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Field DJ, Gauthier JA, King BL, Pisani D, Lyson TR, Peterson KJ. Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles. Evol Dev 2014; 16:189-96. [PMID: 24798503 PMCID: PMC4215941 DOI: 10.1111/ede.12081] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super-alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.
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Affiliation(s)
- Daniel J. Field
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Benjamin L. King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Queen’s Road, Bristol BS8 1RJ, United Kingdom and School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, United Kingdom
| | - Tyler R. Lyson
- Smithsonian National Museum of Natural History, 10 Street and Constitution Avenue, Washington, DC 20013, USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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2
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Lu B, Yang W, Dai Q, Fu J. Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles. PLoS One 2013; 8:e79348. [PMID: 24278129 PMCID: PMC3836853 DOI: 10.1371/journal.pone.0079348] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Ducrest AL, Ursenbacher S, Golay P, Monney JC, Mebert K, Roulin A, Dubey S. Pro-opiomelanocortin gene and melanin-based colour polymorphism in a reptile. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12182] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Anne-Lyse Ducrest
- Department of Ecology and Evolution; University of Lausanne; Biophore Building CH-1015 Lausanne Switzerland
| | - Sylvain Ursenbacher
- Section of Conservation Biology; Department of Environmental Sciences; University of Basel; St Johanns-Vorstadt 10 CH-4056 Basel Switzerland
| | - Philippe Golay
- Department of Ecology and Evolution; University of Lausanne; Biophore Building CH-1015 Lausanne Switzerland
| | - Jean-Claude Monney
- Karch (Centre de coordination pour la protection des amphibiens et des reptiles de Suisse); Passage Maximilien-de-Meuron 6; CH-2000 Neuchâtel Switzerland
| | - Konrad Mebert
- Siebeneichenstrasse 31; CH-5634 Merenschwand Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution; University of Lausanne; Biophore Building CH-1015 Lausanne Switzerland
| | - Sylvain Dubey
- Department of Ecology and Evolution; University of Lausanne; Biophore Building CH-1015 Lausanne Switzerland
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Kálmán M, Somiya H, Lazarevic L, Milosevic I, Ari C, Majorossy K. Absence of post-lesion reactive gliosis in elasmobranchs and turtles and its bearing on the evolution of astroglia. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:351-67. [DOI: 10.1002/jez.b.22505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 01/15/2013] [Accepted: 03/19/2013] [Indexed: 12/14/2022]
Affiliation(s)
- M. Kálmán
- Department of Anatomy; Semmelweis University; Budapest; Hungary
| | - Hiro Somiya
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya; Japan
| | | | | | - Csilla Ari
- Department of Anatomy; Semmelweis University; Budapest; Hungary
| | - K. Majorossy
- Department of Anatomy; Semmelweis University; Budapest; Hungary
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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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Parham JF, Donoghue PCJ, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patané JSL, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood JM, Hipsley CA, Jacobs L, Makovicky PJ, Müller J, Smith KT, Theodor JM, Warnock RCM, Benton MJ. Best practices for justifying fossil calibrations. Syst Biol 2012; 61:346-59. [PMID: 22105867 PMCID: PMC3280042 DOI: 10.1093/sysbio/syr107] [Citation(s) in RCA: 388] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 09/22/2011] [Accepted: 11/14/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- James F Parham
- Alabama Museum of Natural History, University of Alabama, 427 6th Avenue, Smith Hall, Box 870340, Tuscaloosa, AL 35487, USA.
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Lyson TR, Sperling EA, Heimberg AM, Gauthier JA, King BL, Peterson KJ. MicroRNAs support a turtle + lizard clade. Biol Lett 2012; 8:104-7. [PMID: 21775315 PMCID: PMC3259949 DOI: 10.1098/rsbl.2011.0477] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 06/27/2011] [Indexed: 11/12/2022] Open
Abstract
Despite much interest in amniote systematics, the origin of turtles remains elusive. Traditional morphological phylogenetic analyses place turtles outside Diapsida-amniotes whose ancestor had two fenestrae in the temporal region of the skull (among the living forms the tuatara, lizards, birds and crocodilians)-and allied with some unfenestrate-skulled (anapsid) taxa. Nonetheless, some morphological analyses place turtles within Diapsida, allied with Lepidosauria (tuatara and lizards). Most molecular studies agree that turtles are diapsids, but rather than allying them with lepidosaurs, instead place turtles near or within Archosauria (crocodilians and birds). Thus, three basic phylogenetic positions for turtles with respect to extant Diapsida are currently debated: (i) sister to Diapsida, (ii) sister to Lepidosauria, or (iii) sister to, or within, Archosauria. Interestingly, although these three alternatives are consistent with a single unrooted four-taxon tree for extant reptiles, they differ with respect to the position of the root. Here, we apply a novel molecular dataset, the presence versus absence of specific microRNAs, to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and find that this dataset unambiguously supports a turtle + lepidosaur group. We find that turtles and lizards share four unique miRNA gene families that are not found in any other organisms' genome or small RNA library, and no miRNAs are found in all diapsids but not turtles, or in turtles and archosaurs but not in lizards. The concordance between our result and some morphological analyses suggests that there have been numerous morphological convergences and reversals in reptile phylogeny, including the loss of temporal fenestrae.
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Affiliation(s)
- Tyler R. Lyson
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Erik A. Sperling
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Alysha M. Heimberg
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Benjamin L. King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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Shen XX, Liang D, Wen JZ, Zhang P. Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles. Mol Biol Evol 2011; 28:3237-52. [DOI: 10.1093/molbev/msr148] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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