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Marques-Neto JC, de Lima GM, Maciel CMT, Maciel BR, Abrunhosa FA, Sampaio I, Maciel CR. In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data. BMC Genomics 2023; 24:677. [PMID: 37950193 PMCID: PMC10637016 DOI: 10.1186/s12864-023-09770-y] [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: 07/18/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará. RESULTS Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial). CONCLUSIONS It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
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Affiliation(s)
- Jerônimo Costa Marques-Neto
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Gabriel Monteiro de Lima
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Carlos Murilo Tenório Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Bruna Ramalho Maciel
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Fernando Araujo Abrunhosa
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Carcinology, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Iracilda Sampaio
- Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Cristiana Ramalho Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
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Özbek M, Aksu İ, Baytaşoğlu H. A new freshwater amphipod (Amphipoda, Gammaridae), Gammarus tumaf sp. nov. from the Gökgöl Cave, Türkiye. ZOOSYST EVOL 2023. [DOI: 10.3897/zse.99.89957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A new amphipod species belonging to the genus Gammarus is described from the Gökgöl Cave, Zonguldak Province, Türkiye. The newly-identified species is relatively small (13 mm) and is a member of the Gammarus pulex-group by the presence of numerous long setae along the posterior margins of pereopods 3 and 4. The specimens were sampled from a shallow pond located in the dark zone (about 1 km inside the entrance) of the cave. Minute eyes, setose (both peduncle and flagellar segments) second antenna, slightly swollen flagellar segments of the second antenna, setose pereopods 3 and 4 and relatively short endopod/exopod ratio of the third uropod are the character combination of the newly-identified species in addition to lacking body pigmentation. The molecular phylogeny, based on the concatenated dataset (28S+COI, 1495 bp) indicated that the new species was resolved from the other Gammarus species by high bootstrap (NJ: 100, ML: 100). In addition to Gammarus tumafsp. nov., mtDNA COI and nuclear DNA 28S gene data of Gammarus baysaliÖzbek et al., 2013 were recorded for the first time. The newly-identified species was well-differentiated from the genetically closest species, G. baysali, with genetic distance of 12.22% and 0.55% for the COI and 28S genes, respectively. Detailed descriptions and drawings of the extremities of the holotype male were given and the morphology of the newly-identified species is compared with its relatives.
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Koroiva R, Santana DJ. Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae). AN ACAD BRAS CIENC 2022; 94:e20200825. [PMID: 36477987 DOI: 10.1590/0001-3765202220200825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/19/2021] [Indexed: 12/09/2022] Open
Abstract
We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).
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Affiliation(s)
- Ricardo Koroiva
- Universidade Federal da Paraíba, Departamento de Sistemática e Tecnologia, Centro de Ciências Exatas e da Natureza, Laboratório Multiusuário do Programa de Pós-Graduação em Ciências Biológicas/Zoologia, Castelo Branco, Campus Universitário, s/n, 58051900 João Pessoa, PB, Brazil.,Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
| | - Diego José Santana
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
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Turan D, Kaya C, Aksu İ, Bektaş Y. Paracapoeta, a new genus of the Cyprinidae from Mesopotamia, Cilicia and Levant (Teleostei, Cypriniformes). ZOOSYST EVOL 2022. [DOI: 10.3897/zse.98.81463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The molecular and morphological studies carried out within the scope of this study revealed that the scrapers, known as the Mesopotamian group, belong to a different genus. The Paracapoetagen. nov., from the Mesopotomia and Levant, is distinguished from Capoeta and Luciobarbus species by the presence of a strong ligament between the base of the last simple and the first branched rays of the dorsal-fin (vs. no or a very weak ligament). The Paracapoeta further differs from Capoeta by the last simple dorsal-fin ray strongly ossified in adult specimens (more than 75%, vs. less than 75%). The Paracapoeta further differs from Luciobarbus by the lower lip with horny layer (vs. fleshy lips). The molecular phylogeny based on the combined dataset (COI + Cytb, 1312 bp.) showed that the genus Paracapoeta was recovered from the other groups in the subfamily Barbinae with high bootstrap and posterior probability values (BP: 94%, PP: 0.96). Also, Paracapoeta and Capoeta are well differentiated by an average genetic distance of 8.02±0.78%. The morphological and molecular findings have largely overlapped each other. Besides, Capoeta turani is treated as a synonym of Capoeta erhani.
