1
|
Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species. BIOLOGY 2023; 12:biology12030406. [PMID: 36979098 PMCID: PMC10045651 DOI: 10.3390/biology12030406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023]
Abstract
The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important aquaculture reptile with rich nutritional and medicinal values. In recent decades, the wild resources of P. sinensis have been depleting due to natural and artificial factors. Herein, we report the complete mitochondrial genome of four P. sinensis strains, including the Japanese (RB) strain, Qingxi Huabie (HB) strain, Jiangxi (JB) strain, and Qingxi Wubie (WB) strain. The nucleotide composition within the complete mitogenomes was biased towards A + T with a variable frequency ranging from 59.28% (cox3) to 70.31% (atp8). The mitogenomes of all four strains contained 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, 1 control region, and a replication origin region of the L-strand replication (OL), which was consistent with most vertebrates. Additionally, the atp8, nad4l, nad6, and nad3 genes possessed high genetic variation and can be used as potential markers for the identification of these P. sinensis strains. Additionally, all PCGs genes were evolving primarily under purifying selection. Through comparative analysis, it was revealed that most of the tRNAs were structurally different in the TψC stem, DHU stem, and acceptor stem. The length of the tandem repeats in the control region was variable in the four P. sinensis strains, ranging from 2 bp to 50 bp. Phylogenetic analysis indicated that all P. sinensis strains clustered into one branch and were closely related to other Trionychinae species. Overall, this study provides mitochondrial genome information for different P. sinensis strains to support further species identification and germplasm resource conservation.
Collapse
|
2
|
Mitochondrial DNA and Distribution Modelling Evidenced the Lost Genetic Diversity and Wild-Residence of Star Tortoise, Geochelone elegans (Testudines: Testudinidae) in India. Animals (Basel) 2022; 13:ani13010150. [PMID: 36611759 PMCID: PMC9817980 DOI: 10.3390/ani13010150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/04/2023] Open
Abstract
The Indian star tortoise (Geochelone elegans) is a massively traded animal in South Asia. To mitigate this risk, the conservation agencies recommended guidelines to safeguard this charismatic species in nature. We adopted mitochondrial DNA-based investigation and performed species distribution modeling of G. elegans throughout its distribution range in the Indian subcontinent. The genetic analyses revealed weak genetic landscape shape interpolations, low intraspecific distances (0% to 1.5%) with mixed haplotype diversity, and a single molecular operational taxonomic unit (MOTU) in the cytochrome b gene dataset. The star tortoise, G. elegans, and its sister species Geochelone platynota showed a monophyletic clustering in the Bayesian (BA) phylogeny. We also attempt to understand the habitat suitability and quality of G. elegans in its distribution range. Our results suggest that, out of the extant area, only 56,495 km2 (9.90%) is suitable for this species, with regions of highest suitability in Sri Lanka. Comparative habitat quality estimation suggests the patch shape complexity and habitat fragmentation are greater in the western and southern ranges of India, which have been greatly influenced by an increased level of urbanization and agriculture practices. We have also provided a retrospect on the potential threat to G. elegans related to the wildlife trade on the regional and international spectrum. Our results detected multiple trading hubs and junctions overlying within the suitable ranges which need special attention in the vicinity. The present study calls for a proper conservation strategy to combat the fragmented distribution and explicitly recommends intensive genetic screening of founder individuals or isolated adult colonies, implementing scientific breeding, and subsequent wild release to restore the lost genetic diversity of star tortoises.
