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Thomson MM, Fernández-García A. Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning. Virology 2011; 415:30-8. [PMID: 21507449 DOI: 10.1016/j.virol.2011.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/11/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
Subtype C is the most prevalent clade in the HIV-1 pandemic. Previous studies suggested that African HIV-1 subtype C lacks a well-defined phylogenetic structure. Here we show that, by sequential pruning of ambiguously positioned taxa, a well-defined intrasubtype C phylogenetic structure becomes apparent, with 52% African HIV-1 subtype C isolates analyzed in envelope sequences branching within 11 clusters, also supported in a tree of full-length genomes, and all with geographical associations. Among 46 viruses recently transmitted in South Africa, 70% branched within 7 clusters (41% in the largest one) and 15% additional isolates were intercluster recombinants. Choice of the outgroup sequence and inclusion of intrasubtype recombinant viruses in the analyses could greatly affect support of clusters. The identification of clusters comprising a large proportion of African HIV-1 subtype C viruses may have implications for the design of vaccines intended for use in areas where subtype C is prevalent.
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Affiliation(s)
- Michael M Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km. 2, Majadahonda, Madrid, Spain.
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Roos C, Zinner D, Kubatko LS, Schwarz C, Yang M, Meyer D, Nash SD, Xing J, Batzer MA, Brameier M, Leendertz FH, Ziegler T, Perwitasari-Farajallah D, Nadler T, Walter L, Osterholz M. Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys. BMC Evol Biol 2011; 11:77. [PMID: 21435245 PMCID: PMC3068967 DOI: 10.1186/1471-2148-11-77] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 03/24/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera. RESULTS Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing Piliocolobus/Procolobus and langur genera among colobines. Although insufficient data, homoplasy and incomplete lineage sorting might all have contributed to the discordance among gene trees, hybridization is favored as the main cause of the observed discordance. We propose that African colobines are paraphyletic, but might later have experienced female introgression from Piliocolobus/Procolobus into Colobus. In the late Miocene, colobines invaded Eurasia and diversified into several lineages. Among Asian colobines, Semnopithecus diverged first, indicating langur paraphyly. However, unidirectional gene flow from Semnopithecus into Trachypithecus via male introgression followed by nuclear swamping might have occurred until the earliest Pleistocene. CONCLUSIONS Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events. Our results also suggest that sex-specific dispersal patterns, promoted by a respective social organization of the species involved, can result in different hybridization scenarios.
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Affiliation(s)
- Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.
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Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol 2011; 9:e1000602. [PMID: 21423652 PMCID: PMC3057953 DOI: 10.1371/journal.pbio.1000602] [Citation(s) in RCA: 718] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Québec, Canada.
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Proteome evolution and the metabolic origins of translation and cellular life. J Mol Evol 2010; 72:14-33. [PMID: 21082171 DOI: 10.1007/s00239-010-9400-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 10/25/2010] [Indexed: 12/27/2022]
Abstract
The origin of life has puzzled molecular scientists for over half a century. Yet fundamental questions remain unanswered, including which came first, the metabolic machinery or the encoding nucleic acids. In this study we take a protein-centric view and explore the ancestral origins of proteins. Protein domain structures in proteomes are highly conserved and embody molecular functions and interactions that are needed for cellular and organismal processes. Here we use domain structure to study the evolution of molecular function in the protein world. Timelines describing the age and function of protein domains at fold, fold superfamily, and fold family levels of structural complexity were derived from a structural phylogenomic census in hundreds of fully sequenced genomes. These timelines unfold congruent hourglass patterns in rates of appearance of domain structures and functions, functional diversity, and hierarchical complexity, and revealed a gradual build up of protein repertoires associated with metabolism, translation and DNA, in that order. The most ancient domain architectures were hydrolase enzymes and the first translation domains had catalytic functions for the aminoacylation and the molecular switch-driven transport of RNA. Remarkably, the most ancient domains had metabolic roles, did not interact with RNA, and preceded the gradual build-up of translation. In fact, the first translation domains had also a metabolic origin and were only later followed by specialized translation machinery. Our results explain how the generation of structure in the protein world and the concurrent crystallization of translation and diversified cellular life created further opportunities for proteomic diversification.
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Sun G, Yang Z, Ishwar A, Huang J. Algal genes in the closest relatives of animals. Mol Biol Evol 2010; 27:2879-89. [PMID: 20627874 DOI: 10.1093/molbev/msq175] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The spread of photosynthesis is one of the most important but controversial topics in eukaryotic evolution. Because of massive gene transfer from plastids to the nucleus and because of the possibility that plastids have been lost in evolution, algal genes in aplastidic organisms often are interpreted as footprints of photosynthetic ancestors. These putative plastid losses, in turn, have been cited as support for scenarios involving the spread of plastids in broadscale eukaryotic evolution. Phylogenomic analyses identified more than 100 genes of possible algal origin in Monosiga, a unicellular species from choanoflagellates, a group considered to be the closest protozoan relatives of animals and to be primitively heterotrophic. The vast majority of these algal genes appear to be derived from haptophytes, diatoms, or green plants. Furthermore, more than 25% of these algal genes are ultimately of prokaryotic origin and were spread secondarily to Monosiga. Our results show that the presence of algal genes may be expected in many phagotrophs or taxa of phagotrophic ancestry and therefore does not necessarily represent evidence of plastid losses. The ultimate prokaryotic origin of some algal genes and their simultaneous presence in both primary and secondary photosynthetic eukaryotes either suggest recurrent gene transfer events under specific environments or support a more ancient origin of primary plastids.
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Affiliation(s)
- Guiling Sun
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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Pick K, Philippe H, Schreiber F, Erpenbeck D, Jackson D, Wrede P, Wiens M, Alié A, Morgenstern B, Manuel M, Wörheide G. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 2010; 27:1983-7. [PMID: 20378579 PMCID: PMC2922619 DOI: 10.1093/molbev/msq089] [Citation(s) in RCA: 262] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745–749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.