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Malleret MM, Freire MD, Lemes P, Brum FT, Camargo A, Verrastro L. Phylogeography and species delimitation of the Neotropical frog complex (Hylidae:
Scinax granulatus
). ZOOL SCR 2022. [DOI: 10.1111/zsc.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matías M. Malleret
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Marcelo D. Freire
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
| | - Priscila Lemes
- Laboratório de Ecologia e Conservação Departamento de Botânica e Ecologia, Insituto de Biociências, Universidade Federal do Mato Grosso Cuiabá Mato Grosso Brazil
| | - Fernanda T. Brum
- Programa de Pós‐graduação em Ecologia e Conservação Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Arley Camargo
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Laura Verrastro
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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Kartavtsev YP. Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society. Animals (Basel) 2021; 11:1473. [PMID: 34065552 PMCID: PMC8160991 DOI: 10.3390/ani11051473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 01/27/2023] Open
Abstract
Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
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7
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Olsson D, Marquez A, Tellechea J.S, Carvalho PH, Pereira AN, Norbis W. Genetic and morphometric analyzes of Paralichthys species confirm the presence of P. brasiliensis in the Uruguayan waters. NEOTROPICAL BIODIVERSITY 2019. [DOI: 10.1080/23766808.2019.1620407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Daniela Olsson
- Laboratorio de Fisiologia de la Reproduccion y Ecologia de Peces, Departamento de Biologia Animal, Instituto de Biologia. Facultad de Ciencias. Universidad de la Republica, Montevideo, Uruguay
| | - Alejandro Marquez
- Unidad de Microscopía Electrónica de Barrido. Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Javier .S. Tellechea
- Área de Anatomía, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | | | - Alfredo N. Pereira
- Laboratorio de Genética, Dirección Nacional de Recursos Acuáticos, MGAP, Uruguay
| | - Walter Norbis
- Laboratorio de Fisiologia de la Reproduccion y Ecologia de Peces, Departamento de Biologia Animal, Instituto de Biologia. Facultad de Ciencias. Universidad de la Republica, Montevideo, Uruguay
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8
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Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches. Mol Phylogenet Evol 2019; 132:105-116. [DOI: 10.1016/j.ympev.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022]
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9
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Slynko YV, Slynko EE, Pirkova AV, Ladygina LV, Ryabushko VI. Mitochondrial DNA Barcoding of the Pacific Oyster Crassostrea gigas (Thunberg, 1793) (Mollusca: Bivalvia: Ostreidae), Cultivated in the Black Sea. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Lalitha R, Chandavar VR. Analysis of genetic diversity in CYTB and control region sequences of Melanochelys trijuga (Schweigger, 1812) from Karnataka. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2018. [DOI: 10.1016/j.japb.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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11
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Kartavtsev YP, Sharina SN, Chichvarkhin AY, Chichvarkhina OV, Masalkova NA, Lutaenko KA, Oliveira C. Genetic Divergence of Mussels (Mollusca, Mytilidae) Based on the 28S rRNA, 18S rRNA, and H3 Nuclear Gene Sequences. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060078] [Citation(s) in RCA: 7] [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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12
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Yang BT, Zhou Y, Min MS, Matsui M, Dong BJ, Li PP, Fong JJ. Diversity and phylogeography of Northeast Asian brown frogs allied to Rana dybowskii (Anura, Ranidae). Mol Phylogenet Evol 2017; 112:148-157. [DOI: 10.1016/j.ympev.2017.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 04/29/2017] [Indexed: 11/27/2022]
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13
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Slynko YV, Pakunova EN, Statkevich SV, Slynko EE. Genetic diversity of invasive populations of the florida crab (Rhithropanopeus harrisii (Gould, 1841): (Decapoda, Panopidae)). RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417050106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Zhou Y, Wang S, Zhu H, Li P, Yang B, Ma J. Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura). PLoS One 2017; 12:e0175113. [PMID: 28369142 PMCID: PMC5378408 DOI: 10.1371/journal.pone.0175113] [Citation(s) in RCA: 7] [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: 11/08/2016] [Accepted: 03/21/2017] [Indexed: 01/05/2023] Open
Abstract
Few studies have explored the role of Cenozoic tectonic evolution in shaping the patterns and processes of extant animal distributions in and around East Asia. In this study, we selected South Chinese brown frogs as a model to examine the phylogenetic and biogeographical consequences of Miocene tectonic events within South China and its margins. We used mitochondrial and nuclear molecular data to reconstruct phylogenetic interrelationships among Chinese brown frogs using Bayesian and maximum likelihood analyses. The phylogeny results show that there are four main clades of Chinese brown frogs. Excepting the three commonly known Chinese brown frog species groups, R. maoershanensis forms an independent clade nearest to the R. japonica group. Phylogeny and P-distance analyses confirmed R. maoershanensis as a valid species. Among South Chinese brown frogs, there are four subclades associated with four geographical areas: (I) R. maoershanensis; (II) R. japonica; (III) R. chaochiaoensis; and (IV) other species of the R. longicrus species group. Divergence times, estimated using mitochondrial sequences, place the vicariance events among the four subclades in the middle to late Miocene epoch. Our results suggest that (1) South Chinese brown frogs originated due to a vicariance event separating them from the R. chensinensis species group at the time of the Geological movement (~18 million years ago, Ma) in southern Tibet and the Himalayan region; (2) the separation and speciation of R. maoershanensis from the R. japonica group occurred due to the dry climate at approximately 16 Ma; (3) South Chinese brown frogs migrated from South China to Japan at the time (~10.8 Ma) that the global sea-level fell and the East China Sea Shelf Basin was swamp facies, when a land gallery may have formed across the sea to connect the two areas; and (4) R. chaochiaoensis separated from other species of the R. longicrus species group during the uplift of the Tibetan Plateau at approximately 9.5 Ma.
