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de Paula LCB, Dios RDVP, Gudin FM, de Santis MD, Alvarez-Garcia DM, Antunes Júnior M, Freire BV, Marques FPDL, Lahr DJG, Nihei SS. Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships. Cladistics 2024; 40:64-81. [PMID: 37837208 DOI: 10.1111/cla.12562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 08/25/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Tachinidae is the second most species-rich family of Diptera. It comprises four subfamilies, and all of its members have parasitoid habits. We present the first phylogenomic analysis of Tachinidae using transcriptomic data, based on 30 species. We constructed four datasets: three using translated data at the amino acid level (100% coverage, with 106 single-copy protein-coding genes; 75% coverage, with 1359 genes; and 50% coverage, with 1942 genes). The trees were estimated by analysing four matrices using maximum likelihood and maximum parsimony inferences, and only minor differences were found among them. Overall, our topologies are well resolved, with high node support. Polleniidae is corroborated as a sister group to Tachinidae. Within Tachinidae, our results confirm the hypothesis (Phasiinae + Dexiinae) + (Tachininae + Exoristinae). Phasiinae, Dexiinae and Exoristinae are recovered as monophyletic, and Tachininae as polyphyletic. Once again, the tribe Myiophasiini (Tachininae) composes a fifth lineage, clade sister to all the remaining Tachinidae. The Neotropical tribe Iceliini, formerly in Tachininae, is recovered within Exoristinae, sister to Winthemiini. In general, our results are congruent with recent phylogenetic studies that include tachinids, with the important confirmation of the subfamilial relationships and the existence of a fifth lineage of Tachinidae.
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Affiliation(s)
- Letícia Chiara Baldassio de Paula
- Department of Genetics, Institute of Biosciences, University of São Paulo, Rua do Matão, n 277, São Paulo, SP, 05508-090, Brazil
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Rodrigo de Vilhena Perez Dios
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Filipe Macedo Gudin
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Marcelo Domingos de Santis
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut zur Analyse des Biodiversitatswandels, Adenauerallee 127, D-53113, Bonn, Germany
| | - Deivys Moises Alvarez-Garcia
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
- Grupo de Investigación en Zoología y Ecología, Universidad de Sucre, Cra 28 # 5 - 267 Barrio Puerta Roja, Sincelejo, Colombia
| | - Manuel Antunes Júnior
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Beatriz Vieira Freire
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Fernando Portella de Luna Marques
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Daniel José Galafasse Lahr
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
| | - Silvio Shigueo Nihei
- Department of Zoology, Institute of Biosciences, University of São Paulo, Rua do Matão, Travessa 14, n 101, São Paulo, SP, 05508-090, Brazil
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2
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Patané JSL, Martins J, Setubal JC. A Guide to Phylogenomic Inference. Methods Mol Biol 2024; 2802:267-345. [PMID: 38819564 DOI: 10.1007/978-1-0716-3838-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração/Heart Institute Hospital das Clínicas - Faculdade de Medicina da Universidade de São Paulo São Paulo, São Paulo, SP, Brazil
| | - Joaquim Martins
- Integrative Omics group, Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - João Carlos Setubal
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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3
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Henríquez-Piskulich P, Hugall AF, Stuart-Fox D. A supermatrix phylogeny of the world's bees (Hymenoptera: Anthophila). Mol Phylogenet Evol 2024; 190:107963. [PMID: 37967640 DOI: 10.1016/j.ympev.2023.107963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
The increasing availability of large molecular phylogenies has provided new opportunities to study the evolution of species traits, their origins and diversification, and biogeography; yet there are limited attempts to synthesise existing phylogenetic information for major insect groups. Bees (Hymenoptera: Anthophila) are a large group of insect pollinators that have a worldwide distribution, and a wide variation in ecology, morphology, and life-history traits, including sociality. For these reasons, as well as their major economic importance as pollinators, numerous molecular phylogenetic studies of family and genus-level relationships have been published, providing an opportunity to assemble a bee 'tree-of-life'. We used publicly available genetic sequence data, including phylogenomic data, reconciled to a taxonomic database, to produce a concatenated supermatrix phylogeny for the Anthophila comprising 4,586 bee species, representing 23% of species and 82% of genera. At family, subfamily, and tribe levels, support for expected relationships was robust, but between and within some genera relationships remain uncertain. Within families, sampling of genera ranged from 67 to 100% but species coverage was lower (17-41%). Our phylogeny mostly reproduces the relationships found in recent phylogenomic studies with a few exceptions. We provide a summary of these differences and the current state of molecular data available and its gaps. We discuss the advantages and limitations of this bee supermatrix phylogeny (available online at beetreeoflife.org), which may enable new insights into long standing questions about evolutionary drivers in bees, and potentially insects more generally.
