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Francisco Barbosa F, Mermudes JRM, Russo CAM. Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny. PeerJ 2024; 12:e16706. [PMID: 38213769 PMCID: PMC10782957 DOI: 10.7717/peerj.16706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
Recently, many studies have addressed the performance of phylogenetic tree-building methods (maximum parsimony, maximum likelihood, and Bayesian inference), focusing primarily on simulated data. However, for discrete morphological data, there is no consensus yet on which methods recover the phylogeny with better performance. To address this lack of consensus, we investigate the performance of different methods using an empirical dataset for hexapods as a model. As an empirical test of performance, we applied normalized indices to effectively measure accuracy (normalized Robinson-Foulds metric, nRF) and precision, which are measured via resolution, one minus Colless' consensus fork index (1-CFI). Additionally, to further explore phylogenetic accuracy and support measures, we calculated other statistics, such as the true positive rate (statistical power) and the false positive rate (type I error), and constructed receiver operating characteristic plots to visualize the relationship between these statistics. We applied the normalized indices to the reconstructed trees from the reanalyses of an empirical discrete morphological dataset from extant Hexapoda using a well-supported phylogenomic tree as a reference. Maximum likelihood and Bayesian inference applying the k-state Markov (Mk) model (without or with a discrete gamma distribution) performed better, showing higher precision (resolution). Additionally, our results suggest that most available tree topology tests are reliable estimators of the performance measures applied in this study. Thus, we suggest that likelihood-based methods and tree topology tests should be used more often in phylogenetic tree studies based on discrete morphological characters. Our study provides a fair indication that morphological datasets have robust phylogenetic signal.
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Affiliation(s)
| | | | - Claudia A. M. Russo
- Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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2
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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3
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Tidwell H, Nakhleh L. Integrated likelihood for phylogenomics under a no-common-mechanism model. BMC Genomics 2020; 21:219. [PMID: 32299348 PMCID: PMC7161099 DOI: 10.1186/s12864-020-6608-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Multi-locus species phylogeny inference is based on models of sequence evolution on gene trees as well as models of gene tree evolution within the branches of species phylogenies. Almost all statistical methods for this inference task assume a common mechanism across all loci as captured by a single value of each branch length of the species phylogeny. Results In this paper, we pursue a “no common mechanism" (NCM) model, where every gene tree evolves according to its own parameters of the species phylogeny. Based on this model, we derive an analytically integrated likelihood of both species trees and networks given the gene trees of multiple loci under an NCM model. We demonstrate the performance of inference under this integrated likelihood on both simulated and biological data. Conclusions The model presented here will afford opportunities for exploring connections among various criteria for estimating species phylogenies from multiple, independent loci. Furthermore, further development of this model could potentially result in more efficient methods for searching the space of species phylogenies by focusing solely on the topology of the phylogeny.
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Abstract
Background: Locating the root node of the "tree of life" (ToL) is one of the hardest problems in phylogenetics, given the time depth. The root-node, or the universal common ancestor (UCA), groups descendants into organismal clades/domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA, and that Asgard archaea are sister to other archaea. The other 2D-ToL proposes that eukaryotes emerged from within archaea and places Asgard archaea as sister to eukaryotes. Williams et al. ( Nature Ecol. Evol. 4: 138-147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: The poor resolution of the archaea in their analysis, despite employing amino acid alignments from thousands of proteins and the best-fitting substitution models, contradicts their conclusions. We argue that they overlooked important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data. Which 2D-ToL is better supported depends on which kind of molecular features are better for resolving common ancestors at the roots of clades - protein-domains or their component amino acids. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. Clarifications: It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. We show that protein structural-domains support more reliable phylogenetic reconstructions of deep-diverging clades in the ToL. Accordingly, Eukaryotes and Akaryotes are better supported clades in a 2D-ToL.
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Affiliation(s)
| | - David Morrison
- Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, 752 36, Sweden
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Cabra-García J, Hormiga G. Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.
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Affiliation(s)
- Jimmy Cabra-García
- Departamento de Biología, Universidad del Valle, Cali, AA, Colombia
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gustavo Hormiga
- The George Washington University, Department of Biological Sciences, Washington, DC, USA
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Abstract
The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves.