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Affiliation(s)
- Yu Zhou
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
- Feline Research Center of the Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
| | - Sirui Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hedan Zhu
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Pipeng Li
- College of Life Sciences, Shenyang Normal University, Shenyang, Liaoning, China
- * E-mail: (PL); (BY); (JM)
| | - Baotian Yang
- College of Life Sciences, Shenyang Normal University, Shenyang, Liaoning, China
- * E-mail: (PL); (BY); (JM)
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
- Feline Research Center of the Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
- * E-mail: (PL); (BY); (JM)
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Liu QS, Yan SZ, Chen SL. Further resolving the phylogeny of Myxogastria (slime molds) based on COI and SSU rRNA genes. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795414110076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Vakurin AA, Kartavtseva IV, Korablev VP, Pavlenko MV. Some features of cytogenetic differentiation of striped hamsters, Cricetulus barabensis and Cricetulus pseudogriseus (Rodentia, Cricetidae). BIOL BULL+ 2014. [DOI: 10.1134/s1062359014090088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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RETRACTED: Molecular identification and phylogeny of Channa species from Indo-Myanmar biodiversity hotspots using mitochondrial COI gene sequences. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Kartavtsev YP, Rozhkovan KV, Masalkova NA. Phylogeny based on two mtDNA genes (Co-1, Cyt-B) among Sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish in the Russian Far East. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2225-40. [PMID: 25431818 DOI: 10.3109/19401736.2014.984164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The average scores of p-distances at Co-1 and Cyt-b genes revealed a pattern of increased nucleotide diversity for four categories: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores for Co-1 genes were following: (1) 0.24 ± 0.19% (n = 66), (2) 1.54 ± 0.27% (n = 33), (3) 11.57 ± 0.24% (n = 42), and (4) 12.91 ± 0.16% (n = 102); while for Cyt-b genes, those values were (1) 1.92 ± 0.55% (n = 24), (2) 8.19 ± 0.09% (n = 812), (3) 15.42 ± 0.07% (n = 1573), and (4) 23.13 ± 0.19% (n = 211). A concordant increase in the distance score, as the rank of taxa grows, with the minimum at intraspecies level substantiates the concept that speciation in the order Scorpaeniformes mostly follows a geographic mode. Phylogenetic trees for 40 sequences of scorpionfish and four other fishes belonging to Actinopterigii were developed using Co-1 gene and four different analytical approaches: Bayesian, ML, MP, and NJ. Resolution of the Co-1 trees for the three genera that included different species branches was quite distinct in all approaches. Intrafamily branching for Cyt-b in Cottidae was also supported by all four kinds of trees but only for less numerous genera in the research.
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Affiliation(s)
- Yuri Phedorovich Kartavtsev
- a A.V. Zhirmunsky Institute of Marine Biology , Vladivostok , Russian Federation .,b Far Eastern Federal University, Vladivostok, Russian Federation , and
| | | | - Natalya A Masalkova
- a A.V. Zhirmunsky Institute of Marine Biology , Vladivostok , Russian Federation
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Di Lellis MA, Sereda S, Geißler A, Picot A, Arnold P, Lang S, Troschinski S, Dieterich A, Hauffe T, Capowiez Y, Mazzia C, Knigge T, Monsinjon T, Krais S, Wilke T, Triebskorn R, Köhler HR. Phenotypic diversity, population structure and stress protein-based capacitoring in populations of Xeropicta derbentina, a heat-tolerant land snail species. Cell Stress Chaperones 2014; 19:791-800. [PMID: 24609822 PMCID: PMC4389839 DOI: 10.1007/s12192-014-0503-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/03/2014] [Accepted: 02/04/2014] [Indexed: 11/27/2022] Open
Abstract
The shell colour of many pulmonate land snail species is highly diverse. Besides a genetic basis, environmentally triggered epigenetic mechanisms including stress proteins as evolutionary capacitors are thought to influence such phenotypic diversity. In this study, we investigated the relationship of stress protein (Hsp70) levels with temperature stress tolerance, population structure and phenotypic diversity within and among different populations of a xerophilic Mediterranean snail species (Xeropicta derbentina). Hsp70 levels varied considerably among populations, and were significantly associated with shell colour diversity: individuals in populations exhibiting low diversity expressed higher Hsp70 levels both constitutively and under heat stress than those of phenotypically diverse populations. In contrast, population structure (cytochrome c oxidase subunit I gene) did not correlate with phenotypic diversity. However, genetic parameters (both within and among population differences) were able to explain variation in Hsp70 induction at elevated but non-pathologic temperatures. Our observation that (1) population structure had a high explanatory potential for Hsp70 induction and that (2) Hsp70 levels, in turn, correlated with phenotypic diversity while (3) population structure and phenotypic diversity failed to correlate provides empirical evidence for Hsp70 to act as a mediator between genotypic variation and phenotype and thus for chaperone-driven evolutionary capacitance in natural populations.
