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Kitazoe Y, Hasegawa M, Tanaka M, Futami M, Futami J. Mitochondrial determinants of mammalian longevity. Open Biol 2017; 7:rsob.170083. [PMID: 29070610 PMCID: PMC5666079 DOI: 10.1098/rsob.170083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/30/2017] [Indexed: 12/18/2022] Open
Abstract
Current ageing theories are far from satisfactory because of the many determinants involved in ageing. The well-known rate-of-living theory assumes that the product (lifetime energy expenditure, LEE) of maximum lifespan (MLS) and mass-specific basal metabolic rate (msBMR) is approximately constant. Although this theory provides a significant inverse correlation between msBMR and MLS as a whole for mammals, it remains problematic for two reasons. First, several interspecies studies within respective orders (typically within rodents) have shown no inverse relationships between msBMR and MLS. Second, LEE values widely vary in mammals and birds. Here, to solve these two problems, we introduced a new quantity designated as mitochondrial (mt) lifetime energy output, mtLEO = MLS × mtMR, in place of LEE, by using the mt metabolic rate (mtMR) per mitochondrion. Thereby, we found that mtLEO values were distributed more narrowly than LEE ones, and strongly correlated with the four amino-acid variables (AAVs) of Ser, Thr and Cys contents and hydrophobicity of mtDNA-encoded membrane proteins (these variables were related to the stability of these proteins). Consequently, only these two mt items, mtMR and the AAVs, solved the above-mentioned problems in the rate-of-living theory, and thus extensively improved the correlation with MLS compared with that given by LEE.
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Affiliation(s)
- Yasuhiro Kitazoe
- Center of Medical Information Science, Kochi Medical School, Nankoku, Kochi 783-8505, Japan
| | - Masami Hasegawa
- Institute of Statistical Mathematics, Midori-cho 10-3, Tachikawa, Tokyo 190-8562, Japan
| | - Masashi Tanaka
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi, Tokyo 173-0015, Japan
| | - Midori Futami
- Department of Biomedical Engineering, Faculty of Engineering, Okayama University of Science, 1-1 Ridaicho, Okayama 700-0005, Japan
| | - Junichiro Futami
- Department of Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
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Kitazoe Y, Tanaka M. Evolution of mitochondrial power in vertebrate metazoans. PLoS One 2014; 9:e98188. [PMID: 24911874 PMCID: PMC4049578 DOI: 10.1371/journal.pone.0098188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/25/2014] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Basal metabolic rate (BMR) has a very strong body-mass (M) dependence in an individual animal group, and BMR per unit mass (msBMR) converges on a markedly narrow range even across major taxonomic groups. However, it is here a basic question in metazoan biology how much BMR per unit mitochondrion (mtBMR) changes, and then whether mtBMR can be related to the original molecular mechanism of action of mt-encoded membrane proteins (MMPs) playing a central role in cellular energy production. METHODOLOGY/PRINCIPAL FINDINGS Analyzing variations of amino-acid compositions of MMPs across 13 metazoan animal groups, incorporating 2022 sequences, we found a strong inverse correlation between Ser/Thr composition (STC) and hydrophobicity (HYD). A majority of animal groups showed an evolutionary pathway of a gradual increase in HYD and decrease in STC, whereas only the deuterostome lineage revealed a rapid decrease in HYD and increase in STC. The strongest correlations appeared in 5 large subunits (ND4, ND5, ND2, CO1, and CO3) undergoing dynamic conformational changes for the proton-pumping function. The pathway of the majority groups is well understood as reflecting natural selection to reduce mtBMR, since simply raising HYD in MMPs (surrounded by the lipid bilayer) weakens their mobility and strengthens their stability. On the other hand, the marked decrease in HYD of the deuterostome elevates mtBMR, but is accompanied with their instability heightening a turnover rate of mitochondria and then cells. Interestingly, cooperative networks of interhelical hydrogen-bonds between motifs involving Ser and Thr residues can enhance MMP stability. CONCLUSION/SIGNIFICANCE This stability enhancement lowers turnover rates of mitochondria/cells and may prolong even longevity, and was indeed founded by strong positive correlations of STC with both mtBMR and longevity. The lowest HYD and highest STC in Aves and Mammals are congruent with their very high mtBMR and long longevity.