Collapse
|
3
|
Georgalis GL, Macaluso L, Delfino M. A Review of the Fossil Record of Afro-Arabian Turtles of the Clade Testudinoidea. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.3374/014.062.0103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Georgios L. Georgalis
- Palaeontological Institute and Museum, University of Zurich, 8006 Zurich, Switzerland —
| | - Loredana Macaluso
- Dipartimento di Scienze della Terra, Università di Torino, 10125 Torino, Italy
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università di Torino, 10125 Torino, Italy
| |
Collapse
|
4
|
Andreu-Sánchez S, Chen W, Stiller J, Zhang G. Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles. Gigascience 2021; 10:giaa161. [PMID: 33463679 PMCID: PMC7814300 DOI: 10.1093/gigascience/giaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/05/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND During evolutionary history, molecular mechanisms have emerged to cope with deleterious mutations. Frameshift insertions in protein-coding sequences are extremely rare because they disrupt the reading frame. There are a few known examples of their correction through translational frameshifting, a process that enables ribosomes to skip nucleotides during translation to regain proper reading frame. Corrective frameshifting has been proposed to act on the single base pair insertion at position 174 of the mitochondrial NADH dehydrogenase subunit 3 gene (ND3) that has been observed in several turtles and birds. However, the relatively sparse taxonomic representation has hampered our understanding of the evolution of this insertion in vertebrates. RESULTS Here, we analyzed 87,707 ND3 sequences from 10,309 vertebrate taxa to reveal the evolutionary history of this insertion and its common genomic characteristics. We confirmed that the insertion only appears in turtles and birds and reconstructed that it evolved independently in both groups with complex patterns of gains and losses. The insertion was observed in almost all bird orders but was absent in all members of the diverse Passeriformes. We found strong conservation in the nucleotides surrounding the insertion in both turtles and birds, which implies that the insertion enforces structural constraints that could be involved in its correction. CONCLUSIONS Our study demonstrates that frameshifts can be widespread and can be retained for millions of years if they are embedded in a conserved sequence theme.
Collapse
Affiliation(s)
- Sergio Andreu-Sánchez
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Present Address: University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands
| | - Wanjun Chen
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
| |
Collapse
|
5
|
Early preference for face-like stimuli in solitary species as revealed by tortoise hatchlings. Proc Natl Acad Sci U S A 2020; 117:24047-24049. [PMID: 32929003 PMCID: PMC7533828 DOI: 10.1073/pnas.2011453117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
At the beginning of life, inexperienced babies and human fetuses, domestic chicks, and monkeys exhibit a preference for faces and face-like configurations (three blobs arranged like an upside-down triangle). Because all of these species have parental care, it is not clear whether the early preference for faces is a mechanism for orienting toward the conspecifics and sustaining parental care, or a more general mechanism to attend to living beings. We contrasted these hypotheses by testing inexperienced hatchlings of five species of tortoises, solitary animals with no parental care. If early face-like preference evolved in the context of parental care, solitary species should not exhibit it. We observed that visually naïve tortoises prefer to approach face-like patterns over alternative configurations. The predisposition to approach face-like stimuli observed in hatchlings of these solitary species suggests the presence of an ancient mechanism, ancestral to the evolution of reptiles and mammals, that sustains the exploratory responses, and potentially learning, in both solitary and social species.
Collapse
|
6
|
Garcia G, Pinton A, Valentin X, Kostopoulos DS, Merceron G, de Bonis L, Koufos GD. The earliest known crown-Testudo tortoise from the late Miocene (Vallesian, 9 Ma) of Greece. PLoS One 2020; 15:e0224783. [PMID: 32267839 PMCID: PMC7141670 DOI: 10.1371/journal.pone.0224783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 10/21/2019] [Indexed: 11/19/2022] Open
Abstract
We here report on fossil remains of the earliest known crown-Testudo, an extant clade of Mediterranean testudinid tortoises from the late Miocene (Vallesian, MN 10) from the hominoid locality Ravin de la Pluie (RPl) in Greece. The material studied is a small, nearly complete carapace with a clearly distinct hypo-xiphiplastral hinge. This supports the sensu stricto generic assignment. This new terrestrial testudinid specimen is characterized by a possible tectiform, narrow, elongated shell with a pentagonal pygal and a long, posteriorly elevated, lenticular and rounded dorsal epiplastral lip. These unique features differ from those of other known Mediterranean hinged forms and allow the erection of the new species Testudo hellenica sp. nov. This taxon is phylogenetically close to two Greek species, the extant T. marginata and the fossil T. marmorum (Turolian, around 7.3 Ma). This record provides evidence for the first appearance of the genus Testudo sensu stricto at a minimum age of 9 Ma.
