effect. An unexpected outcome is the recovery of miniaturization in Testudona (<30 cm carapace length) that emerged sometime between the Oligocene and Early Miocene. No clear correlation between body size evolution and climate is apparent, but increased taxon sampling may nevertheless demonstrate the role of cooling and warming as one of many influential variables.
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Affiliation(s)
- Evangelos Vlachos
- CONICET - Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, Chubut, 9100, Argentina.,School of Geology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Márton Rabi
- Central Natural Science Collections, Martin-Luther University Halle-Wittenberg, Domplatz 4, 06108, Halle (Saale), Germany.,Department of Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074, Tübingen, Germany
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16
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de la Fuente MS, Zacarías GG, Vlachos E. A Review of the Fossil Record of South American Turtles of the Clade Testudinoidea. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2018. [DOI: 10.3374/014.059.0201] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Gerardo G. Zacarías
- CONICET, Universidad Nacional de Salta sede regional Orán, 4530 San Ramón de la Nueva Orán, Salta, Argentina
| | - Evangelos Vlachos
- CONICET, Museo Paleontológico Egidio Feruglio, 9100 Trelew, Chubut, Argentina
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17
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Vlachos E. A Review of the Fossil Record of North American Turtles of the Clade Pan-Testudinoidea. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2018. [DOI: 10.3374/014.059.0101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Evangelos Vlachos
- CONICET and Museo Paleontológico Egidio Feruglio, 9100 Trelew, Chubut, Argentina —
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18
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Vlachos E. A Review of the Fossil Record of North American Turtles of the CladePan-Testudinoidea. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2018. [DOI: 10.3374/014.058.0201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Evangelos Vlachos
- CONICET and Museo Paleontológico Egidio Feruglio, 9100 Trelew, Chubut, Argentina —
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19
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Jasinski SE. A new slider turtle (Testudines: Emydidae: Deirochelyinae: Trachemys) from the late Hemphillian (late Miocene/early Pliocene) of eastern Tennessee and the evolution of the deirochelyines. PeerJ 2018; 6:e4338. [PMID: 29456887 PMCID: PMC5815335 DOI: 10.7717/peerj.4338] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/17/2018] [Indexed: 11/30/2022] Open
Abstract
Trachemys (Testudines: Emydidae) represents one of the most well-known turtle genera today. The evolution of Trachemys, while being heavily documented with fossil representatives, is not well understood. Numerous fossils from the late Hemphillian Gray Fossil Site (GFS) in northeastern Tennessee help to elucidate its evolution. The fossil Trachemys at the GFS represent a new species. The new taxon, Trachemys haugrudi, is described, and currently represents the most thoroughly described fossil emydid species known. A phylogenetic analysis, including 31 species, focusing on the subfamily Deirochelyinae is performed that includes the new fossil species, along with numerous other modern and fossil deirochelyine species, representing the first phylogenetic analysis published that includes several fossil deirochelyines. The phylogenetic analysis, utilizing morphological evidence, provides monophyletic clades of all modern deirochelyines, including Chrysemys, Deirochelys, Pseudemys, Malaclemys, Graptemys, and Trachemys. A strict consensus tree finds the recently described fossil species Graptemys kerneri to be part of a clade of Graptemys + Malaclemys. Three fossil taxa, including one previously referred to Pseudemys (Pseudemys caelata) and two to Deirochelys (Deirochelys carri and Deirochelys floridana) are found to form a clade with modern Deirochelys reticularia reticularia, with D. floridana sister to the other members of the clade. Chrysemys is found to be part of a basal polytomy with Deirochelys in relation to other deirochelyine taxa. Two fossil taxa previously referred to Chrysemys (Chrysemys timida and Chrysemys williamsi) form a paraphyly with the modern Chrysemys picta picta and Deirochelys, and may be referable to distinct genera. Additionally, fossil taxa previously attributed to Trachemys (Trachemys hillii, Trachemys idahoensis, Trachemys inflata, and Trachemys platymarginata) and T. haugrudi are found to form a clade separate from clades of northern and southern Trachemys species, potentially suggesting a distinct lineage of Trachemys with no modern survivors. Hypotheses of phylogenetic relationships mostly agree between the present study and previous ones, although the inclusion of fossil taxa provides further clues to the evolution of parts of the Deirochelyinae. The inclusion of more fossil taxa and characters may help resolve the placement of some taxa, and further elucidate the evolution of these New World turtles.