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Affiliation(s)
- Maddalena A. Di Lellis
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Sergej Sereda
- />Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, D-35392 Giessen, Germany
| | - Anna Geißler
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Adrien Picot
- />Laboratory of Ecotoxicology (LEMA), EA 3222 PRES Normandie, Le Havre University, 25 Rue Philippe Lebon, F-76058 Le Havre Cedex, France
| | - Petra Arnold
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Stefanie Lang
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Sandra Troschinski
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Andreas Dieterich
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Torsten Hauffe
- />Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, D-35392 Giessen, Germany
| | - Yvan Capowiez
- />Université d’Avignon et des Pays de Vaucluse, Laboratoire de Toxicologie Environnementale, UMR 406 UAPV/INRA, Domaine St Paul, Site Agroparc, F-84914 Avignon Cedex 9, France
| | - Christophe Mazzia
- />IMBE UMR 7263, Institut Mediterranéen de Biodiversité et d’Ecologie marine et continentale, Université d’Avignon et des Pays de Vaucluse, Pole Agrosciences, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon cedex 9, France
| | - Thomas Knigge
- />Laboratory of Ecotoxicology (LEMA), EA 3222 PRES Normandie, Le Havre University, 25 Rue Philippe Lebon, F-76058 Le Havre Cedex, France
| | - Tiphaine Monsinjon
- />Laboratory of Ecotoxicology (LEMA), EA 3222 PRES Normandie, Le Havre University, 25 Rue Philippe Lebon, F-76058 Le Havre Cedex, France
| | - Stefanie Krais
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
| | - Thomas Wilke
- />Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, D-35392 Giessen, Germany
| | - Rita Triebskorn
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
- />Steinbeis-Transfer Center Ecotoxicology and Ecophysiology Rottenburg, Blumenstr. 13, D-72108 Rottenburg, Germany
| | - Heinz-R. Köhler
- />Animal Physiological Ecology, Institute of Evolution and Ecology, Tübingen University, Konrad-Adenauer-Str. 20, D-72072 Tübingen, Germany
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Bachevskaja LT, Pereverzeva VV, Ivanova GD, Agapova GA. Nucleotide variation in the mitochondrial DNA cytochrome oxidase 1 gene in the Siberian sucker (Catostomus catostomus rostratus) from Kolyma River. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414100019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Turanov SV, Kartavtsev YP, Lipinsky VV, Zemnukhov VV, Balanov AA, Lee YH, Jeong D. DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups. ACTA ACUST UNITED AC 2014; 27:1188-209. [DOI: 10.3109/19401736.2014.945525] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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22
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Zhou N, Shen H, Chen C, Sun B, Zheng P, Wang C. Genetic structure of Onchidium "struma" (Mollusca: Gastropoda: Eupulmonata) from the coastal area of China based on mtCO I. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1319-23. [PMID: 25103423 DOI: 10.3109/19401736.2014.945575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The genetic diversity and population genetic structure of Onchidium "struma" were investigated using mitochondrial cytochrome c oxidase subunit I (CO I) gene sequences. A total of 240 individuals representing 10 collection sites from across a large portion of its known range were included in the analysis. Overall, 42 haplotypes were defined and 97 polymorphic sites were observed. The O. "struma" populations had high haplotype diversity (0.9280) and nucleotide diversity (0.0404). We inferred that the early maturity and extensive survival habitat led to high genetic diversity of O. "struma" populations in China. Bayesian analysis and SAMOVA analysis showed significant genetic differentiation among populations and all populations were divided into two groups, (HK and HN) versus (GY, DF, CX, CN, ND and XM). The Mantel test revealed no significant correlation between geographic distance and genetic distance (r = 0.251; p = 0.058). Restricted gene flow caused by a shorter term pelagic veliger stage and limited dispersal potential were inferred to result in genetic differentiation among populations based on nested analysis. HK population might be an invasive species by artificial transplantation.
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Affiliation(s)
- Na Zhou
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education, Shanghai Ocean University , Shanghai , China
| | - Heding Shen
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education, Shanghai Ocean University , Shanghai , China
| | - Cheng Chen
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education, Shanghai Ocean University , Shanghai , China
| | - Bianna Sun
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education, Shanghai Ocean University , Shanghai , China
| | - Pei Zheng
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education, Shanghai Ocean University , Shanghai , China
| | - Chengnuan Wang
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education, Shanghai Ocean University , Shanghai , China
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23
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Torgunakova OA, Egorova TA, Semenova SK. Comparative analysis of variability of three mitochondrial genes of cytochrome oxidase complex (cox1, cox2, and cox3) in wild and domestic carp (Cyprinus carpio L.). RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412120149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Zeng L, Wang J, Sheng J, Gu Q, Hong Y. Molecular characteristics of mitochondrial DNA and phylogenetic analysis of the loach (Misgurnus anguillicaudatus) from the Poyang Lake. ACTA ACUST UNITED AC 2012; 23:187-200. [PMID: 22651231 DOI: 10.3109/19401736.2012.668893] [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 goal of our study was to investigate the molecular characteristics of mitochondrial DNA (mtDNA) and phylogenetic construction of the weather loach (Misgurnus anguillicaudatus) in Poyang Lake. The complete mitochondrial genome was 16,634 bp, and the gene order was identical to that of teleost fishes. Compared with the previous reported weather loach in China, there were numerous nucleotide substitutions and length polymorphisms on the structural genes of mitochondrial DNA in the loach from the Poyang Lake. The Phylogenetic tree indicated that the loach had its own molecular characteristics and was somewhat different from those in other regions of China. Fourteen unique haplotypes of the cytochrome b (cyt b) gene were obtained from 300 weather loaches. The Phylogenetic tree based on the cyt b gene showed that the loaches were substructured into two different populations in The Poyang Lake. Results indicated that the loaches in Poyang Lake not only showed the same phylogeny as the loaches in other areas of China, but also generated its own unique phylogenetic relationships.