Collapse
Affiliation(s)
- Géraldine Garcia
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - Aurélie Pinton
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - Xavier Valentin
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | | | - Gildas Merceron
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - Louis de Bonis
- PALEVOPRIM, UMR CNRS 7262, Université de Poitiers, Poitiers, France
| | - George D. Koufos
- Department of Geology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
7
|
Iwasaki SI, Erdoğan S, Asami T. Evolutionary Specialization of the Tongue in Vertebrates: Structure and Function. FEEDING IN VERTEBRATES 2019. [DOI: 10.1007/978-3-030-13739-7_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
8
|
Vlachos E, Rabi M. Total evidence analysis and body size evolution of extant and extinct tortoises (Testudines: Cryptodira: Pan-Testudinidae). Cladistics 2018; 34:652-683. [PMID: 34706483 DOI: 10.1111/cla.12227] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 01/18/2023] Open
Abstract
Testudinidae (tortoises) is an extant clade of terrestrial turtles of worldwide distribution and with a rich fossil record that provides an exceptional context for studying their evolutionary history. Because of the lack of global phylogenetic analyses integrating extinct taxa, our current knowledge of the relationships of the total clade of Testudinidae is rather poor. To resolve this issue, we performed the first total evidence analysis of Pan-Testudinidae. The total evidence trees are congruent with the molecular topology and agree on the dichotomy of derived Testudinidae (=Testudininae; Converted Clade Name) into two previously recognized major clades, Testudona and Geochelona (New Clade Name). The integration of extinct taxa into the analysis allowed the stratigraphic fit of the total evidence trees, indicating that crown Testudininae, Testudona and Geochelona all originated by the Late Eocene, in agreement with recent molecular estimates. Ghost lineage analysis indicates high diversification in the Late Eocene and in the Miocene. The age of crown Testudo is Late Miocene, again in accordance with some molecular dates. Phylogenetic placement of fossils demonstrates that giant body size independently evolved in multiple continental mainland taxa and confirms recent results deduced from living taxa-giantism in Testudinidae is not linked to the insular effect. An unexpected outcome is the recovery of miniaturization in Testudona (<30 cm carapace length) that emerged sometime between the Oligocene and Early Miocene. No clear correlation between body size evolution and climate is apparent, but increased taxon sampling may nevertheless demonstrate the role of cooling and warming as one of many influential variables.
Collapse
Affiliation(s)
- Evangelos Vlachos
- CONICET - Museo Paleontológico Egidio Feruglio, Av. Fontana 140, Trelew, Chubut, 9100, Argentina.,School of Geology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Márton Rabi
- Central Natural Science Collections, Martin-Luther University Halle-Wittenberg, Domplatz 4, 06108, Halle (Saale), Germany.,Department of Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074, Tübingen, Germany
| |
Collapse
|
9
|
Chang CH, Dai WY, Chen TY, Lee AH, Hou HY, Liu SH, Jang-Liaw NH. DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens. Genome 2018; 61:615-624. [PMID: 29916730 DOI: 10.1139/gen-2017-0264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.
Collapse
Affiliation(s)
- Chia-Hao Chang
- a Department of Animal Biology, University of Illinois, 202 Shelford Vivarium, 606 East Healey St., Champaign, IL 61820, USA
| | - Wei-Yu Dai
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Ting-Yu Chen
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - An-Hsin Lee
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Hsuan-Yi Hou
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Shih-Hui Liu
- c Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei City 11529, Taiwan
| | - Nian-Hong Jang-Liaw
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| |
Collapse
|
10
|
|
11
|
Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles. Mol Phylogenet Evol 2017; 113:59-66. [DOI: 10.1016/j.ympev.2017.05.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/13/2017] [Accepted: 05/09/2017] [Indexed: 11/19/2022]
|
12
|
Shi Q, Wang J, Liu J, Jiang H, Nie L. The complete mitochondrial genome of Geochelone sulcata. Mitochondrial DNA B Resour 2017; 2:463-464. [PMID: 33473863 PMCID: PMC7800827 DOI: 10.1080/23802359.2017.1357437] [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: 06/05/2017] [Accepted: 07/17/2017] [Indexed: 10/31/2022] Open
Abstract
The complete mitochondrial genome of Geochelone sulcata was determined using PCR, Long-PCR with length of 16,692 bp. The genome organization, gene order, and base composition was similar to typical vertebrate. Gene content included 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. Otherwise, the lack of C, as same as in the other species of Testudinidae, was detected in arms of tRNALys gene in G. sulcata. In addition, an extra nucleotide A was discovered in ND3 gene in G. sulcata. The complete mitogenome of G. sulcata provides the basic data to research molecular systematics of Testudinidae.
