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Shen Y, Yang N, Liu Z, Chen Q, Li Y. Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes. Genomics 2020; 112:3511-3517. [PMID: 32105795 DOI: 10.1016/j.ygeno.2020.02.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022]
Abstract
The Acipenseriformes, as one of the earliest extant vertebrates, plays an important role in the evolution of fishes and even the whole vertebrates. Here we collected and analyzed all complete mitochondrial genomes of Acipenseriformes species. Phylogenetic analyses demonstrated that the polytomous branch included Acipenseridae and Polyodontidae formed five clades. The Polyodontidae clade and the Scaphirhynchus clade both were monophyletic group, whereas the Acipenser species and the Huso species both were polyphyletic group. The Bayesian divergence times showed that the origin time for Acipenseriformes was at 318.0 Mya, which was similar to the some previous results of 312.1 Mya, 346.9 Mya and 389.7 Mya. The result was in good consistent with the paleontological data available and the split time of the Pacific and Atlantic Oceans from the Jurassic to the Cretaceous (Laurasia splits in North America and Eurasia). The dN/dS ratios showed the evolutionary rates gradually slow down in five major Acipenseriformes clades from the Clade A (the Pacific sturgeons species) to Clade C (the genus Scaphirhynchus), which was related to the process of geographical formation.
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Affiliation(s)
- Yanjun Shen
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
| | - Na Yang
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Zhihao Liu
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Qiliang Chen
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yingwen Li
- Chongqing Key Laboratory of Animal Biology, School of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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2
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Nedoluzhko AV, Sharko FS, Tsygankova SV, Boulygina ES, Barmintseva AE, Krasivskaya AA, Ibragimova AS, Gruzdeva NM, Rastorguev SM, Mugue NS. Molecular phylogeny of one extinct and two critically endangered Central Asian sturgeon species (genus Pseudoscaphirhynchus) based on their mitochondrial genomes. Sci Rep 2020; 10:722. [PMID: 31959974 PMCID: PMC6971001 DOI: 10.1038/s41598-020-57581-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/03/2020] [Indexed: 01/12/2023] Open
Abstract
The enigmatic and poorly studied sturgeon genus Pseudoscaphirhynchus (Scaphirhynchinae: Acipenseridae) comprises three species: the Amu Darya shovelnose sturgeon (Pseudoscaphirhynchus kaufmanni (Bogdanow)), dwarf Amu Darya shovelnose sturgeon P. hermanni (Kessler), and Syr Darya shovelnose sturgeon (P. fedtschenkoi (Bogdanow). Two species - P. hermanni and P. kaufmanni - are critically endangered due to the Aral Sea area ecological disaster, caused by massive water use for irrigation to support cotton agriculture, subsequent pesticide pollution and habitat degradation. For another species - P. fedtschenkoi - no sightings have been reported since 1960-s and it is believed to be extinct, both in nature and in captivity. In this study, complete mitochondrial (mt) genomes of these three species of Pseudoscaphirhynchus were characterized using Illumina and Sanger sequencing platforms. Phylogenetic analyses showed the significant divergence between Amu Darya and Syr Darya freshwater sturgeons and supported the monophyletic origin of the Pseudoscaphirhynchus species. We confirmed that two sympatric Amu Darya species P. kaufmanni and P. hermanni form a single genetic cluster, which may require further morphological and genetic study to assess possible hybridization, intraspecific variation and taxonomic status and to develop conservation measures to protect these unique fishes.
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Affiliation(s)
- Artem V Nedoluzhko
- Nord University, Faculty of Biosciences and Aquaculture, Bodø, 8049, Norway.
| | - Fedor S Sharko
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 117312, Russia
| | | | | | - Anna E Barmintseva
- Russian Federal Research Institute of Fisheries and Oceanography, Moscow, 107140, Russia
| | | | | | | | | | - Nikolai S Mugue
- Russian Federal Research Institute of Fisheries and Oceanography, Moscow, 107140, Russia
- Koltzov Institute for Developmental Biology of the Russian Academy of Sciences, Moscow, 117808, Russia
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3
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Harter TS, Brauner CJ. The O 2 and CO 2 Transport System in Teleosts and the Specialized Mechanisms That Enhance Hb–O 2 Unloading to Tissues. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/bs.fp.2017.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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4
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Mugue N, Barmintseva A, Schepetov D, Shalgimbayeva G, Isbekov K. Complete mitochondrial genomes of the critically endangered Ship sturgeon Acipenser nudiventris from two seas. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:195-197. [PMID: 33644342 PMCID: PMC7871871 DOI: 10.1080/23802359.2016.1144103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Two complete mitochondrial genome sequences of ship sturgeon Acipenser nudiventris from the Caspian Sea and from Balkhash Lake (introduced from the Aral Sea during the last century) were determined by PCR-based sequencing method. The whole mitogenome sequences have been deposited in GenBank under accession numbers KU321568 and KU321569.
