1
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SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2
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Chen MY, Liang D, Zhang P. Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences. Genome Biol Evol 2018; 9:1998-2012. [PMID: 28830116 PMCID: PMC5737624 DOI: 10.1093/gbe/evx147] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2017] [Indexed: 12/12/2022] Open
Abstract
The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing "hard" polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life.
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Affiliation(s)
- Meng-Yun Chen
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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3
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Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia. Cladistics 2016; 33:295-332. [DOI: 10.1111/cla.12170] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Affiliation(s)
- John Gatesy
- Department of Biology University of California Riverside CA 92521 USA
| | - Robert W. Meredith
- Department of Biology and Molecular Biology Montclair State University Montclair NJ 07043 USA
| | - Jan E. Janecka
- Department of Biological Sciences Duquesne University Pittsburgh PA 15282 USA
| | - Mark P. Simmons
- Department of Biology Colorado State University Fort Collins CO 80523 USA
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA
| | - Mark S. Springer
- Department of Biology University of California Riverside CA 92521 USA
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4
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Arcila ML, Betizeau M, Cambronne XA, Guzman E, Doerflinger N, Bouhallier F, Zhou H, Wu B, Rani N, Bassett DS, Borello U, Huissoud C, Goodman RH, Dehay C, Kosik KS. Novel primate miRNAs coevolved with ancient target genes in germinal zone-specific expression patterns. Neuron 2014; 81:1255-1262. [PMID: 24583023 DOI: 10.1016/j.neuron.2014.01.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2013] [Indexed: 01/15/2023]
Abstract
Major nonprimate-primate differences in cortico-genesis include the dimensions, precursor lineages, and developmental timing of the germinal zones (GZs). microRNAs (miRNAs) of laser-dissected GZ compartments and cortical plate (CP) from embryonic E80 macaque visual cortex were deep sequenced. The CP and the GZ including ventricular zone (VZ) and outer and inner subcompartments of the outer subventricular zone (OSVZ) in area 17 displayed unique miRNA profiles. miRNAs present in primate, but absent in rodent, contributed disproportionately to the differential expression between GZ subregions. Prominent among the validated targets of these miRNAs were cell-cycle and neurogenesis regulators. Coevolution between the emergent miRNAs and their targets suggested that novel miRNAs became integrated into ancient gene circuitry to exert additional control over proliferation. We conclude that multiple cell-cycle regulatory events contribute to the emergence of primate-specific cortical features, including the OSVZ, generated enlarged supragranular layers, largely responsible for the increased primate cortex computational abilities.
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Affiliation(s)
- Mary L Arcila
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Marion Betizeau
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Xiaolu A Cambronne
- Vollum Institute, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97068, USA
| | - Elmer Guzman
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Nathalie Doerflinger
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Frantz Bouhallier
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Hongjun Zhou
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Bian Wu
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Neha Rani
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Danielle S Bassett
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ugo Borello
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France
| | - Cyril Huissoud
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France; Service de gynécologie-obstétrique, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, 69004 Lyon, France
| | - Richard H Goodman
- Vollum Institute, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97068, USA
| | - Colette Dehay
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003 Lyon, France.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Department Cellular Molecular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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5
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Lin J, Chen G, Gu L, Shen Y, Zheng M, Zheng W, Hu X, Zhang X, Qiu Y, Liu X, Jiang C. Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate. Mol Phylogenet Evol 2013; 71:193-200. [PMID: 24333622 DOI: 10.1016/j.ympev.2013.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 11/25/2013] [Accepted: 12/02/2013] [Indexed: 11/26/2022]
Abstract
Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly.
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Affiliation(s)
- Jiannan Lin
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Guangfeng Chen
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchangzhong Rd, Shanghai 200072, China.
| | - Liang Gu
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Yuefeng Shen
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Meizhu Zheng
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Weisheng Zheng
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Xinjie Hu
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Xiaobai Zhang
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
| | - Yu Qiu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchangzhong Rd, Shanghai 200072, China.
| | - Xiaoqing Liu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchangzhong Rd, Shanghai 200072, China.
| | - Cizhong Jiang
- Shanghai Tenth People's Hospital, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.
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Hu JY, Zhang YP, Yu L. Summary of Laurasiatheria (mammalia) phylogeny. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2013; 33:E65-74. [PMID: 23266984 DOI: 10.3724/sp.j.1141.2012.e05-06e65] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.
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7
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Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. A phylogenetic blueprint for a modern whale. Mol Phylogenet Evol 2012; 66:479-506. [PMID: 23103570 DOI: 10.1016/j.ympev.2012.10.012] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/10/2012] [Accepted: 10/12/2012] [Indexed: 11/16/2022]
Abstract
The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti - toothed whales), and others that batch feed using racks of baleen (Mysticeti - baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.
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Affiliation(s)
- John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA.