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Affiliation(s)
- Liugen Zeng
- Key Laboratory of Molecular Biology and Genetic Engineering in Jiangxi, College of Life Science and Food Engineering, Nanchang University, Nanchang, PR China
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25
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Barbanera F, Guerrini M, Beccani C, Forcina G, Anayiotos P, Panayides P. Conservation of endemic and threatened wildlife: Molecular forensic DNA against poaching of the Cypriot mouflon (Ovis orientalis ophion, Bovidae). Forensic Sci Int Genet 2012; 6:671-5. [DOI: 10.1016/j.fsigen.2011.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022]
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26
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Turanov SV, Kartavtsev YP, Zemnukhov VV. Molecular phylogenetic study of several eelpout fishes (Perciformes, Zoarcoidei) from Far Eastern seas on the basis of the nucleotide sequences of the mitochondrial cytochrome oxidase 1 gene (Co-1). RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412020159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Singh M, Lakra WS, Bahuguna SN, Kartavtsev YP. Cytochrome b gene sequence divergence of seven sisorid species of catfish genus Glyptothorax (siluriformes, sisoridae) from India. Mol Biol Rep 2011; 39:4275-82. [PMID: 21789484 DOI: 10.1007/s11033-011-1214-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 07/14/2011] [Indexed: 11/28/2022]
Abstract
Samples of seven Sisorid catfish species of the genus Glyptothorax (G. garhwali, G. dakpathari, G. brevipinnis, G. ngapang, G. granulus, G. ventrolineatus, and G. davissinghi) were collected from the Himalayan region and the Western Ghats of India. They were analyzed for the mitochondrial cytochrome b gene (Cyt b). Out of 1152 nucleotide positions analyzed, 269 (23.3%) were found to be variable and 235 (20.3%) were parsimoniously informative. The sequences showed 111 (9.6%) fourfold degenerate sites. The overall transition/transversion bias was R = 3.457. The average proportion of base substitutions measured as P-distance for all sequences of seven Glyptothorax species and other five species comprising four comparison groups was intraspecies, P = 0.17 ± 0.05%, intragenus, P = 10.75 ± 0.48%, intrafamily, P = 20.07 ± 1.43%, and intraorder, P = 21.10 ± 0.45%. Within the Glyptothorax genus maximum divergence was obtained among G. brevipinnis sequences, whereas the least divergence was obtained within G. davissinghi. The phylogenetic trees for 193 and 47 sequences of Sisorid catfishes together were developed using the Cyt b gene and four different analytical approaches: Bayesian (BA), neighbour-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML). The analysis revealed a monophyletic origin for the all investigated representatives of the genus Glyptothorax (99, 100, 99, and 73% support level in our BA, NJ, MP, and ML analyses respectively) and with some reservations for Sisoridae, which is the principal family investigated. The monophyletic origin of the two subfamilies of Sisorid catfish defined in the literature was partly also supported by molecular phylogenetic data.
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Affiliation(s)
- Mahender Singh
- National Bureau of Fish Genetic Resources, Lucknow, 226002, Uttra Pradesh, India.
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28
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Baird HP, Miller KJ, Stark JS. Evidence of hidden biodiversity, ongoing speciation and diverse patterns of genetic structure in giant Antarctic amphipods. Mol Ecol 2011; 20:3439-54. [PMID: 21733028 DOI: 10.1111/j.1365-294x.2011.05173.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Recent molecular research on Antarctic benthic organisms has challenged traditional taxonomic classifications, suggesting that our current perceptions of Antarctic biodiversity and species distributions must be thoroughly revised. Furthermore, genetic differentiation at the intraspecific level remains poorly understood, particularly in eastern Antarctica. We addressed these issues using DNA sequence data for two sibling amphipod species that could be collected on a circum-Antarctic scale: Eusirus perdentatus and Eusirus giganteus. Haplotype networks and Bayesian phylogenies based on mitochondrial (COI, CytB) and nuclear (ITS2) DNA provided strong evidence of multiple cryptic species of Eusirus, with several occurring in sympatry and at least one likely to have a true circum-Antarctic distribution. Within species, gene flow was often highly restricted, consistent with a brooding life history and in some cases suggestive of current or future allopatric speciation. Patterns of genetic structure were not always predictable: one cryptic species showed preliminary evidence of high genetic differentiation across ∼150 km in eastern Antarctica (F(ST) > 0.47, P < 0.01), yet another was remarkably homogenous across ∼5000 km (F(ST) = 0.00, P = 1.00). Genetic diversity also varied among cryptic species, independent of sample size (π = 0.00-0.99). These results indicate several hidden levels of genetic complexity in these Antarctic amphipods that are neither apparent from previous taxonomic or ecological studies nor predictable from their life history. Such genetic diversity and structure may reflect different modes of survival for Antarctic benthic organisms during historic glacial cycles, and/or subsequent re-establishment of populations on the shelf, and highlight our misunderstanding of Antarctic marine species diversity.