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Affiliation(s)
- K.S. Pick
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - H. Philippe
- Centre Robert-Cedergren, Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - F. Schreiber
- Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - D. Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - D.J. Jackson
- Department of Geobiology, Courant Research Center Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - P. Wrede
- Department of Applied Molecular Biology, Institute for Physiological Chemistry and Pathobiochemistry, Mainz, Germany
| | - M. Wiens
- Department of Applied Molecular Biology, Institute for Physiological Chemistry and Pathobiochemistry, Mainz, Germany
| | - A. Alié
- University Pierre & Marie Curie (UPMC), Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Department UMR7138 Systématique, Adaptation, Evolution. UPMC, Paris, France
| | - B. Morgenstern
- Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - M. Manuel
- University Pierre & Marie Curie (UPMC), Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Department UMR7138 Systématique, Adaptation, Evolution. UPMC, Paris, France
| | - G. Wörheide
- Department of Earth and Environmental Sciences, Palaeontology and Geobiology GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- Corresponding author: E-mail:
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Zhu J, Braun EL, Kohno S, Antenos M, Xu EY, Cook RW, Lin SJ, Moore BC, Guillette LJ, Jardetzky TS, Woodruff TK. Phylogenomic analyses reveal the evolutionary origin of the inhibin alpha-subunit, a unique TGFbeta superfamily antagonist. PLoS One 2010; 5:e9457. [PMID: 20209104 PMCID: PMC2832003 DOI: 10.1371/journal.pone.0009457] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 02/01/2010] [Indexed: 11/18/2022] Open
Abstract
Transforming growth factor-beta (TGFβ) homologues form a diverse superfamily that arose early in animal evolution and control cellular function through membrane-spanning, conserved serine-threonine kinases (RII and RI receptors). Activin and inhibin are related dimers within the TGFβ superfamily that share a common β-subunit. The evolution of the inhibin α-subunit created the only antagonist within the TGFβ superfamily and the only member known to act as an endocrine hormone. This hormone introduced a new level of complexity and control to vertebrate reproductive function. The novel functions of the inhibin α-subunit appear to reflect specific insertion-deletion changes within the inhibin β-subunit that occurred during evolution. Using phylogenomic analysis, we correlated specific insertions with the acquisition of distinct functions that underlie the phenotypic complexity of vertebrate reproductive processes. This phylogenomic approach presents a new way of understanding the structure-function relationships between inhibin, activin, and the larger TGFβ superfamily.
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Affiliation(s)
- Jie Zhu
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Satomi Kohno
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Monica Antenos
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Eugene Y. Xu
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Robert W. Cook
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - S. Jack Lin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Brandon C. Moore
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Louis J. Guillette
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Theodore S. Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Teresa K. Woodruff
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail:
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Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, Schmitz J. Rodent Evolution: Back to the Root. Mol Biol Evol 2010; 27:1315-26. [DOI: 10.1093/molbev/msq019] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Belinky F, Cohen O, Huchon D. Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol Biol Evol 2009; 27:441-51. [PMID: 19864469 DOI: 10.1093/molbev/msp263] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Insertions and deletions (indels) are considered to be rare evolutionary events, the analysis of which may resolve controversial phylogenetic relationships. Indeed, indel characters are often assumed to be less homoplastic than amino acid and nucleotide substitutions and, consequently, more reliable markers for phylogenetic reconstruction. In this study, we analyzed indels from over 1,000 metazoan orthologous genes. We studied the impact of different species sampling, ortholog data sets, lengths of included indels, and indel-coding methods on the resulting metazoan tree. Our results show that, similar to sequence substitutions, indels are homoplastic characters, and their analysis is sensitive to the long-branch attraction artifact. Furthermore, improving the taxon sampling and choosing a closely related outgroup greatly impact the phylogenetic inference. Our indel-based inferences support the Ecdysozoa hypothesis over the Coelomata hypothesis and suggest that sponges are a sister clade to other animals.
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Yip CW, Hon CC, Shi M, Lam TTY, Chow KYC, Zeng F, Leung FCC. Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses. INFECTION GENETICS AND EVOLUTION 2009; 9:1185-96. [PMID: 19800030 PMCID: PMC7106296 DOI: 10.1016/j.meegid.2009.09.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 08/09/2009] [Accepted: 09/24/2009] [Indexed: 11/24/2022]
Abstract
Severe Acute Respiratory Syndrome (SARS) is a respiratory disease caused by a zoonotic coronavirus (CoV) named SARS-CoV (SCoV), which rapidly swept the globe after its emergence in rural China during late 2002. The origins of SCoV have been mysterious and controversial, until the recent discovery of SARS-like CoV (SLCoV) in bats and the proposal of bats as the natural reservior of the Coronaviridae family. In this article, we focused on discussing how phylogenetics contributed to our understanding towards the emergence and transmission of SCoV. We first reviewed the epidemiology of SCoV from a phylogenetic perspective and discussed the controversies over its phylogenetic origins. Then, we summarized the phylogenetic findings in relation to its zoonotic origins and the proposed inter-species viral transmission events. Finally, we also discussed how the discoveries of SCoV and SLCoV expanded our knowledge on the evolution of the Coronaviridae family as well as its implications on the possible future re-emergence of SCoV.
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Affiliation(s)
- Chi Wai Yip
- The School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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62
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Nozaki H, Maruyama S, Matsuzaki M, Nakada T, Kato S, Misawa K. Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Mol Phylogenet Evol 2009; 53:872-80. [PMID: 19698794 DOI: 10.1016/j.ympev.2009.08.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 06/15/2009] [Accepted: 08/13/2009] [Indexed: 11/16/2022]
Abstract
The phylogenetic positions of the primary photosynthetic eukaryotes, or Archaeplastida (green plants, red algae, and glaucophytes) and the secondary photosynthetic chromalveolates, Haptophyta, vary depending on the data matrices used in the previous nuclear multigene phylogenetic studies. Here, we deduced the phylogeny of three groups of Archaeplastida and Haptophyta on the basis of sequences of the multiple slowly evolving nuclear genes and reduced the gaps or missing data, especially in glaucophyte operational taxonomic units (OTUs). The present multigene phylogenetic analyses resolved that Haptophyta and two other groups of Chromalveolata, stramenopiles and Alveolata, form a monophyletic group that is sister to the green plants and that the glaucophytes and red algae are basal to the clade composed of green plants and Chromalveolata. The bootstrap values supporting these phylogenetic relationships increased with the exclusion of long-branched OTUs. The close relationship between green plants and Chromalveolata is further supported by the common replacement in two plastid-targeted genes.