Collapse
Affiliation(s)
- Qiong Shi
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Jue Wang
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Jianjun Liu
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Hui Jiang
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| | - Liuwang Nie
- Life Science College, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China
| |
Collapse
|
13
|
Wang Y, Dai X, Wang M, Nie L. The complete mitochondrial genome of the Heosemys depressa (Testudines, Geoemydidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:437-438. [PMID: 33473854 PMCID: PMC7800218 DOI: 10.1080/23802359.2017.1357438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The complete mitochondrial genome of Heosemys depressa was obtained and characterized in this study. The mitochondrial genome is a circular molecule of 16,773bp in length, and harbours 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding D-loop region (control region). Its gene arrangement type is identical to the type of most vertebrate. Phylogenetic analysis suggests that H. depressa is closely related to H. annandalii than to the other species. Our data provide a useful resource for the phylogenetic studies of genus Heosemys.
Collapse
Affiliation(s)
- Yuqin Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Xueting Dai
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Meng Wang
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Liuwang Nie
- Life Science College, Anhui Normal University, Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| |
Collapse
|
14
|
Yan C, Mou B, Meng Y, Tu F, Fan Z, Price M, Yue B, Zhang X. A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history. PLoS One 2017; 12:e0181649. [PMID: 28742865 PMCID: PMC5526529 DOI: 10.1371/journal.pone.0181649] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/05/2017] [Indexed: 01/16/2023] Open
Abstract
The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.
Collapse
Affiliation(s)
- Chaochao Yan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Biqin Mou
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yang Meng
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Feiyun Tu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
- Institute of Wildlife Conservation, Jiangxi Academy of Forestry, Nanchang, P.R. China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| |
Collapse
|
15
|
Mautner AK, Latimer AE, Fritz U, Scheyer TM. An updated description of the osteology of the pancake tortoiseMalacochersus tornieri(Testudines: Testudinidae) with special focus on intraspecific variation. J Morphol 2017; 278:321-333. [DOI: 10.1002/jmor.20640] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/23/2016] [Accepted: 12/04/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Anna-Katharina Mautner
- University of Zurich, Palaeontological Institute and Museum; Karl Schmid-Strasse 4 Zurich CH-8006 Switzerland
| | - Ashley E. Latimer
- University of Zurich, Palaeontological Institute and Museum; Karl Schmid-Strasse 4 Zurich CH-8006 Switzerland
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde); A. B. Meyer Building Dresden D-01109 Germany
| | - Torsten M. Scheyer
- University of Zurich, Palaeontological Institute and Museum; Karl Schmid-Strasse 4 Zurich CH-8006 Switzerland
| |
Collapse
|
16
|
Hofmeyr MD, Vamberger M, Branch W, Schleicher A, Daniels SR. Tortoise (Reptilia, Testudinidae) radiations in Southern Africa from the Eocene to the present. ZOOL SCR 2016. [DOI: 10.1111/zsc.12223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Margaretha D. Hofmeyr
- Chelonian Biodiversity and Conservation; Department of Biodiversity and Conservation Biology; University of the Western Cape; Private Bag X17 Bellville 7535 South Africa
| | - Melita Vamberger
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building 01109 Dresden Germany
| | - William Branch
- Department of Herpetology; Port Elizabeth Museum; P.O. Box 13147 Humewood 6013 South Africa
- Department of Zoology; Nelson Mandela Metropolitan University; P.O. Box 77000 Port Elizabeth 6031 South Africa
| | | | - Savel R. Daniels
- Department of Botany and Zoology; University of Stellenbosch; Private Bag X1 Matieland 7602 South Africa
| |
Collapse
|
17
|
Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
Collapse
Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
| |
Collapse
|
18
|
Luján ÀH, Delfino M, Robles JM, Alba DM. The Miocene tortoiseTestudo catalaunicaBataller, 1926, and a revised phylogeny of extinct species of genusTestudo(Testudines: Testudinidae). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12414] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Àngel H. Luján
- Institut Català de Paleontologia Miquel Crusafont; Universitat Autònoma de Barcelona; Edifici ICTA-ICP, Carrer de les Columnes s/n, Campus de la UAB 08193 Cerdanyola del Vallès, Barcelona Spain
| | - Massimo Delfino
- Institut Català de Paleontologia Miquel Crusafont; Universitat Autònoma de Barcelona; Edifici ICTA-ICP, Carrer de les Columnes s/n, Campus de la UAB 08193 Cerdanyola del Vallès, Barcelona Spain
- Dipartimento di Scienze della Terra; Università di Torino; Via Valperga Caluso 35 10125 Torino Italy
| | - Josep M. Robles
- Institut Català de Paleontologia Miquel Crusafont; Universitat Autònoma de Barcelona; Edifici ICTA-ICP, Carrer de les Columnes s/n, Campus de la UAB 08193 Cerdanyola del Vallès, Barcelona Spain
- FOSSILIA Serveis Paleontològics i Geològics; S.L., Carrer Jaume I núm. 87, 1er 5a 08470 Sant Celoni, Barcelona Spain
| | - David M. Alba
- Institut Català de Paleontologia Miquel Crusafont; Universitat Autònoma de Barcelona; Edifici ICTA-ICP, Carrer de les Columnes s/n, Campus de la UAB 08193 Cerdanyola del Vallès, Barcelona Spain
| |
Collapse
|
19
|
Li DH, Shi W, Munroe TA, Gong L, Kong XY. Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes). PLoS One 2015; 10:e0134580. [PMID: 26237419 PMCID: PMC4523187 DOI: 10.1371/journal.pone.0134580] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 07/12/2015] [Indexed: 12/20/2022] Open
Abstract
Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.