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Affiliation(s)
- Steven E. Jasinski
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA, USA
- Section of Paleontology and Geology, State Museum of Pennsylvania, Harrisburg, PA, USA
- Department of Biological Sciences, Don Sundquist Center of Excellence in Paleontology, Johnson City, TN, USA
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20
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Thomson RC, Spinks PQ, Shaffer HB. Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys). Mol Phylogenet Evol 2017; 121:61-70. [PMID: 29242165 DOI: 10.1016/j.ympev.2017.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/13/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022]
Abstract
The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies. We make use of an empirical prior on rates of molecular evolution to estimate divergence times with a molecular clock under a coalescent framework. Together, the phylogeny and divergence time estimates suggest that diversification has been both more recent and more rapid than has so far been suspected. We provide a well-supported evolutionary framework for Graptemys that is necessary for understanding map turtle diversity, biogeography, and for conservation of this threatened clade of turtles.
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Affiliation(s)
- Robert C Thomson
- Department of Biology, University of Hawai'i, Honolulu, HI 96822, USA.
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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21
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Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles. Mol Phylogenet Evol 2017; 113:59-66. [DOI: 10.1016/j.ympev.2017.05.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/13/2017] [Accepted: 05/09/2017] [Indexed: 11/19/2022]
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22
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Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire JY, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H. Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nat Ecol Evol 2017; 1:1370-1378. [PMID: 28890940 PMCID: PMC5584656 DOI: 10.1038/s41559-017-0240-5] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on "standards" for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes and some relationships remain controversial. We tested a novel bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and find this phylotranscriptomic approach successful and highly cost-effective. Increased sequencing effort up to ca. 10Gbp allows recovering more genes, but shallower sequencing (1.5Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large curated nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
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Affiliation(s)
- Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78464, Germany. .,Systematic Biology Program, Department of Organismal Biology, Univeristy of Uppsala, Norbyvägen 18D, Uppsala, 75236, Sweden.
| | - Denis Baurain
- InBioS-Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège, 4000, Belgium
| | - Henner Brinkmann
- Leibniz-Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, 34095, France
| | - Jean-Yves Sire
- Institut de Biologie Paris-Seine, UMR7138, Sorbonne Universities, Paris, 75005, France
| | - Alexander Kupfer
- Department of Zoology, Stuttgart State Museum of Natural History, Stuttgart, 70191, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78464, Germany
| | - Miguel Vences
- Zoological Institute, Braunschweig University of Technology, Braunschweig, 38106, Germany
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, Moulis, 09200, France. .,Departement de Biochimie, Université de Montréal, Montréal, QC, H3C3J7, Canada.