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Affiliation(s)
- Helena P Baird
- Private Bag 129, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia.
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29
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Kartavtsev YP. Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics. Mar Genomics 2011; 4:71-81. [DOI: 10.1016/j.margen.2011.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 01/26/2011] [Accepted: 02/23/2011] [Indexed: 11/15/2022]
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30
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Wang J, Shen T, Ju J, Yang G. The complete mitochondrial genome of the Chinese longsnout catfish Leiocassis longirostris (Siluriformes: Bagridae) and a time-calibrated phylogeny of ostariophysan fishes. Mol Biol Rep 2010; 38:2507-16. [PMID: 21104148 DOI: 10.1007/s11033-010-0388-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
The complete mitogenome sequence of the Chinese longsnout catfish Leiocassis longirostris was determined using long-polymerase chain reaction (long-PCR) and directly sequenced with primer walking method. The complete mtDNA was 16,534 bp in length and contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. Phylogenetic relationship of 15 ostariophysan fishes was reconstructed using Bayesian inference and maximum likelihood methods based on a total of 15,658 nucleotides from all the 13 protein-coding, two rRNA, and 22 tRNA genes, using recently developed models of rate autocorrelation, which resolved the phylogenetic relationship of the major ostariophysan lineages with a high statistical support. The present result was consistent with some previous molecular cladistic work which supported the grouping of (((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), Gonorynchiformes), outgroup). The Chinese longsnout catfish together with the Bagrid catfish (both from the same family Bagridae) had a closer affinity with Amblycipitidae than with other four analyzed catfish families. The relaxed molecular clock method incorporated into the program BEAST vl.5.3 was used to estimate divergence dates among ostariophysan lineages, which revealed that the major ostariophysan lineages diversified in the middle Jurassic (around 164.5 million years ago (Mya)) and the split of Leiocassis/Pseudobagrus occurred in the Oligocene to Miocene (8.9-25.1 Mya). The time-calibrated tree generated in this study would provide a powerful evolutionary tool for broad-scale comparative studies of the catfishes and the ostariophysan fishes.
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Affiliation(s)
- Jialian Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
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31
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A reappraisal of the evolution of Asian snakehead fishes (Pisces, Channidae) using molecular data from multiple genes and fossil calibration. Mol Phylogenet Evol 2010; 56:707-17. [PMID: 20359539 DOI: 10.1016/j.ympev.2010.03.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 03/18/2010] [Accepted: 03/23/2010] [Indexed: 11/22/2022]
Abstract
Freshwater snakehead fishes (Channidae) provide an interesting target for phylogenetic analysis for the following reasons, their unusual biology, potential for cryptic diversity and availability of a good fossil record. Here, a multi-locus molecular phylogeny was constructed and calibrated using two fossil dates to estimate divergence times within the family. Sampling aimed to explore interspecific divergence of Channa species across Southeast Asia and intra-specific variation where species possessed natural geographical ranges that were extensive. Results contradict divergence times estimated previously independently from single locus mitochondrial data or the fossil record and suggest that after divergence from African taxa 40-50 Ma, evolution of Asian snakeheads has been heavily influenced by multiple broad scale dispersal events across India and Southeast Asia. A similar pattern of divergence within multiple clades suggests that west-east dispersal was limited for many taxa during the Miocene. Deep intra-specific divergence was inferred for C. striata, indicating that long historical periods of isolation ( approximately 8Ma) have not resulted in the evolution of reproductive isolation within this species. Results support suggestions that C. marulia like fishes in northern Cambodia may constitute an undescribed species, and that Indian C. diplogramma warrants taxonomic recognition as being distinct from Southeast Asian C. micropeltes, with the two taxa last sharing a common ancestor in the mid- to late-Miocene.
