1
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Özel MN, Gibbs CS, Holguera I, Soliman M, Bonneau R, Desplan C. Coordinated control of neuronal differentiation and wiring by sustained transcription factors. Science 2022; 378:eadd1884. [PMID: 36480601 DOI: 10.1126/science.add1884] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The large diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of on average 10 continuously expressed transcription factors. We show that targeted modifications of this terminal selector code induce predictable conversions of neuronal fates that appear morphologically and transcriptionally complete. Cis-regulatory analysis of open chromatin links one of these genes to an upstream patterning factor that specifies neuronal fates in stem cells. Experimentally validated network models describe the synergistic regulation of downstream effectors by terminal selectors and ecdysone signaling during brain wiring. Our results provide a generalizable framework of how specific fates are implemented in postmitotic neurons.
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Affiliation(s)
| | - Claudia Skok Gibbs
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Isabel Holguera
- Department of Biology, New York University, New York, NY 10003, USA
| | - Mennah Soliman
- Department of Biology, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10003, USA.,Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY 10010, USA.,Center for Data Science, New York University, New York, NY 10003, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA.,New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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2
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Giacomelli M, Rossi ME, Lozano-Fernandez J, Feuda R, Pisani D. Resolving tricky nodes in the tree of life through amino acid recoding. iScience 2022; 25:105594. [PMID: 36458253 PMCID: PMC9706708 DOI: 10.1016/j.isci.2022.105594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 09/05/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic data allowed a detailed resolution of the Tree of Life, but "tricky nodes" such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic-scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact.
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Affiliation(s)
- Mattia Giacomelli
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Maria Eleonora Rossi
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, & Biodiversity Research Institute (IRBio), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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3
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Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022; 14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Affiliation(s)
- Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal 643, 08028 Barcelona, Spain
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra), Passeig marítim de la Barcelona 37-49, 08003 Barcelona, Spain
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4
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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5
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Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat Commun 2021; 12:1783. [PMID: 33741994 PMCID: PMC7979703 DOI: 10.1038/s41467-021-22074-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.
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6
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Fleming JF, Feuda R, Roberts NW, Pisani D. A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans. Genome Biol Evol 2020; 12:3906-3916. [PMID: 32031627 PMCID: PMC7058159 DOI: 10.1093/gbe/evaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 12/02/2022] Open
Abstract
Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.
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Affiliation(s)
- James F Fleming
- School of Earth Sciences, University of Bristol, United Kingdom.,Faculty of Environment and Information Studies, Keio University, Tsuruoka, Yamagata, Japan
| | - Roberto Feuda
- School of Earth Sciences, University of Bristol, United Kingdom
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, United Kingdom
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7
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Edgecombe GD. Arthropod Origins: Integrating Paleontological and Molecular Evidence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-124437] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phylogenomics underpins a stable and mostly well-resolved hypothesis for the interrelationships of extant arthropods. Exceptionally preserved fossils are integrated into this framework by coding their morphological characters, as exemplified by total-evidence dating approaches that treat fossils as dated tips in analyses numerically dominated by molecular data. Cambrian fossils inform on the sequence of character acquisition in the arthropod stem group and in the stems of its main extant clades. The arthropod head problem incorporates unique appendage combinations and remains of the nervous system in fossils into a scheme mostly based on neuroanatomy and Hox expression domains for extant forms. Molecular estimates of arthropod origins in the Cryogenian or Ediacaran predate a coherent picture from the arthropod fossil record, which commences as trace fossils in the earliest Cambrian. Probabilistic morphological clock analysis of trilobites, which exemplify the earliest arthropod body fossils, supports a Cambrian origin, without the need to posit an unfossilized Ediacaran history.
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Affiliation(s)
- Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
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8
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Vorster PJ, Goetsch P, Wijeratne TU, Guiley KZ, Andrejka L, Tripathi S, Larson BJ, Rubin SM, Strome S, Lipsick JS. A long lost key opens an ancient lock: Drosophila Myb causes a synthetic multivulval phenotype in nematodes. Biol Open 2020; 9:bio051508. [PMID: 32295830 PMCID: PMC7225089 DOI: 10.1242/bio.051508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/05/2020] [Indexed: 01/14/2023] Open
Abstract
The five-protein MuvB core complex is highly conserved in animals. This nuclear complex interacts with RB-family tumor suppressor proteins and E2F-DP transcription factors to form DREAM complexes that repress genes that regulate cell cycle progression and cell fate. The MuvB core complex also interacts with Myb family oncoproteins to form the Myb-MuvB complexes that activate many of the same genes. We show that animal-type Myb genes are present in Bilateria, Cnidaria and Placozoa, the latter including the simplest known animal species. However, bilaterian nematode worms lost their animal-type Myb genes hundreds of millions of years ago. Nevertheless, amino acids in the LIN9 and LIN52 proteins that directly interact with the MuvB-binding domains of human B-Myb and Drosophila Myb are conserved in Caenorhabditiselegans Here, we show that, despite greater than 500 million years since their last common ancestor, the Drosophila melanogaster Myb protein can bind to the nematode LIN9-LIN52 proteins in vitro and can cause a synthetic multivulval (synMuv) phenotype in vivo This phenotype is similar to that caused by loss-of-function mutations in C. elegans synMuvB-class genes including those that encode homologs of the MuvB core, RB, E2F and DP. Furthermore, amino acid substitutions in the MuvB-binding domain of Drosophila Myb that disrupt its functions in vitro and in vivo also disrupt these activities in C. elegans We speculate that nematodes and other animals may contain another protein that can bind to LIN9 and LIN52 in order to activate transcription of genes repressed by DREAM complexes.