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23
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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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24
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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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25
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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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26
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Hofmeyr MD, Vamberger M, Branch W, Schleicher A, Daniels SR. Tortoise (Reptilia, Testudinidae) radiations in Southern Africa from the Eocene to the present. ZOOL SCR 2016. [DOI: 10.1111/zsc.12223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Margaretha D. Hofmeyr
- Chelonian Biodiversity and Conservation; Department of Biodiversity and Conservation Biology; University of the Western Cape; Private Bag X17 Bellville 7535 South Africa
| | - Melita Vamberger
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - William Branch
- Department of Herpetology; Port Elizabeth Museum; P.O. Box 13147 Humewood 6013 South Africa
- Department of Zoology; Nelson Mandela Metropolitan University; P.O. Box 77000 Port Elizabeth 6031 South Africa
| | | | - Savel R. Daniels
- Department of Botany and Zoology; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
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Spinks PQ, Thomson RC, McCartney-Melstad E, Shaffer HB. Phylogeny and temporal diversification of the New World pond turtles (Emydidae). Mol Phylogenet Evol 2016; 103:85-97. [DOI: 10.1016/j.ympev.2016.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 06/03/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022]
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Zhou H, Jiang Y, Nie L, Yin H, Li H, Dong X, Zhao F, Zhang H, Pu Y, Huang Z, Song J, Sun E. The Historical Speciation of Mauremys Sensu Lato: Ancestral Area Reconstruction and Interspecific Gene Flow Level Assessment Provide New Insights. PLoS One 2015; 10:e0144711. [PMID: 26657158 PMCID: PMC4678219 DOI: 10.1371/journal.pone.0144711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022] Open
Abstract
Mauremys sensu lato was divided into Mauremys, Chinemys, Ocadia, and Annamemys based on earlier research on morphology. Phylogenetic research on this group has been controversial because of disagreements regarding taxonomy, and the historical speciation is still poorly understood. In this study, 32 individuals of eight species that are widely distributed in Eurasia were collected. The complete mitochondrial (mt) sequences of 14 individuals of eight species were sequenced. Phylogenetic relationships, interspecific divergence times, and ancestral area reconstructions were explored using mt genome data (10,854 bp). Subsequent interspecific gene flow level assessment was performed using five unlinked polymorphic microsatellite loci. The Bayesian and maximum likelihood analyses revealed a paraphyletic relationship among four old genera (Mauremys, Annamemys, Chinemys, and Ocadia) and suggested the four old genera should be merged into the genus (Mauremys). Ancestral area reconstruction and divergence time estimation suggested Southeast Asia may be the area of origin for the common ancestral species of this genus and genetic drift may have played a decisive role in species divergence due to the isolated event of a glacial age. However, M. japonica may have been speciated due to the creation of the island of Japan. The detection of extensive gene flow suggested no vicariance occurred between Asia and Southeast Asia. Inconsistent results between gene flow assessment and phylogenetic analysis revealed the hybrid origin of M. mutica (Southeast Asian). Here ancestral area reconstruction and interspecific gene flow level assessment were first used to explore species origins and evolution of Mauremys sensu lato, which provided new insights on this genus.
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Affiliation(s)
- Huaxing Zhou
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Yuan Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liuwang Nie
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Huazong Yin
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Haifeng Li
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Xianmei Dong
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Feifei Zhao
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Huanhuan Zhang
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Youguang Pu
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Zhenfeng Huang
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Jiaolian Song
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Entao Sun
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
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29
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Héritier L, Badets M, Du Preez LH, Aisien MS, Lixian F, Combes C, Verneau O. Evolutionary processes involved in the diversification of chelonian and mammal polystomatid parasites (Platyhelminthes, Monogenea, Polystomatidae) revealed by palaeoecology of their hosts. Mol Phylogenet Evol 2015; 92:1-10. [DOI: 10.1016/j.ympev.2015.05.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 11/16/2022]
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Natchev N, Tzankov N, Werneburg I, Heiss E. Feeding behaviour in a 'basal' tortoise provides insights on the transitional feeding mode at the dawn of modern land turtle evolution. PeerJ 2015; 3:e1172. [PMID: 26339550 PMCID: PMC4558077 DOI: 10.7717/peerj.1172] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/20/2015] [Indexed: 11/20/2022] Open
Abstract
Almost all extant testudinids are highly associated with terrestrial habitats and the few tortoises with high affinity to aquatic environments are found within the genus Manouria. Manouria belongs to a clade which forms a sister taxon to all remaining tortoises and is suitable as a model for studying evolutionary transitions within modern turtles. We analysed the feeding behaviour of Manouria emys and due to its phylogenetic position, we hypothesise that the species might have retained some ancestral features associated with an aquatic lifestyle. We tested whether M. emys is able to feed both in aquatic and terrestrial environments. In fact, M. emys repetitively tried to reach submerged food items in water, but always failed to grasp them—no suction feeding mechanism was applied. When feeding on land, M. emys showed another peculiar behaviour; it grasped food items by its jaws—a behaviour typical for aquatic or semiaquatic turtles—and not by the tongue as generally accepted as the typical feeding mode in all tortoises studied so far. In M. emys, the hyolingual complex remained retracted during all food uptake sequences, but the food transport was entirely lingual based. The kinematical profiles significantly differed from those described for other tortoises and from those proposed from the general models on the function of the feeding systems in lower tetrapods. We conclude that the feeding behaviour of M. emys might reflect a remnant of the primordial condition expected in the aquatic ancestor of the tortoises.