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Affiliation(s)
- Yasuhiro Kitazoe
- Center of Medical Information Science, Kochi Medical School, Nankoku, Kochi, Japan
| | - Masashi Tanaka
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
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LIVEZEY BRADLEYC. Phylogenetics of modern shorebirds (Charadriiformes) based on phenotypic evidence: analysis and discussion. Zool J Linn Soc 2010. [DOI: 10.1111/j.1096-3642.2010.00635.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci U S A 2009; 106:8986-91. [PMID: 19416880 DOI: 10.1073/pnas.0900233106] [Citation(s) in RCA: 251] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. However, because convergence mimics shared ancestry and is not accommodated by current phylogenetic methods, it can strongly mislead phylogenetic inference when it does occur. Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions (primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny. The relevant sites generally evolved slowly but converged between ancient lineages of snakes and agamids. We estimate that approximately 44 of 113 predicted convergent changes distributed across all 13 mitochondrial protein-coding genes are expected to have arisen from nonneutral causes-a remarkably large number. Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution.
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Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates. PLoS One 2008; 3:e3343. [PMID: 18836526 PMCID: PMC2553178 DOI: 10.1371/journal.pone.0003343] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 09/12/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The mitochondrial (mt) gene tree of placental mammals reveals a very strong acceleration of the amino acid (AA) replacement rate and a change in AA compositional bias in the lineage leading to the higher primates (simians), in contrast to the nuclear gene tree. Whether this acceleration and compositional bias were caused by adaptive evolution at the AA level or directional mutation pressure at the DNA level has been vigorously debated. METHODOLOGY/PRINCIPAL FINDINGS Our phylogenetic analysis indicates that the rate acceleration in the simian lineage is accompanied by a marked increase in threonine (Thr) residues in the transmembrane helix regions of mt DNA-encoded proteins. This Thr increase involved the replacement of hydrophobic AAs in the membrane interior. Even after accounting for lack of independence due to phylogeny, a regression analysis reveals a statistical significant positive correlation between Thr composition and longevity in primates. CONCLUSION/SIGNIFICANCE Because crucial roles of Thr and Ser in membrane proteins have been proposed to be the formation of hydrogen bonds enhancing helix-helix interactions, the Thr increase detected in the higher primates might be adaptive by serving to reinforce stability of mt proteins in the inner membrane. The correlation between Thr composition in the membrane interior and the longevity of animals is striking, especially because some mt functions are thought to be involved in aging.
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O'Loughlin SM, Okabayashi T, Honda M, Kitazoe Y, Kishino H, Somboon P, Sochantha T, Nambanya S, Saikia PK, Dev V, Walton C. Complex population history of two Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change rather than human-mediated effects. J Evol Biol 2008; 21:1555-69. [PMID: 18800997 DOI: 10.1111/j.1420-9101.2008.01606.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anopheles dirus and Anopheles baimaii are closely related species which feed on primates, particularly humans, and transmit malaria in the tropical forests of mainland Southeast Asia. Here, we report an in-depth phylogeographic picture based on 269 individuals from 21 populations from mainland Southeast Asia. Analysis of 1537 bp of mtDNA sequence revealed that the population history of A. baimaii is far more complex than previously thought. An old expansion (pre-300 kyr BP) was inferred in northern India/Bangladesh with a wave of south-eastwards expansion arriving at the Thai border (ca 135-173 kyr BP) followed by leptokurtic dispersal very recently (ca 16 kyr BP) into peninsular Thailand. The long and complex population history of these anthropophilic species suggests their expansions are not in response to the relatively recent (ca 40 kyr BP) human expansions in mainland Southeast Asia but, rather, fit well with our understanding of Pleistocene climatic change there.