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Affiliation(s)
- Paul J Vorster
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Paul Goetsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Laura Andrejka
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Braden J Larson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joseph S Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
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9
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McCarthy CGP, Fitzpatrick DA. Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom. ADVANCES IN GENETICS 2017; 100:211-266. [PMID: 29153401 DOI: 10.1016/bs.adgen.2017.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.
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10
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Filloramo GV, Saunders GW. Application of multigene phylogenetics and site-stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta). JOURNAL OF PHYCOLOGY 2016; 52:339-355. [PMID: 27037902 DOI: 10.1111/jpy.12418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/28/2016] [Indexed: 06/05/2023]
Abstract
Previous molecular assessments of the red algal order Rhodymeniales have confirmed its monophyly and distinguished the six currently recognized families (viz. Champiaceae, Faucheaceae, Fryeellaceae, Hymenocladiaceae, Lomentariaceae, and Rhodymeniaceae); however, relationships among most of these families have remained unresolved possibly as a result of substitution saturation at deeper phylogenetic nodes. The objective of the current study was to improve rhodymenialean systematics by increasing taxonomic representation and using a more robust multigene dataset of mitochondrial (COB, COI/COI-5P), nuclear (LSU, EF2) and plastid markers (psbA, rbcL). Additionally, we aimed to prevent phylogenetic inference problems associated with substitution saturation (particularly at the interfamilial nodes) by removing fast-evolving sites and analyzing a series of progressively more conservative alignments. The Rhodymeniales was resolved as two major lineages: (i) the Fryeellaceae as sister to the Faucheaceae and Lomentariaceae; and (ii) the Rhodymeniaceae allied to the Champiaceae and Hymenocladiaceae. Support at the interfamilial nodes was highest when 20% of variable sites were removed. Inclusion of Binghamiopsis, Chamaebotrys, and Minium, which were absent in previous phylogenetic investigations, established their phylogenetic affinities while assessment of two genera consistently polyphyletic in phylogenetic analyses, Erythrymenia and Lomentaria, resulted in the proposition of the novel genera Perbella and Fushitsunagia. The taxonomic position of Drouetia was reinvestigated with re-examination of holotype material of D. coalescens to clarify tetrasporangial development in this genus. In addition, we added three novel Australian species to Drouetia as a result of ongoing DNA barcoding assessments-D. aggregata sp. nov., D. scutellata sp. nov., and D. viridescens sp. nov.
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Affiliation(s)
- Gina V Filloramo
- Centre for Environmental and Molecular Algal Research, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada, E3B 5A3
| | - Gary W Saunders
- Centre for Environmental and Molecular Algal Research, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada, E3B 5A3
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11
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De Oliveira Martins L, Mallo D, Posada D. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Syst Biol 2016; 65:397-416. [PMID: 25281847 PMCID: PMC4851173 DOI: 10.1093/sysbio/syu082] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 09/30/2014] [Indexed: 11/16/2022] Open
Abstract
Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.
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Affiliation(s)
| | - Diego Mallo
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
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12
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Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G. Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A 2015; 112:15402-7. [PMID: 26621703 PMCID: PMC4687580 DOI: 10.1073/pnas.1518127112] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.
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Affiliation(s)
- Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom; School of Biological Sciences, University of Bristol, Bristol BS8 1TG, United Kingdom;
| | - Walker Pett
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Martin Dohrmann
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany
| | - Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige 38010, Italy
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France; Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montreal, QC, Canada H3C 3J7
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, 69622 Villeurbanne cedex, France
| | - Gert Wörheide
- Department of Earth & Environmental Sciences & GeoBio-Center, Ludwig-Maximilians-Universität München, Munich 80333, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Munich 80333, Germany
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13
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Akanni WA, Wilkinson M, Creevey CJ, Foster PG, Pisani D. Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140436. [PMID: 26361544 PMCID: PMC4555849 DOI: 10.1098/rsos.140436] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 07/06/2015] [Indexed: 05/14/2023]
Abstract
Since their advent, supertrees have been increasingly used in large-scale evolutionary studies requiring a phylogenetic framework and substantial efforts have been devoted to developing a wide variety of supertree methods (SMs). Recent advances in supertree theory have allowed the implementation of maximum likelihood (ML) and Bayesian SMs, based on using an exponential distribution to model incongruence between input trees and the supertree. Such approaches are expected to have advantages over commonly used non-parametric SMs, e.g. matrix representation with parsimony (MRP). We investigated new implementations of ML and Bayesian SMs and compared these with some currently available alternative approaches. Comparisons include hypothetical examples previously used to investigate biases of SMs with respect to input tree shape and size, and empirical studies based either on trees harvested from the literature or on trees inferred from phylogenomic scale data. Our results provide no evidence of size or shape biases and demonstrate that the Bayesian method is a viable alternative to MRP and other non-parametric methods. Computation of input tree likelihoods allows the adoption of standard tests of tree topologies (e.g. the approximately unbiased test). The Bayesian approach is particularly useful in providing support values for supertree clades in the form of posterior probabilities.
