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Hong YH, Yuan YN, Li K, Storey KB, Zhang JY, Zhang SS, Yu DN. Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation. Int J Mol Sci 2024; 25:5967. [PMID: 38892163 PMCID: PMC11172996 DOI: 10.3390/ijms25115967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.
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Affiliation(s)
- Yue-Huan Hong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Ni Yuan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ke Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Sheng Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Main DC, Taft JM, Geneva AJ, Jansenvan Vuuren B, Tolley KA. The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons. PeerJ 2024; 12:e17076. [PMID: 38708350 PMCID: PMC11067893 DOI: 10.7717/peerj.17076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/19/2024] [Indexed: 05/07/2024] Open
Abstract
Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.
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Affiliation(s)
- Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Jody M. Taft
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
| | - Anthony J. Geneva
- Department of Biology, Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States of America
| | - Bettine Jansenvan Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
| | - Krystal A. Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, Gauteng, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, South Africa
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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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He J, Zhan L, Meng S, Wang Z, Gao L, Wang W, Storey KB, Zhang Y, Yu D. Differential Mitochondrial Genome Expression of Three Sympatric Lizards in Response to Low-Temperature Stress. Animals (Basel) 2024; 14:1158. [PMID: 38672309 PMCID: PMC11047653 DOI: 10.3390/ani14081158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/28/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Ecological factors related to climate extremes have a significant influence on the adaptability of organisms, especially for ectotherms such as reptiles that are sensitive to temperature change. Climate extremes can seriously affect the survival and internal physiology of lizards, sometimes even resulting in the loss of local populations or even complete extinction. Indeed, studies have shown that the expression levels of the nuclear genes and mitochondrial genomes of reptiles change under low-temperature stress. At present, the temperature adaptability of reptiles has rarely been studied at the mitochondrial genome level. In the present study, the mitochondrial genomes of three species of lizards, Calotes versicolor, Ateuchosaurus chinensis, and Hemidactylus bowringii, which live in regions of sympatry, were sequenced. We used RT-qPCR to explore the level of mitochondrial gene expression under low-temperature stress, as compared to a control temperature. Among the 13 protein-coding genes (PCGs), the steady-state transcript levels of ND4L, ND1, ATP6, and COII were reduced to levels of 0.61 ± 0.06, 0.50 ± 0.08, 0.44 ± 0.16, and 0.41 ± 0.09 in C. versicolor, respectively, compared with controls. The transcript levels of the ND3 and ND6 genes fell to levels of just 0.72 ± 0.05 and 0.67 ± 0.05 in H. bowringii, compared with controls. However, the transcript levels of ND3, ND5, ND6, ATP6, ATP8, Cytb, and COIII genes increased to 1.97 ± 0.15, 2.94 ± 0.43, 1.66 ± 0.07, 1.59 ± 0.17, 1.46 ± 0.04, 1.70 ± 0.16, and 1.83 ± 0.07 in A. chinensis. Therefore, the differences in mitochondrial gene expression may be internally related to the adaptative strategy of the three species under low-temperature stress, indicating that low-temperature environments have a greater impact on A. chinensis, with a small distribution area. In extreme environments, the regulatory trend of mitochondrial gene expression in reptiles is associated with their ability to adapt to extreme climates, which means differential mitochondrial genome expression can be used to explore the response of different lizards in the same region to low temperatures. Our experiment aims to provide one new research method to evaluate the potential extinction of reptile species in warm winter climates.
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Affiliation(s)
- Jingyi He
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
| | - Lemei Zhan
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
| | - Siqi Meng
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
| | - Zhen Wang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
| | - Lulu Gao
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
| | - Wenjing Wang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Yongpu Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Danna Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China; (J.H.); (L.Z.); (S.M.); (Z.W.); (L.G.); (W.W.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Complete Mitogenome of Oreolalax Omeimontis Reveals Phylogenetic Status and Novel Gene Arrangement of Archaeobatrachia. Genes (Basel) 2022; 13:genes13112089. [DOI: 10.3390/genes13112089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/23/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Species of the genus Oreolalax displayed crucial morphological characteristics of vertebrates transitioning from aquatic to terrestrial habitats; thus, they can be regarded as a representative vertebrate genus for this landing phenomenon. But the present phylogenetic status of Oreolalax omeimontis has been controversial with morphological and molecular approaches, and specific gene rearrangements were discovered in all six published Oreolalax mitogenomes, which are rarely observed in Archaeobatrachia. Therefore, this study determined the complete mitogenome of O. omeimontis with the aim of identifying its precise phylogenetic position and novel gene arrangement in Archaeobatrachia. Phylogenetic analysis with Bayesian inference and maximum likelihood indicates O. omeimontis is a sister group to O. lichuanensis, which is consistent with previous phylogenetic analysis based on morphological characteristics, but contrasts with other studies using multiple gene fragments. Moreover, although the duplication of trnM occurred in all seven Oreolalax species, the translocation of trnQ and trnM occurred differently in O. omeimontis to the other six, and this unique rearrangement would happen after the speciation of O. omeimontis. In general, this study sheds new light on the phylogenetic relationships and gene rearrangements of Archaeobatrachia.
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Wu N, Liu J, Wang S, Guo X. Comparative Analysis of Mitochondrial Genomes in Two Subspecies of the Sunwatcher Toad-Headed Agama (Phrynocephalus helioscopus): Prevalent Intraspecific Gene Rearrangements in Phrynocephalus. Genes (Basel) 2022; 13:genes13020203. [PMID: 35205248 PMCID: PMC8872181 DOI: 10.3390/genes13020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 01/27/2023] Open
Abstract
Intraspecific rearrangements of mitochondrial genomes are rarely reported in reptiles, even in vertebrates. The sunwatcher toad-headed agama, Phryncoephalus helioscopus, can serve as an excellent model for investigating the dynamic mitogenome structure at intraspecific level. To date, seven subspecies of P. helioscopus are well recognized, but little is known about the mitogenomic evolution among different subspecies. In this study, complete mitogenomes of subspecies P. helioscopus varius II and P. helioscopus cameranoi were determined by next-generation sequencing, and another P. helioscopus varius I retrieved from GenBank was compiled for comparative analysis. The nucleotide composition and the codon usage are similar to those previously published from toad-headed agamas. P. helioscopus varius II and P. helioscopus cameranoi have 23 tRNA genes, including standard 22 tRNA genes and one extra tRNA-Phe (tRNA-Phe duplication). Gene order and phylogenetic analyses in the genus Phrynocephalus support prevalent intraspecific gene rearrangement in P. helioscopus and other congener species including P. erythrurus, P. vlangalii, and P. forsythii. Six different mitochondrial gene arrangements are observed in Phrynocephalus. Overall, the occurrence of rearrangements may result from multiple independent structural dynamic events. The split of the two subspecies in P. helioscopus was dated at approximately 2.34 million years ago (Ma). Two types of gene rearrangements are found in the three mitogenomes of P. helioscopus, and this intraspecific rearrangement phenomenon can be explained by the tandem duplication/random loss (TDRL) model. Post duplication, the alternative loss types can occur in 0.23–0.72 Ma, suggesting that the duplication and fixation of these rearrangements can occur quite quickly. These findings highlight the need for more mitogenomes at the population level in order to better understand the potentially rampant intraspecific mitogenomic reorganization in Phrynocephalus.