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32
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Kim JK, Kim YH, Kim MJ, Park JY. Genetic diversity, relationships and demographic history of the small yellow croaker,Larimichthys polyactis(Pisces: Sciaenidae) from Korea and China inferred from mitochondrial control region sequence data. Anim Cells Syst (Seoul) 2010. [DOI: 10.1080/19768351003764973] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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33
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Sequence diversity at cytochrome oxidase 1 (Co-1) gene among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish of Russia Far East with phylogenetic and taxonomic insights. Genes Genomics 2009. [DOI: 10.1007/bf03191151] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Ryu JH, Kim JK, Park JY. Comparison of the genetic relationships and osteological aspects in six branchiostegid fish species (perciformes). Anim Cells Syst (Seoul) 2009. [DOI: 10.1080/19768354.2009.9647225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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35
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Radchenko OA, Chereshnev IA, Petrovskaya AV, Nazarkin MV, Chegodaeva EA. Nucleotide sequence variation of the mitochondrial COI gene in several eelpout species of the genus Zoarces (Zoarcidae, Pisces). RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408070077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Kartavtsev YP, Park TJ, Lee JS, Vinnikov KA, Ivankov VN, Sharina SN, Ponomarev AS. Phylogenetic inferences introduced on cytochrome b gene sequences data for six flatfish species (Teleostei, Pleuronectidae) and species synonymy between representatives of genera Pseudopleuronectes and Hippoglossoides from far eastern seas. RUSS J GENET+ 2008. [DOI: 10.1134/s102279540804011x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Ferreira KM, Lino e Silva O, Arias MC, Del Lama MA. Cytochrome-b variation in Apis mellifera samples and its association with COI-COII patterns. Genetica 2008; 135:149-55. [PMID: 18373204 DOI: 10.1007/s10709-008-9264-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 03/18/2008] [Indexed: 11/29/2022]
Abstract
Five Mbo I (Mbo-A, Mbo-M, Mbo-C(1), Mbo-C(2) and Mbo-C(3)) and Hinf I (Hinf-1 to Hinf-5) patterns were observed in Apis mellifera samples after restriction of a 485 bp fragment of the mitochondrial cytochrome-b (cyt-b) gene. Associating the cyt-b Restriction fragment length polymorphism (RFLP) pattern of each sample to its respective previously established COI-COII (Dra I sites) pattern, five restriction patterns (Mbo-C(1), Mbo-C(2), Mbo-C(3), Hinf-1 and Hinf-4) were observed in samples of maternal origin associated to the evolutionary branch C. No deletions or insertions were observed and the nucleotide substitution rate was estimated at 5.4%. Higher nucleotide diversity was observed among the branch C-haplotypes when compared with A and M lineages. Further studies are needed to confirm if the cyt-b + COI-COII haplotypes help to assign certain phylogeographic patterns to the branch C and to clarify phylogenetic relationships among A. mellifera subspecies.
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Affiliation(s)
- Kátia M Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo, Rodovia Washington Luís km 235, São Carlos, São Paulo, 13565.905, Brazil
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38
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Price BW, Barker NP, Villet MH. Patterns and processes underlying evolutionary significant units in the Platypleura stridula L. species complex (Hemiptera: Cicadidae) in the Cape Floristic Region, South Africa. Mol Ecol 2008; 16:2574-88. [PMID: 17561914 DOI: 10.1111/j.1365-294x.2007.03328.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cicadas have been shown to be useful organisms for examining the effects of distribution, plant association and geographical barriers on gene flow between populations. The cicadas of the Platypleura stridula species complex are restricted to the biologically diverse Cape Floristic Region (CFR) of South Africa. They are thus an excellent study group for elucidating the mechanisms by which hemipteran diversity is generated and maintained in the CFR. Phylogeographical analysis of this species complex using mitochondrial DNA Cytochrome Oxidase I (COI) and ribosomal 16S sequence data, coupled with preliminary morphological and acoustic data, resolves six clades, each of which has specific host-plant associations and distinct geographical ranges. The phylogeographical structure implies simultaneous or near-simultaneous radiation events, coupled with shifts in host-plant associations. When calibrated using published COI and 16S substitution rates typical for related insects, these lineages date back to the late Pliocene - early Pleistocene, coincident with vegetation change, altered drainage patterns and accelerated erosion in response to neotectonic crustal uplift and cyclic Pleistocene climate change, and glaciation-associated changes in climate and sea level.
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Affiliation(s)
- B W Price
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa.
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39
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Djong TH, Matsui M, Kuramoto M, Belabut DM, Sen YH, Nishioka M, Sumida M. Morphological divergence, reproductive isolating mechanism, and molecular phylogenetic relationships among Indonesia, Malaysia, and Japan populations of the Fejervarya limnocharis complex (Anura, Ranidae). Zoolog Sci 2008; 24:1197-212. [PMID: 18271636 DOI: 10.2108/zsj.24.1197] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 08/26/2007] [Indexed: 11/17/2022]
Abstract
In order to elucidate the taxonomic status of the Fejervarya limnocharis complex relative to Malaysia and Japan populations, morphological observations and molecular phylogenetic analysis were carried out using three populations from Indonesia (type locality), Malaysia, and Japan. In addition, we conducted histological and spermatogenic observations using hybrids among these populations. Principal component and cluster analyses demonstrated that these populations could be clearly separated from one another. Abnormal testes were found in the hybrids between the Japan and Indonesia populations and between the Japan and Malaysia populations, but testes of the controls and hybrids between the Malaysia and Indonesia populations were quite normal. The mean number of univalents per cell was 5.42, 4.58, and 0.20 in hybrids between the Indonesia and Japan populations, Malaysia and Japan populations, and Indonesia and Malaysia populations, respectively. Sequence divergences in 16S rRNA and Cyt b genes were 0-0.4% (xbar=0.2%) and 0.3-1.5% (xbar=1.0%), respectively, between the Malaysia and Indonesia populations, and 2.4-2.6% (xbar=2.5%) and 11.0-12.0% (xbar=11.5%) between the Japan population and F. limnocharis complex, including the Malaysia and Indonesia populations and F. multistriata from China. This study indicated that the Malaysia population and F. multistriata from China should be designated as a subspecies of topotypic F. limnocharis, and that the Japan population should be regarded as a distinct species.