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Affiliation(s)
| | - Andrew F Hugall
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia; Department of Sciences, Museums Victoria, Melbourne, Victoria, Australia.
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
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4
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Chesters D, Ferrari RR, Lin X, Orr MC, Staab M, Zhu CD. Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects. Mol Ecol Resour 2023; 23:1556-1573. [PMID: 37265018 DOI: 10.1111/1755-0998.13817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species-level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species-comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine-readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species-comprehensive phylogenies for biological research.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Rafael R Ferrari
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Michael Staab
- Ecological Networks, Technische Universität Darmstadt, Darmstadt, Germany
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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5
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Sanchez-Fernandez C, Bolatti EM, Culasso ACA, Chouhy D, Kowalewski MM, Stella EJ, Schurr TG, Rinas MA, Liotta DJ, Campos RH, Giri AA, Badano I. Identification and evolutionary analysis of papillomavirus sequences in New World monkeys (genera Sapajus and Alouatta) from Argentina. Arch Virol 2022; 167:1257-1268. [PMID: 35353206 DOI: 10.1007/s00705-022-05420-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/03/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE In this study, we investigated the occurrence of papillomavirus (PV) infection in non-human primates (NHPs) in northeastern Argentina. We also explored their evolutionary history and evaluated the co-speciation hypothesis in the context of primate evolution. METHODS We obtained DNA samples from 57 individuals belonging to wild and captive populations of Alouatta caraya, Sapajus nigritus, and Sapajus cay. We assessed PV infection by PCR amplification with the CUT primer system and sequencing of 337 bp (112 amino acids) of the L1 gene. The viral sequences were analyzed by phylogenetic and Bayesian coalescence methods to estimate the time to the most common recent ancestor (tMRCA) using BEAST, v1.4.8 software. We evaluated viral/host tree congruence with TreeMap v3.0. RESULTS We identified two novel putative PV sequences of the genus Gammapapillomavirus in Sapajus spp. and Alouatta caraya (SPV1 and AcPV1, respectively). The tMRCA of SPV1 was estimated to be 11,941,682 years before present (ybp), and that of AcPV1 was 46,638,071 ybp, both before the coalescence times of their hosts (6.4 million years ago [MYA] and 6.8 MYA, respectively). Based on the comparison of primate and viral phylogenies, we found that the PV tree was no more congruent with the host tree than a random tree would be (P > 0.05), thus allowing us to reject the model of virus-host coevolution. CONCLUSION This study presents the first evidence of PV infection in platyrrhine species from Argentina, expands the range of described hosts for these viruses, and suggests new scenarios for their origin and dispersal.
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Affiliation(s)
- C Sanchez-Fernandez
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - E M Bolatti
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - A C A Culasso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - D Chouhy
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - M M Kowalewski
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Estación Biológica Corrientes (EBCo-MACN-CONICET), Corrientes, Argentina
| | - E J Stella
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina
| | - T G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - M A Rinas
- Ministerio de Ecología y Recursos Naturales Renovables, Posadas, Misiones, Argentina
| | - D J Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.,Instituto Nacional de Medicina Tropical, ANLIS, Pto. Iguazú, Misiones, Argentina
| | - R H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - A A Giri
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - I Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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6
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Mongiardino Koch N, Thompson JR, Hiley AS, McCowin MF, Armstrong AF, Coppard SE, Aguilera F, Bronstein O, Kroh A, Mooi R, Rouse GW. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. eLife 2022; 11:72460. [PMID: 35315317 PMCID: PMC8940180 DOI: 10.7554/elife.72460] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Earth & Planetary Sciences, Yale University, New Haven, United States.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Jeffrey R Thompson
- Department of Earth Sciences, Natural History Museum, London, United Kingdom.,University College London Center for Life's Origins and Evolution, London, United Kingdom
| | - Avery S Hiley
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Marina F McCowin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - A Frances Armstrong
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Simon E Coppard
- Bader International Study Centre, Queen's University, Herstmonceux Castle, East Sussex, United Kingdom
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Rich Mooi
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
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7
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Karmeinski D, Meusemann K, Goodheart JA, Schroedl M, Martynov A, Korshunova T, Wägele H, Donath A. Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia. BMC Ecol Evol 2021; 21:226. [PMID: 34963462 PMCID: PMC8895541 DOI: 10.1186/s12862-021-01944-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01944-0.