Collapse
Affiliation(s)
- Dong-He Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Shi
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, China
- * E-mail: (WS); (XYK)
| | - Thomas A. Munroe
- National Systematics Laboratory NMFS/NOAA, Post Office Box 37012, Smithsonian Institution NHB, WC 60, MRC-153, Washington, D.C., 20013–7012, United States of America
| | - Li Gong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Yu Kong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- * E-mail: (WS); (XYK)
| |
Collapse
|
20
|
Crawford NG, Parham JF, Sellas AB, Faircloth BC, Glenn TC, Papenfuss TJ, Henderson JB, Hansen MH, Simison WB. A phylogenomic analysis of turtles. Mol Phylogenet Evol 2015; 83:250-7. [DOI: 10.1016/j.ympev.2014.10.021] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/16/2014] [Accepted: 10/28/2014] [Indexed: 11/25/2022]
|
21
|
Angielczyk KD, Burroughs RW, Feldman CR. Do turtles follow the rules? Latitudinal gradients in species richness, body size, and geographic range area of the world's turtles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:270-94. [DOI: 10.1002/jez.b.22602] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/10/2014] [Accepted: 09/29/2014] [Indexed: 11/11/2022]
Affiliation(s)
| | - Robert W. Burroughs
- Jackson School of Geosciences; The University of Texas at Austin; Austin Texas
| | | |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Eight new mtDNA sequences of glass sponges reveal an extensive usage of +1 frameshifting in mitochondrial translation. Gene 2013; 535:336-44. [PMID: 24177232 DOI: 10.1016/j.gene.2013.10.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 11/22/2022]
Abstract
Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate the mechanism of frameshifting, we determined eight new complete or nearly complete mtDNA sequences from glass sponges and examined individual mitochondrial genes from three others. We found nine new instances of single nucleotide insertions in these sequences and analyzed them both comparatively and phylogenetically. The base insertions appear to have been gained and lost repeatedly in hexactinellid mt protein genes, suggesting no functional significance for the frameshifting sites. A high degree of sequence conservation, the presence of unusual tRNAs, and a distinct pattern of codon usage suggest the "out-of-frame pairing" model of translational frameshifting. Additionally, we provide evidence that relaxed selection pressure on glass sponge mtDNA - possibly a result of their low growth rates and deep-water lifestyle - has allowed frameshift insertions to be tolerated for hundreds of millions of years. Our study provides the first example of a phylogenetically diverse and extensive usage of translational frameshifting in animal mitochondrial coding sequences.
Collapse
|
24
|
Weisrock DW. Concordance analysis in mitogenomic phylogenetics. Mol Phylogenet Evol 2012; 65:194-202. [DOI: 10.1016/j.ympev.2012.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 05/22/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
|
25
|
Drosopoulou E, Tsiamis G, Mavropoulou M, Vittas S, Katselidis KA, Schofield G, Palaiologou D, Sartsidis T, Bourtzis K, Pantis J, Scouras ZG. The complete mitochondrial genome of the loggerhead turtle Caretta caretta (Testudines: Cheloniidae): genome description and phylogenetic considerations. ACTA ACUST UNITED AC 2012; 23:1-12. [PMID: 22295859 DOI: 10.3109/19401736.2011.637109] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The marine turtle Caretta caretta is a widely distributed species that is facing critical population decline, especially in the Mediterranean rookeries. Molecular markers, such as mitochondrial DNA (mtDNA) sequences, are of great importance for the description and monitoring of turtle migratory populations. The complete sequence of the C. caretta mitochondrial genome is presented here. The genome comprises 16,440 base pairs, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes), and a control region, all organized similar to the majority of vertebrate mitogenomes. MtDNA length polymorphism and heteroplasmy were observed among, and within, individuals due to the variable size of a microsatellite repeat residing at the 3' end of the control region. The use of the above repeat as a marker for individual fingerprinting is discussed. Furthermore, phylogenetic analyses among Testudines based on complete mitogenomes, as well as among marine turtles based on partial mtDNA sequences, are considered.