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Affiliation(s)
- Wasiu A. Akanni
- Department of Biology, The National University of Ireland, Maynooth, Co. Kildare, Republic of Ireland
- Department of Life Science, The Natural History Museum, London SW7 5BD, UK
| | - Mark Wilkinson
- Department of Life Science, The Natural History Museum, London SW7 5BD, UK
| | - Christopher J. Creevey
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Ceredigion SY23 3FG, UK
| | - Peter G. Foster
- Department of Life Science, The Natural History Museum, London SW7 5BD, UK
| | - Davide Pisani
- School of Biological Sciences and School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TG, UK
- Author for correspondence: Davide Pisani e-mail:
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Chaudhary R, Boussau B, Burleigh JG, Fernández-Baca D. Assessing approaches for inferring species trees from multi-copy genes. Syst Biol 2014; 64:325-39. [PMID: 25540456 DOI: 10.1093/sysbio/syu128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the availability of genomic sequence data, there is increasing interest in using genes with a possible history of duplication and loss for species tree inference. Here we assess the performance of both nonprobabilistic and probabilistic species tree inference approaches using gene duplication and loss and coalescence simulations. We evaluated the performance of gene tree parsimony (GTP) based on duplication (Only-dup), duplication and loss (Dup-loss), and deep coalescence (Deep-c) costs, the NJst distance method, the MulRF supertree method, and PHYLDOG, which jointly estimates gene trees and species tree using a hierarchical probabilistic model. We examined the effects of gene tree and species sampling, gene tree error, and duplication and loss rates on the accuracy of phylogenetic estimates. In the 10-taxon duplication and loss simulation experiments, MulRF is more accurate than the other methods when the duplication and loss rates are low, and Dup-loss is generally the most accurate when the duplication and loss rates are high. PHYLDOG performs well in 10-taxon duplication and loss simulations, but its run time is prohibitively long on larger data sets. In the larger duplication and loss simulation experiments, MulRF outperforms all other methods in experiments with at most 100 taxa; however, in the larger simulation, Dup-loss generally performs best. In all duplication and loss simulation experiments with more than 10 taxa, all methods perform better with more gene trees and fewer missing sequences, and they are all affected by gene tree error. Our results also highlight high levels of error in estimates of duplications and losses from GTP methods and demonstrate the usefulness of methods based on generic tree distances for large analyses.
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Affiliation(s)
- Ruchi Chaudhary
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; and Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France Department of Computer Science, Iowa State University, Ames, IA 50011, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; and Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France
| | - Bastien Boussau
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; and Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France
| | - J Gordon Burleigh
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; and Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France
| | - David Fernández-Baca
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; and Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France
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15
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Alderson RG, Barker D, Mitchell JBO. One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. J Mol Evol 2014; 79:117-29. [PMID: 25185655 PMCID: PMC4185109 DOI: 10.1007/s00239-014-9639-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 08/11/2014] [Indexed: 01/04/2023]
Abstract
Bacteria use metallo-β-lactamase enzymes to hydrolyse lactam rings found in many antibiotics, rendering them ineffective. Metallo-β-lactamase activity is thought to be polyphyletic, having arisen on more than one occasion within a single functionally diverse homologous superfamily. Since discovery of multiple origins of enzymatic activity conferring antibiotic resistance has broad implications for the continued clinical use of antibiotics, we test the hypothesis of polyphyly further; if lactamase function has arisen twice independently, the most recent common ancestor (MRCA) is not expected to possess lactam-hydrolysing activity. Two major problems present themselves. Firstly, even with a perfectly known phylogeny, ancestral sequence reconstruction is error prone. Secondly, the phylogeny is not known, and in fact reconstructing a single, unambiguous phylogeny for the superfamily has proven impossible. To obtain a more statistical view of the strength of evidence for or against MRCA lactamase function, we reconstructed a sample of 98 MRCAs of the metallo-β-lactamases, each based on a different tree in a bootstrap sample of reconstructed phylogenies. InterPro sequence signatures and homology modelling were then used to assess our sample of MRCAs for lactamase functionality. Only 5 % of these models conform to our criteria for metallo-β-lactamase functionality, suggesting that the ancestor was unlikely to have been a metallo-β-lactamase. On the other hand, given that ancestral proteins may have had metallo-β-lactamase functionality with variation in sequence and structural properties compared with extant enzymes, our criteria are conservative, estimating a lower bound of evidence for metallo-β-lactamase functionality but not an upper bound.