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Affiliation(s)
- S M O'Loughlin
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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Springer MS, Meredith RW, Eizirik E, Teeling E, Murphy WJ. Morphology and Placental Mammal Phylogeny. Syst Biol 2008; 57:499-503. [DOI: 10.1080/10635150802164504] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California
Riverside, CA 92521, USA; E-mail: (M.S.S.)
| | - Robert W. Meredith
- Department of Biology, University of California
Riverside, CA 92521, USA; E-mail: (M.S.S.)
| | - Eduardo Eizirik
- Faculdade de Biociencias, PUCRS
Porto Alegre, RS 90619-900, Brazil
| | - Emma Teeling
- School of Biological and Environmental Sciences, University College Dublin Belfield
Dublin, 4, Ireland
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University
College Station, TX 77843-4458, USA
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Abstract
Recent progress resolving the phylogenetic relationships of the major lineages of mammals has had a broad impact in evolutionary biology, comparative genomics and the biomedical sciences. Novel insights into the timing and historical biogeography of early mammalian diversification have resulted from a new molecular tree for placental mammals coupled with dating approaches that relax the assumption of the molecular clock. We highlight the numerous applications to come from a well-resolved phylogeny and genomic prospecting in multiple lineages of mammals, from identifying regulatory elements in mammalian genomes to assessing the functional consequences of mutations in human disease loci and those driving adaptive evolution.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Affiliation(s)
- Gerton Lunter
- Gerton Lunter () University of Oxford, Oxford, United Kingdom
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Kitazoe Y, Kishino H, Waddell PJ, Nakajima N, Okabayashi T, Watabe T, Okuhara Y. Robust time estimation reconciles views of the antiquity of placental mammals. PLoS One 2007; 2:e384. [PMID: 17440620 PMCID: PMC1849890 DOI: 10.1371/journal.pone.0000384] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 03/28/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Molecular studies have reported divergence times of modern placental orders long before the Cretaceous-Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution. METHODOLOGY/PRINCIPAL FINDINGS New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described. We used a variant of the multidimensional vector space (MVS) procedure to take account of possible convergent evolution. Numerical simulations of abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods. Application to complete mitochondrial genomes identified marked rate accelerations and decelerations, which are not obtained with current methods. The root of placental mammals is estimated to be approximately 18 million years more recent than when assuming a log Brownian motion model. Correcting the pairwise distances for convergent evolution using MVS lowers the age of the root about another 20 million years compared to using standard maximum likelihood tree branch lengths. These two procedures combined revise the root time of placental mammals from around 122 million years ago to close to 84 million years ago. As a result, the estimated distribution of molecular divergence times is broadly consistent with quantitative analysis of the North American fossil record and traditional morphological views. CONCLUSIONS/SIGNIFICANCE By including the dual effects of abrupt rate change and directly accounting for convergent evolution at the molecular level, these estimates provide congruence between the molecular results, paleontological analyses and morphological expectations. The programs developed here are provided along with sample data that reproduce the results of this study and are especially applicable studies using genome-scale sequence lengths.
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Affiliation(s)
- Yasuhiro Kitazoe
- Center of Medical Information Science, Kochi Medical School, Nankoku, Kochi, Japan.