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Affiliation(s)
- Nikolai Mugue
- Laboratory of Molecular Genetics, Russian Institut for Fisheries and Oceanography (VNIRO), Moscow, Russian Federation.,Laboratory of Experimental Embryology, Koltzov Institute of Developmental Biology, Moscow, Russian Federation
| | - Anna Barmintseva
- Laboratory of Molecular Genetics, Russian Institut for Fisheries and Oceanography (VNIRO), Moscow, Russian Federation.,Laboratory of Experimental Embryology, Koltzov Institute of Developmental Biology, Moscow, Russian Federation
| | - Dmitry Schepetov
- Laboratory of Molecular Genetics, Russian Institut for Fisheries and Oceanography (VNIRO), Moscow, Russian Federation.,Laboratory of Experimental Embryology, Koltzov Institute of Developmental Biology, Moscow, Russian Federation
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5
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Jiang L, Ruan Q, Chen W. The complete mitochondrial genome sequence of the Xizang Plateau frog, Nanorana parkeri (Anura: Dicroglossidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3184-5. [PMID: 25758045 DOI: 10.3109/19401736.2015.1007327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Xizang Plateau frog (Nanorana parkeri) belongs to the family Dicroglossidae, which distributes in southern and eastern Xizang, southern-most Qinghai in China, high elevations of north-central Nepal, Himalayan Bhutan, northeastern Kashmir and India. In this study, the complete mitochondrial genome of N. parkeri was sequenced. The mitogenome was 17,837 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a non-coding control region (CR). As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. The overall base composition of the N. parkeri is A: 27.7 % A, T: 30.1 % T, C: 26.6% and G: 15.6%. The alignment of the Nanorana species CRs exhibited high genetic variability and rich A + T content. In comparison with the mtDNA sequences typical of vertebrates, a tandem duplication of the tRNA(Met) gene and a rearrangement of the tRNA(Thr), tRNA(Pro) and tRNA(Leu) (CUN) genes were found. The complete mitogenome of N. parkeri can provided an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.
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Affiliation(s)
- Lichun Jiang
- a Key Laboratory for Molecular Biology and Biopharmaceutics , School of Life Science and Technology and
| | - Qiping Ruan
- a Key Laboratory for Molecular Biology and Biopharmaceutics , School of Life Science and Technology and
| | - Wei Chen
- b Ecological Security and Protection Key Laboratory of Sichuan Province , Mianyang Normal University , Mianyang , Sichuan , P.R. China
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6
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Sallan LC. Major issues in the origins of ray-finned fish (Actinopterygii) biodiversity. Biol Rev Camb Philos Soc 2014; 89:950-71. [DOI: 10.1111/brv.12086] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/02/2014] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Lauren C. Sallan
- Department of Organismal Biology and Anatomy; University of Chicago; Chicago IL 60637 U.S.A
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 U.S.A
- Michigan Society of Fellows; University of Michigan; Ann Arbor MI 48109 U.S.A
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7
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Li C, Cheng L, Li JT, Lu CY, Wang Y, Sun XW. Complete mitochondrial genome of sterlet (Acipenser ruthenus). MITOCHONDRIAL DNA 2013; 26:259-60. [PMID: 24021000 DOI: 10.3109/19401736.2013.823188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of sterlet (Acipenser ruthenus) was determined in this study. The mitogenome is 16,790 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (the control region and the putative origin of the light strand replication) with a typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand is 30.26% for A, 29.00% for C, 16.23% for G and 24.51% for T, with a slight AT bias of 54.77%.
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Affiliation(s)
- Chao Li
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University , Harbin , P. R. China
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8
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Wang H, Zhang B, Li L, Chen J. The complete mitochondrial genome of the Acipenser schrenckii (Acipenseridae: Acipenser). ACTA ACUST UNITED AC 2013; 26:137-8. [DOI: 10.3109/19401736.2013.815174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Hui Wang
- School of Life Science, Anhui University, Hefei, Anhui, China and
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China
| | - Baowei Zhang
- School of Life Science, Anhui University, Hefei, Anhui, China and
| | - Linmiao Li
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China
| | - Jinping Chen
- Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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Chen XW, Jiang S, Shi ZY, Li Q, Xun XR, Guo DQ. Mitochondrial genome of the Siberian sturgeon Acipenser baerii. MITOCHONDRIAL DNA 2012; 23:120-2. [PMID: 22409751 DOI: 10.3109/19401736.2011.653804] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Siberian sturgeon Acipenser baerii had been determined. The total length of the mitogenome was 16,763 bp and had 13 protein-coding, 22 tRNA, and 2 rRNA genes. Except for the eight tRNA and Nd6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 30.3% A, 24.3% T, 29.1% C, 16.3% G, with an AT content of 54.6%. The DNA sequence of A. baerii shared 97.8, 97.6, 93.5, 91.6, 93.6, and 87.1% sequence homology with that of Acipenser sinensis, Acipenser gueldenstaedtii, Acipenser transmontanus, Acipenser dabryanus, Acipenser stellatus, and Polyodon spathula. Molecular data presented here provide a useful tool for evolutionary as well as population genetics studied.