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Affiliation(s)
- Na Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (N.W.); (J.L.); (S.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinlong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (N.W.); (J.L.); (S.W.)
| | - Song Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (N.W.); (J.L.); (S.W.)
- College of Life Sciences and Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (N.W.); (J.L.); (S.W.)
- Correspondence:
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Chakraborty S, Basumatary P, Nath D, Paul S, Uddin A. Compositional features and pattern of codon usage for mitochondrial CO genes among reptiles. Mitochondrion 2021; 62:111-121. [PMID: 34793987 DOI: 10.1016/j.mito.2021.11.004] [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: 04/07/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 11/27/2022]
Abstract
The phenomenon of non-random occurrence of synonymous nucleotide triplets (codons) in the coding sequences of genes is the codon usage bias (CUB). In this study, we used bioinformatic tool kit to analyze the compositional pattern and CUB of mitogenes namely COI, COII and COIII across different orders of reptiles. Estimation of overall base composition in the protein-coding sequences of COI, COII and COIII genes of the reptilian orders revealed an uneven usage of nucleotides. The overall count of A nucleotide was found to be the highest while the overall count of G nucleotide was the least. The CO genes across the three reptilian orders were prominently AT biased. Comparison of the GC proportion at each codon position displayed that GC1 percentage ranked the highest in all the three CO genes of the reptilian orders. SCUO values indicated weaker CUB, while considerable variation of SCUO values existed in the three CO genes across the studied reptiles. Relative synonymous codon usage (RSCU) values indicated that mostly the A ending codons were preferred. Based on the parameters namely neutrality plot, mutational responsive index and translational selection, we could conclude that natural selection was the major evolutionary force in COI, COII and COIII genes in the studied reptilian orders. However, correspondence analysis, parity plot and correlation studies indicated the existence of mutation pressure as well on the CO genes.
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Affiliation(s)
- Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
| | | | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Sunanda Paul
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi788150, Assam, India.
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Valdes J, Samoluk SS, Abdala CS, Baldo D, Seijo G. Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels. PeerJ 2021; 9:e10677. [PMID: 33828904 PMCID: PMC7996074 DOI: 10.7717/peerj.10677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/09/2020] [Indexed: 11/20/2022] Open
Abstract
Liolaemus is the most specious genus of the Squamata lizards in South America, presenting exceptional evolutionary radiation and speciation patterns. This recent diversification complicates the formal taxonomic treatment and the phylogenetic analyses of this group, causing relationships among species to remain controversial. Here we used Next-Generation Sequencing to do a comparative analysis of the structure and organization of the complete mitochondrial genomes of three differently related species of Liolaemus and with different reproductive strategies and ploidy levels. The annotated mitochondrial genomes of ca. 17 kb are the first for the Liolaemidae family. Despite the high levels of sequence similarity among the three mitochondrial genomes over most of their lengths, the comparative analyses revealed variations at the stop codons of the protein coding genes and the structure of the tRNAs among species. The presence of a non-canonical dihydrouridine loop is a novelty for the pleurodonts iguanians. But the highest level of variability was observed in two repetitive sequences of the control region, which were responsible for most of the length heterogeneity of the mitochondrial genomes. These tandem repeats may be useful markers to analyze relationships of closely related species of Liolaemus and related genera and to conduct population and phylogenetic studies.
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Affiliation(s)
- Julian Valdes
- Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes Capital, Corrientes, Argentina
| | | | - Cristian Simón Abdala
- Unidad ejecutora Lillo (CONICET), Facultad de Ciencias Naturales e Instituto Miguel Lillo (IML), Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes Capital, Corrientes, Argentina.,Facultad de Ciencias Exactas y Naturales y Agrimensura, FaCENA-UNNE, Corrientes Capital, Corrientes, Argentina
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Xu X, Wang Q, Wu Q, Xu J, Wang J, Wang Z. The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura. Biochem Genet 2021; 59:617-636. [PMID: 33415669 DOI: 10.1007/s10528-020-10025-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (- 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.
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Affiliation(s)
- Xinyi Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qi Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qiong Wu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jiayan Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jie Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China.
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Cao J, Wang Y, Guo X, Wang G, Li W, Murányi D. Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6137693. [PMID: 33590866 PMCID: PMC7885146 DOI: 10.1093/jisesa/ieab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 06/01/2023]
Abstract
The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.
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Affiliation(s)
- Jinjun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Xuan Guo
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Guoquan Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, China
| | - Weihai Li
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, China
| | - Dávid Murányi
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
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12
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Loria SF, Prendini L. Out of India, thrice: diversification of Asian forest scorpions reveals three colonizations of Southeast Asia. Sci Rep 2020; 10:22301. [PMID: 33339838 PMCID: PMC7749168 DOI: 10.1038/s41598-020-78183-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
The 'Out of India' hypothesis is often invoked to explain patterns of distribution among Southeast Asian taxa. According to this hypothesis, Southeast Asian taxa originated in Gondwana, diverged from their Gondwanan relatives when the Indian subcontinent rifted from Gondwana in the Late Jurassic, and colonized Southeast Asia when it collided with Eurasia in the early Cenozoic. A growing body of evidence suggests these events were far more complex than previously understood, however. The first quantitative reconstruction of the biogeography of Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) is presented here. Divergence time estimation, ancestral range estimation, and diversification analyses are used to determine the origins, dispersal and diversification patterns of these scorpions, providing a timeline for their biogeographical history that can be summarized into four major events. (1) Heterometrinae diverged from other Scorpionidae on the African continent after the Indian subcontinent became separated in the Cretaceous. (2) Environmental stresses during the Cretaceous-Tertiary (KT) mass extinction caused range contraction, restricting one clade of Heterometrinae to refugia in southern India (the Western Ghats) and Sri Lanka (the Central Highlands). (3) Heterometrinae dispersed to Southeast Asia three times during India's collision with Eurasia, the first dispersal event occurring as the Indian subcontinent brushed up against the western side of Sumatra, and the other two events occurring as India moved closer to Eurasia. (4) Indian Heterometrinae, confined to southern India and Sri Lanka during the KT mass extinction, recolonized the Deccan Plateau and northern India, diversifying into new, more arid habitats after environmental conditions stabilized. These hypotheses, which are congruent with the geological literature and biogeographical analyses of other taxa from South and Southeast Asia, contribute to an improved understanding of the dispersal and diversification patterns of taxa in this biodiverse and geologically complex region.