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Affiliation(s)
- Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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64
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Schneider A, Cannarozzi GM. Support patterns from different outgroups provide a strong phylogenetic signal. Mol Biol Evol 2009; 26:1259-72. [PMID: 19240194 DOI: 10.1093/molbev/msp034] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It is known that the accuracy of phylogenetic reconstruction decreases when more distant outgroups are used. We quantify this phenomenon with a novel scoring method, the outgroup score pOG. This score expresses if the support for a particular branch of a tree decreases with increasingly distant outgroups. Large-scale simulations confirmed that the outgroup support follows this expectation and that the pOG score captures this pattern. The score often identifies the correct topology even when the primary reconstruction methods fail, particularly in the presence of model violations. In simulations of problematic phylogenetic scenarios such as rate variation among lineages (which can lead to long-branch attraction artifacts) and quartet-based reconstruction, the pOG analysis outperformed the primary reconstruction methods. Because the pOG method does not make any assumptions about the evolutionary model (besides the decreasing support from increasingly distant outgroups), it can detect cases of violations not treated by a specific model or too strong to be fully corrected. When used as an optimization criterion in the construction of a tree of 23 mammals, the outgroup signal confirmed many well-accepted mammalian orders and superorders. It supports Atlantogenata, a clade of Afrotheria and Xenarthra, and suggests an Artiodactyla-Chiroptera clade.
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Affiliation(s)
- Adrian Schneider
- ETH Zurich, Department of Computer Science, Zurich, Switzerland.
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Deveaux Y, Toffano-Nioche C, Claisse G, Thareau V, Morin H, Laufs P, Moreau H, Kreis M, Lecharny A. Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis. BMC Evol Biol 2008; 8:291. [PMID: 18950478 PMCID: PMC2584047 DOI: 10.1186/1471-2148-8-291] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 10/24/2008] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The Wuschel related homeobox (WOX) family proteins are key regulators implicated in the determination of cell fate in plants by preventing cell differentiation. A recent WOX phylogeny, based on WOX homeodomains, showed that all of the Physcomitrella patens and Selaginella moellendorffii WOX proteins clustered into a single orthologous group. We hypothesized that members of this group might preferentially share a significant part of their function in phylogenetically distant organisms. Hence, we first validated the limits of the WOX13 orthologous group (WOX13 OG) using the occurrence of other clade specific signatures and conserved intron insertion sites. Secondly, a functional analysis using expression data and mutants was undertaken. RESULTS The WOX13 OG contained the most conserved plant WOX proteins including the only WOX detected in the highly proliferating basal unicellular and photosynthetic organism Ostreococcus tauri. A large expansion of the WOX family was observed after the separation of mosses from other land plants and before monocots and dicots have arisen. In Arabidopsis thaliana, AtWOX13 was dynamically expressed during primary and lateral root initiation and development, in gynoecium and during embryo development. AtWOX13 appeared to affect the floral transition. An intriguing clade, represented by the functional AtWOX14 gene inside the WOX13 OG, was only found in the Brassicaceae. Compared to AtWOX13, the gene expression profile of AtWOX14 was restricted to the early stages of lateral root formation and specific to developing anthers. A mutational insertion upstream of the AtWOX14 homeodomain sequence led to abnormal root development, a delay in the floral transition and premature anther differentiation. CONCLUSION Our data provide evidence in favor of the WOX13 OG as the clade containing the most conserved WOX genes and established a functional link to organ initiation and development in Arabidopsis, most likely by preventing premature differentiation. The future use of Ostreococcus tauri and Physcomitrella patens as biological models should allow us to obtain a better insight into the functional importance of WOX13 OG genes.
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Affiliation(s)
- Yves Deveaux
- Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
| | - Claire Toffano-Nioche
- Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
| | - Gaelle Claisse
- Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
| | - Vincent Thareau
- Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
| | - Halima Morin
- Laboratoire de Biologie Cellulaire, Institut J. P. Bourgin, INRA, 78026 Versailles Cedex, France
| | - Patrick Laufs
- Laboratoire de Biologie Cellulaire, Institut J. P. Bourgin, INRA, 78026 Versailles Cedex, France
| | - Hervé Moreau
- Observatoire Océanologique, Laboratoire Arago, Unité Mixte de Recherche 7628, CNRS-Université Pierre et Marie Curie, BP44, 66651 Banyuls sur Mer Cedex, France
| | - Martin Kreis
- Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
| | - Alain Lecharny
- Université Paris-Sud 11, Institut de Biotechnologie des Plantes, Bâtiment 630, UMR/CNRS 8618, F-91405 Orsay, France
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Tan KSW. New insights on classification, identification, and clinical relevance of Blastocystis spp. Clin Microbiol Rev 2008; 21:639-65. [PMID: 18854485 PMCID: PMC2570156 DOI: 10.1128/cmr.00022-08] [Citation(s) in RCA: 459] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
SUMMARY Blastocystis is an unusual enteric protozoan parasite of humans and many animals. It has a worldwide distribution and is often the most commonly isolated organism in parasitological surveys. The parasite has been described since the early 1900s, but only in the last decade or so have there been significant advances in our understanding of Blastocystis biology. However, the pleomorphic nature of the parasite and the lack of standardization in techniques have led to confusion and, in some cases, misinterpretation of data. This has hindered laboratory diagnosis and efforts to understand its mode of reproduction, life cycle, prevalence, and pathogenesis. Accumulating epidemiological, in vivo, and in vitro data strongly suggest that Blastocystis is a pathogen. Many genotypes exist in nature, and recent observations indicate that humans are, in reality, hosts to numerous zoonotic genotypes. Such genetic diversity has led to a suggestion that previously conflicting observations on the pathogenesis of Blastocystis are due to pathogenic and nonpathogenic genotypes. Recent epidemiological, animal infection, and in vitro host-Blastocystis interaction studies suggest that this may indeed be the case. This review focuses on such recent advances and also provides updates on laboratory and clinical aspects of Blastocystis spp.