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Affiliation(s)
- Tjong Hon Djong
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima 739-8526, Japan
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40
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Radchenko OA, Chereshnev IA, Nazarkin MV, Petrovskaya AV, Chegodaeva EA. Restriction fragment variation of the mitochondrial gene of cytochrome b in some taxa of the Eelpout Family (Pisces, Perciformes, Zoarcidae) from the northern Sea of Okhotsk. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408010122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Kartavtsev YP, Jung SO, Lee YM, Byeon HK, Lee JS. Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes. Gene 2007; 396:13-27. [PMID: 17434693 DOI: 10.1016/j.gene.2007.01.027] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 01/27/2007] [Accepted: 01/31/2007] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA (mtDNA) from the bullhead torrent catfish, Liobagrus obesus, was isolated by long-polymerase chain reaction (Long-PCR) with universal primers and was fully sequenced by primer working using flanking sequences. The complete mtDNA from L. obesus was 16,531 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, demonstrating a structure very similar to that of other bony fish. An analysis of the protein-coding genes revealed a statistically substantiated bias in (T+C): (A+G) content, supporting earlier findings regarding this peculiarity. As indicated by a chi-square test, the observed scores for pyrimidine and purine content were different from those expected assuming a 50:50 ratio: chi(2)=41.63, d.f.=5, p<0.000001 for three categories, including the 1st, 2nd, and 3rd codon positions. Further, there was a difference in nucleotide content between ND6 and the other 12 protein-coding genes in L. obesus. The values of p-distances, as summarized for different scales of evolutionary history at the Cyt b gene, revealed a clear pattern of increased nucleotide diversity at four levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intraorder. Scores of average p-distances of the four categories in catfish were (1) 1.59+/-0.54%, (2) 5.28+/-1.72% (3) 16.37+/-1.26%, and (4) 19.81+/-0.14%, respectively. These data support the hypothesis that speciation in the order Siluriformes, in most cases, follows a geographic mode through the accumulation of a numerous small genetic changes over a long time period. A phylogenetic tree for the bullhead torrent catfish and several other fish species belonging to the order Siluriformes was developed on the basis of respective Cyt b sequences (1138 bp); the analysis revealed a monophyletic origin for the five examined families. A species-specific clustering of sequences from single species was obtained, supporting additionally basic phylogenetic information for the catfish and the barcoding suitability of Cyt b sequence data. Lastly, one of the well-supported properties of our phylogenetic tree (99% repetition level in our analysis) was the monophyletic placement of all catfish (order Siluriformes) among other ray-finned fish of the class Actinopterigii. Also discussed herein are the aspects of phylogeny based on the 16S rRNA gene.
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Affiliation(s)
- Yuri P Kartavtsev
- Department of Chemistry, and the National Research Lab of Marine Molecular and Environmental Bioscience, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea
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Jungt SO, Lee YM, Kartavtsev Y, Park IS, Kim DS, Lee JS. The complete mitochondrial genome of the Korean soft-shelled turtle Pelodiscus sinensis (Testudines, Trionychidae). ACTA ACUST UNITED AC 2007; 17:471-83. [PMID: 17381049 DOI: 10.1080/10425170600760091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We isolated Korean soft-shelled turtle, Pelodiscus sinensis, mitochondrial DNA by long-polymerase chain reaction (long-PCR) with conserved primers and sequenced this mitochondrial genome (mitogenome) with primer walking using flanking sequences. The P. sinensis mitochondrial DNA has 17,042 bp and its structural organization is conserved compared to those of other reptiles and mammals. To unveil the phylogenetic relationship of the turtles, we used the NJ, MP, and ML analysis methods after inferring those sequences from the mitochondrial 16S rRNA gene. We also compared two P. sinensis variants from Korea and China using the mitochondrial genome. In this study, we report the basic characteristics of the P. sinensis mitochondrial genome, including structural organization and base composition of the rRNAs, tRNAs and protein-coding genes, as well as characteristics of tRNAs. These features are applicable for the study of phylogenetic relationships in turtles.
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Affiliation(s)
- Sang-Oun Jungt
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, Korea
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