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Affiliation(s)
- Rosanna G. Alderson
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, Purdie Building, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland, UK
| | - Daniel Barker
- Sir Harold Mitchell Building, School of Biology, University of St Andrews, St Andrews, KY16 9TH Scotland, UK
| | - John B. O. Mitchell
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, Purdie Building, University of St Andrews, North Haugh, St Andrews, KY16 9ST Scotland, UK
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16
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Akanni WA, Creevey CJ, Wilkinson M, Pisani D. L.U.St: a tool for approximated maximum likelihood supertree reconstruction. BMC Bioinformatics 2014; 15:183. [PMID: 24925766 PMCID: PMC4073192 DOI: 10.1186/1471-2105-15-183] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/02/2014] [Indexed: 12/29/2022] Open
Abstract
Background Supertrees combine disparate, partially overlapping trees to generate a synthesis that provides a high level perspective that cannot be attained from the inspection of individual phylogenies. Supertrees can be seen as meta-analytical tools that can be used to make inferences based on results of previous scientific studies. Their meta-analytical application has increased in popularity since it was realised that the power of statistical tests for the study of evolutionary trends critically depends on the use of taxon-dense phylogenies. Further to that, supertrees have found applications in phylogenomics where they are used to combine gene trees and recover species phylogenies based on genome-scale data sets. Results Here, we present the L.U.St package, a python tool for approximate maximum likelihood supertree inference and illustrate its application using a genomic data set for the placental mammals. L.U.St allows the calculation of the approximate likelihood of a supertree, given a set of input trees, performs heuristic searches to look for the supertree of highest likelihood, and performs statistical tests of two or more supertrees. To this end, L.U.St implements a winning sites test allowing ranking of a collection of a-priori selected hypotheses, given as a collection of input supertree topologies. It also outputs a file of input-tree-wise likelihood scores that can be used as input to CONSEL for calculation of standard tests of two trees (e.g. Kishino-Hasegawa, Shimidoara-Hasegawa and Approximately Unbiased tests). Conclusion This is the first fully parametric implementation of a supertree method, it has clearly understood properties, and provides several advantages over currently available supertree approaches. It is easy to implement and works on any platform that has python installed. Availability: bitBucket page - https://afro-juju@bitbucket.org/afro-juju/l.u.st.git. Contact: Davide.Pisani@bristol.ac.uk.
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Affiliation(s)
| | | | | | - Davide Pisani
- Department of Biology, The National University of Ireland, Maynooth, Maynooth, Kildare, Ireland.
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17
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Schierwater B, Stadler P, Desalle R, Podsiadlowski L. Mitogenomics and metazoan evolution. Mol Phylogenet Evol 2014; 69:311-2. [PMID: 24010851 DOI: 10.1016/j.ympev.2013.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Bernd Schierwater
- ITZ, TiHo Hannover, Buenteweg 17d, 30559 Hannover, Germany; Yale University, MCDB, 165 Prospect St, New Haven, CT 06511, USA; AMNH New York, Central Park West at 79th Street, New York, NY 10024, USA
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18
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Holton TA, Wilkinson M, Pisani D. The Shape of Modern Tree Reconstruction Methods. Syst Biol 2014; 63:436-41. [DOI: 10.1093/sysbio/syt103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Paczesniak D, Jokela J, Larkin K, Neiman M. Discordance between nuclear and mitochondrial genomes in sexual and asexual lineages of the freshwater snail Potamopyrgus antipodarum. Mol Ecol 2013; 22:4695-710. [PMID: 23957656 DOI: 10.1111/mec.12422] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/29/2013] [Accepted: 06/05/2013] [Indexed: 11/30/2022]
Abstract
The presence and extent of mitonuclear discordance in coexisting sexual and asexual lineages provides insight into 1) how and when asexual lineages emerged, and 2) the spatial and temporal scales at which the ecological and evolutionary processes influencing the evolution of sexual and asexual reproduction occur. Here, we used nuclear single-nucleotide polymorphism (SNP) markers and a mitochondrial gene to characterize phylogeographic structure and the extent of mitonuclear discordance in Potamopyrgus antipodarum. This New Zealand freshwater snail is often used to study the evolution and maintenance of sex because obligately sexual and obligately asexual individuals often coexist. While our data indicate that sexual and asexual P. antipodarum sampled from the same lake population are often genetically similar, suggesting recent origin of these asexuals from sympatric sexual P. antipodarum, we also found significantly more population structure in sexuals vs. asexuals. This latter result suggests that some asexual lineages originated in other lakes and/or in the relatively distant past. When comparing mitochondrial and nuclear population genetic structure, we discovered that one mitochondrial haplotype ('1A') was rare in sexuals, but common and widespread in asexuals. Haplotype 1A frequency and nuclear genetic diversity were not associated, suggesting that the commonness of this haplotype cannot be attributed entirely to genetic drift and pointing instead to a role for selection.