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Affiliation(s)
- Kevin S W Tan
- Department of Microbiology, Laboratory of Molecular and Cellular Parasitology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
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Brinkmann H, Philippe H. The Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 607:20-37. [DOI: 10.1007/978-0-387-74021-8_2] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Pilgrim EM, von Dohlen CD, Pitts JP. Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies. ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00340.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Soria-Carrasco V, Castresana J. Estimation of Phylogenetic Inconsistencies in the Three Domains of Life. Mol Biol Evol 2008; 25:2319-29. [DOI: 10.1093/molbev/msn176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Lartillot N, Philippe H. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci 2008; 363:1463-72. [PMID: 18192187 DOI: 10.1098/rstb.2007.2236] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (maximum likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. We applied this approach to a dataset of 94 genes and 79 species using CAT, a previously developed model accounting for site-specific amino acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothesis, and, with a lower statistical support, the paraphyly of Deuterostomia. These results, in particular the status of deuterostomes, need further confirmation, both through increased taxonomic sampling, and future improvements of probabilistic models.
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Affiliation(s)
- Nicolas Lartillot
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, CNRS-Université de Montpellier 2, 34392 Montpellier Cedex 5, France
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Boore JL, Fuerstenberg SI. Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. Philos Trans R Soc Lond B Biol Sci 2008; 363:1445-51. [PMID: 18192190 DOI: 10.1098/rstb.2007.2234] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been the comparisons of the relative arrangements of genes, which has convincingly resolved numerous branch points, including those that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for comparison, there is also a potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, the presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing owing to their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, thereby reducing the occurrence of homoplasy. The comparisons of organelle genomes pioneered the way for using such features for phylogenetic reconstructions, and it is almost certainly true, as ever more genomic sequence becomes available, that further use of genome-level characters will play a big role in outlining the relationships among major animal groups.
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73
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A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol Phylogenet Evol 2008; 48:103-11. [DOI: 10.1016/j.ympev.2008.03.033] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 03/01/2008] [Accepted: 03/17/2008] [Indexed: 11/15/2022]
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Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)? Mol Phylogenet Evol 2008; 48:313-25. [PMID: 18490181 DOI: 10.1016/j.ympev.2008.04.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 04/04/2008] [Accepted: 04/07/2008] [Indexed: 11/23/2022]
Abstract
Despite sampling of up to 25kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable phylogenetic hypothesis in these parts of the tree. The main reason for this is probably a combination of rapid radiation and substitution rate heterogeneity. Poor resolution among closely related species are often explained by low levels of variation in chloroplast data, but the problem with our data appear to be high levels of homoplasy. Tree-like cpDNA evolution cannot be rejected, but apparent incongruent patterns between different regions are evaluated with the possibility of ancient interspecific chloroplast recombination as explanatory model. However, several major phylogenetic relationships, previously not recognized, are confidently resolved, e.g. the grouping of the two SW Anatolian taxa S. cryptoneura and S. sordida strongly disagrees with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. The closely related S. atocioides and S. aegyptiaca form a sister group to Lychnis and the rest of Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data.
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75
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Clare EL, Kerr KCR, von Königslöw TE, Wilson JJ, Hebert PDN. Diagnosing Mitochondrial DNA Diversity: Applications of a Sentinel Gene Approach. J Mol Evol 2008; 66:362-7. [DOI: 10.1007/s00239-008-9088-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 01/23/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
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Whitfield JB, Kjer KM. Ancient rapid radiations of insects: challenges for phylogenetic analysis. ANNUAL REVIEW OF ENTOMOLOGY 2008; 53:449-72. [PMID: 17877448 DOI: 10.1146/annurev.ento.53.103106.093304] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Phylogenies of major groups of insects based on both morphological and molecular data have sometimes been contentious, often lacking the data to distinguish between alternative views of relationships. This paucity of data is often due to real biological and historical causes, such as shortness of time spans between divergences for evolution to occur and long time spans after divergences for subsequent evolutionary changes to obscure the earlier ones. Another reason for difficulty in resolving some of the relationships using molecular data is the limited spectrum of genes so far developed for phylogeny estimation. For this latter issue, there is cause for current optimism owing to rapid increases in our knowledge of comparative genomics. At least some historical patterns of divergence may, however, continue to defy our attempts to completely reconstruct them with confidence, at least using current strategies.
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Affiliation(s)
- James B Whitfield
- Department of Entomology, University of Illinois, Urbana, IL 61821, USA.
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77
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Mulkidjanian AY, Makarova KS, Galperin MY, Koonin EV. Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nat Rev Microbiol 2007; 5:892-9. [PMID: 17938630 DOI: 10.1038/nrmicro1767] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rotary proton- and sodium-translocating ATPases are reversible molecular machines present in all cellular life forms that couple ion movement across membranes with ATP hydrolysis or synthesis. Sequence and structural comparisons of F- and V-type ATPases have revealed homology between their catalytic and membrane subunits, but not between the subunits of the central stalk that connects the catalytic and membrane components. Based on this pattern of homology, we propose that these ATPases originated from membrane protein translocases, which, themselves, evolved from RNA translocases. We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer.
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Talavera G, Castresana J. Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments. Syst Biol 2007; 56:564-77. [PMID: 17654362 DOI: 10.1080/10635150701472164] [Citation(s) in RCA: 3593] [Impact Index Per Article: 199.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
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Affiliation(s)
- Gerard Talavera
- Department of Physiology, Institute of Molecular Biology of Barcelona, Barcelona, Spain
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79
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Nozaki H, Iseki M, Hasegawa M, Misawa K, Nakada T, Sasaki N, Watanabe M. Phylogeny of Primary Photosynthetic Eukaryotes as Deduced from Slowly Evolving Nuclear Genes. Mol Biol Evol 2007; 24:1592-5. [PMID: 17488739 DOI: 10.1093/molbev/msm091] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.