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Affiliation(s)
- Stephanie F Loria
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA.
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA.
| | - Lorenzo Prendini
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA
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13
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Complete mitochondrial genome of a blue-tailed skink Plestiodon capito (Reptilia, Squamata, Scincidae) and comparison with other Scincidae lizards. Genetica 2020; 148:229-241. [PMID: 33044712 DOI: 10.1007/s10709-020-00107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 09/24/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular genome is 17,344 bp long, showing a typical vertebrate pattern with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (CR). The gene organization, nucleotide composition, and codon usage are similar to those from skinks previously published. Twelve out of 13 PCGs initiates with canonical start codon (ATG), while COX1 starts with GTG. The codon usage analysis revealed a preferential use of the LeuCUN (Leu1), Pro, and Thr codons with the A/U ending. All tRNAs in P. capito were predicted to fold into typical clover-leaf secondary structure, except tRNA-Ser AGY. The secondary structures of 12S rRNA and 16S rRNA comprises 34 helices and 56 helices, respectively. The alignment of the Plesitodon species CRs exhibited high genetic variability and rich A + T content. Besides, variable types and numbers of tandem repeat units were also identified in the CR of Plestiodon. Phylogenetic analyses recovered P. capito as the sister species to P. tunganus; monophyly of the Scincidae is well supported. Our results will help to better understand structure and evolution of the mitochondrial DNA control region in reptiles as well as the evolutionary status of P. capito, and to lay foundation for further phylogenetic study of skinks in a mitogenomic framework.
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14
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Cabañas N, Becerra A, Romero D, Govezensky T, Espinosa-Aguirre JJ, Camacho-Carranza R. Repetitive DNA profile of the amphibian mitogenome. BMC Bioinformatics 2020; 21:197. [PMID: 32429835 PMCID: PMC7236288 DOI: 10.1186/s12859-020-3532-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/05/2020] [Indexed: 11/20/2022] Open
Abstract
Background Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not been extensively explored. We consider that the data of mitochondrial genomes in the NCBI database are a valuable alternative to generate a better understanding of the molecular dynamic of the repeat sequences in the amphibians. Results This work presents the development of a strategy to identify and quantify the total amount of repeat sequences with lengths from 5 to 30 base pairs in the amphibian mitogenomes. The results show differences in the abundance of repeat sequences among amphibians and bias to specific genomic regions that are not easily associated with the classical amphibian ancestry. Conclusions Derived from these analyses, we show that great variability of the repeat sequences exists among amphibians, demonstrating that the mitogenomes of these organisms are dynamic.
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Affiliation(s)
- Noel Cabañas
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - David Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Tzipe Govezensky
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Jesús Javier Espinosa-Aguirre
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico
| | - Rafael Camacho-Carranza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico. .,Facultad de Ciencias, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Cd. Mx., Mexico.
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Trivalairat P, Kunya K, Chanhome L, Sumontha M, Vasaruchapong T, Chomngam N, Chiangkul K. Acanthosaura aurantiacrista (Squamata: Agamidae), a new long horn lizard from northern Thailand. Biodivers Data J 2020; 8:e48587. [PMID: 32489275 PMCID: PMC7244599 DOI: 10.3897/bdj.8.e48587] [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: 11/18/2019] [Accepted: 05/10/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND In Thailand, five species of Acanthosaura have been recorded so far, including Acanthosaura armata from the southern region, A. cardamomensis from the eastern region, A. crucigera from the western region, A. lepidogaster from the northern region and A. phuketensis from the Phuket Island and south-western region. However, comprehensive studies of diversity patterns and distribution of Acanthosaura are still lacking in some areas and need further information for designating areas of special conservation importance and nature protection planning in Thailand. NEW INFORMATION Acanthosaura aurantiacrista is a new species of long-horned lizard of the genus Acanthosaura from northern Thailand. It is distinguished from all other species of Acanthosaura by a dagger-like nuchal spine with yellowish-orange colouration in females, bright yellow colouration in males and a combination of other morphological characters: a greater tail length to snout-vent length ratio; a larger postorbital spine, nuchal spine, dorsal spine and occipital spine compared to its head length; a smaller diastema to snout-vent length ratio; a greater number of subdigital lamellae on the fourth finger and fourth toe; and a larger gular pouch than other Acanthosaura species. Analysis of mitochondrial ND2 gene sequences revealed a sister clade between the A. aurantiacrista lineage and the A. crucigera lineage with a 100% probability of divergence, according to Bayesian analysis and strong support value for Maximum Likelihood analysis. The pairwise distance ranged from 13.8-15.0% between A. aurantiacrista and A. cardamomensis, 10.9-14.5% between A. aurantiacrista and A. crucigera and 0-1.2% amongst A. aurantiacrista populations. The discovery of this lizard increases the known endemic herpetological diversity and underscores the importance of conservation in the mountain rainforest region of northern Thailand.