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Affiliation(s)
- Xiao Wu Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, P.R. China
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11
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Robins JH, McLenachan PA, Phillips MJ, McComish BJ, Matisoo-Smith E, Ross HA. Evolutionary relationships and divergence times among the native rats of Australia. BMC Evol Biol 2010; 10:375. [PMID: 21126350 PMCID: PMC3014932 DOI: 10.1186/1471-2148-10-375] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 12/02/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. RESULTS Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. CONCLUSIONS Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.
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Affiliation(s)
- Judith H Robins
- Department of Anthropology and School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Recuero E, Cruzado-Cortes J, Parra-Olea G, Zamudio KR. Urban Aquatic Habitats and Conservation of Highly Endangered Species: The Case ofAmbystoma mexicanum(Caudata, Ambystomatidae). ANN ZOOL FENN 2010. [DOI: 10.5735/086.047.0401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Regan MD, Brauner CJ. The evolution of Root effect hemoglobins in the absence of intracellular pH protection of the red blood cell: insights from primitive fishes. J Comp Physiol B 2010; 180:695-706. [PMID: 20213180 DOI: 10.1007/s00360-010-0450-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 01/25/2010] [Accepted: 01/26/2010] [Indexed: 11/26/2022]
Abstract
The Root effect, a reduction in blood oxygen (O(2)) carrying capacity at low pH, is used by many fish species to maximize O(2) delivery to the eye and swimbladder. It is believed to have evolved in the basal actinopterygian lineage of fishes, species that lack the intracellular pH (pH(i)) protection mechanism of more derived species' red blood cells (i.e., adrenergically activated Na(+)/H(+) exchangers; betaNHE). These basal actinopterygians may consequently experience a reduction in blood O(2) carrying capacity, and thus O(2) uptake at the gills, during hypoxia- and exercise-induced generalized blood acidoses. We analyzed the hemoglobins (Hbs) of seven species within this group [American paddlefish (Polyodon spathula), white sturgeon (Acipenser transmontanus), spotted gar (Lepisosteus oculatus), alligator gar (Atractosteus spatula), bowfin (Amia calva), mooneye (Hiodon tergisus), and pirarucu (Arapaima gigas)] for their Root effect characteristics so as to test the hypothesis of the Root effect onset pH value being lower than those pH values expected during a generalized acidosis in vivo. Analysis of the haemolysates revealed that, although each of the seven species displayed Root effects (ranging from 7.3 to 40.5% desaturation of Hb with O(2), i.e., Hb O(2) desaturation), the Root effect onset pH values of all species are considerably lower (ranging from pH 5.94 to 7.04) than the maximum blood acidoses that would be expected following hypoxia or exercise (pH(i) 7.15-7.3). Thus, although these primitive fishes possess Hbs with large Root effects and lack any significant red blood cell betaNHE activity, it is unlikely that the possession of a Root effect would impair O(2) uptake at the gills following a generalized acidosis of the blood. As well, it was shown that both maximal Root effect and Root effect onset pH values increased significantly in bowfin over those of the more basal species, toward values of similar magnitude to those of most of the more derived teleosts studied to date. This is paralleled by the initial appearance of the choroid rete in bowfin, as well as a significant decrease in Hb buffer value and an increase in Bohr/Haldane effects, together suggesting bowfin as the most basal species capable of utilizing its Root effect to maximize O(2) delivery to the eye.
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Affiliation(s)
- Matthew D Regan
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada.
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14
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The transition in hemoglobin proton-binding characteristics within the basal actinopterygian fishes. J Comp Physiol B 2010; 180:521-30. [DOI: 10.1007/s00360-009-0438-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 12/05/2009] [Accepted: 12/08/2009] [Indexed: 10/20/2022]
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15
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The complete mitochondrial genome of the large-headed frog, Limnonectes bannaensis (Amphibia: Anura), and a novel gene organization in the vertebrate mtDNA. Gene 2009; 442:119-27. [PMID: 19397958 DOI: 10.1016/j.gene.2009.04.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2008] [Revised: 04/16/2009] [Accepted: 04/17/2009] [Indexed: 11/20/2022]
Abstract
We determined the complete nucleotide sequence of the mitochondrial (mt) genome of the large-headed frog, Limnonectes bannaensis (Amphibia, Anura) by using polymerase chain reaction (PCR). The entire mtDNA sequence is 16,867 bp in length with a novel case of tRNAs in vertebrates. This mt genome is characterized by three distinctive features: (1) a tandem duplication of tRNA(Met) gene is observed, (2) the tRNA(Ala), tRNA(Asn), tRNA(Cys) and tRNA(Glu) genes coded on the L-strand are absent from the L. bannaensis mtDNA, the tRNA(Cys) and tRNA(Glu) genes change into tRNA pseudogenes by reason of degenerative anticodon, and a noncoding sequence of 206 nt long (NC1) has replaced the original position of other two tRNAs, (3) besides NC1, another three noncoding spacers (NC2-4) longer than 50 bp are found in the broken WANCY region and the region NC3-ND5-NC4-ND6-PsiE-Cytb-CR of the new sequence. These features could be explained by a model of gene duplication and deletion. The new sequence data was used to assess the phylogenetic relationships among 25 species of Anura using neighbor-joining, Bayesian, and maximum likelihood methods, and the phylogenetic tree shows the rice frog Fejervarya limnocharis is closest to L. bannaensis in the study.