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Okabayashi T, Kitazoe Y, Kishino H, Watabe T, Nakajima N, Okuhara Y, O'Loughlin S, Walton C. Core set approach to reduce uncertainty of gene trees. BMC Evol Biol 2006; 6:41. [PMID: 16712735 PMCID: PMC1508163 DOI: 10.1186/1471-2148-6-41] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Accepted: 05/20/2006] [Indexed: 11/18/2022] Open
Abstract
Background A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more closely related than interspecific ones, detailed information on the evolutionary process may be available by determining all the node sequences of trees and provide insight into functional constraints and adaptations. However, strong evolutionary correlations on a few lineages make this determination difficult as a whole, and the maximum parsimony (MP) method frequently allows a number of topologies with a same total branching length. Results Kitazoe et al. developed multidimensional vector-space representation of phylogeny. It converts additivity of evolutionary distances to orthogonality among the vectors expressing branches, and provides a unified index to measure deviations from the orthogoality. In this paper, this index is used to detect and exclude sequences with large deviations from orthogonality, and then selects a maximum subset ("core set") of sequences for which MP generates a single solution. Once the core set tree is formed whose all the node sequences are given, the excluded sequences are found to have basically two phylogenetic positions on this tree, respectively. Fortunately, since multiple substitutions are rare in intra-species sequences, the variance of nucleotide transitions is confined to a small range. By applying the core set approach to 38 partial env sequences of HIV-1 in a single patient and also 198 mitochondrial COI and COII DNA sequences of Anopheles dirus, we demonstrate how consistently this approach constructs the tree. Conclusion In the HIV dataset, we confirmed that the obtained core set tree is the unique maximum set for which MP proposes a single tree. In the mosquito data set, the fluctuation of nucleotide transitions caused by the sequences excluded from the core set was very small. We reproduced this core-set tree by simulation based on random process, and applied our approach to many sets of the obtained endpoint sequences. Consequently, the ninety percent of the endpoint sequences was identified as the core sets and the obtained node sequences were perfectly identical to the true ones.
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Affiliation(s)
- Takahisa Okabayashi
- Center of Medical Information Science, Kochi Medical School, Kochi University, Okoho-cho, Nankoku, Kochi 783-8505, Japan
| | - Yasuhiro Kitazoe
- Center of Medical Information Science, Kochi Medical School, Kochi University, Okoho-cho, Nankoku, Kochi 783-8505, Japan
| | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Teruaki Watabe
- Center of Medical Information Science, Kochi Medical School, Kochi University, Okoho-cho, Nankoku, Kochi 783-8505, Japan
| | - Noriaki Nakajima
- Center of Medical Information Science, Kochi Medical School, Kochi University, Okoho-cho, Nankoku, Kochi 783-8505, Japan
| | - Yoshiyasu Okuhara
- Center of Medical Information Science, Kochi Medical School, Kochi University, Okoho-cho, Nankoku, Kochi 783-8505, Japan
| | | | - Catherine Walton
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
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Marsh L. Evolution of Structural Shape in Bacterial Globin-Related Proteins. J Mol Evol 2006; 62:575-87. [PMID: 16612536 DOI: 10.1007/s00239-005-0025-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2005] [Accepted: 12/31/2005] [Indexed: 10/24/2022]
Abstract
The globin family of proteins has a characteristic structural pattern of helix interactions that nonetheless exhibits some variation. A simplified model for globin structural evolution was developed in which protein shape evolved by random change of contacts between helices. A conserved globin domain of 15 bacterial proteins representing four structural families was studied. Using a parsimony approach ancestral structural states could be reconstructed. The distribution of number of contact changes per site for a fixed topology tree fit a gamma distribution. Homoplasy was high, with multiple changes per site and no support for an invariant class of residue-residue contacts. Contacts changed more slowly than sequence. A phylogenetic reconstruction using a distance measure based on the proportion of shared contacts was generally consistent with a sequence-based phylogeny but not highly resolved. Contact pattern convergence between members of different globin family proteins could not be detected. Simulation studies indicated the convergence test was sensitive enough to have detected convergence involving only 10% of the contacts, suggesting a limit on the extent of selection for a specific contact pattern. Contact site methods may provide additional approaches to study the relationship between protein structure and sequence evolution.
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Affiliation(s)
- Lorraine Marsh
- Department of Biology, Long Island University, 1 University Plaza, Brooklyn, NY 11201, USA.