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8
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Resolution of the laurasiatherian phylogeny: Evidence from genomic data. Mol Phylogenet Evol 2012; 64:685-9. [DOI: 10.1016/j.ympev.2012.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 04/03/2012] [Accepted: 04/17/2012] [Indexed: 11/17/2022]
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9
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Voloch CM, Schrago CG. Impact of the partitioning scheme on divergence times inferred from Mammalian genomic data sets. Evol Bioinform Online 2012; 8:207-18. [PMID: 22654486 PMCID: PMC3362329 DOI: 10.4137/ebo.s9627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Data partitioning has long been regarded as an important parameter for phylogenetic inference. The division of heterogeneous multigene data sets into partitions with similar substitution patterns is known to increase the performance of probabilistic phylogenetic methods. However, the effect of the partitioning scheme on divergence time estimates has generally been ignored. To investigate the impact of data partitioning on the estimation of divergence times, we have constructed two genomic data sets. The first one with 15 nuclear genes comprising 50,928 bp were selected from the OrthoMam database; the second set was composed of complete mitochondrial genomes. We studied two partitioning schemes: concatenated supermatrices and partitioned gene analysis. We have also measured the impact of taxonomic sampling on the estimates. After drawing divergence time inferences using the uncorrelated relaxed clock in BEAST, we have compared the age estimates between the partitioning schemes. Our results show that, in general, both schemes resulted in similar chronological estimates, however the concatenated data sets were more efficient than the partitioned ones in attaining suitable effective sample sizes.
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Affiliation(s)
- Carolina M Voloch
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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10
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Zhou X, Xu S, Xu J, Chen B, Zhou K, Yang G. Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals. Syst Biol 2012; 61:150-64. [PMID: 21900649 PMCID: PMC3243735 DOI: 10.1093/sysbio/syr089] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 04/06/2011] [Accepted: 06/23/2011] [Indexed: 11/24/2022] Open
Abstract
Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian mammals with draft genome sequences were reconstructed based on 1608 exons (2,175,102 bp). Our reconstructions resolve the interordinal relationships within Laurasiatheria and corroborate the clades Scrotifera, Fereuungulata, and Cetartiodactyla. Furthermore, we tested alternative topologies within Laurasiatheria, and among alternatives for the phylogenetic position of Perissodactyla, a sister-group relationship with Cetartiodactyla receives the highest support. Thus, Pegasoferae (Perissodactyla + Carnivora + Pholidota + Chiroptera) does not appear to be a natural group. Divergence time estimates from these genes were compared with published estimates for splits within Laurasiatheria. Our estimates were similar to those of several studies and suggest that the divergences among these orders occurred within just a few million years.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Junxiao Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Bingyao Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Meredith RW, Janečka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simão TLL, Stadler T, Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub NA, Springer MS, Murphy WJ. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 2011; 334:521-4. [PMID: 21940861 DOI: 10.1126/science.1211028] [Citation(s) in RCA: 919] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.
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Affiliation(s)
- Robert W Meredith
- Department of Biology, University of California, Riverside, CA 92521, USA
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12
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Arbiza L, Patricio M, Dopazo H, Posada D. Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol Evol 2011; 3:896-908. [PMID: 21824869 PMCID: PMC3175760 DOI: 10.1093/gbe/evr080] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
At a genomic scale, the patterns that have shaped molecular evolution are believed to be largely heterogeneous. Consequently, comparative analyses should use appropriate probabilistic substitution models that capture the main features under which different genomic regions have evolved. While efforts have concentrated in the development and understanding of model selection techniques, no descriptions of overall relative substitution model fit at the genome level have been reported. Here, we provide a characterization of best-fit substitution models across three genomic data sets including coding regions from mammals, vertebrates, and Drosophila (24,000 alignments). According to the Akaike Information Criterion (AIC), 82 of 88 models considered were selected as best-fit models at least in one occasion, although with very different frequencies. Most parameter estimates also varied broadly among genes. Patterns found for vertebrates and Drosophila were quite similar and often more complex than those found in mammals. Phylogenetic trees derived from models in the 95% confidence interval set showed much less variance and were significantly closer to the tree estimated under the best-fit model than trees derived from models outside this interval. Although alternative criteria selected simpler models than the AIC, they suggested similar patterns. All together our results show that at a genomic scale, different gene alignments for the same set of taxa are best explained by a large variety of different substitution models and that model choice has implications on different parameter estimates including the inferred phylogenetic trees. After taking into account the differences related to sample size, our results suggest a noticeable diversity in the underlying evolutionary process. All together, we conclude that the use of model selection techniques is important to obtain consistent phylogenetic estimates from real data at a genomic scale.
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Affiliation(s)
- Leonardo Arbiza
- Department of Biochemistry, Genetics, and Immunology, University of Vigo, Vigo, Spain
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Gunbin KV, Suslov VV, Turnaev II, Afonnikov DA, Kolchanov NA. Molecular evolution of cyclin proteins in animals and fungi. BMC Evol Biol 2011; 11:224. [PMID: 21798004 PMCID: PMC3162929 DOI: 10.1186/1471-2148-11-224] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 07/28/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi. RESULTS We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution. CONCLUSIONS The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.
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Affiliation(s)
- Konstantin V Gunbin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Valentin V Suslov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Igor I Turnaev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
- Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
- Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
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14
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Neuronal morphology in the African elephant (Loxodonta africana) neocortex. Brain Struct Funct 2010; 215:273-98. [DOI: 10.1007/s00429-010-0288-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 10/15/2010] [Indexed: 12/24/2022]
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