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16
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Kim DW, Kang A, Choi SH, Kim ZG, Kim WJ, Kim HC, Park HS. Evolutionary characterization of a highly repetitive sequence identified from the false killer whale (Pseudorca crassidens). Genes Genet Syst 2009; 84:185-9. [DOI: 10.1266/ggs.84.185] [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] Open
Affiliation(s)
- Dae-Won Kim
- Genome Research Center, Korea Research Institute of Bioscience and Biotechnology
| | - Aram Kang
- Genome Research Center, Korea Research Institute of Bioscience and Biotechnology
- Department of Functional Genome, University of Science and Technology
| | - Sang-Haeng Choi
- Genome Research Center, Korea Research Institute of Bioscience and Biotechnology
| | - Zang Geun Kim
- Cetacean Research Institute, National Fisheries Research and Development Institute
| | - Woo-Jin Kim
- Biotechnology Research Institute, National Fisheries Research and Development Institute
| | - Hyung-Cheol Kim
- Genome Research Center, Korea Research Institute of Bioscience and Biotechnology
| | - Hong-Seog Park
- Genome Research Center, Korea Research Institute of Bioscience and Biotechnology
- Department of Functional Genome, University of Science and Technology
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17
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Hallström BM, Janke A. Gnathostome phylogenomics utilizing lungfish EST sequences. Mol Biol Evol 2008; 26:463-71. [PMID: 19029191 DOI: 10.1093/molbev/msn271] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The relationship between the Chondrichthyes (cartilaginous fishes), the Actinopterygii (ray-finned fishes), and the piscine Sarcopterygii (lobe-finned fishes) and how the Tetrapoda (four-limbed terrestrial vertebrates) are related to these has been a contentious issue for more than a century. A general consensus about the relationship of these vertebrate clades has gradually emerged among morphologists, but no molecular study has yet provided conclusive evidence for any specific hypothesis. In order to examine these relationships on the basis of more extensive sequence data, we have produced almost 1,000,000 bp of expressed sequence tags (ESTs) from the African marbled lungfish, Protopterus aethiopicus. This new data set yielded 771 transcribed nuclear sequences that had not been previously described. The lungfish EST sequences were combined with EST data from two cartilaginous fishes and whole genome data from an agnathan, four ray-finned fishes, and four tetrapods. Phylogenomic analysis of these data yielded, for the first time, significant maximum likelihood support for a traditional gnathostome tree with a split between the Chondrichthyes and remaining (bone) gnathostomes. Also, the sister group relationship between Dipnoi (lungfishes) and Tetrapoda received conclusive support. Previously proposed hypotheses, such as the monophyly of fishes, could be rejected significantly. The divergence time between lungfishes and tetrapods was estimated to 382-388 Ma by the current data set and six calibration points.
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Affiliation(s)
- Björn M Hallström
- Department of Cell and Organism Biology, Division of Evolutionary Molecular Systematics, University of Lund, Sweden.
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18
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Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2008; 49:586-97. [DOI: 10.1016/j.ympev.2008.08.020] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/16/2008] [Accepted: 08/28/2008] [Indexed: 11/20/2022]
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19
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Robins JH, McLenachan PA, Phillips MJ, Craig L, Ross HA, Matisoo-Smith E. Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Mol Phylogenet Evol 2008; 49:460-6. [PMID: 18725306 DOI: 10.1016/j.ympev.2008.08.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 04/20/2008] [Accepted: 08/01/2008] [Indexed: 11/20/2022]
Abstract
The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.
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Affiliation(s)
- Judith H Robins
- Department of Anthropology and Allan Wilson Centre for Molecular Ecology and Evolution, The University of Auckland, Auckland, New Zealand.