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Kriegs JO, Churakov G, Kiefmann M, Jordan U, Brosius J, Schmitz J. Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 2006; 4:e91. [PMID: 16515367 PMCID: PMC1395351 DOI: 10.1371/journal.pbio.0040091] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 01/23/2006] [Indexed: 11/30/2022] Open
Abstract
Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods, as well as directional mutation pressure, can produce molecular homoplasies, similar characteristics lacking common ancestors. Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics. By computationally scanning more than 160,000 chromosomal loci and judiciously selecting from only phylogenetically informative retroposons for experimental high-throughput PCR applications, we recovered 28 clear, independent monophyly markers that conclusively verify the earliest divergences in placental mammalian evolution. Using tests that take into account ancestral polymorphisms, multiple long interspersed elements and long terminal repeat element insertions provide highly significant evidence for the monophyletic clades Boreotheria (synonymous with Boreoeutheria), Supraprimates (synonymous with Euarchontoglires), and Laurasiatheria. More importantly, two retropositions provide new support for a prior scenario of early mammalian evolution that places the basal placental divergence between Xenarthra and Epitheria, the latter comprising all remaining placentals. Due to its virtually homoplasy-free nature, the analysis of retroposon presence/absence patterns avoids the pitfalls of other molecular methodologies and provides a rapid, unequivocal means for revealing the evolutionary history of organisms. The authors identified and sequenced retroposons in mammalian genomes. The presence and absence of these retroposons provided evolutionary markers from which the authors reconstructed the phylogenetic history of placental mammals.
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Affiliation(s)
- Jan Ole Kriegs
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Gennady Churakov
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Martin Kiefmann
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Ursula Jordan
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Jürgen Brosius
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Jürgen Schmitz
- 1Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, Münster, Germany
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van Rheede T, Bastiaans T, Boone DN, Hedges SB, de Jong WW, Madsen O. The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians. Mol Biol Evol 2005; 23:587-97. [PMID: 16291999 DOI: 10.1093/molbev/msj064] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Morphological data supports monotremes as the sister group of Theria (extant marsupials + eutherians), but phylogenetic analyses of 12 mitochondrial protein-coding genes have strongly supported the grouping of monotremes with marsupials: the Marsupionta hypothesis. Various nuclear genes tend to support Theria, but a comprehensive study of long concatenated sequences and broad taxon sampling is lacking. We therefore determined sequences from six nuclear genes and obtained additional sequences from the databases to create two large and independent nuclear data sets. One (data set I) emphasized taxon sampling and comprised five genes, with a concatenated length of 2,793 bp, from 21 species (two monotremes, six marsupials, nine placentals, and four outgroups). The other (data set II) emphasized gene sampling and comprised eight genes and three proteins, with a concatenated length of 10,773 bp or 3,669 amino acids, from five taxa (a monotreme, a marsupial, a rodent, human, and chicken). Both data sets were analyzed by parsimony, minimum evolution, maximum likelihood, and Bayesian methods using various models and data partitions. Data set I gave bootstrap support values for Theria between 55% and 100%, while support for Marsupionta was at most 12.3%. Taking base compositional bias into account generally increased the support for Theria. Data set II exclusively supported Theria, with the highest possible values and significantly rejected Marsupionta. Independent phylogenetic evidence in support of Theria was obtained from two single amino acid deletions and one insertion, while no supporting insertions and deletions were found for Marsupionta. On the basis of our data sets, the time of divergence between Monotremata and Theria was estimated at 231-217 MYA and between Marsupialia and Eutheria at 193-186 MYA. The morphological evidence for a basal position of Monotremata, well separated from Theria, is thus fully supported by the available molecular data from nuclear genes.
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Affiliation(s)
- Teun van Rheede
- Department of Biochemistry, Radboud University Nijmegen, Nijmegen, The Netherlands
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Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome Res 2005; 15:998-1006. [PMID: 15998912 PMCID: PMC1172044 DOI: 10.1101/gr.3493405] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2004] [Accepted: 05/03/2005] [Indexed: 11/25/2022]
Abstract
Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.
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Affiliation(s)
- Ali Bashir
- Bioinformatics Program, University of California San Diego, La Jolla, California 92093-0114, USA.
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