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80
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Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 2007; 7 Suppl 1:S4. [PMID: 17288577 PMCID: PMC1796613 DOI: 10.1186/1471-2148-7-s1-s4] [Citation(s) in RCA: 426] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the tree is accurate. Systematic errors, such as the Long Branch Attraction (LBA) artefact, can be misleading, in particular when the taxon sampling is poor, or the outgroup is distant. In an otherwise consistent probabilistic framework, systematic errors in genome-wide analyses can be traced back to model mis-specification problems, which suggests that better models of sequence evolution should be devised, that would be more robust to tree reconstruction artefacts, even under the most challenging conditions. METHODS We focus on a well characterized LBA artefact analyzed in a previous phylogenomic study of the metazoan tree, in which two fast-evolving animal phyla, nematodes and platyhelminths, emerge either at the base of all other Bilateria, or within protostomes, depending on the outgroup. We use this artefactual result as a case study for comparing the robustness of two alternative models: a standard, site-homogeneous model, based on an empirical matrix of amino-acid replacement (WAG), and a site-heterogeneous mixture model (CAT). In parallel, we propose a posterior predictive test, allowing one to measure how well a model acknowledges sequence saturation. RESULTS Adopting a Bayesian framework, we show that the LBA artefact observed under WAG disappears when the site-heterogeneous model CAT is used. Using cross-validation, we further demonstrate that CAT has a better statistical fit than WAG on this data set. Finally, using our statistical goodness-of-fit test, we show that CAT, but not WAG, correctly accounts for the overall level of saturation, and that this is due to a better estimation of site-specific amino-acid preferences. CONCLUSION The CAT model appears to be more robust than WAG against LBA artefacts, essentially because it correctly anticipates the high probability of convergences and reversions implied by the small effective size of the amino-acid alphabet at each site of the alignment. More generally, our results provide strong evidence that site-specificities in the substitution process need be accounted for in order to obtain more reliable phylogenetic trees.
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Affiliation(s)
- Nicolas Lartillot
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS-Université de Montpellier 2, 161, rue Ada, 34392 Montpellier Cedex 5, France
| | - Henner Brinkmann
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec Canada
| | - Hervé Philippe
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec Canada
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81
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LIVEZEY BRADLEYC, ZUSI RICHARDL. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zool J Linn Soc 2007; 149:1-95. [PMID: 18784798 PMCID: PMC2517308 DOI: 10.1111/j.1096-3642.2006.00293.x] [Citation(s) in RCA: 282] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.
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Affiliation(s)
- BRADLEY C LIVEZEY
- Section of Birds, Carnegie Museum of Natural History4400 Forbes Avenue, Pittsburgh, PA 15213-4080, USA
| | - RICHARD L ZUSI
- Division of Birds, National Museum of Natural HistoryWashington, DC 20013-7012, USA
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82
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Savard J, Tautz D, Richards S, Weinstock GM, Gibbs RA, Werren JH, Tettelin H, Lercher MJ. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genes Dev 2006; 16:1334-8. [PMID: 17065606 PMCID: PMC1626634 DOI: 10.1101/gr.5204306] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 04/03/2006] [Indexed: 11/25/2022]
Abstract
Comparative studies require knowledge of the evolutionary relationships between taxa. However, neither morphological nor paleontological data have been able to unequivocally resolve the major groups of holometabolous insects so far. Here, we utilize emerging genome projects to assemble and analyze a data set of 185 nuclear genes, resulting in a fully resolved phylogeny of the major insect model species. Contrary to the most widely accepted phylogenetic hypothesis, bees and wasps (Hymenoptera) are basal to the other major holometabolous orders, beetles (Coleoptera), moths (Lepidoptera), and flies (Diptera). We validate our results by meticulous examination of potential confounding factors. Phylogenomic approaches are thus able to resolve long-standing questions about the phylogeny of insects.
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Affiliation(s)
- Joël Savard
- Abteilung für Evolutionsgenetik, Institut für Genetik, Universität zu Köln, Köln 50674, Germany
| | - Diethard Tautz
- Abteilung für Evolutionsgenetik, Institut für Genetik, Universität zu Köln, Köln 50674, Germany
| | - Stephen Richards
- Human Genome Sequencing Centre, Baylor College of Medicine, Houston, Texas 77002, USA
| | - George M. Weinstock
- Human Genome Sequencing Centre, Baylor College of Medicine, Houston, Texas 77002, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Centre, Baylor College of Medicine, Houston, Texas 77002, USA
| | - John H. Werren
- Department of Biology, University of Rochester, New York 14627, USA
| | - Hervé Tettelin
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Martin J. Lercher
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
- European Molecular Biology Laboratory, 69012 Heidelberg, Germany
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83
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Shao R, Barker SC. Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution. Parasitology 2006; 134:153-67. [PMID: 17032475 DOI: 10.1017/s0031182006001429] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 08/15/2006] [Accepted: 08/15/2006] [Indexed: 11/05/2022]
Abstract
Over 39000 species of arthropods parasitize humans, domestic animals and wildlife. Despite their medical, veterinary and economic importance, most aspects of the population genetics and evolution of the vast majority of parasitic arthropods are poorly understood. Mitochondrial genomes are a rich source of markers for studies of population genetics and evolution. These markers include (1) nucleotide sequences of each of the 37 mitochondrial genes and non-coding regions; (2) concatenated nucleotide sequences of 2 or more genes; and (3) genomic features, such as gene duplications, gene rearrangements, and changes in gene content and secondary structures of RNAs. To date, the mitochondrial genomes of over 700 species of multi-cellular animals have been sequenced entirely, however, only 24 of these species are parasitic arthropods. Of the mitochondrial genome markers, only the nucleotide sequences of 4 mitochondrial genes,cox1,cob,rrnSandrrnL, have been well explored in population genetic and evolutionary studies of parasitic arthropods whereas the sequences of the other 33 genes, and various genomic features have not. We review current knowledge of the mitochondrial genomes of parasitic arthropods, summarize applications of mitochondrial genes and genomic features in population genetic and evolutionary studies, and highlight prospects for future research.
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Affiliation(s)
- R Shao
- Parasitology Section, School of Molecular and Microbial Sciences, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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84
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Liu YJ, Hodson MC, Hall BD. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol Biol 2006; 6:74. [PMID: 17010206 PMCID: PMC1599754 DOI: 10.1186/1471-2148-6-74] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 09/29/2006] [Indexed: 11/10/2022] Open
Abstract
Background At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Results Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. Conclusion In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.