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Affiliation(s)
- Dario Karmeinski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Karen Meusemann
- Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany.,Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), National Facilities and Collections, Clunies Ross Street, Acton, Canberra, ACT, 2601, Australia
| | - Jessica A Goodheart
- Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Michael Schroedl
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, Munich, Germany.,GeoBioCenter LMU und Biozentrum, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Alexander Martynov
- Zoological Museum of the Moscow State University, Bolshaya Nikitskaya Str. 6, 125009, Moscow, Russia
| | - Tatiana Korshunova
- Koltzov Institute of Developmental Biology, Vavilova Str. 26, 119334, Moscow, Russia
| | - Heike Wägele
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany.
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8
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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: 23] [Impact Index Per Article: 7.7] [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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9
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Toussaint EFA, Gauthier J, Bilat J, Gillett CPDT, Gough HM, Lundkvist H, Blanc M, Muñoz-Ramírez CP, Alvarez N. HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution. Genome Biol Evol 2021; 13:6275686. [PMID: 33988685 PMCID: PMC8480185 DOI: 10.1093/gbe/evab112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/27/2022] Open
Abstract
Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.
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Affiliation(s)
| | | | - Julia Bilat
- Natural History Museum of Geneva, Switzerland
| | - Conrad P D T Gillett
- University of Hawai'i Insect Museum, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Harlan M Gough
- Florida Natural History Museum, University of Florida, Gainesville, Florida, USA
| | | | | | - Carlos P Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.,Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Chile
| | - Nadir Alvarez
- Natural History Museum of Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Switzerland
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10
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Minh BQ, Hahn MW, Lanfear R. New Methods to Calculate Concordance Factors for Phylogenomic Datasets. Mol Biol Evol 2021; 37:2727-2733. [PMID: 32365179 PMCID: PMC7475031 DOI: 10.1093/molbev/msaa106] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).
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Affiliation(s)
- Bui Quang Minh
- Research School of Computer Science, Australian National University, Canberra, ACT, Australia.,Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,Department of Computer Science, Indiana University, Bloomington, IN
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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11
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Takezaki N. Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data. Genome Biol Evol 2021; 13:6178791. [PMID: 33739405 PMCID: PMC8103497 DOI: 10.1093/gbe/evab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: 1) 412 genes from 12 species, 2) 772 genes from 15 species, 3) 1,062 genes from 30 species, and 4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the data sets (1)–(3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE data set (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
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12
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Bayless KM, Trautwein MD, Meusemann K, Shin S, Petersen M, Donath A, Podsiadlowski L, Mayer C, Niehuis O, Peters RS, Meier R, Kutty SN, Liu S, Zhou X, Misof B, Yeates DK, Wiegmann BM. Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics. BMC Biol 2021; 19:23. [PMID: 33557827 PMCID: PMC7871583 DOI: 10.1186/s12915-020-00944-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge. RESULTS Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila's superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the 'Modified Oviscapt Clade' containing Tephritoidea, Nerioidea, and other families, and the 'Cleft Pedicel Clade' containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data. CONCLUSIONS Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.
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Affiliation(s)
- Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, Australia.
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA.
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA.
| | - Michelle D Trautwein
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, Australia
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstraße 1, Freiburg i. Br., Germany
| | - Seunggwan Shin
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Malte Petersen
- Max-Planck-Institut of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstraße 1, Freiburg i. Br., Germany
| | - Ralph S Peters
- Centre of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, People's Republic of China
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, Australia
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
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13
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Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM. Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae). Proc Biol Sci 2020; 287:20202102. [PMID: 33290680 PMCID: PMC7739936 DOI: 10.1098/rspb.2020.2102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/13/2020] [Indexed: 11/12/2022] Open
Abstract
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Carl R. Hutter
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L. Wood
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA 92505, USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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14
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Szucsich NU, Bartel D, Blanke A, Böhm A, Donath A, Fukui M, Grove S, Liu S, Macek O, Machida R, Misof B, Nakagaki Y, Podsiadlowski L, Sekiya K, Tomizuka S, Von Reumont BM, Waterhouse RM, Walzl M, Meng G, Zhou X, Pass G, Meusemann K. Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. BMC Evol Biol 2020; 20:144. [PMID: 33148176 PMCID: PMC7640414 DOI: 10.1186/s12862-020-01699-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
Background Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data. Results We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda. Conclusions Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.