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Affiliation(s)
- Poramad Trivalairat
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, ThailandAnimal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart UniversityBangkokThailand
| | - Kirati Kunya
- Nakhonratchasima Zoo, 111 M.1, Ratchasima-Pak Tongchai Rd., Chaimongkol, Muang Nakhonrajsima, ThailandNakhonratchasima Zoo, 111 M.1, Ratchasima-Pak Tongchai Rd., ChaimongkolMuang NakhonrajsimaThailand
| | - Lawan Chanhome
- Head of Snake Farm Queen Saovabha Memorial Institute The Thai Red Cross Society 1871 Rama IV Rd., Bangkok, ThailandHead of Snake Farm Queen Saovabha Memorial Institute The Thai Red Cross Society 1871 Rama IV Rd.BangkokThailand
| | - Montri Sumontha
- Ranong Marine Fisheries Station, 157 M. 1 Saphan Pla Road, Pak Nam, Muang, Ranong, ThailandRanong Marine Fisheries Station, 157 M. 1 Saphan Pla Road, Pak Nam, MuangRanongThailand
| | - Taksa Vasaruchapong
- Head of Snake Farm Queen Saovabha Memorial Institute The Thai Red Cross Society 1871 Rama IV Rd., Bangkok, ThailandHead of Snake Farm Queen Saovabha Memorial Institute The Thai Red Cross Society 1871 Rama IV Rd.BangkokThailand
| | - Nirut Chomngam
- 54 M. 2, Tha Pha Subdistrict, Ban Pong District, Ratchaburi, Thailand54 M. 2, Tha Pha Subdistrict, Ban Pong DistrictRatchaburiThailand
| | - Krittiya Chiangkul
- Animal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, ThailandAnimal Systematics and Ecology Speciality Research Unit, Department of Zoology, Faculty of Science, Kasetsart UniversityBangkokThailand
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16
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Liu J, Yu J, Zhou M, Yang J. Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species. Int J Biol Macromol 2019; 125:423-431. [DOI: 10.1016/j.ijbiomac.2018.12.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
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17
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Qiu QB, Zhu GY, Yu XL, Du Y. The complete mitochondrial genome of the Draco maculatus (Squamata: Agamidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1547159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Qing-Bo Qiu
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
| | - Guan-Yan Zhu
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xiu-Li Yu
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
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18
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Areesirisuk P, Muangmai N, Kunya K, Singchat W, Sillapaprayoon S, Lapbenjakul S, Thapana W, Kantachumpoo A, Baicharoen S, Rerkamnuaychoke B, Peyachoknagul S, Han K, Srikulnath K. Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage. PeerJ 2018; 6:e6121. [PMID: 30581685 PMCID: PMC6295329 DOI: 10.7717/peerj.6121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55-75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.
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Affiliation(s)
- Prapatsorn Areesirisuk
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Kirati Kunya
- Nakhon Ratchasima Zoo, Nakhon Ratchasima, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
| | - Sorravis Lapbenjakul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
| | - Watcharaporn Thapana
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand), Kasetsart University, Bangkok, Thailand
| | - Attachai Kantachumpoo
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand), Kasetsart University, Bangkok, Thailand
| | - Sudarath Baicharoen
- Bureau of Conservation and Research, Zoological Park Organization under the Royal Patronage of His Majesty the King, Bangkok, Thailand
| | - Budsaba Rerkamnuaychoke
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand), Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
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Poulsen JY, Miller MJ, Sado T, Hanel R, Tsukamoto K, Miya M. Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders. PLoS One 2018; 13:e0199982. [PMID: 30044814 PMCID: PMC6059418 DOI: 10.1371/journal.pone.0199982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 06/14/2018] [Indexed: 11/24/2022] Open
Abstract
Deep-sea midwater "saccopharyngiform" eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the general anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as "Leptocephalus holti", which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial gene orders.
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Affiliation(s)
- Jan Y. Poulsen
- Department of Fish and Shellfish, Greenland Institute of Natural Resources, Kivioq, Nuuk, Greenland
- Fish Section, Australian Museum, Sydney NSW, Australia
| | - Michael J. Miller
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Aoba-cho, Chuo-ku, Chiba, Japan
| | | | - Katsumi Tsukamoto
- Department of Marine Science and Resources, Nihon University, Fujisawa, Japan
| | - Masaki Miya
- Thunen-Institute of Fisheries Ecology, Hamburg, Germany
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20
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Qian L, Wang H, Yan J, Pan T, Jiang S, Rao D, Zhang B. Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes. BMC Genomics 2018; 19:354. [PMID: 29747572 PMCID: PMC5946542 DOI: 10.1186/s12864-018-4717-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes. RESULTS In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome. CONCLUSIONS The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
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Affiliation(s)
- Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
| | - Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Shanqun Jiang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, China.
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Molnar JL, Diaz RE, Skorka T, Dagliyan G, Diogo R. Comparative musculoskeletal anatomy of chameleon limbs, with implications for the evolution of arboreal locomotion in lizards and for teratology. J Morphol 2017; 278:1241-1261. [DOI: 10.1002/jmor.20708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/10/2017] [Accepted: 05/01/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Julia L. Molnar
- Department of Anatomy; Howard University College of Medicine; 520 W Street NW Washington DC 20059
| | - Raul E. Diaz
- Department of Biology; La Sierra University; 4500 Riverwalk Parkway Riverside California 92505
| | - Tautis Skorka
- Keck School of Medicine, Molecular Imaging Center, University of Southern California; 2250 Alcazar Street Los Angeles California 90033
| | - Grant Dagliyan
- Keck School of Medicine, Molecular Imaging Center, University of Southern California; 2250 Alcazar Street Los Angeles California 90033
| | - Rui Diogo
- Department of Anatomy; Howard University College of Medicine; 520 W Street NW Washington DC 20059
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22
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Grandjean F, Tan MH, Gan HM, Lee YP, Kawai T, Distefano RJ, Blaha M, Roles AJ, Austin CM. Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish. ZOOL SCR 2017. [DOI: 10.1111/zsc.12247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Frederic Grandjean
- UMR CNRS 7267 Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions; 5 rue Albert Turpin Poitiers Cedex France
| | - Mun Hua Tan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Han Ming Gan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Yin Peng Lee
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
| | - Tadashi Kawai
- Fisheries Research Department; Wakkanai Fisheries Research Institute; 4-5-15 Suehiro Wakkanai-shi 097-0001 Hokkaido Japan
| | - Robert J. Distefano
- Missouri Department of Conservation; East Gans Road Columbia Missouri 65201 USA
| | - Martin Blaha
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Zátiší 728/II Vodňany Czech Republic
| | - Angela J. Roles
- Biology Department; Oberlin College, Oberlin; Ohio 44074 USA
| | - Christopher M. Austin
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
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23
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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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24
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Wei M, Liu Y, Guo H, Zhao F, Chen S. Characterization of the complete mitochondrial genome of Cynoglossus gracilis and a comparative analysis with other Cynoglossinae fishes. Gene 2016; 591:369-75. [PMID: 27312953 DOI: 10.1016/j.gene.2016.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 11/29/2022]
Abstract
Mitochondrial genomes can provide basic information for phylogenetic analysis and evolutionary studies. We present here the mitochondrial genome of Cynoglossus gracilis, which is 16,565bp in length. Numerous distinct regions were identified, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, a light-strand replication origin, and a control region. Interestingly, we detected rearrangement of genes in C. gracilis, including a control region translocation, tRNA(Gln) gene inversion, and tRNA(Ile) gene shuffling. Additionally, a phylogenetic analysis based on the nucleotide sequences of the 13 PCGs using maximum likelihood and Bayesian inference methods reveals that C. gracilis is closely related to Cynoglossus semilaevis. This study provides important mitogenomic data for analyzing phylogenetic relationships in the Cynoglossinae.