Collapse
Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Fielder D, Vernes K, Alacs E, Georges A. Mitochondrial variation among Australian freshwater turtles (genus Myuchelys), with special reference to the Endangered M. bellii. ENDANGER SPECIES RES 2012. [DOI: 10.3354/esr00417] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
27
|
Reid BN, LE M, McCord WP, Iverson JB, Georges A, Bergmann T, Amato G, Desalle R, Naro-Maciel E. Comparing and combining distance-based and character-based approaches for barcoding turtles. Mol Ecol Resour 2011; 11:956-67. [PMID: 21635698 DOI: 10.1111/j.1755-0998.2011.03032.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Molecular barcoding can serve as a powerful tool in wildlife forensics and may prove to be a vital aid in conserving organisms that are threatened by illegal wildlife trade, such as turtles (Order Testudines). We produced cytochrome oxidase subunit one (COI) sequences (650 bp) for 174 turtle species and combined these with publicly available sequences for 50 species to produce a data set representative of the breadth of the order. Variability within the barcode region was assessed, and the utility of both distance-based and character-based methods for species identification was evaluated. For species in which genetic material from more than one individual was available (n = 69), intraspecific divergences were 1.3% on average, although divergences greater than the customary 2% barcode threshold occurred within 15 species. High intraspecific divergences could indicate species with a high degree of internal genetic structure or possibly even cryptic species, although introgression is also probable in some of these taxa. Divergences between species of the same genus were 6.4% on average; however, 49 species were <2% divergent from congeners. Low levels of interspecific divergence could be caused by recent evolutionary radiations coupled with the low rates of mtDNA evolution previously observed in turtles. Complementing distance-based barcoding with character-based methods for identifying diagnostic sets of nucleotides provided better resolution in several cases where distance-based methods failed to distinguish species. An online identification engine was created to provide character-based identifications. This study constitutes the first comprehensive barcoding effort for this seriously threatened order.
Collapse
Affiliation(s)
- B N Reid
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Eda M, Kuro-o M, Higuchi H, Hasegawa H, Koike H. Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses). Genes Genet Syst 2010; 85:129-39. [PMID: 20558899 DOI: 10.1266/ggs.85.129] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.
Collapse
Affiliation(s)
- Masaki Eda
- Graduate School of Social and Cultural Studies, Kyusyu University.
| | | | | | | | | |
Collapse
|
29
|
Fritz U, Daniels SR, Hofmeyr MD, González J, Barrio-Amorós CL, Široký P, Hundsdörfer AK, Stuckas H. Mitochondrial phylogeography and subspecies of the wide-ranging sub-Saharan leopard tortoise Stigmochelys pardalis (Testudines: Testudinidae) - a case study for the pitfalls of pseudogenes and GenBank sequences. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00565.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
30
|
Zhang Y, Nie L, Huang Y, Pu Y, Zhang L. The mitochondrial DNA control region comparison studies of four hinged turtles and its phylogentic significance of the genusCuora sensu lato (Testudinata: Geoemydidae). Genes Genomics 2009. [DOI: 10.1007/bf03191253] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
31
|
Genetic assessment, illegal trafficking and management of the Mediterranean spur-thighed tortoise in Southern Spain and Northern Africa. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9982-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
32
|
Russell RD, Beckenbach AT. Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code. J Mol Evol 2009; 67:682-95. [PMID: 19030769 PMCID: PMC2706983 DOI: 10.1007/s00239-008-9179-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 10/24/2008] [Indexed: 12/02/2022]
Abstract
A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the widespread nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises reveal general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker’s snake-neck turtle (Chelodina parkeri), the first known example of this in vertebrate mitochondria.