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20
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Historical presence of the sturgeon Acipenser sturio in the Rhône basin determined by the analysis of ancient DNA cytochrome b sequences. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9549-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Claiborne JB, Choe KP, Morrison-Shetlar AI, Weakley JC, Havird J, Freiji A, Evans DH, Edwards SL. Molecular detection and immunological localization of gill Na+/H+ exchanger in the dogfish (Squalus acanthias). Am J Physiol Regul Integr Comp Physiol 2007; 294:R1092-102. [PMID: 18094061 DOI: 10.1152/ajpregu.00718.2007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The dogfish (Squalus acanthias) can make rapid adjustments to gill acid-base transfers to compensate for internal acidosis/alkalosis. Branchial Na+/H+ exchange (NHE) has been postulated as one mechanism driving the excretion of H+ following acidosis. We have cloned gill cDNA that includes an open reading frame coding for a 770-residue protein most homologous (approximately 71%) to mammalian NHE2. RT-PCR revealed NHE2 transcripts predominantly in gill, stomach, rectal gland, intestine, and kidney. In situ hybridization with an antisense probe against NHE2 in gill sections revealed a strong mRNA signal from a subset of interlamellar and lamellae cells. We developed dogfish-specific polyclonal antibodies against NHE2 that detected a approximately 70-kDa protein in Western blots and immunologically recognized branchial cells having two patterns of protein expression. Cytoplasmic and apical NHE2 immunoreactivity were observed in cells coexpressing basolateral Na+-K+-ATPase. Other large ovoid cells more generally staining for NHE2 also were strongly positive for basolateral H+-ATPase. Gill mRNA levels for NHE2 and H+-ATPase did not change following systemic acidosis (as measured by quantitative PCR 2 h after a 1- or 2-meq/kg acid infusion). These data indicate that posttranslational adjustments of NHE2 and other transport systems (e.g., NHE3) following acidosis may be of importance in the short-term pH adjustment and net branchial H+ efflux observed in vivo. NHE2 may play multiple roles in the gills, involved with H+ efflux from acid-secreting cells, basolateral H+ reabsorption for pHi regulation, and in parallel with H+-ATPase for the generation of HCO3(-) in base-secreting cells.
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Affiliation(s)
- James B Claiborne
- Department of Biology, Georgia Southern University, Statesboro, GA 30460, USA.
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Metcalf VJ, George PM, Brennan SO. Lungfish albumin is more similar to tetrapod than to teleost albumins: Purification and characterisation of albumin from the Australian lungfish, Neoceratodus forsteri. Comp Biochem Physiol B Biochem Mol Biol 2007; 147:428-37. [DOI: 10.1016/j.cbpb.2007.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 02/21/2007] [Accepted: 02/21/2007] [Indexed: 11/25/2022]
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Mallatt J, Winchell CJ. Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star. Mol Phylogenet Evol 2007; 43:1005-22. [PMID: 17276090 DOI: 10.1016/j.ympev.2006.11.023] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 10/27/2006] [Accepted: 11/22/2006] [Indexed: 01/08/2023]
Abstract
This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the approximately 45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and 'vertebrates plus cephalochordates'; and (2) lungfishes are the closest living relatives of tetrapods.
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Affiliation(s)
- Jon Mallatt
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Peng Z, Ludwig A, Wang D, Diogo R, Wei Q, He S. Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes). Mol Phylogenet Evol 2007; 42:854-62. [PMID: 17158071 DOI: 10.1016/j.ympev.2006.09.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2006] [Revised: 09/11/2006] [Accepted: 09/18/2006] [Indexed: 11/28/2022]
Affiliation(s)
- Zuogang Peng
- Laboratory of Fish Phylogenetics and Biogeography, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Dijkstra JM, Katagiri T, Hosomichi K, Yanagiya K, Inoko H, Ototake M, Aoki T, Hashimoto K, Shiina T. A third broad lineage of major histocompatibility complex (MHC) class I in teleost fish; MHC class II linkage and processed genes. Immunogenetics 2007; 59:305-21. [PMID: 17318646 DOI: 10.1007/s00251-007-0198-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 01/09/2007] [Indexed: 10/23/2022]
Abstract
Most of the previously studied teleost MHC class I molecules can be classified into two broad lineages: "U" and "Z/ZE." However, database reports on genes in cyprinid and salmonid fishes show that there is a third major lineage, which lacks detailed analysis so far. We designated this lineage "L" because of an intriguing linkage characteristic. Namely, one zebrafish L locus is closely linked with MHC class II loci, despite the extensively documented nonlinkage of teleost class I with class II. The L lineage consists of highly variable, nonclassical MHC class I genes, and has no apparent orthologues outside teleost fishes. Characteristics that distinguish the L lineage from most other MHC class I are (1) absence of two otherwise highly conserved tryptophan residues W51 and W60 in the alpha1 domain, (2) a low GC content of the alpha1 and alpha2 exons, and (3) an HINLTL motif including a possible glycosylation site in the alpha3 domain. In rainbow trout (Oncorhynchus mykiss) we analyzed several intact L genes in detail, including their genomic organization and transcription pattern. The gene Onmy-LAA is quite different from the genes Onmy-LBA, Onmy-LCA, Onmy-LDA, and Onmy-LEA, while the latter four are similar and categorized as "Onmy-LBA-like." Whereas the Onmy-LAA gene is organized like a canonical MHC class I gene, the Onmy-LBA-like genes are processed and lack all introns except intron 1. Onmy-LAA is predominantly expressed in the intestine, while the Onmy-LBA-like transcripts display a rather homogeneous tissue distribution. To our knowledge, this is the first description of an MHC class I lineage with multiple copies of processed genes, which are intact and transcribed. The present study significantly improves the knowledge of MHC class I variation in teleosts.