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Affiliation(s)
- Nikolay Natchev
- Department of Integrative Zoology, Vienna University , Vienna , Austria ; Faculty of Natural Science, Shumen University , Shumen , Bulgaria
| | - Nikolay Tzankov
- Section Vertebrates, National Museum of Natural History, Bulgarian Academy of Sciences , Sofia , Bulgaria
| | - Ingmar Werneburg
- Museum für Naturkunde, Leibniz-Institut für Evolutions- & Biodiversitätsforschung an der Humboldt-Universität zu Berlin , Berlin , Germany ; Institut für Biologie, Humboldt-Universität zu Berlin , Berlin , Germany
| | - Egon Heiss
- Institute of Systematic Zoology and Evolutionary Biology, Friedrich-Schiller-University Jena , Jena , Germany
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31
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Nicholson DB, Holroyd PA, Benson RBJ, Barrett PM. Climate-mediated diversification of turtles in the Cretaceous. Nat Commun 2015; 6:7848. [PMID: 26234913 PMCID: PMC4532850 DOI: 10.1038/ncomms8848] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/19/2015] [Indexed: 12/25/2022] Open
Abstract
Chelonians are ectothermic, with an extensive fossil record preserved in diverse palaeoenvironmental settings: consequently, they represent excellent models for investigating organismal response to long-term environmental change. We present the first Mesozoic chelonian taxic richness curve, subsampled to remove geological/collection biases, and demonstrate that their palaeolatitudinal distributions were climate mediated. At the Jurassic/Cretaceous transition, marine taxa exhibit minimal diversity change, whereas non-marine diversity increases. A Late Cretaceous peak in 'global' non-marine subsampled richness coincides with high palaeolatitude occurrences and the Cretaceous thermal maximum (CTM): however, this peak also records increased geographic sampling and is not recovered in continental-scale diversity patterns. Nevertheless, a model-detrended richness series (insensitive to geographic sampling) also recovers a Late Cretaceous peak, suggesting genuine geographic range expansion among non-marine turtles during the CTM. Increased Late Cretaceous diversity derives from intensive North American sampling, but subsampling indicates that Early Cretaceous European/Asian diversity may have exceeded that of Late Cretaceous North America.