Collapse
Affiliation(s)
- R David Russell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6
| | | |
Collapse
|
33
|
Lee JCI, Tsai LC, Liao SP, Linacre A, Hsieh HM. Species identification using the cytochrome b gene of commercial turtle shells. Forensic Sci Int Genet 2008; 3:67-73. [PMID: 19215874 DOI: 10.1016/j.fsigen.2008.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 10/09/2008] [Accepted: 10/14/2008] [Indexed: 10/21/2022]
Abstract
Turtle shells and their gelled products are familiar in some countries as foods, tonics and medicines. These shells may come from endangered and protected species, requiring the identification of the species present to enforce national and international legislation. We report on the design of five combinations of primer pairs for the identification of turtle shells and shell fragments used as ornaments, food products and medicines. The types of samples used are those encountered frequently and will typically contain highly degraded DNA. The success rate for species identification using the test described is dependent upon the choice of primer sets used and the length of the expected amplification product. Gelled products were simulated by the process of decoction for up to 12 h, after which all the turtle species could be identified from the liquid samples. This study establishes a method for the identification of commercial turtle shells and illustrates a simulated case using gelled products.
Collapse
Affiliation(s)
- James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan, ROC
| | | | | | | | | |
Collapse
|
34
|
Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Mol Phylogenet Evol 2008; 49:514-25. [PMID: 18761096 DOI: 10.1016/j.ympev.2008.08.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 08/01/2008] [Accepted: 08/05/2008] [Indexed: 11/21/2022]
Abstract
We present a strategy for phylogenetic marker development in non-model systems. Rather than using the traditional approach of comparing distantly related taxa to develop conserved primers for unknown species, we explore an alternative strategy that builds primers directly from a single, relatively well characterized species and applies those primers to increasingly distantly related taxa. We develop and test our protocol with turtles. Using a single BAC end-sequence library consisting of 3461 sequences totaling 2.43 million base pairs of data, we outline a procedure to flag repeat elements, followed by a BLAST approach to categorize sequences into high, low, and no similarity compartments compared to GenBank sequences. We developed and tested a panel of 96 primer pairs with a set of turtle tissues that forms a series of increasingly distantly related taxa with respect to the BAC reference species. Finally, we sequenced 11 of these newly discovered markers across a diverse set of 18 turtle species that spans the 210 million years of chelonian crown-group history and that includes representatives of most of the major clades of extant turtles. Our results indicate that large numbers of new, phylogenetically informative markers can be developed quickly and inexpensively from a single BAC, EST, or similar genomic resource, and that those markers provide reliable phylogenetic information across both shallow and deep levels of phylogenetic history. Our results also highlight the importance of screening for and managing repetitive elements found in randomly sequenced DNA fragments. We presume that our strategy should work well across any similarly divergent clade, suggesting that many-marker datasets can be developed quickly and efficiently for phylogenetic analysis.
Collapse
|
35
|
RIVERA GABRIEL, CLAUDE JULIEN. Environmental media and shape asymmetry: a case study on turtle shells. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01008.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
36
|
Parham JF, Papenfuss TJ. High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9544-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
37
|
Zhang L, Nie L, Cao C, Zhan Y. The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups. J Genet Genomics 2008; 35:33-40. [DOI: 10.1016/s1673-8527(08)60005-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 07/26/2007] [Accepted: 07/26/2007] [Indexed: 11/28/2022]
|
38
|
Zhang L, Nie LW, Zhang Y, Rui JL, Zhang YY. Complete sequence and organization of the mitochondrial genome of Cyclemys atripons (Testudines, Geoemydidae). Genet Mol Biol 2008. [DOI: 10.1590/s1415-47572008000400027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
39
|
Boore JL. Requirements and standards for organelle genome databases. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 10:119-26. [PMID: 16901216 DOI: 10.1089/omi.2006.10.119] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mitochondria and plastids (collectively called organelles) descended from prokaryotes that adopted an intracellular, endosymbiotic lifestyle within early eukaryotes. Comparisons of their remnant genomes address a wide variety of biological questions, especially when including the genomes of their prokaryotic relatives and the many genes transferred to the eukaryotic nucleus during the transitions from endosymbiont to organelle. The pace of producing complete organellar genome sequences now makes it unfeasible to do broad comparisons using the primary literature and, even if it were feasible, it is now becoming uncommon for journals to accept detailed descriptions of genome-level features. Unfortunately, no database is completely useful for this task, since they have little standardization and are riddled with error. Further, the descriptors necessary to make full use of these data are generally lacking. Here, I outline what is currently wrong and what must be done to make this data useful to the scientific community.