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Affiliation(s)
- Nikolaus U Szucsich
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria. .,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria.
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Blanke
- Institute for Zoology, Biocenter, University of Cologne, D-50674, Cologne, Germany.,Institute of Evolutionary Biology and Animal Ecology, University of Bonn, D-53121, Bonn, Germany
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Makiko Fukui
- Department of Biology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Simon Grove
- Invertebrate Zoology, Collections and Research Facility, Tasmanian Museum and Art Gallery, Rosny, Tasmania, 7018, Australia
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Oliver Macek
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria.,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Yasutaka Nakagaki
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Kaoru Sekiya
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | | | - Björn M Von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Animal Venomics, Institute for Insect Biotechnology, University of Giessen, Heinrich Buff Ring 26-32, D-35394, Giessen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Manfred Walzl
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Guanliang Meng
- Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Günther Pass
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany. .,Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, D-79104, Freiburg, Germany. .,Australian National Insect Collection, National Research Collections Australia, CSIRO, ACT, Canberra, 2601, Australia.
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15
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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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16
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Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM. Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana). Mol Phylogenet Evol 2020; 151:106899. [PMID: 32590046 DOI: 10.1016/j.ympev.2020.106899] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 06/17/2020] [Indexed: 01/01/2023]
Abstract
Using FrogCap, a recently-developed sequence-capture protocol, we obtained >12,000 highly informative exons, introns, and ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation error, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS). We then estimated species trees using concatenated datasets and Maximum Likelihood (IQ-TREE) in addition to summary (ASTRAL-III), distance-based (ASTRID), and site-based (SVDQuartets) multispecies coalescent methods. Topological congruence and branch support were examined using traditional bootstrap, local posterior probabilities, gene concordance factors, quartet frequencies, and quartet scores. Our results did not yield a single concordant topology. Instead, introns, exons, and UCEs clearly possessed different phylogenetic signals, resulting in conflicting, yet strongly-supported phylogenetic estimates. However, a combined analysis comprising the most informative introns, exons, and UCEs converged on a similar topology across all analyses, with the exception of SVDQuartets. Bootstrap values were consistently high despite high levels of incongruence and high proportions of gene trees supporting conflicting topologies. Although low bootstrap values did indicate low heuristic support, high bootstrap support did not necessarily reflect congruence or support for the correct topology. This study reiterates findings of some previous studies, which demonstrated that traditional bootstrap values can produce positively misleading measures of support in large phylogenomic datasets. We also showed a remarkably strong positive relationship between branch length and topological congruence across all datasets, implying that very short internodes remain a challenge to resolve, even with orders of magnitude more data than ever before. Overall, our results demonstrate that more data from unfiltered or combined datasets produced superior results. Although data filtering reduced gene tree incongruence, decreased amounts of data also biased phylogenetic estimation. A point of diminishing returns was evident, at which higher congruence (from more stringent filtering) at the expense of amount of data led to topological error as assessed by comparison to more complete datasets across different genomic markers. Additionally, we showed that applying a parameter-rich model to a partitioned analysis of concatenated data produces better results compared to unpartitioned, or even partitioned analysis using model selection. Despite some lingering uncertainties, a combined analysis of our genomic data and sequences supplemented from GenBank (on the basis of a few gene regions) revealed highly supported novel systematic arrangements. Based on these new findings, we transfer Amnirana nicobariensis into the genus Indosylvirana; and I. milleti and Hylarana celebensis to the genus Papurana. We also provisionally place H. attigua in the genus Papurana pending verification from positively identified (voucher substantiated) samples.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377, Singapore.