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Affiliation(s)
- David B. Nicholson
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Patricia A. Holroyd
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, California 94720, USA
| | - Roger B. J. Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Paul M. Barrett
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Loire E, Chiari Y, Bernard A, Cahais V, Romiguier J, Nabholz B, Lourenço JM, Galtier N. Population genomics of the endangered giant Galápagos tortoise. Genome Biol 2013; 14:R136. [PMID: 24342523 PMCID: PMC4053747 DOI: 10.1186/gb-2013-14-12-r136] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 12/16/2013] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The giant Galápagos tortoise, Chelonoidis nigra, is a large-sized terrestrial chelonian of high patrimonial interest. The species recently colonized a small continental archipelago, the Galápagos Islands, where it has been facing novel environmental conditions and limited resource availability. To explore the genomic consequences of this ecological shift, we analyze the transcriptomic variability of five individuals of C. nigra, and compare it to similar data obtained from several continental species of turtles. RESULTS Having clarified the timing of divergence in the Chelonoidis genus, we report in C. nigra a very low level of genetic polymorphism, signatures of a weakened efficacy of purifying selection, and an elevated mutation load in coding and regulatory sequences. These results are consistent with the hypothesis of an extremely low long-term effective population size in this insular species. Functional evolutionary analyses reveal a reduced diversity of immunity genes in C. nigra, in line with the hypothesis of attenuated pathogen diversity in islands, and an increased selective pressure on genes involved in response to stress, potentially related to the climatic instability of its environment and its elongated lifespan. Finally, we detect no population structure or homozygosity excess in our five-individual sample. CONCLUSIONS These results enlighten the molecular evolution of an endangered taxon in a stressful environment and point to island endemic species as a promising model for the study of the deleterious effects on genome evolution of a reduced long-term population size.
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Affiliation(s)
- Etienne Loire
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Ylenia Chiari
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Aurélien Bernard
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Vincent Cahais
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Jonathan Romiguier
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Benoît Nabholz
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Joao Miguel Lourenço
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
| | - Nicolas Galtier
- Université Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Place E. Bataillon, 34095 Montpellier, France
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Joyce WG, Schoch RR, Lyson TR. The girdles of the oldest fossil turtle, Proterochersis robusta, and the age of the turtle crown. BMC Evol Biol 2013; 13:266. [PMID: 24314094 PMCID: PMC4077068 DOI: 10.1186/1471-2148-13-266] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/26/2013] [Indexed: 12/02/2022] Open
Abstract
Background Proterochersis robusta from the Late Triassic (Middle Norian) of Germany is the oldest known fossil turtle (i.e. amniote with a fully formed turtle shell), but little is known about its anatomy. A newly prepared, historic specimen provides novel insights into the morphology of the girdles and vertebral column of this taxon and the opportunity to reassess its phylogenetic position. Results The anatomy of the pectoral girdle of P. robusta is similar to that of other primitive turtles, including the Late Triassic (Carnian) Proganochelys quenstedti, in having a vertically oriented scapula, a large coracoid foramen, a short acromion process, and bony ridges that connect the acromion process with the dorsal process, glenoid, and coracoid, and by being able to rotate along a vertical axis. The pelvic elements are expanded distally and suturally attached to the shell, but in contrast to modern pleurodiran turtles the pelvis is associated with the sacral ribs. Conclusions The primary homology of the character “sutured pelvis” is unproblematic between P. robusta and extant pleurodires. However, integration of all new observations into the most complete phylogenetic analysis that support the pleurodiran nature of P. robusta reveals that this taxon is more parsimoniously placed along the phylogenetic stem of crown Testudines. All current phylogenetic hypotheses therefore support the basal placement of this taxon, imply that the sutured pelvis of this taxon developed independently from that of pleurodires, and conclude that the age of the turtle crown is Middle Jurassic.
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Affiliation(s)
- Walter G Joyce
- Department of Geosciences, University of Tübingen, Hölderlinstr, 12, 72074 Tübingen, Germany.