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Affiliation(s)
- Min Wei
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Yang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Hua Guo
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Fazhen Zhao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
| | - Songlin Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China.
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25
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Shi W, Gong L, Wang SY, Miao XG, Kong XY. Tandem Duplication and Random Loss for mitogenome rearrangement in Symphurus (Teleost: Pleuronectiformes). BMC Genomics 2015; 16:355. [PMID: 25943439 PMCID: PMC4430869 DOI: 10.1186/s12864-015-1581-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/24/2015] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial genomes (mitogenomes) of flatfishes (Pleuronectiformes) exhibit highly diversified types of large-scale gene rearrangements. We have reported that the mitogenomes of Crossorhombus azureus (Bothidae), Samariscus latus (Samaridae) and Cynoglossus fishes (Cynoglossidae) show different types of gene rearrangements. Results In the present study, the complete mitogenomes of two Symphurus species (Cynoglossidae), Symphurus plagiusa and Symphurus orientalis, were determined. The gene order in the S. plagiusa mitogenome is the same as that of a typical vertebrate (without any gene rearrangements). Surprisingly, large-scale gene rearrangements have occurred in S. orientalis. In the rearranged fragment from the control region (CR) to the WANCY tRNA cluster (tRNA cluster of tRNA-W, tRNA-A, tRNA-N, tRNA-C and tRNA-Y) in the S. orientalis mitogenome, tRNA-V and tRNA-M have been translocated to the 3’ end of the 16S rRNA gene, with six large intergenic spacers over 20 bp in length. In addition, an origin for light-strand replication (OL) structure that is typically located in the WANCY region was absent in both the S. plagiusa and S. orientalis mitogenomes. It is generally recognized that a sequence in the WANCY region that encodes tRNAs forms a hairpin structure (OL-like structure) and can act as the OL when the typical locus is lost. Moreover, an additional OL-like structure was identified near the control region in the S. plagiusa mitogenome. Conclusions The positions of the intergenic spacers and the rearranged genes of the S. orientalis mitogenome strongly indicate that the mechanism underlying the rearrangement of this mitogenome was Tandem Duplication and Random Loss. Additionally, two OL-like regions substituting for the typical locus were found in the S. plagiusa mitogenome. We speculate that the ancestral mitogenomes of S. plagiusa and S. orientalis also had this characteristic, such that if both OL-like structures functioned during mitochondrial replication, they could initiate duplicate replications of the light strand (L-strand), leading to duplication of the region between the two structures. We consider that this mechanism may account for the gene duplication that occurred during the gene rearrangement process in the evolution of the ancestral mitogenome to the S. orientalis mitogenome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1581-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Li Gong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Shu-Ying Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Xian-Guang Miao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
| | - Xiao-Yu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, PR China.
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26
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Chen D, Zhou T, Guo X. The complete mitochondrial genome of Phrynocephalus forsythii (Reptilia, Squamata, Agamidae), a toad-headed agama endemic to the Taklamakan Desert. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4046-4048. [PMID: 25600730 DOI: 10.3109/19401736.2014.1003837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome was sequenced from a viviparous toad-headed agama, Phrynocephalus forsythii, which is endemic to the Taklamakan Desert. The mitogenome sequence was 17,542 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region (D-loop). The gene arrangement and composition of P. forsythii is identical to the mitogenome of P. theobaldi in that tRNA-Pro was translocated immediately downstream of tRNA-Phe. The D-loop comprised two parts, one existing between tRNA-Thr and tRNA-Phe, and another containing 12 copies of 36-bp tandem repeats inserting between tRNA-Pro and 12S rRNA. The complete mitogenome sequence of P. forsythii may provide fundamental data for unveiling the phylogenetic origin and adaptive evolution related to Phrynocephalus viviparity.
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Affiliation(s)
- Dali Chen
- a Department of Parasitology , West China School of Preclinical and Forensic Medicine, Sichuan University , Chengdu , Sichuan , People's Republic of China
| | - Tianhe Zhou
- b Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , People's Republic of China , and.,c University of Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Xianguang Guo
- b Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , People's Republic of China , and
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27
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MacDonald AJ, Knopp T, Pepper M, Keogh JS, Sarre SD. The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge). AUST J ZOOL 2015. [DOI: 10.1071/zo14092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming to the typical vertebrate gene order. The overall mitochondrial nucleotide composition is 31.7% A, 24.5% T, 30.5% C and 13.2% G. This corresponds to a total A+T content of 56.3%, which is similar to that of other squamate lizard genomes.
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28
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Kumazawa Y, Miura S, Yamada C, Hashiguchi Y. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics 2014; 15:930. [PMID: 25344428 PMCID: PMC4223735 DOI: 10.1186/1471-2164-15-930] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 10/13/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Vertebrate mitochondrial genomes (mitogenomes) are 16-18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study. RESULTS We determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNAArg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNAArg gene appears to have been converted to a tRNAGln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNALeu genes, as well as a translocation of the tRNAAla gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNAGlu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNAGlu gene adjacent to the 5' end of the major noncoding region. CONCLUSIONS The present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.
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Affiliation(s)
- Yoshinori Kumazawa
- Department of Information and Biological Sciences and Research Center for Biological Diversity, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya 467-8501, Japan.
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29
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Shi W, Miao XG, Kong XY. A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes). BMC Genomics 2014; 15:352. [PMID: 24885702 PMCID: PMC4035078 DOI: 10.1186/1471-2164-15-352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 04/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements. RESULTS In the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained. CONCLUSIONS We propose a "Double Replications and Random Loss" model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.