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Affiliation(s)
- Dorota Paczesniak
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH-Zürich, Universitätstrasse 16, 8092, Zürich, Switzerland
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20
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Starrett J, Hedin M, Ayoub N, Hayashi CY. Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae. Gene 2013; 524:175-86. [DOI: 10.1016/j.gene.2013.04.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/18/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
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Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, O'Connell MJ. Heterogeneous models place the root of the placental mammal phylogeny. Mol Biol Evol 2013; 30:2145-56. [PMID: 23813979 PMCID: PMC3748356 DOI: 10.1093/molbev/mst117] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
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Affiliation(s)
- Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
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22
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Metazoan innovation: from aromatic amino acids to extracellular signaling. Amino Acids 2013; 45:359-67. [PMID: 23690137 DOI: 10.1007/s00726-013-1509-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
Abstract
Tyrosine depletion in metazoan proteins was recently explained to be due to the appearance of tyrosine kinases in Metazoa. Here, we present a complementary explanation for the depletion of tyrosine, stating the importance of tyrosine in signaling not only as a phosphorylation target but also as a precursor for catecholamines and hormones. Molecules (dopamine, norepinephrine, and epinephrine, and to a lesser extent serotonin and melatonin) critical to metazoan multicellular signaling are also greatly dependent on a supply of tyrosine. These signaling molecules are synthesized in two highly linked pathways specific to metazoans. In addition, the shikimate pathway that non-metazoans use to synthesize the aromatic amino acids is not present in metazoans. These important pathway changes have occurred between Metazoa and other eukaryotes, causing significant changes to tyrosine metabolism and rendering tyrosine crucial for extracellular signaling. In addition, the evolutionary and functional linkage between these two pathways and the resulting implications for neuropathology are discussed.
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Struck TH. The impact of paralogy on phylogenomic studies - a case study on annelid relationships. PLoS One 2013; 8:e62892. [PMID: 23667537 PMCID: PMC3647064 DOI: 10.1371/journal.pone.0062892] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/26/2013] [Indexed: 12/15/2022] Open
Abstract
Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus) including the robust bootstrap support could be attributed to the presence of paralogous sequences in two partitions. Excluding these sequences resulted in a different, weaker supported placement for these taxa. Moreover, the analyses revealed that paralogous sequences impacted the reconstruction when only a single taxon represented a previously supported higher taxon such as a polychaete family. One possibility of a priori detection of wrongly assigned paralogous sequences could combine 1) a screening of single-partition analyses based on criteria such as nodal support or internal branch length with 2) blast searches of suspicious cases as presented herein. Also possible are a posteriori approaches in which support for specific clades is investigated by comparing alternative hypotheses based on differences in per-site likelihoods. Increasing the sizes of EST libraries will also decrease the likelihood of wrongly assigned paralogous sequences, and in the case of orthology prediction methods like HaMStR it is likewise decreased by using more than one reference taxon.
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Bigot T, Daubin V, Lassalle F, Perrière G. TPMS: a set of utilities for querying collections of gene trees. BMC Bioinformatics 2013; 14:109. [PMID: 23530580 PMCID: PMC3655882 DOI: 10.1186/1471-2105-14-109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 03/12/2013] [Indexed: 01/02/2023] Open
Abstract
Background The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible. Results In this paper, we present TPMS (Tree Pattern-Matching Suite), a set of programs for handling and retrieving gene trees according to different criteria. The programs from the suite include utilities for tree collection building, specific tree-pattern search strategies and tree rooting. Use of TPMS is illustrated through three examples: systematic search for incongruencies in a large tree collection, a short study on the Coelomata/Ecdysozoa controversy and an evaluation of the level of support for a recently published Mammal phylogeny. Conclusion TPMS is a powerful suite allowing to quickly retrieve sets of trees matching complex patterns in large collection or to root trees using more rigorous approaches than the classical midpoint method. As it is made of a set of command-line programs, it can be easily integrated in any sequence analysis pipeline for an automated use.
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Affiliation(s)
- Thomas Bigot
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd, du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
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25
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Hill N, Leow A, Bleidorn C, Groth D, Tiedemann R, Selbig J, Hartmann S. Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information. Theory Biosci 2012; 132:93-104. [DOI: 10.1007/s12064-012-0173-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 11/30/2012] [Indexed: 11/29/2022]
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26
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Wolf YI, Makarova KS, Yutin N, Koonin EV. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct 2012; 7:46. [PMID: 23241446 PMCID: PMC3534625 DOI: 10.1186/1745-6150-7-46] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/11/2012] [Indexed: 12/17/2022] Open
Abstract
Background Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. Reviewers This article was reviewed by (for complete reviews see the Reviewers’ Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
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Parkinson J, Wasmuth JD, Salinas G, Bizarro CV, Sanford C, Berriman M, Ferreira HB, Zaha A, Blaxter ML, Maizels RM, Fernández C. A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation. PLoS Negl Trop Dis 2012; 6:e1897. [PMID: 23209850 PMCID: PMC3510090 DOI: 10.1371/journal.pntd.0001897] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/25/2012] [Indexed: 01/14/2023] Open
Abstract