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34
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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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Rabi M, Zhou CF, Wings O, Ge S, Joyce WG. A new xinjiangchelyid turtle from the Middle Jurassic of Xinjiang, China and the evolution of the basipterygoid process in Mesozoic turtles. BMC Evol Biol 2013; 13:203. [PMID: 24053145 PMCID: PMC3852240 DOI: 10.1186/1471-2148-13-203] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/16/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Most turtles from the Middle and Late Jurassic of Asia are referred to the newly defined clade Xinjiangchelyidae, a group of mostly shell-based, generalized, small to mid-sized aquatic froms that are widely considered to represent the stem lineage of Cryptodira. Xinjiangchelyids provide us with great insights into the plesiomorphic anatomy of crown-cryptodires, the most diverse group of living turtles, and they are particularly relevant for understanding the origin and early divergence of the primary clades of extant turtles. RESULTS Exceptionally complete new xinjiangchelyid material from the ?Qigu Formation of the Turpan Basin (Xinjiang Autonomous Province, China) provides new insights into the anatomy of this group and is assigned to Xinjiangchelys wusu n. sp. A phylogenetic analysis places Xinjiangchelys wusu n. sp. in a monophyletic polytomy with other xinjiangchelyids, including Xinjiangchelys junggarensis, X. radiplicatoides, X. levensis and X. latiens. However, the analysis supports the unorthodox, though tentative placement of xinjiangchelyids and sinemydids outside of crown-group Testudines. A particularly interesting new observation is that the skull of this xinjiangchelyid retains such primitive features as a reduced interpterygoid vacuity and basipterygoid processes. CONCLUSIONS The homology of basipterygoid processes is confidently demonstrated based on a comprehensive review of the basicranial anatomy of Mesozoic turtles and a new nomenclatural system is introduced for the carotid canal system of turtles. The loss of the basipterygoid process and the bony enclosure of the carotid circulation system occurred a number of times independently during turtle evolution suggesting that the reinforcement of the basicranial region was essential for developing a rigid skull, thus paralleling the evolution of other amniote groups with massive skulls.
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Affiliation(s)
- Márton Rabi
- Institut für Geowissenschaften, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
- Department of Paleontology & MTA–ELTE Lendület Dinosaur Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Chang-Fu Zhou
- Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang 110034, China
| | - Oliver Wings
- Niedersächsisches Landesmuseum Hannover, 5 Willy-Brandt-Allee, Hannover 530169, Germany
| | - Sun Ge
- Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang 110034, China
| | - Walter G Joyce
- Institut für Geowissenschaften, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
- Yale Peabody Museum of Natural History, 170 Whitney Avenue, New Haven, Connecticut 06511, USA
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36
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Pincheira-Donoso D, Bauer AM, Meiri S, Uetz P. Global taxonomic diversity of living reptiles. PLoS One 2013; 8:e59741. [PMID: 23544091 PMCID: PMC3609858 DOI: 10.1371/journal.pone.0059741] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 02/21/2013] [Indexed: 11/19/2022] Open
Abstract
Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world's diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of lineage richness remain qualitatively identical, hence reinforcing our conclusions about the fractal nature of reptile biodiversity.
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Affiliation(s)
- Daniel Pincheira-Donoso
- Laboratory of Evolutionary Ecology of Adaptations, School of Life Sciences, University of Lincoln, Riseholme Park, Lincoln, Lincolnshire, United Kingdom.
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Cadena EA, Ksepka DT, Norell MA. New material ofMongolemys elegansKhosatzky and Mlynarski, 1971 (Testudines: Lindholmemydidae), from the Late Cretaceous of Mongolia with Comments on Bone Histology and Phylogeny. AMERICAN MUSEUM NOVITATES 2013. [DOI: 10.1206/3766.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Lourenço JM, Glémin S, Chiari Y, Galtier N. The determinants of the molecular substitution process in turtles. J Evol Biol 2012; 26:38-50. [PMID: 23176666 DOI: 10.1111/jeb.12031] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 09/13/2012] [Accepted: 09/17/2012] [Indexed: 12/28/2022]
Abstract
Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic rate, generation time and longevity (LON) - have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT - faster evolution in the tropics - and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms.
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Affiliation(s)
- J M Lourenço
- Institut des Sciences de l'Evolution, Université Montpellier 2, Montpellier Cedex, France.
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Chiari Y, Cahais V, Galtier N, Delsuc F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol 2012; 10:65. [PMID: 22839781 PMCID: PMC3473239 DOI: 10.1186/1741-7007-10-65] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 07/27/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. RESULTS In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. CONCLUSIONS These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.
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Affiliation(s)
- Ylenia Chiari
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Vincent Cahais
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
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