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Affiliation(s)
| | | | - Xiao-Yu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China.
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30
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Monod L, Prendini L. Evidence for Eurogondwana: the roles of dispersal, extinction and vicariance in the evolution and biogeography of Indo-Pacific Hormuridae (Scorpiones: Scorpionoidea). Cladistics 2014; 31:71-111. [DOI: 10.1111/cla.12067] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lionel Monod
- Département des arthropodes et d'entomologie I; Muséum d'histoire naturelle; Route de Malagnou 1 1208 Genève Switzerland
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
| | - Lorenzo Prendini
- Division of Invertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024-5192 USA
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31
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Gan HM, Schultz MB, Austin CM. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 2014; 14:19. [PMID: 24484414 PMCID: PMC3915555 DOI: 10.1186/1471-2148-14-19] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/29/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. RESULTS The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. CONCLUSIONS We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.
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Affiliation(s)
- Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia.
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32
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Havird JC, Santos SR. Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data. PLoS One 2014; 9:e84080. [PMID: 24454717 PMCID: PMC3891902 DOI: 10.1371/journal.pone.0084080] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/11/2013] [Indexed: 12/04/2022] Open
Abstract
Mitochondrial (mt) genes are some of the most popular and widely-utilized genetic loci in phylogenetic studies of metazoan taxa. However, their linked nature has raised questions on whether using the entire mitogenome for phylogenetics is overkill (at best) or pseudoreplication (at worst). Moreover, no studies have addressed the comparative phylogenetic utility of mitochondrial genes across individual lineages within the entire Metazoa. To comment on the phylogenetic utility of individual mt genes as well as concatenated subsets of genes, we analyzed mitogenomic data from 1865 metazoan taxa in 372 separate lineages spanning genera to subphyla. Specifically, phylogenies inferred from these datasets were statistically compared to ones generated from all 13 mt protein-coding (PC) genes (i.e., the “supergene” set) to determine which single genes performed “best” at, and the minimum number of genes required to, recover the “supergene” topology. Surprisingly, the popular marker COX1 performed poorest, while ND5, ND4, and ND2 were most likely to reproduce the “supergene” topology. Averaged across all lineages, the longest ∼2 mt PC genes were sufficient to recreate the “supergene” topology, although this average increased to ∼5 genes for datasets with 40 or more taxa. Furthermore, concatenation of the three “best” performing mt PC genes outperformed that of the three longest mt PC genes (i.e, ND5, COX1, and ND4). Taken together, while not all mt PC genes are equally interchangeable in phylogenetic studies of the metazoans, some subset can serve as a proxy for the 13 mt PC genes. However, the exact number and identity of these genes is specific to the lineage in question and cannot be applied indiscriminately across the Metazoa.
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Affiliation(s)
- Justin C. Havird
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, Alabama, United States of America
- Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
| | - Scott R. Santos
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, Alabama, United States of America
- Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama, United States of America
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Zheng C, Nie L, Wang J, Zhou H, Hou H, Wang H, Liu J. Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big-headed turtle, Platysternon megacephalum. PLoS One 2013; 8:e82854. [PMID: 24367563 PMCID: PMC3867392 DOI: 10.1371/journal.pone.0082854] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 10/29/2013] [Indexed: 01/24/2023] Open
Abstract
Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3' end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.
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Affiliation(s)
- Chenfei Zheng
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Liuwang Nie
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Jue Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Huaxing Zhou
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Huazhen Hou
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Hao Wang
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
| | - Juanjuan Liu
- Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, P.R. China
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Undersampling taxa will underestimate molecular divergence dates: an example from the South american lizard clade liolaemini. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2013; 2013:628467. [PMID: 24222886 PMCID: PMC3809987 DOI: 10.1155/2013/628467] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 08/30/2013] [Accepted: 08/31/2013] [Indexed: 11/24/2022]
Abstract
Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.
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Jones MEH, Anderson CL, Hipsley CA, Müller J, Evans SE, Schoch RR. Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara). BMC Evol Biol 2013; 13:208. [PMID: 24063680 PMCID: PMC4016551 DOI: 10.1186/1471-2148-13-208] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively derived in their morphology (e.g. Brachyrhinodon), an earlier unknown history of Lepidosauria is implied. However, molecular age estimates for Lepidosauria have been problematic; dates for the most recent common ancestor of all lepidosaurs range between approximately 226 and 289 Mya whereas estimates for crown-group Squamata (lizards and snakes) vary more dramatically: 179 to 294 Mya. This uncertainty restricts inferences regarding the patterns of diversification and evolution of Lepidosauria as a whole. RESULTS Here we report on a rhynchocephalian fossil from the Middle Triassic of Germany (Vellberg) that represents the oldest known record of a lepidosaur from anywhere in the world. Reliably dated to 238-240 Mya, this material is about 12 million years older than previously known lepidosaur records and is older than some but not all molecular clock estimates for the origin of lepidosaurs. Using RAG1 sequence data from 76 extant taxa and the new fossil specimens two of several calibrations, we estimate that the most recent common ancestor of Lepidosauria lived at least 242 Mya (238-249.5), and crown-group Squamata originated around 193 Mya (176-213). CONCLUSION A Early/Middle Triassic date for the origin of Lepidosauria disagrees with previous estimates deep within the Permian and suggests the group evolved as part of the faunal recovery after the end-Permain mass extinction as the climate became more humid. Our origin time for crown-group Squamata coincides with shifts towards warmer climates and dramatic changes in fauna and flora. Most major subclades within Squamata originated in the Cretaceous postdating major continental fragmentation. The Vellberg fossil locality is expected to become an important resource for providing a more balanced picture of the Triassic and for bridging gaps in the fossil record of several other major vertebrate groups.