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Sasaki T, Sato T, Miura S, Bwathondi POJ, Ngatunga BP, Okada N. Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught in Tanzania. Gene 2006; 389:73-9. [PMID: 17113246 DOI: 10.1016/j.gene.2006.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 09/11/2006] [Accepted: 09/22/2006] [Indexed: 10/24/2022]
Abstract
In recent years, a large number of individuals of the species Latimeria chalumnae, one of the living fossil coelacanths, have been landed off the coast of Tanzania. Although L. chalumnae specimens have also been landed at other localities in the western Indian Ocean, so far, viable populations of this species have been identified only at two localities, Comoros and South Africa. Therefore, the recent active catch off Tanzania suggests a new habitat for L. chalumnae. To examine the genetic background of the Tanzanian fish, we analyzed complete mtDNA sequences of two Tanzanian individuals (Kigombe-9 and Songo Mnara-1) collected from the north and south coasts of Tanzania. Using the recently reported criteria for six haplotypes established in a population genetic study for coelacanths living in the western Indian Ocean [Schartl, M., Hornung, U., Hissman, K., Schauer, J., Fricke, H., 2005. Relatedness among east African coelacanths. Nature 435, 901.], we characterized Songo Mnara-1 as haplotype 1 and Kigombe-9 as haplotype 5. We suggest that the Songo Mnara specimen is a member of the Comoran group, but was swept away by the South Equatorial current. The individual from Kigombe may be a member of an undiscovered population that exists near the boundary between Tanzania and Kenya. Further analysis using more than 19 individuals recently captured off the north coast of Tanzania will reveal whether a new population exists there. Our sequence data suggest additional variable sites in the mtDNA sequence that may define the population structure of coelacanths in the western Indian Ocean and also raise the possibility that the previously published Comoran coelacanth mtDNA sequence contains several critical errors including base changes and indels.
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Affiliation(s)
- Takeshi Sasaki
- Department of Evolutionary Biology and Biodiversity, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, 444-8585, Japan
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Andersen Ø, Aas TS, Skugor S, Takle H, van Nes S, Grisdale-Helland B, Helland SJ, Terjesen BF. Purine-induced expression of urate oxidase and enzyme activity in Atlantic salmon (Salmo salar). Cloning of urate oxidase liver cDNA from three teleost species and the African lungfish Protopterus annectens. FEBS J 2006; 273:2839-50. [PMID: 16759232 DOI: 10.1111/j.1742-4658.2006.05288.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The peroxisomal enzyme urate oxidase plays a pivotal role in the degradation of purines in both prokaryotes and eukaryotes. However, knowledge about the purine-induced expression of the encoding gene is lacking in vertebrates. These are the first published sequences of fish urate oxidase, which were predicted from PCR amplified liver cDNAs of Atlantic salmon (Salmo salar), Atlantic cod (Gadus morhua), Atlantic halibut (Hippoglossus hippoglossus) and African lungfish (Protopterus annectens). Sequence alignment of different vertebrate urate oxidases revealed amino acid substitutions of putative functional importance in the enzyme of chicken and lungfish. In the adult salmon, expression of urate oxidase mRNA predominated in liver, but was also identified in several nonhepatic organs including brain, but not in skeletal muscle and kidney. Juvenile salmon fed diets containing bacterial protein meal (BPM) rich in nucleic acids showed a significant increase in liver urate oxidase enzyme activity, and urea concentrations in plasma, muscle and liver were elevated. Whereas salmon fed the 18% BPM diet showed a nonsignificant increase in liver mRNA levels of urate oxidase compared with the 0% BPM-fed fish, no further increase in mRNA levels was found in fish receiving 36% BPM. The discrepancy between urate oxidase mRNA and enzyme activity was explained by rapid mRNA degradation or alternatively, post-translational control of the activity. Although variable plasma and liver levels of urate were detected, the substrate increased only slightly in 36% BPM-fed fish, indicating that the uricolytic pathway of Atlantic salmon is intimately regulated to handle high dietary purine levels.
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Affiliation(s)
- Øivind Andersen
- AKVAFORSK, Institute of Aquaculture Research AS, As, Norway.