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Affiliation(s)
- Yajuan J Liu
- Departments of Biology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Matthew C Hodson
- Departments of Biology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin D Hall
- Departments of Biology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
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85
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Macario AJL, Brocchieri L, Shenoy AR, Conway de Macario E. Evolution of a Protein-Folding Machine: Genomic and Evolutionary Analyses Reveal Three Lineages of the Archaeal hsp70(dnaK) Gene. J Mol Evol 2006; 63:74-86. [PMID: 16788741 DOI: 10.1007/s00239-005-6207-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Accepted: 03/14/2006] [Indexed: 11/27/2022]
Abstract
The stress chaperone protein Hsp70 (DnaK) (abbreviated DnaK) and its co-chaperones Hsp40(DnaJ) (or DnaJ) and GrpE are universal in bacteria and eukaryotes but occur only in some archaea clustered in the order 5'-grpE-dnaK-dnaJ-3' in a locus termed Locus I. Three structural varieties of Locus I, termed Types I, II, and III, were identified, respectively, in Methanosarcinales, in Thermoplasmatales and Methanothermobacter thermoautotrophicus, and in Halobacteriales. These Locus I types corresponded to three groups identified by phylogenetic trees of archaeal DnaK proteins including the same archaeal subdivisions. These archaeal DnaK groups were not significantly interrelated, clustering instead with DnaKs from three bacterial lineages, Methanosarcinales with Firmicutes, Thermoplasmatales and M. thermoautotrophicus with Thermotoga, and Halobacteriales with Actinobacteria, suggesting that the three archaeal types of Locus I were acquired by independent events of lateral gene transfer. These associations, however, lacked strong bootstrap support and were sensitive to dataset choice and tree-reconstruction method. Structural features of dnaK loci in bacteria revealed that Methanosarcinales and Firmicutes shared a similar structure, also common to most other bacterial groups. Structural differences were observed instead in Thermotoga compared to Thermoplasmatales and M. thermoautotrophicus, and in Actinobacteria compared to Halobacteriales. It was also found that the association between the DnaK sequences from Halobacteriales and Actinobacteria likely reflects common biases in their amino acid compositions. Although the loci structural features and the DnaK trees suggested the possibility of lateral gene transfer between Firmicutes and Methanosarcinales, the similarity between the archaeal and the ancestral bacterial loci favors the more parsimonious hypothesis that all archaeal sequences originated from a unique prokaryotic ancestor.
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Affiliation(s)
- Alberto J L Macario
- Division of Molecular Medicine, Wadsworth Center, Room B-749, New York State Department of Health, Empire State Plaza, P.O. Box 509, Albany, NY 12201-0509, USA
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86
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Teeling H, Gloeckner FO. RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics 2006; 7:66. [PMID: 16476165 PMCID: PMC1421441 DOI: 10.1186/1471-2105-7-66] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Accepted: 02/13/2006] [Indexed: 11/28/2022] Open
Abstract
Background Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs, RibAlign has been developed to fill this gap. Results RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to eubacterial ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as exporting aligned, concatenated and filtered sequence files that can directly be used in conjunction with the PHYLIP and MrBayes phylogenetic reconstruction programs. Conclusion Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements. However, hundreds of full and draft genome sequencing projects are on the way, and advances in cluster-computing and algorithms make phylogenetic reconstructions feasible even with large alignments of concatenated marker genes. RibAlign is a first step in this direction and may be particularly interesting to scientists involved in whole genome sequencing of representatives of new or sparsely studied eubacterial phyla. RibAlign is available at
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Affiliation(s)
- Hanno Teeling
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Frank Oliver Gloeckner
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
- International University Bremen, D-28759 Bremen, Germany
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87
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Challis RJ, Goodacre SL, Hewitt GM. Evolution of spider silks: conservation and diversification of the C-terminus. INSECT MOLECULAR BIOLOGY 2006; 15:45-56. [PMID: 16469067 DOI: 10.1111/j.1365-2583.2005.00606.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Analysis of DNA sequences coding for the C-terminus of spider silk proteins from a range of spiders suggests that many silk C-termini share a common origin, and that their physical properties have been highly conserved over several hundred million years. These physical properties are compatible with roles in protein synthesis, silk function and in recruiting accessory proteins. Phylogenetic relationships among different silk genes suggest that any recombination has been insufficient to homogenize the different types of silk gene, which appear to have evolved independently of one another. The types of nucleotide substitutions that have occurred suggest that selection may have operated differently in the various silk lineages. Amino acid sequences of flagelliform silk C-termini differ substantially from the other types of spider silk studied, but they are expected to have very similar physical properties and may perform a similar function.
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Affiliation(s)
- R J Challis
- IEB, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, UK
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88
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García-Moreno J, Cortés N, García-Deras GM, Hernández-Baños BE. Local origin and diversification among Lampornis hummingbirds: A Mesoamerican taxon. Mol Phylogenet Evol 2006; 38:488-98. [PMID: 16257241 DOI: 10.1016/j.ympev.2005.08.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 08/16/2005] [Accepted: 08/24/2005] [Indexed: 11/21/2022]
Abstract
The huge biodiversity found in Mesoamerica is often explained by its geographic situation as a natural bridge between two large biogeographic regions. Often overlooked, however, are the high levels of speciation and diversification in the area. Here we assess the phylogenetic relationships within a Mesoamerican group of hummingbirds (Lampornis). We sequenced both mtDNA (1,143 bp of cyt b and 727 bp of ND5) and nuclear genes (505 bp of AK-5 intron and 567 bp of c-mos) for each of the seven recognised species and outgroups. We find two or three clades of similar age within this genus: L. clemenciae and L. amethystinus (singly or as each other's sister taxa) and a Central American clade. This Central-American clade presents a clear bipartition between northern (L. viridipallens and L. sybillae) and southern Mesoamerica, which is shared with many other Mesoamerican organisms. Our analyses suggest that L. hemileucus does not belong in the genus Lampornis. While we refrain to apply a time-scale to our data because of the lack of an appropriate calibration, our results indicate that the genus Lampornis predates the uprising of the Panama land-bridge, and that diversification among the isthmian species (L. castaneoventris and L. calolaema) is a very recent event. Our results strongly suggest a local Mesoamerican origin for this genus.