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Goloboff PA, Pittman M, Pol D, Xu X. Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model. Syst Biol 2019; 68:494-504. [PMID: 30445627 DOI: 10.1093/sysbio/syy077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/11/2018] [Accepted: 11/13/2018] [Indexed: 01/30/2023] Open
Abstract
The Mkv evolutionary model, based on minor modifications to models of molecular evolution, is being increasingly used to infer phylogenies from discrete morphological data, often producing different results from parsimony. The critical difference between Mkv and parsimony is the assumption of a "common mechanism" in the Mkv model, with branch lengths determining that probability of change for all characters increases or decreases at the same tree branches by the same exponential factor. We evaluate whether the assumption of a common mechanism applies to morphology, by testing the implicit prediction that branch lengths calculated from different subsets of characters will be significantly correlated. Our analysis shows that DNA (38 data sets tested) is often compatible with a common mechanism, but morphology (86 data sets tested) generally is not, showing very disparate branch lengths for different character partitions. The low levels of branch length correlation demonstrated for morphology (fitting models without a common mechanism) suggest that the Mkv model is too unrealistic and inadequate for the analysis of most morphological data sets. [Bayesian analysis; Mkv model; morphological data; phylogenetics.].
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo (UEL), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), S.M. Tucumán, Argentina
| | - Michael Pittman
- Vertebrate Palaeontology Laboratory, Department of Earth Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Diego Pol
- Museo Egidio Feruglio, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Trelew, Argentina
| | - Xing Xu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
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8
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Goloboff PA, Arias JS. Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion. Cladistics 2019; 35:695-716. [DOI: 10.1111/cla.12380] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 01/09/2023] Open
Affiliation(s)
- Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas Fundación Miguel Lillo Miguel Lillo 251 4000 S.M. de Tucumán Argentina
| | - J. Salvador Arias
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas Fundación Miguel Lillo Miguel Lillo 251 4000 S.M. de Tucumán Argentina
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Staley JT, Caetano-Anollés G. Archaea-First and the Co-Evolutionary Diversification of Domains of Life. Bioessays 2018; 40:e1800036. [PMID: 29944192 DOI: 10.1002/bies.201800036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/12/2018] [Indexed: 12/13/2022]
Abstract
The origins and evolution of the Archaea, Bacteria, and Eukarya remain controversial. Phylogenomic-wide studies of molecular features that are evolutionarily conserved, such as protein structural domains, suggest Archaea is the first domain of life to diversify from a stem line of descent. This line embodies the last universal common ancestor of cellular life. Here, we propose that ancestors of Euryarchaeota co-evolved with those of Bacteria prior to the diversification of Eukarya. This co-evolutionary scenario is supported by comparative genomic and phylogenomic analyses of the distributions of fold families of domains in the proteomes of free-living organisms, which show horizontal gene recruitments and informational process homologies. It also benefits from the molecular study of cell physiologies responsible for membrane phospholipids, methanogenesis, methane oxidation, cell division, gas vesicles, and the cell wall. Our theory however challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis, demanding phylogenetic reconciliation. Also see the video abstract here: https://youtu.be/9yVWn_Q9faY.
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Affiliation(s)
- James T Staley
- Department of Microbiology and Astrobiology Program, University of Washington, Seattle, WA, 98195, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, C. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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10
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Brower AVZ. Statistical consistency and phylogenetic inference: a brief review. Cladistics 2017; 34:562-567. [DOI: 10.1111/cla.12216] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2017] [Indexed: 11/29/2022] Open
Affiliation(s)
- Andrew V. Z. Brower
- Evolution and Ecology Group Department of Biology Middle Tennessee State University Murfreesboro TN 37132 USA
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11
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Peloso PL, Frost DR, Richards SJ, Rodrigues MT, Donnellan S, Matsui M, Raxworthy CJ, Biju S, Lemmon EM, Lemmon AR, Wheeler WC. The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura, Microhylidae). Cladistics 2015; 32:113-140. [DOI: 10.1111/cla.12118] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2015] [Indexed: 02/02/2023] Open
Affiliation(s)
- Pedro L.V. Peloso
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
- Richard Gilder Graduate School American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Darrel R. Frost
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - Stephen J. Richards
- Herpetology Department South Australian Museum North Terrace Adelaide SA 5000 Australia
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo, Rua do Matão Trav. 14, n 321, Cidade Universitária, Caixa Postal 11461 CEP 05422‐970 São Paulo São Paulo Brazil
| | - Stephen Donnellan
- Centre for Evolutionary Biology and Biodiversity The University of Adelaide Adelaide SA 5005 Australia
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies Kyoto University Sakyo‐ku Kyoto 606‐8501 Japan
| | - Cristopher J. Raxworthy