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29
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Goricki S, Trontelj P. Structure and evolution of the mitochondrial control region and flanking sequences in the European cave salamander Proteus anguinus. Gene 2006; 378:31-41. [PMID: 16764998 DOI: 10.1016/j.gene.2006.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Revised: 04/18/2006] [Accepted: 04/20/2006] [Indexed: 10/24/2022]
Abstract
The European cave salamander Proteus anguinus Laurenti 1768 is one of the best-known subterranean animals, yet its evolutionary history and systematic relationships remain enigmatic. This is the first comprehensive study on molecular evolution within the taxon, using an mtDNA segment containing the control region (CR) and adjacent sequences. Two to seven tandem repeats of 24-32 bp were found in the intergenic spacer region (VNTR1), and three, four or six repeats, 59-77 bp each, in the 3' end of the CR (VNTR2). Different molecular mechanisms account for VNTR2 formation in different lineages of Proteus. The overall CR variation was lower than that of the spacer region, the 3' end of the cytb gene, or the tRNA genes. Individual genes and the concatenated non-repetitive sequences produced similar, well resolved maximum likelihood, Bayesian inference and parsimony trees. The numbers of repeat elements as well as the genealogy of the VNTR2 repeat units were mostly inconsistent with the groupings of the non-repetitive sequences. Different degrees of repeat array homogenization were detected in all major groups. Orthology was established for the first and the second VNTR2 elements of some populations. These two copies may therefore be used for analyses at the population level. The pattern of CR sequence variation points to strong genetic isolation of hydrographically separated populations. Genetic separation of the major groups of populations is incongruent with the current division into subspecies.
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Affiliation(s)
- Spela Goricki
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
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Rowe G, Harris DJ, Beebee TJC. Lusitania revisited: A phylogeographic analysis of the natterjack toad Bufo calamita across its entire biogeographical range. Mol Phylogenet Evol 2006; 39:335-46. [PMID: 16230033 DOI: 10.1016/j.ympev.2005.08.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 08/18/2005] [Accepted: 08/23/2005] [Indexed: 10/25/2022]
Abstract
Attempts to understand the current distributions of plants and animals require both historical and ecological information. Phylogeography has proved highly effective in elucidating historical events such as postglacial colonisations in north temperate zones. However, interesting questions still await resolution. Lusitanian distributions of fauna and flora in western Europe, for example, have puzzled biogeographers for more than 150 years. Lusitanian species have highly disjunct distributions in Ireland and in Iberia, often with few or no other populations inbetween. Despite much debate, no agreed explanation for Lusitanian distributions has yet emerged. We investigated the phylogeographic structure of one Lusitanian species, the natterjack toad Bufo calamita, using mitochondrial DNA control region sequences and allelic variation at eight microsatellite loci. Our results show that this amphibian must have survived in north European refugia, as well as in Iberia, during and since the last (Weichselian) glacial maximum around 20,000 years before present (BP). Subsequent local recolonisation after the Younger Dryas cooling around 11,000 years BP best explains the Lusitanian aspect of natterjack toad distribution.
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Affiliation(s)
- Graham Rowe
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
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31
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Bohl E, Lancaster P. Implementation of a Markov model for phylogenetic trees. J Theor Biol 2006; 239:324-33. [PMID: 16171829 DOI: 10.1016/j.jtbi.2005.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 07/04/2005] [Accepted: 08/01/2005] [Indexed: 11/27/2022]
Abstract
A recently developed mathematical model for the analysis of phylogenetic trees is applied to comparative data for 48 species. The model represents a return to fundamentals and makes no hypothesis with respect to the reversibility of the process. The species have been analysed in all subsets of three, and a measure of reliability of the results is provided. The numerical results of the computations on 17,296 triples of species are made available on the Internet. These results are discussed and the development of reliable tree structures for several species is illustrated. It is shown that, indeed, the Markov model is capable of considerably more interesting predictions than has been recognized to date.
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Affiliation(s)
- Erich Bohl
- Fakultät für Mathematik, Universität Konstanz, Postfach D 194, 78457 Konstanz, Germany.
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32
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Abstract
The phylogenetic relationships among deuterostome animals have been debated for many years, and a diversity of hypotheses have been proposed based on both morphological and molecular data. Here we have assembled sequences of 217 nuclear-encoded proteins to address specific questions concerning their relationships and times of origin. We recovered significant support for urochordates as the closest relative of vertebrates with an analysis of 59 proteins (17,400 amino acids) and suggest that the basal position of urochordates found in previous molecular studies may have been the result of long-branch attraction biases. Our results also support Ambulacraria, the pairing of hemichordates with echinoderms (nine proteins; 2,382 amino acids), and Cyclostomata, the pairing of lampreys with hagfish (25 proteins; 6,895 amino acids). In addition, 325 shared proteins (102,110 amino acids) were obtained from the complete genomes of six vertebrates and a urochordate for phylogenetic analysis and divergence time estimation. An evolutionary timescale was estimated using a local (Bayesian) molecular clock method. We found that most major lineages of deuterostomes arose prior to the Cambrian Explosion of fossils (approximately 520 MYA) and that several lineages had originated before periods of global glaciation in the Precambrian.