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Affiliation(s)
- Jaime García-Moreno
- Max Planck Institiute for Ornithology, Vogelwarte Radolfzell, Schlossalleé 2, D-78315 Radolfzell, Germany.
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89
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Philippe H, Delsuc F, Brinkmann H, Lartillot N. Phylogenomics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2005. [DOI: 10.1146/annurev.ecolsys.35.112202.130205] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada; , ,
| | - Frédéric Delsuc
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada; , ,
| | - Henner Brinkmann
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada; , ,
| | - Nicolas Lartillot
- Laboratoire d'Informatique, de Robotique et de Mathématiques de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, 34392 Montpellier Cedex 5, France;
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90
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Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H. An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics. Syst Biol 2005; 54:743-57. [PMID: 16243762 DOI: 10.1080/10635150500234609] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene data sets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long-branch attraction artefact (LBA) using real instead of simulated sequences. Two fast-evolving eukaryotic lineages, whose evolutionary positions are well established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large data set was assembled (44 species, 133 genes, and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood-based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast-evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast-evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the nonphylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.
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Affiliation(s)
- Henner Brinkmann
- Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
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91
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Oda H, Tagawa K, Akiyama-Oda Y. Diversification of epithelial adherens junctions with independent reductive changes in cadherin form: identification of potential molecular synapomorphies among bilaterians. Evol Dev 2005; 7:376-89. [PMID: 16174032 DOI: 10.1111/j.1525-142x.2005.05043.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The adherens junction (AJ) is the most universal junction found in bilaterian epithelia and may represent one of the earliest types of cell-cell junctions. The adhesion molecules responsible for forming AJs are the classic cadherins (referred to simply as cadherins), whose extracellular domain organization displays marked variety among species examined so far. In this study, we attempted to reconstruct the evolution of cadherin by analyzing new data from several arthropods (two insects, one non-insect hexapod, three crustaceans, and one chelicerate) and previously published sequences for Drosophila melanogaster and other animals. The results of comparative analyses using the BLAST tool and immunohistochemical analyses revealed that the extracellular domain organizations of a decapod, an isopod, a spider, and a starfish cadherin, which are present at AJs in the embryonic epithelia are homologous. Independent reductive changes from the ancestral state were evident in the epithelia of hexapods+branchiopod, vertebrates+urochordates, and a cephalochordate. The form of cadherins in hexapods is more closely related to that of a branchiopod than to that of malacostracan crustaceans, and one of those of vertebrates is more closely related to that of urochordates than to that of a cephalochordate. Although the sampling of taxa is limited at this stage of research, we hypothesize that the reductive events in cadherin structure related to AJ formation in the epithelia may possess information about bilaterian relationships as molecular synapomorphies.
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Affiliation(s)
- Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
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92
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Raina SZ, Faith JJ, Disotell TR, Seligmann H, Stewart CB, Pollock DD. Evolution of base-substitution gradients in primate mitochondrial genomes. Genome Res 2005; 15:665-73. [PMID: 15867428 PMCID: PMC1088294 DOI: 10.1101/gr.3128605] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Inferences of phylogenies and dates of divergence rely on accurate modeling of evolutionary processes; they may be confounded by variation in substitution rates among sites and changes in evolutionary processes over time. In vertebrate mitochondrial genomes, substitution rates are affected by a gradient along the genome of the time spent being single-stranded during replication, and different types of substitutions respond differently to this gradient. The gradient is controlled by biological factors including the rate of replication and functionality of repair mechanisms; little is known, however, about the consistency of the gradient over evolutionary time, or about how evolution of this gradient might affect phylogenetic analysis. Here, we evaluate the evolution of response to this gradient in complete primate mitochondrial genomes, focusing particularly on A-->G substitutions, which increase linearly with the gradient. We developed a methodology to evaluate the posterior probability densities of the response parameter space, and used likelihood ratio tests and mixture models with different numbers of classes to determine whether groups of genomes have evolved in a similar fashion. Substitution gradients usually evolve slowly in primates, but there have been at least two large evolutionary jumps: on the lineage leading to the great apes, and a convergent change on the lineage leading to baboons (Papio). There have also been possible convergences at deeper taxonomic levels, and different types of substitutions appear to evolve independently. The placements of the tarsier and the tree shrew within and in relation to primates may be incorrect because of convergence in these factors.
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Affiliation(s)
- Sameer Z Raina
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
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93
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Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol Biol Evol 2005; 22:1948-63. [PMID: 15944438 DOI: 10.1093/molbev/msi191] [Citation(s) in RCA: 173] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.
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Affiliation(s)
- Jim Leebens-Mack
- Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of Life Sciences, The Pennsylvania State University, PA, USA.
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94
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Holland B, Delsuc F, Moulton V. Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. Syst Biol 2005; 54:66-76. [PMID: 15805011 DOI: 10.1080/10635150590906055] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Many phylogenetic methods produce large collections of trees as opposed to a single tree, which allows the exploration of support for various evolutionary hypotheses. However, to be useful, the information contained in large collections of trees should be summarized; frequently this is achieved by constructing a consensus tree. Consensus trees display only those signals that are present in a large proportion of the trees. However, by their very nature consensus trees require that any conflicts between the trees are necessarily disregarded. We present a method that extends the notion of consensus trees to allow the visualization of conflicting hypotheses in a consensus network. We demonstrate the utility of this method in highlighting differences amongst maximum likelihood bootstrap values and Bayesian posterior probabilities in the placental mammal phylogeny, and also in comparing the phylogenetic signal contained in amino acid versus nucleotide characters for hexapod monophyly.