- Division of Vertebrate Zoology (Herpetology) American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - S.D. Biju
- Systematics Lab Department of Environmental Studies University of Delhi Delhi 110 007 India
| | | | - Alan R. Lemmon
- Department of Scientific Computing Florida State University Dirac Science Library Tallahassee FL 32306‐4120 USA
| | - Ward C. Wheeler
- Division of Invertebrate Zoology American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
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12
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Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP. Strepsiptera, phylogenomics and the long branch attraction problem. PLoS One 2014; 9:e107709. [PMID: 25272037 PMCID: PMC4182670 DOI: 10.1371/journal.pone.0107709] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022] Open
Abstract
Insect phylogeny has recently been the focus of renewed interest as advances in sequencing techniques make it possible to rapidly generate large amounts of genomic or transcriptomic data for a species of interest. However, large numbers of markers are not sufficient to guarantee accurate phylogenetic reconstruction, and the choice of the model of sequence evolution as well as adequate taxonomic sampling are as important for phylogenomic studies as they are for single-gene phylogenies. Recently, the sequence of the genome of a strepsipteran has been published and used to place Strepsiptera as sister group to Coleoptera. However, this conclusion relied on a data set that did not include representatives of Neuropterida or of coleopteran lineages formerly proposed to be related to Strepsiptera. Furthermore, it did not use models that are robust against the long branch attraction artifact. Here we have sequenced the transcriptomes of seven key species to complete a data set comprising 36 species to study the higher level phylogeny of insects, with a particular focus on Neuropteroidea (Coleoptera, Strepsiptera, Neuropterida), especially on coleopteran taxa considered as potential close relatives of Strepsiptera. Using models robust against the long branch attraction artifact we find a highly resolved phylogeny that confirms the position of Strepsiptera as a sister group to Coleoptera, rather than as an internal clade of Coleoptera, and sheds new light onto the phylogeny of Neuropteroidea.
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Affiliation(s)
- Bastien Boussau
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Zaak Walton
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Juan A. Delgado
- Departamento de Zoologia y Antropologia Fisica, Facultad de Biologia, Universidad de Murcia, Murcia, Spain
| | - Francisco Collantes
- Departamento de Zoologia y Antropologia Fisica, Facultad de Biologia, Universidad de Murcia, Murcia, Spain
| | - Laura Beani
- Dipartimento di Biologia, Università di Firenze, Sesto Fiorentino, Firenze, Italia
| | - Isaac J. Stewart
- Fisher High School, Fisher, IL, United States of America
- Department of Entomology, University of Illinois, Urbana, IL, United States of America
| | - Sydney A. Cameron
- Department of Entomology, University of Illinois, Urbana, IL, United States of America
| | - James B. Whitfield
- Department of Entomology, University of Illinois, Urbana, IL, United States of America
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, United States of America
| | - Peter W.H. Holland
- Department of Zoology, University of Oxford, Oxford, England, United Kingdom
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | | | - John P. Huelsenbeck
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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13
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Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. BIOLOGY 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
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Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
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14
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Martins LDO, Posada D. Proving universal common ancestry with similar sequences. TRENDS IN EVOLUTIONARY BIOLOGY 2012; 4:e5. [PMID: 23814665 PMCID: PMC3694314 DOI: 10.4081/eb.2012.e5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer (HGT) and to the quality of sequence alignment.
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15
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Wagner PJ. Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates. Biol Lett 2011; 8:143-6. [PMID: 21795266 DOI: 10.1098/rsbl.2011.0523] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rate distributions are important considerations when testing hypotheses about morphological evolution or phylogeny. They also have implications about general processes underlying character evolution. Molecular systematists often assume that rates are Poisson processes with gamma distributions. However, morphological change is the product of multiple probabilistic processes and should theoretically be affected by hierarchical integration of characters. Both factors predict lognormal rate distributions. Here, a simple inverse modelling approach assesses the best single-rate, gamma and lognormal models given observed character compatibility for 115 invertebrate groups. Tests reject the single-rate model for nearly all cases. Moreover, the lognormal outperforms the gamma for character change rates and (especially) state derivation rates. The latter in particular is consistent with integration affecting morphological character evolution.
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Affiliation(s)
- Peter J Wagner
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
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16
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Affiliation(s)
- Mike Steel
- Allan Wilson Centre for Molecular Ecology and Evolution, Biomathematics Research Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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