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92505, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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17
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Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020; 20:64. [PMID: 32493355 PMCID: PMC7268685 DOI: 10.1186/s12862-020-01631-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. RESULTS Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. CONCLUSION Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
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Affiliation(s)
- Alexandros Vasilikopoulos
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
- Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Doria Lieberz
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743, Jena, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, 64283, Darmstadt, Germany
| | - Jes Rust
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Ralph S Peters
- Centre for Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325, Frankfurt, Germany
| | - James E Jepson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, T23 N73K, Cork, Ireland
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), 1090, Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
- Zoological Department II, Natural History Museum of Vienna, 1010, Vienna, Austria
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18
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Prasanna AN, Gerber D, Kijpornyongpan T, Aime MC, Doyle VP, Nagy LG. Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships. Syst Biol 2020; 69:17-37. [PMID: 31062852 DOI: 10.1093/sysbio/syz029] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.
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Affiliation(s)
- Arun N Prasanna
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
| | - Daniel Gerber
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary.,Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA
| | - Laszlo G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
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19
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Simon S, Letsch H, Bank S, Buckley TR, Donath A, Liu S, Machida R, Meusemann K, Misof B, Podsiadlowski L, Zhou X, Wipfler B, Bradler S. Old World and New World Phasmatodea: Phylogenomics Resolve the Evolutionary History of Stick and Leaf Insects. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00345] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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20
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Vasilikopoulos A, Balke M, Beutel RG, Donath A, Podsiadlowski L, Pflug JM, Waterhouse RM, Meusemann K, Peters RS, Escalona HE, Mayer C, Liu S, Hendrich L, Alarie Y, Bilton DT, Jia F, Zhou X, Maddison DR, Niehuis O, Misof B. Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error. Mol Phylogenet Evol 2019; 135:270-285. [DOI: 10.1016/j.ympev.2019.02.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
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21
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Parker E, Dornburg A, Domínguez-Domínguez O, Piller KR. Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae). Mol Phylogenet Evol 2019; 134:282-290. [DOI: 10.1016/j.ympev.2019.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 01/18/2023]
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22
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Laumer CE. Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices. Integr Comp Biol 2019; 58:623-639. [PMID: 29982611 DOI: 10.1093/icb/icy075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Contemporary phylogeneticists enjoy an embarrassment of riches, not only in the volumes of data now available, but also in the diversity of bioinformatic tools for handling these data. Here, I discuss a subset of these tools I consider well-suited to the task of inferring ancient relationships with coding sequence data in particular, encompassing data generation, orthology assignment, alignment and gene tree inference, supermatrix construction, and analysis under the best-fitting models applicable to large-scale datasets. Throughout, I compare and critique methods, considering both their theoretical principles and the details of their implementation, and offering practical tips on usage where appropriate. I also entertain different motivations for analyzing what are almost always originally DNA sequence data as codons, amino acids, and higher-order recodings. Although presented in a linear order, I see value in using the diversity of tools available to us to assess the sensitivity of clades of biological interest to different gene and taxon sets and analytical modes, which can be an indication of the presence of systematic error, of which a few forms remain poorly controlled by even the best available inference methods.
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Affiliation(s)
- Christopher E Laumer
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, EBML-EBI South Building, Hinxton CB10 1SD, UK
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23
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Jiang J, Yuan H, Zheng X, Wang Q, Kuang T, Li J, Liu J, Song S, Wang W, Cheng F, Li H, Huang J, Li C. Gene markers for exon capture and phylogenomics in ray-finned fishes. Ecol Evol 2019; 9:3973-3983. [PMID: 31015981 PMCID: PMC6468074 DOI: 10.1002/ece3.5026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/30/2022] Open
Abstract
Gene capture coupled with the next-generation sequencing has become one of the preferred methods of subsampling genomes for phylogenomic studies. Many exon markers have been developed in plants, sharks, frogs, reptiles, fishes, and others, but no universal exon markers have been tested in ray-finned fishes. Here, we identified a suite of "single-copy" protein-coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and nine orders or higher clades: Acipenseriformes, Lepisosteiformes, Elopomorpha, Osteoglossomorpha, Clupeiformes, Cypriniformes, Gobiaria, Carangaria, and Eupercaria; sensu Betancur et al. 2013). Sorting the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray-finned fishes at different taxonomic levels. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may greatly enrich the batteries of exon markers for phylogenomic study in ray-finned fishes.