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Affiliation(s)
- Jaime E Blair
- NASA Astrobiology Institute and Department of Biology, The Pennsylvania State University, University Park, USA.
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Samuels AK, Weisrock DW, Smith JJ, France KJ, Walker JA, Putta S, Voss SR. Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes. Gene 2005; 349:43-53. [PMID: 15780978 DOI: 10.1016/j.gene.2004.12.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 11/11/2004] [Accepted: 12/22/2004] [Indexed: 12/01/2022]
Abstract
We report on a study that extended mitochondrial transcript information from a recent EST project to obtain complete mitochondrial genome sequence for 5 tiger salamander complex species (Ambystoma mexicanum, A. t. tigrinum, A. andersoni, A. californiense, and A. dumerilii). We describe, for the first time, aspects of mitochondrial transcription in a representative amphibian, and then use complete mitochondrial sequence data to examine salamander phylogeny at both deep and shallow levels of evolutionary divergence. The available mitochondrial ESTs for A. mexicanum (N=2481) and A. t. tigrinum (N=1205) provided 92% and 87% coverage of the mitochondrial genome, respectively. Complete mitochondrial sequences for all species were rapidly obtained by using long distance PCR and DNA sequencing. A number of genome structural characteristics (base pair length, base composition, gene number, gene boundaries, codon usage) were highly similar among all species and to other distantly related salamanders. Overall, mitochondrial transcription in Ambystoma approximated the pattern observed in other vertebrates. We inferred from the mapping of ESTs onto mtDNA that transcription occurs from both heavy and light strand promoters and continues around the entire length of the mtDNA, followed by post-transcriptional processing. However, the observation of many short transcripts corresponding to rRNA genes indicates that transcription may often terminate prematurely to bias transcription of rRNA genes; indeed an rRNA transcription termination signal sequence was observed immediately following the 16S rRNA gene. Phylogenetic analyses of salamander family relationships consistently grouped Ambystomatidae in a clade containing Cryptobranchidae and Hynobiidae, to the exclusion of Salamandridae. This robust result suggests a novel alternative hypothesis because previous studies have consistently identified Ambystomatidae and Salamandridae as closely related taxa. Phylogenetic analyses of tiger salamander complex species also produced robustly supported trees. The D-loop, used in previous molecular phylogenetic studies of the complex, was found to contain a relatively low level of variation and we identified mitochondrial regions with higher rates of molecular evolution that are more useful in resolving relationships among species. Our results show the benefit of using complete genome mitochondrial information in studies of recently and rapidly diverged taxa.
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Affiliation(s)
- Amy K Samuels
- University of Kentucky, Department of Biology, Lexington, KY 40506, USA.
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Zhang P, Zhou H, Liang D, Liu YF, Chen YQ, Qu LH. The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene 2005; 346:133-43. [PMID: 15716017 DOI: 10.1016/j.gene.2004.10.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 10/01/2004] [Accepted: 10/14/2004] [Indexed: 11/21/2022]
Abstract
In this study, we have determined the complete sequence of the mitochondrial genome of an Old World tree frog Polypedates megacephalus (Anura: Rhacophoridae) by using a long polymerase chain reaction (PCR) technique and shotgun strategy of sequencing. The entire mtDNA sequence is 16,473 nt long with a novel mitogenomic gene organization in amphibians. Unlike other neobatrachian frogs, the transfer ribonucleic acid (tRNA)-Leu(CUN) and tRNA-Thr genes exchange their positions in P. megacephalus and form a Thr-Leu(CUN)-Pro-Phe tRNA gene tetrad. Moreover, we found that the ATP8 gene was replaced by a noncoding sequence of 853 nt long and that the ND5 gene was absent in the new mitogenome. These peculiar features of P. megacephalus mtDNA were further studied among related anuran species by PCR amplification. The new sequence data was used to assess the phylogenetic relationships of the three living amphibian orders using neighbor-joining, maximum likelihood, and Bayesian methods. In agreement with most morphological studies, phylogenetic analyses of a whole mitochondrial genome data set suggest a close relationship between salamanders and frogs. Moreover, using a molecular clock-independent Bayesian approach for inferring dating information from molecular phylogenies, we have provided a rough timescale for living amphibian evolution. This timescale provides a working framework for future paleontological researches on amphibian evolution and improves our understanding of the evolutionary history of modern amphibians.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, Biotechnology Research Center, Zhongshan University, Guangzhou 510275, PR China
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