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Affiliation(s)
- Marc EH Jones
- Research Department of Cell and Developmental Biology, Anatomy Building, UCL, University College London, Gower Street, London WCIE 6BT, UK
- School of Earth and Environmental Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Cajsa Lisa Anderson
- University of Gothenburg, Department of Plant and Environmental Sciences, Gothenburg, Sweden
| | - Christy A Hipsley
- Museum für Naturkunde – Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Müller
- Museum für Naturkunde – Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Susan E Evans
- Research Department of Cell and Developmental Biology, Anatomy Building, UCL, University College London, Gower Street, London WCIE 6BT, UK
| | - Rainer R Schoch
- Staatliches Museum für Naturkunde, Rosenstein 1, D-70191, Stuttgart, Germany
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Jones MEH, Anderson CL, Hipsley CA, Müller J, Evans SE, Schoch RR. Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara). BMC Evol Biol 2013. [PMID: 24063680 DOI: 10.1186/1471-2148-23-208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively derived in their morphology (e.g. Brachyrhinodon), an earlier unknown history of Lepidosauria is implied. However, molecular age estimates for Lepidosauria have been problematic; dates for the most recent common ancestor of all lepidosaurs range between approximately 226 and 289 Mya whereas estimates for crown-group Squamata (lizards and snakes) vary more dramatically: 179 to 294 Mya. This uncertainty restricts inferences regarding the patterns of diversification and evolution of Lepidosauria as a whole. RESULTS Here we report on a rhynchocephalian fossil from the Middle Triassic of Germany (Vellberg) that represents the oldest known record of a lepidosaur from anywhere in the world. Reliably dated to 238-240 Mya, this material is about 12 million years older than previously known lepidosaur records and is older than some but not all molecular clock estimates for the origin of lepidosaurs. Using RAG1 sequence data from 76 extant taxa and the new fossil specimens two of several calibrations, we estimate that the most recent common ancestor of Lepidosauria lived at least 242 Mya (238-249.5), and crown-group Squamata originated around 193 Mya (176-213). CONCLUSION A Early/Middle Triassic date for the origin of Lepidosauria disagrees with previous estimates deep within the Permian and suggests the group evolved as part of the faunal recovery after the end-Permain mass extinction as the climate became more humid. Our origin time for crown-group Squamata coincides with shifts towards warmer climates and dramatic changes in fauna and flora. Most major subclades within Squamata originated in the Cretaceous postdating major continental fragmentation. The Vellberg fossil locality is expected to become an important resource for providing a more balanced picture of the Triassic and for bridging gaps in the fossil record of several other major vertebrate groups.
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Affiliation(s)
- Marc E H Jones
- Research Department of Cell and Developmental Biology, Anatomy Building, UCL, University College London, Gower Street, London WCIE 6BT, UK.
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VanBuren CS, Bonnan M. Forearm posture and mobility in quadrupedal dinosaurs. PLoS One 2013; 8:e74842. [PMID: 24058633 PMCID: PMC3776758 DOI: 10.1371/journal.pone.0074842] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 08/07/2013] [Indexed: 11/18/2022] Open
Abstract
Quadrupedality evolved four independent times in dinosaurs; however, the constraints associated with these transitions in limb anatomy and function remain poorly understood, in particular the evolution of forearm posture and rotational ability (i.e., active pronation and supination). Results of previous qualitative studies are inconsistent, likely due to an inability to quantitatively assess the likelihood of their conclusions. We attempt to quantify antebrachial posture and mobility using the radius bone because its morphology is distinct between extant sprawled taxa with a limited active pronation ability and parasagittal taxa that have an enhanced ability to actively pronate the manus. We used a sliding semi-landmark, outline-based geometric morphometric approach of the proximal radial head and a measurement of the angle of curvature of the radius in a sample of 189 mammals, 49 dinosaurs, 35 squamates, 16 birds, and 5 crocodilians. Our results of radial head morphology showed that quadrupedal ceratopsians, bipedal non-hadrosaurid ornithopods, and theropods had limited pronation/supination ability, and sauropodomorphs have unique radial head morphology that likely allowed limited rotational ability. However, the curvature of the radius showed that no dinosaurian clade had the ability to cross the radius about the ulna, suggesting parallel antebrachial elements for all quadrupedal dinosaurs. We conclude that the bipedal origins of all quadrupedal dinosaur clades could have allowed for greater disparity in forelimb posture than previously appreciated, and future studies on dinosaur posture should not limit their classifications to the overly simplistic extant dichotomy.
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Affiliation(s)
- Collin S. VanBuren
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Matthew Bonnan
- Biology Program, The Richard Stockton College of New Jersey, Galloway, New Jersey, United States of America
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Head JJ, Gunnell GF, Holroyd PA, Hutchison JH, Ciochon RL. Giant lizards occupied herbivorous mammalian ecospace during the Paleogene greenhouse in Southeast Asia. Proc Biol Sci 2013; 280:20130665. [PMID: 23740779 PMCID: PMC3774227 DOI: 10.1098/rspb.2013.0665] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Mammals dominate modern terrestrial herbivore ecosystems, whereas extant herbivorous reptiles are limited in diversity and body size. The evolution of reptile herbivory and its relationship to mammalian diversification is poorly understood with respect to climate and the roles of predation pressure and competition for food resources. Here, we describe a giant fossil acrodontan lizard recovered with a diverse mammal assemblage from the late middle Eocene Pondaung Formation of Myanmar, which provides a historical test of factors controlling body size in herbivorous squamates. We infer a predominately herbivorous feeding ecology for the new acrodontan based on dental anatomy, phylogenetic relationships and body size. Ranking body masses for Pondaung Formation vertebrates indicates that the lizard occupied a size niche among the larger herbivores and was larger than most carnivorous mammals. Paleotemperature estimates of Pondaung Formation environments based on the body size of the new lizard are approximately 2–5°C higher than modern. These results indicate that competitive exclusion and predation by mammals did not restrict body size evolution in these herbivorous squamates, and elevated temperatures relative to modern climates during the Paleogene greenhouse may have resulted in the evolution of gigantism through elevated poikilothermic metabolic rates and in response to increases in floral productivity.
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Affiliation(s)
- Jason J Head
- Department of Earth and Atmospheric Sciences and Nebraska State Museum of Natural History, University of Nebraska-Lincoln, , Lincoln, NE 68588, USA.