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Affiliation(s)
- Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Hao Yuan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Xin Zheng
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Qian Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Ting Kuang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Jingyan Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Junning Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Shuli Song
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Weicai Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Fangyuan Cheng
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Hongjie Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Junman Huang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
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24
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Ballesteros JA, Sharma PP. A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error. Syst Biol 2019; 68:896-917. [DOI: 10.1093/sysbio/syz011] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/20/2018] [Accepted: 02/10/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractHorseshoe crabs (Xiphosura) are traditionally regarded as sister group to the clade of terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent phylogenomic analyses, but the non-monophyly of Arachnida has consistently been disregarded as artifactual. We re-evaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic data set to date, expanding outgroup sampling, and including data from whole genome sequencing projects. In spite of uncertainty in the placement of some arachnid clades, all analyses show Xiphosura consistently nested within Arachnida as the sister group to Ricinulei (hooded tick spiders). It is apparent that the radiation of arachnids is an old one and occurred over a brief period of time, resulting in several consecutive short internodes, and thus is a potential case for the confounding effects of incomplete lineage sorting (ILS). We simulated coalescent gene trees to explore the effects of increasing levels of ILS on the placement of horseshoe crabs. In addition, common sources of systematic error were evaluated, as well as the effects of fast-evolving partitions and the dynamics of problematic long branch orders. Our results indicated that the placement of horseshoe crabs cannot be explained by missing data, compositional biases, saturation, or ILS. Interrogation of the phylogenetic signal showed that the majority of loci favor the derived placement of Xiphosura over a monophyletic Arachnida. Our analyses support the inference that horseshoe crabs represent a group of aquatic arachnids, comparable to aquatic mites, breaking a long-standing paradigm in chelicerate evolution and altering previous interpretations of the ancestral transition to the terrestrial habitat. Future studies testing chelicerate relationships should approach the task with a sampling strategy where the monophyly of Arachnida is not held as the premise.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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25
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Wang Y, Zhou X, Wang L, Liu X, Yang D, Rokas A. Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data. Int J Mol Sci 2019; 20:E1072. [PMID: 30832228 PMCID: PMC6429444 DOI: 10.3390/ijms20051072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 11/30/2022] Open
Abstract
Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.
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Affiliation(s)
- Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
- Department of Entomology, China Agricultural University, Beijing 100193, China.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China.
| | - Liming Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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26
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Narayanan Kutty S, Meusemann K, Bayless KM, Marinho MAT, Pont AC, Zhou X, Misof B, Wiegmann BM, Yeates D, Cerretti P, Meier R, Pape T. Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera. Cladistics 2019; 35:605-622. [DOI: 10.1111/cla.12375] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sujatha Narayanan Kutty
- Department of Biological Sciences National University of Singapore 14 Science Dr 4 Singapore 117543 Singapore
| | - Karen Meusemann
- Biology I, Evolutionary Biology & Ecology University of Freiburg Hauptstraße 1 Freiburg (Brsg.) Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
- Australian National Insect Collection CSIRO National Research Collections Australia (NRCA) Acton, ACT Canberra Australia
| | - Keith M. Bayless
- Department of Entomology California Academy of Sciences San Francisco CA USA
- Department of Entomology North Carolina State University Raleigh NC 27695 USA
| | - Marco A. T. Marinho
- Departamento de Ecologia, Zoologia e Genética Instituto de Biologia Universidade Federal de Pelotas Pelotas RS Brazil
| | - Adrian C. Pont
- Oxford University Museum of Natural History Parks Road Oxford OX1 3PW UK
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing 100193 China
- Department of Entomology China Agricultural University Beijing 100193 China
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Brian M. Wiegmann
- Department of Entomology North Carolina State University Raleigh NC 27695 USA
| | - David Yeates
- Australian National Insect Collection CSIRO National Research Collections Australia (NRCA) Acton, ACT Canberra Australia
| | - Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’ Sapienza Università di Roma Rome Italy
| | - Rudolf Meier
- Department of Biological Sciences National University of Singapore 14 Science Dr 4 Singapore 117543 Singapore
| | - Thomas Pape
- Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 Copenhagen DK–2100 Denmark
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27
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Wipfler B, Letsch H, Frandsen PB, Kapli P, Mayer C, Bartel D, Buckley TR, Donath A, Edgerly-Rooks JS, Fujita M, Liu S, Machida R, Mashimo Y, Misof B, Niehuis O, Peters RS, Petersen M, Podsiadlowski L, Schütte K, Shimizu S, Uchifune T, Wilbrandt J, Yan E, Zhou X, Simon S. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proc Natl Acad Sci U S A 2019; 116:3024-3029. [PMID: 30642969 PMCID: PMC6386694 DOI: 10.1073/pnas.1817794116] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.