Collapse
Affiliation(s)
- Jeffrey L Boore
- Department of Energy (DOE) Joint Genome Institute and Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94598, USA.
| |
Collapse
|
40
|
Fritz U, Bininda-Emonds ORP. When genes meet nomenclature: Tortoise phylogeny and the shifting generic concepts of Testudo and Geochelone. ZOOLOGY 2007; 110:298-307. [PMID: 17611092 DOI: 10.1016/j.zool.2007.02.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 02/08/2007] [Accepted: 02/09/2007] [Indexed: 10/23/2022]
Abstract
We used a five-gene data set (mtDNA: 12S rRNA, 16S rRNA, cyt-b; nDNA: Cmos, Rag2) comprising approximately two-thirds of all extant testudinid species and, for the first time, including all five Testudo species to investigate the question of whether all western Palaearctic testudinids are monophyletic. Further, we examined whether the recently suggested allocation of the African Geochelone pardalis in the otherwise exclusively South African genus Psammobates and of the Malagasy G. yniphora in the monotypic genus Angonoka is justified in the face of considerable morphological evidence against such placements. Our phylogenetic analyses do not support the paraphyly and generic break-up of Testudo, as suggested by previous papers using a smaller taxon sampling and mtDNA data only. We propose a continued usage of the generic name Testudo for all five western Palaearctic tortoise species. Within Testudo, two monophyletic subclades are present, one containing T. hermanni+T. horsfieldii, and the other comprising (T. kleinmanni+T. marginata)+T. graeca. Nomenclaturally, we demonstrate that Eurotestudo Lapparent de Broin et al., 2006, which was recently erected with the type species T. hermanni, is an objective junior synonym of Chersine Merrem, 1820 and Medaestia Wussow, 1916. Recognition of a monotypic genus Angonoka for G. yniphora is unwarranted according to both our re-analysis of sequence data and morphological data. Acknowledging the strong morphological similarity between G. yniphora and G. radiata, we suggest placing both species into the genus Astrochelys. Although sequence data for only one of the three Psammobates species was available for analysis, there is currently no cause to challenge the monophyly of this genus as established on the basis of morphological evidence. Thus, we hypothesize that G. pardalis is sister to a monophyletic Psammobates. In light of the clear morphological gap between G. pardalis and Psammobates species, the recognition of a distinct genus Stigmochelys for the former seems justified.
Collapse
Affiliation(s)
- Uwe Fritz
- Museum of Zoology, Natural History State Collections Dresden, A.B. Meyer Building, D-01109 Dresden, Germany.
| | | |
Collapse
|
41
|
|
42
|
Fritz U, Auer M, Bertolero A, Cheylan M, Fattizzo T, Hundsdorfer AK, Martin Sampayo M, Pretus JL, ŠirokY P, Wink M. A rangewide phylogeography of Hermann's tortoise, Testudo hermanni (Reptilia: Testudines: Testudinidae): implications for taxonomy. ZOOL SCR 2006. [DOI: 10.1111/j.1463-6409.2006.00242.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
43
|
Le M, Raxworthy CJ, McCord WP, Mertz L. A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes. Mol Phylogenet Evol 2006; 40:517-31. [PMID: 16678445 DOI: 10.1016/j.ympev.2006.03.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2005] [Revised: 03/01/2006] [Accepted: 03/02/2006] [Indexed: 11/29/2022]
Abstract
Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.
Collapse
Affiliation(s)
- Minh Le
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
| | | | | | | |
Collapse
|
44
|
Parham JF, Feldman CR, Boore JL. The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA. BMC Evol Biol 2006; 6:11. [PMID: 16464263 PMCID: PMC1403801 DOI: 10.1186/1471-2148-6-11] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 02/07/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis. RESULTS We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles. CONCLUSION Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, including Platysternon.
Collapse
Affiliation(s)
- James F Parham
- Department of Evolutionary Genomics, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Museum of Paleontology, University of California, Berkeley, CA, 94720, USA
| | - Chris R Feldman
- Department of Biology, Utah State University, Logan, UT, 84322, USA
| | - Jeffrey L Boore
- Department of Evolutionary Genomics, DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Integrative Biology, 3060 Valley Life Science Building, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
45
|
Simison WB, Lindberg DR, Boore JL. Rolling circle amplification of metazoan mitochondrial genomes. Mol Phylogenet Evol 2005; 39:562-7. [PMID: 16360323 DOI: 10.1016/j.ympev.2005.11.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 11/07/2005] [Accepted: 11/07/2005] [Indexed: 11/24/2022]
Affiliation(s)
- W Brian Simison
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.
| | | | | |
Collapse
|