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Affiliation(s)
- Barbara Holland
- The Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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95
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Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005; 6:361-75. [PMID: 15861208 DOI: 10.1038/nrg1603] [Citation(s) in RCA: 756] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
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Affiliation(s)
- Frédéric Delsuc
- Canadian Institute for Advanced Research, Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
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96
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97
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Caetano-Anollés G, Caetano-Anollés D. Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life. J Mol Evol 2005; 60:484-98. [PMID: 15883883 DOI: 10.1007/s00239-004-0221-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 10/11/2004] [Indexed: 11/30/2022]
Abstract
Protein evolution is imprinted in both the sequence and the structure of evolutionary building blocks known as protein domains. These domains share a common ancestry and can be unified into a comparatively small set of folding architectures, the protein folds. We have traced the distribution of protein folds between and within proteomes belonging to Eukarya, Archaea, and Bacteria along the branches of a universal phylogeny of protein architecture. This tree was reconstructed from global fold-usage statistics derived from a structural census of proteomes. We found that folds shared by the three organismal domains were placed almost exclusively at the base of the rooted tree and that there were marked heterogeneities in fold distribution and clear evolutionary patterns related to protein architecture and organismal diversification. These include a relative timing for the emergence of prokaryotes, congruent episodes of architectural loss and diversification in Archaea and Bacteria, and a late and quite massive rise of architectural novelties in Eukarya perhaps linked to multicellularity.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois, 332 NSRC, 1101 West Peabody Drive, Urbana, IL, 61801, USA.
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98
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Hubert N, Bonillo C, Paugy D. Does elision account for molecular saturation: Case study based on mitochondrial ribosomal DNA among Characiform fishes (Teleostei: Ostariophysii). Mol Phylogenet Evol 2005; 35:300-8. [PMID: 15737600 DOI: 10.1016/j.ympev.2005.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 01/11/2005] [Accepted: 01/11/2005] [Indexed: 11/26/2022]
Affiliation(s)
- Nicolas Hubert
- Département Milieux et peuplements aquatique, Unité Biodiversité et dynamique des communautés aquatiques, US MNHN 0403, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris Cedex 05, France.
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99
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Arisue N, Maki Y, Yoshida H, Wada A, Sánchez LB, Müller M, Hashimoto T. Comparative analysis of the ribosomal components of the hydrogenosome-containing protist, Trichomonas vaginalis. J Mol Evol 2005; 59:59-71. [PMID: 15383908 DOI: 10.1007/s00239-004-2604-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Accepted: 01/12/2004] [Indexed: 10/26/2022]
Abstract
The ribosomes of the amitochondriate but hydrogenosome-containing protist lineage, the trichomonads, have previously been reported to be prokaryotic or primitive eukaryotic, based on evidence that they have a 70S sedimentation coefficient and a small number of proteins, similar to prokaryotic ribosomes. In order to determine whether the components of the trichomonad ribosome indeed differ from those of typical eukaryotic ribosomes, the ribosome of a representative trichomonad, Trichomonas vaginalis, was characterized. The sedimentation coefficient of the T. vaginalis ribosome was smaller than that of Saccharomyces cerevisiae and larger than that of Escherichia coli. Based on two-dimensional PAGE analysis, the number of different ribosomal proteins was estimated to be approximately 80. This number is the same as those obtained for typical eukaryotes (approximately 80) but larger than that of E. coli (approximately 55). N-Terminal amino acid sequencing of 18 protein spots and the complete sequences of 4 ribosomal proteins as deduced from their genes revealed these sequences to display typical eukaryotic features. Phylogenetic analyses of the five ribosomal proteins currently available also clearly confirmed that the T. vaginalis sequences are positioned within a eukaryotic clade. Comparison of deduced secondary structure models of the small and large subunit rRNAs of T. vaginalis with those of other eukaryotes revealed that all helices commonly found in typical eukaryotes are present and conserved in T. vaginalis, while variable regions are shortened or lost. These lines of evidence demonstrate that the T. vaginalis ribosome has no prokaryotic or primitive eukaryotic features but is clearly a typical eukaryotic type.
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Affiliation(s)
- Nobuko Arisue
- Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
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100
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Moreira D, López-García P, Vickerman K. An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea. Int J Syst Evol Microbiol 2005; 54:1861-1875. [PMID: 15388756 DOI: 10.1099/ijs.0.63081-0] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Given their ecological and medical importance, the classification of the kinetoplastid protists (class Kinetoplastea) has attracted much scientific attention for a long time. Morphology-based taxonomic schemes distinguished two major kinetoplastid groups: the strictly parasitic, uniflagellate trypanosomatids and the biflagellate bodonids. Molecular phylogenetic analyses based on 18S rRNA sequence comparison suggested that the trypanosomatids emerged from within the bodonids. However, these analyses revealed a huge evolutionary distance between the kinetoplastids and their closest relatives (euglenids and diplonemids) that makes very difficult the correct inference of the phylogenetic relationships between the different kinetoplastid groups. Using direct PCR amplification of 18S rRNA genes from hydrothermal vent samples, several new kinetoplastid-like sequences have been reported recently. Three of them emerge robustly at the base of the kinetoplastids, breaking the long branch leading to the euglenids and diplonemids. One of these sequences belongs to a close relative of Ichthyobodo necator (a fish parasite) and of the 'Perkinsiella amoebae'-like endosymbiont of Neoparamoeba spp. amoebae. The authors have studied the reliability of their basal position and used all these slow-evolving basal-emerging sequences as a close outgroup to analyse the phylogeny of the apical kinetoplastids. They thus find a much more stable and resolved kinetoplastid phylogeny, which supports the monophyly of groups that very often emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences. A new classification of the class Kinetoplastea is proposed based on the results of the phylogenetic analysis presented. This class is now subdivided into two new subclasses, Prokinetoplastina (accommodating the basal species I. necator and 'Perkinsiella amoebae') and Metakinetoplastina (containing the Trypanosomatida together with three additional new orders: Eubodonida, Parabodonida and Neobodonida). The classification of the species formerly included in the genus Bodo is also revised, with the amendment of this genus and the genus Parabodo and the creation of a new genus, Neobodo.
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Affiliation(s)
- David Moreira
- UMR CNRS 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, bâtiment 360, 91405 Orsay Cedex, France
| | - Purificación López-García
- UMR CNRS 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, bâtiment 360, 91405 Orsay Cedex, France
| | - Keith Vickerman
- Division of Environmental & Evolutionary Biology, University of Glasgow, Glasgow G12 8QQ, UK
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