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Poulsen JY, Byrkjedal I, Willassen E, Rees D, Takeshima H, Satoh TP, Shinohara G, Nishida M, Miya M. Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei). BMC Evol Biol 2013; 13:111. [PMID: 23731841 PMCID: PMC3682873 DOI: 10.1186/1471-2148-13-111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 05/20/2013] [Indexed: 11/24/2022] Open
Abstract
Background A skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes – the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass. Myctophids possess a unique communication system of species-specific photophore patterns and traditional intrafamilial classification has been established to reflect arrangements of photophores. Myctophids present the most diverse array of larval body forms found in fishes although this attribute has both corroborated and confounded phylogenetic hypotheses based on adult morphology. No molecular phylogeny is available for Myctophiformes, despite their importance within all ocean trophic cycles, open-ocean speciation and as an important part of neoteleost divergence. This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements. Results Mitogenomic evidence from DNA sequences and unique gene orders are highly congruent concerning phylogenetic resolution on several myctophiform classification levels, corroborating evidence from osteology, larval ontogeny and photophore patterns, although the lack of larval morphological characters within the subfamily Lampanyctinae stands out. Neoscopelidae is resolved as the sister family to myctophids with Solivomer arenidens positioned as a sister taxon to the remaining neoscopelids. The enigmatic Notolychnus valdiviae is placed as a sister taxon to all other myctophids and exhibits an unusual second copy of the tRNA-Met gene – a gene order rearrangement reminiscent of that found in the tribe Diaphini although our analyses show it to be independently derived. Most tribes are resolved in accordance with adult morphology although Gonichthyini is found within a subclade of the tribe Myctophini consisting of ctenoid scaled species. Mitogenomic sequence data from this study recognize 10 reciprocally monophyletic lineages within Myctophidae, with five of these clades delimited from additional rearranged gene orders or intergenic non-coding sequences. Conclusions Mitogenomic results from DNA sequences and unique gene orders corroborate morphology in phylogeny reconstruction and provide a likely scenario for the phylogenetic history of Myctophiformes. The extent of gene order rearrangements found within the mitochondrial genomes of myctophids is unique for phylogenetic purposes.
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Affiliation(s)
- Jan Y Poulsen
- Natural History Collections, University Museum of Bergen, University of Bergen, Allégaten 41, P.O. Box 7800, Bergen N-5020, Norway.
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Pyron RA, Burbrink FT, Wiens JJ. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol Biol 2013; 13:93. [PMID: 23627680 PMCID: PMC3682911 DOI: 10.1186/1471-2148-13-93] [Citation(s) in RCA: 962] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. RESULTS The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. CONCLUSIONS We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA
| | - Frank T Burbrink
- Department of Biology, The Graduate School and University Center, The City University of New York, 365 5th Ave., New York, NY 10016, USA
- Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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Quemeneur S, de Buffrénil V, Laurin M. Microanatomy of the amniote femur and inference of lifestyle in limbed vertebrates. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12066] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonia Quemeneur
- UMR 7207, CNRS/MNHN/UPMC; Département Histoire de la Terre; Muséum National d'Histoire Naturelle; 43 rue Buffon; 75005; Paris; France
| | - Vivian de Buffrénil
- UMR 7207, CNRS/MNHN/UPMC; Département Histoire de la Terre; Muséum National d'Histoire Naturelle; 43 rue Buffon; 75005; Paris; France
| | - Michel Laurin
- UMR 7207, CNRS/MNHN/UPMC; Département Histoire de la Terre; Muséum National d'Histoire Naturelle; 43 rue Buffon; 75005; Paris; France
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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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Chen D, Guo X, Li J. The complete mitochondrial genome of secret toad-headed agama,Phrynocephalus mystaceus(Reptilia, Squamata, Agamidae). ACTA ACUST UNITED AC 2013; 25:19-20. [DOI: 10.3109/19401736.2013.775269] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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44
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Grechko VV. The problems of molecular phylogenetics with the example of squamate reptiles: Mitochondrial DNA markers. Mol Biol 2013. [DOI: 10.1134/s0026893313010056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Esteve-Altava B, Marugán-Lobón J, Botella H, Rasskin-Gutman D. Structural Constraints in the Evolution of the Tetrapod Skull Complexity: Williston’s Law Revisited Using Network Models. Evol Biol 2012. [DOI: 10.1007/s11692-012-9200-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Campione NE, Evans DC. A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biol 2012; 10:60. [PMID: 22781121 PMCID: PMC3403949 DOI: 10.1186/1741-7007-10-60] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Body size is intimately related to the physiology and ecology of an organism. Therefore, accurate and consistent body mass estimates are essential for inferring numerous aspects of paleobiology in extinct taxa, and investigating large-scale evolutionary and ecological patterns in the history of life. Scaling relationships between skeletal measurements and body mass in birds and mammals are commonly used to predict body mass in extinct members of these crown clades, but the applicability of these models for predicting mass in more distantly related stem taxa, such as non-avian dinosaurs and non-mammalian synapsids, has been criticized on biomechanical grounds. Here we test the major criticisms of scaling methods for estimating body mass using an extensive dataset of mammalian and non-avian reptilian species derived from individual skeletons with live weights. RESULTS Significant differences in the limb scaling of mammals and reptiles are noted in comparisons of limb proportions and limb length to body mass. Remarkably, however, the relationship between proximal (stylopodial) limb bone circumference and body mass is highly conserved in extant terrestrial mammals and reptiles, in spite of their disparate limb postures, gaits, and phylogenetic histories. As a result, we are able to conclusively reject the main criticisms of scaling methods that question the applicability of a universal scaling equation for estimating body mass in distantly related taxa. CONCLUSIONS The conserved nature of the relationship between stylopodial circumference and body mass suggests that the minimum diaphyseal circumference of the major weight-bearing bones is only weakly influenced by the varied forces exerted on the limbs (that is, compression or torsion) and most strongly related to the mass of the animal. Our results, therefore, provide a much-needed, robust, phylogenetically corrected framework for accurate and consistent estimation of body mass in extinct terrestrial quadrupeds, which is important for a wide range of paleobiological studies (including growth rates, metabolism, and energetics) and meta-analyses of body size evolution.
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Affiliation(s)
- Nicolás E Campione
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S 3B2
| | - David C Evans
- Department of Palaeobiology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
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Marine turtle mitogenome phylogenetics and evolution. Mol Phylogenet Evol 2012; 65:241-50. [PMID: 22750111 DOI: 10.1016/j.ympev.2012.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022]
Abstract
The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.
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Gauthier JA, Kearney M, Maisano JA, Rieppel O, Behlke AD. Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2012. [DOI: 10.3374/014.053.0101] [Citation(s) in RCA: 352] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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: 378] [Impact Index Per Article: 31.5] [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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Abstract
Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.
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Affiliation(s)
- Miguel Vences
- Division of Evolutionary Biology Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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