Background The cestode Echinococcus granulosus - the agent of cystic echinococcosis, a zoonosis affecting humans and domestic animals worldwide - is an excellent model for the study of host-parasite cross-talk that interfaces with two mammalian hosts. To develop the molecular analysis of these interactions, we carried out an EST survey of E. granulosus larval stages. We report the salient features of this study with a focus on genes reflecting physiological adaptations of different parasite stages. Methodology/Principal Findings We generated ∼10,000 ESTs from two sets of full-length enriched libraries (derived from oligo-capped and trans-spliced cDNAs) prepared with three parasite materials: hydatid cyst wall, larval worms (protoscoleces), and pepsin/H+-activated protoscoleces. The ESTs were clustered into 2700 distinct gene products. In the context of the biology of E. granulosus, our analyses reveal: (i) a diverse group of abundant long non-protein coding transcripts showing homology to a middle repetitive element (EgBRep) that could either be active molecular species or represent precursors of small RNAs (like piRNAs); (ii) an up-regulation of fermentative pathways in the tissue of the cyst wall; (iii) highly expressed thiol- and selenol-dependent antioxidant enzyme targets of thioredoxin glutathione reductase, the functional hub of redox metabolism in parasitic flatworms; (iv) candidate apomucins for the external layer of the tissue-dwelling hydatid cyst, a mucin-rich structure that is critical for survival in the intermediate host; (v) a set of tetraspanins, a protein family that appears to have expanded in the cestode lineage; and (vi) a set of platyhelminth-specific gene products that may offer targets for novel pan-platyhelminth drug development. Conclusions/Significance This survey has greatly increased the quality and the quantity of the molecular information on E. granulosus and constitutes a valuable resource for gene prediction on the parasite genome and for further genomic and proteomic analyses focused on cestodes and platyhelminths. Cestodes are a neglected group of platyhelminth parasites, despite causing chronic infections to humans and domestic animals worldwide. We used Echinococcus granulosus as a model to study the molecular basis of the host-parasite cross-talk during cestode infections. For this purpose, we carried out a survey of the genes expressed by parasite larval stages interfacing with definitive and intermediate hosts. Sequencing from several high quality cDNA libraries provided numerous insights into the expression of genes involved in important aspects of E. granulosus biology, e.g. its metabolism (energy production and antioxidant defences) and the synthesis of key parasite structures (notably, the one exposed to humans and livestock intermediate hosts). Our results also uncovered the existence of an intriguing set of abundant repeat-associated non-protein coding transcripts that may participate in the regulation of gene expression in all surveyed stages. The dataset now generated constitutes a valuable resource for gene prediction on the parasite genome and for further genomic and proteomic studies focused on cestodes and platyhelminths. In particular, the detailed characterization of a range of newly discovered genes will contribute to a better understanding of the biology of cestode infections and, therefore, to the development of products allowing their efficient control.
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Affiliation(s)
- John Parkinson
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - James D. Wasmuth
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Gustavo Salinas
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Cristiano V. Bizarro
- Laboratório de Biologia Molecular de Cestódeos and Laboratorio de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Chris Sanford
- Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Matthew Berriman
- Parasite Genomics, The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Henrique B. Ferreira
- Laboratório de Biologia Molecular de Cestódeos and Laboratorio de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Arnaldo Zaha
- Laboratório de Biologia Molecular de Cestódeos and Laboratorio de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mark L. Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rick M. Maizels
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (RMM); (CF)
| | - Cecilia Fernández
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- * E-mail: (RMM); (CF)
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Abstract
All known visual pigments in Neuralia (Cnidaria, Ctenophora, and Bilateria) are composed of an opsin (a seven-transmembrane G protein-coupled receptor), and a light-sensitive chromophore, generally retinal. Accordingly, opsins play a key role in vision. There is no agreement on the relationships of the neuralian opsin subfamilies, and clarifying their phylogeny is key to elucidating the origin of this protein family and of vision. We used improved methods and data to resolve the opsin phylogeny and explain the evolution of animal vision. We found that the Placozoa have opsins, and that the opsins share a common ancestor with the melatonin receptors. Further to this, we found that all known neuralian opsins can be classified into the same three subfamilies into which the bilaterian opsins are classified: the ciliary (C), rhabdomeric (R), and go-coupled plus retinochrome, retinal G protein-coupled receptor (Go/RGR) opsins. Our results entail a simple scenario of opsin evolution. The first opsin originated from the duplication of the common ancestor of the melatonin and opsin genes in a eumetazoan (Placozoa plus Neuralia) ancestor, and an inference of its amino acid sequence suggests that this protein might not have been light-sensitive. Two more gene duplications in the ancestral neuralian lineage resulted in the origin of the R, C, and Go/RGR opsins. Accordingly, the first animal with at least a C, an R, and a Go/RGR opsin was a neuralian progenitor.
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Hinchliff CE, Roalson EH. Using supermatrices for phylogenetic inquiry: an example using the sedges. Syst Biol 2012; 62:205-19. [PMID: 23103590 DOI: 10.1093/sysbio/sys088] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In this article, we use supermatrix data-mining methods to reconstruct a large, highly inclusive phylogeny of Cyperaceae from nucleotide data available on GenBank. We explore the properties of these trees and their utility for phylogenetic inference, and show that even the highly incomplete alignments characteristic of supermatrix approaches may yield very good estimates of phylogeny. We present a novel pipeline for filtering sparse alignments to improve their phylogenetic utility by maximizing the partial decisiveness of the matrices themselves through a technique we call "phylogenetic scaffolding," and we present a new method of scoring tip instability (i.e. "rogue taxa") based on the I statistic implemented in the software Mesquite. The modified statistic, which we call I(S), is somewhat more straightforward to interpret than similar statistics, and our implementation of it may be applied to large sets of large trees. The largest sedge trees presented here contain more than 1500 tips (about one quarter of all sedge species) and are based on multigene alignments with more than 20 000 sites and more than 90% missing data. These trees match well with previously supported phylogenetic hypotheses, but have lower overall support values and less resolution than more heavily filtered trees. Our best-resolved trees are characterized by stronger support values than any previously published sedge phylogenies, and show some relationships that are incongruous with previous studies. Overall, we show that supermatrix methods offer powerful means of pursuing phylogenetic study and these tools have high potential value for many systematic biologists.
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Affiliation(s)
- Cody E Hinchliff
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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Cohen E, Chor B. Detecting Phylogenetic Signals in Eukaryotic Whole Genome Sequences. J Comput Biol 2012; 19:945-56. [DOI: 10.1089/cmb.2012.0122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Eyal Cohen
- School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Benny Chor
- School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
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Hartmann S, Helm C, Nickel B, Meyer M, Struck TH, Tiedemann R, Selbig J, Bleidorn C. Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS One 2012; 7:e29843. [PMID: 22276131 PMCID: PMC3262807 DOI: 10.1371/journal.pone.0029843] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 12/06/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms. METHODOLOGY Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. CONCLUSIONS Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.
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Affiliation(s)
- Stefanie Hartmann
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Conrad Helm
- University of Leipzig, Institute for Biology II, Molecular Evolution and Systematics of Animals, Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
| | | | - Ralph Tiedemann
- Department of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Joachim Selbig
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christoph Bleidorn
- University of Leipzig, Institute for Biology II, Molecular Evolution and Systematics of Animals, Leipzig, Germany
- Department of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom. J Mol Evol 2011; 73:116-33. [PMID: 21938499 DOI: 10.1007/s00239-011-9461-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 09/07/2011] [Indexed: 01/02/2023]
Abstract
We have used three independent phylogenomic approaches (concatenated alignments, single-, and multi-gene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from single- and multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom.
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Campbell LI, Rota-Stabelli O, Edgecombe GD, Marchioro T, Longhorn SJ, Telford MJ, Philippe H, Rebecchi L, Peterson KJ, Pisani D. MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci U S A 2011; 108:15920-4. [PMID: 21896763 PMCID: PMC3179045 DOI: 10.1073/pnas.1105499108] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations--comparisons of model fit, signal dissection, and taxonomic pruning--we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.
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Affiliation(s)
- Lahcen I. Campbell
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
| | - Omar Rota-Stabelli
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
| | - Gregory D. Edgecombe
- Department of Palaeontology, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Trevor Marchioro
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, 41125 Modena, Italy
| | - Stuart J. Longhorn
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
| | - Maximilian J. Telford
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Hervé Philippe
- Centre Robert-Cedergren, Département de Biochimie, Université de Montréal, Montréal, QC, Canada H3C3J7; and
| | - Lorena Rebecchi
- Dipartimento di Biologia, Università di Modena e Reggio Emilia, 41125 Modena, Italy
| | | | - Davide Pisani
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
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Pisani D, Feuda R, Peterson KJ, Smith AB. Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships. Mol Phylogenet Evol 2011; 62:27-34. [PMID: 21945533 DOI: 10.1016/j.ympev.2011.08.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 07/08/2011] [Accepted: 08/31/2011] [Indexed: 10/17/2022]
Abstract
Resolving evolutionary relationships in groups that underwent fast radiation in deep time is a problem for molecular phylogeny, as the scant phylogenetic signal that characterises short internal branches is generally swamped by more recent substitutions. We implement an approach, that maps how the support for rival phylogenies changes when analysing subsets of sites with either faster and more heterogeneous rates or slower and more homogeneous rates, to address a long-standing problem in deuterostome phylogeny - the interrelationships of the eleutherozoan echinoderm classes. We show that miRNA genes are phylogenetically uninformative as to the relationships of asteroids, echinoids and ophiuroids, consistent with a rapid radiation of these groups as suggested by their fossil record. Using three nuclear rRNAs and seven nuclear housekeeping genes, we map the support for the three possible phylogenetic arrangements of asteroids, ophiuroids and echinoids when moving between subsets of the data with very similar or very different rates of evolution. Only one of the three possible topologies (asteroids (ophiuroids+echinoids)) strengthens when the most rate-homogeneous subset of data are analysed. The other two possible pairings become stronger in a less reliable data subset, which includes the fastest and thus homoplasy-rich data in our alignment. Thus, while superficial analysis of our concatenated alignment identifies asteroids and ophiuroids as sister taxa, more thorough analyses suggest that ophiuroids may be more closely related to echinoids. Divergence of these echinoderm groups, using a relaxed molecular clock, is estimated to have occurred within ≈ 5 million years. Our results illustrate that the analytic approach of phylogenetic signal dissection can be a powerful tool to investigate rapid radiations in deep geologic time.
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Affiliation(s)
- Davide Pisani
- The National University of Ireland, Maynooth, Co. Kildare, Ireland
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Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. Statistics and truth in phylogenomics. Mol Biol Evol 2011; 29:457-72. [PMID: 21873298 DOI: 10.1093/molbev/msr202] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Phylogenomics refers to the inference of historical relationships among species using genome-scale sequence data and to the use of phylogenetic analysis to infer protein function in multigene families. With rapidly decreasing sequencing costs, phylogenomics is becoming synonymous with evolutionary analysis of genome-scale and taxonomically densely sampled data sets. In phylogenetic inference applications, this translates into very large data sets that yield evolutionary and functional inferences with extremely small variances and high statistical confidence (P value). However, reports of highly significant P values are increasing even for contrasting phylogenetic hypotheses depending on the evolutionary model and inference method used, making it difficult to establish true relationships. We argue that the assessment of the robustness of results to biological factors, that may systematically mislead (bias) the outcomes of statistical estimation, will be a key to avoiding incorrect phylogenomic inferences. In fact, there is a need for increased emphasis on the magnitude of differences (effect sizes) in addition to the P values of the statistical test of the null hypothesis. On the other hand, the amount of sequence data available will likely always remain inadequate for some phylogenomic applications, for example, those involving episodic positive selection at individual codon positions and in specific lineages. Again, a focus on effect size and biological relevance, rather than the P value, may be warranted. Here, we present a theoretical overview and discuss practical aspects of the interplay between effect sizes, bias, and P values as it relates to the statistical inference of evolutionary truth in phylogenomics.
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Affiliation(s)
- Sudhir Kumar
- Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Arizona, USA.
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Gunbin KV, Suslov VV, Turnaev II, Afonnikov DA, Kolchanov NA. Molecular evolution of cyclin proteins in animals and fungi. BMC Evol Biol 2011; 11:224. [PMID: 21798004 PMCID: PMC3162929 DOI: 10.1186/1471-2148-11-224] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 07/28/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The passage through the cell cycle is controlled by complexes of cyclins, the regulatory units, with cyclin-dependent kinases, the catalytic units. It is also known that cyclins form several families, which differ considerably in primary structure from one eukaryotic organism to another. Despite these lines of evidence, the relationship between the evolution of cyclins and their function is an open issue. Here we present the results of our study on the molecular evolution of A-, B-, D-, E-type cyclin proteins in animals and fungi. RESULTS We constructed phylogenetic trees for these proteins, their ancestral sequences and analyzed patterns of amino acid replacements. The analysis of infrequently fixed atypical amino acid replacements in cyclins evidenced that accelerated evolution proceeded predominantly during paralog duplication or after it in animals and fungi and that it was related to aromorphic changes in animals. It was shown also that evolutionary flexibility of cyclin function may be provided by consequential reorganization of regions on protein surface remote from CDK binding sites in animal and fungal cyclins and by functional differentiation of paralogous cyclins formed in animal evolution. CONCLUSIONS The results suggested that changes in the number and/or nature of cyclin-binding proteins may underlie the evolutionary role of the alterations in the molecular structure of cyclins and their involvement in diverse molecular-genetic events.
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Affiliation(s)
- Konstantin V Gunbin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Valentin V Suslov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Igor I Turnaev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
- Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev ave., 10, Novosibirsk, Russia
- Novosibirsk state University, Pirogova, 2, Novosibirsk, Russia
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Ness RW, Graham SW, Barrett SCH. Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae. Mol Biol Evol 2011; 28:3009-18. [PMID: 21633114 DOI: 10.1093/molbev/msr119] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most plant phylogenetic inference has used DNA sequence data from the plastid genome. This genome represents a single genealogical sample with no recombination among genes, potentially limiting the resolution of evolutionary relationships in some contexts. In contrast, nuclear DNA is inherently more difficult to employ for phylogeny reconstruction because major mutational events in the genome, including polyploidization, gene duplication, and gene extinction can result in homologous gene copies that are difficult to identify as orthologs or paralogs. Gene tree parsimony (GTP) can be used to infer the rooted species tree by fitting gene genealogies to species trees while simultaneously minimizing the estimated number of duplications needed to reconcile conflicts among them. Here, we use GTP for five nuclear gene families and a previously published plastid data set to reconstruct the phylogenetic backbone of the aquatic plant family Pontederiaceae. Plastid-based phylogenetic studies strongly supported extensive paraphyly of Eichhornia (one of the four major genera) but also depicted considerable ambiguity concerning the true root placement for the family. Our results indicate that species trees inferred from the nuclear genes (alone and in combination with the plastid data) are highly congruent with gene trees inferred from plastid data alone. Consideration of optimal and suboptimal gene tree reconciliations place the root of the family at (or near) a branch leading to the rare and locally restricted E. meyeri. We also explore methods to incorporate uncertainty in individual gene trees during reconciliation by considering their individual bootstrap profiles and relate inferred excesses of gene duplication events on individual branches to whole-genome duplication events inferred for the same branches. Our study improves understanding of the phylogenetic history of Pontederiaceae and also demonstrates the utility of GTP for phylogenetic analysis.
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Affiliation(s)
- Rob W Ness
- Department of Ecology & Evolutionary Biology, University of Toronto, Ontario, Canada.
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Telford MJ, Copley RR. Improving animal phylogenies with genomic data. Trends Genet 2011; 27:186-95. [DOI: 10.1016/j.tig.2011.02.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 02/04/2023]
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Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. Higher-level metazoan relationships: recent progress and remaining questions. ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0044-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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