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Affiliation(s)
- Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, 1030 Vienna, Austria
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84604
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Daniela Bartel
- Department of Integrative Zoology, Universität Wien, 1090 Vienna, Austria
| | - Thomas R Buckley
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Janice S Edgerly-Rooks
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA 95053
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Yuta Mashimo
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, 79104 Freiburg, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kai Schütte
- Tierökologie und Naturschutz, Universität Hamburg, 20146 Hamburg, Germany
| | - Shota Shimizu
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Toshiki Uchifune
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
- Yokosuka City Museum, Fukadadai, Kanagawa 238-0016, Japan
| | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Evgeny Yan
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Borissiak Palaeontological Institute, Russian Academy of Sciences, 123 Moscow, Russia
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100083, China
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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28
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Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 2019; 35:518-522. [PMID: 29077904 PMCID: PMC5850222 DOI: 10.1093/molbev/msx281] [Citation(s) in RCA: 3975] [Impact Index Per Article: 795.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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Affiliation(s)
- Diep Thi Hoang
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Le Sy Vinh
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
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29
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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30
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Evangelista DA, Wipfler B, Béthoux O, Donath A, Fujita M, Kohli MK, Legendre F, Liu S, Machida R, Misof B, Peters RS, Podsiadlowski L, Rust J, Schuette K, Tollenaar W, Ware JL, Wappler T, Zhou X, Meusemann K, Simon S. An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea). Proc Biol Sci 2019; 286:20182076. [PMID: 30963947 PMCID: PMC6364590 DOI: 10.1098/rspb.2018.2076] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/04/2019] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.
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Affiliation(s)
- Dominic A. Evangelista
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Dabney Hall, 1416 Circle Dr., Knoxville, TN 37996, USA
| | - Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum, Friedrich-Schiller Universität Jena, Vor dem Neutor 1, 07743 Jena, Germany
- Center for Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Olivier Béthoux
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, Paris, France
- Muséum national d'Histoire naturelle, 57 rue Cuvier, CP38, 75005 Paris, France
| | - Alexander Donath
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Manpreet K. Kohli
- Federated Department of Biological Sciences, Rutgers, The State University of New Jersey and NJIT, 195 University Ave, Newark, NJ 07102, USA
| | - Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Ralph S. Peters
- Center for Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
| | - Jes Rust
- Steinmann-Institute, Institute for Paleontology, University of Bonn, Nussallee 8, 53115 Bonn, Germany
| | - Kai Schuette
- Animal Ecology and Conservation, Zoological Institute, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ward Tollenaar
- Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jessica L. Ware
- Federated Department of Biological Sciences, Rutgers, The State University of New Jersey and NJIT, 195 University Ave, Newark, NJ 07102, USA
| | - Torsten Wappler
- Hessisches Landesmuseum Darmstadt, Friedensplatz 1, 64283 Darmstadt, Germany
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Karen Meusemann
- Center for Molecular Biodiversity Research (ZMB), Zoological Research Museum Alexander Koenig (ZFMK), Adenauerallee 160, 53113 Bonn, Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, Australian Capital Territory, Australia
- Evolutionary Biology and Ecology, Institute for Biology I, University of Freiburg, Hauptstr. 1, 79104 Freiburg (Brsg.), Germany
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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31
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Johnson KP, Dietrich CH, Friedrich F, Beutel RG, Wipfler B, Peters RS, Allen JM, Petersen M, Donath A, Walden KKO, Kozlov AM, Podsiadlowski L, Mayer C, Meusemann K, Vasilikopoulos A, Waterhouse RM, Cameron SL, Weirauch C, Swanson DR, Percy DM, Hardy NB, Terry I, Liu S, Zhou X, Misof B, Robertson HM, Yoshizawa K. Phylogenomics and the evolution of hemipteroid insects. Proc Natl Acad Sci U S A 2018; 115:12775-12780. [PMID: 30478043 PMCID: PMC6294958 DOI: 10.1073/pnas.1815820115] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.
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Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820;
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Frank Friedrich
- Institut für Zoologie, Universität Hamburg, 20146 Hamburg, Germany
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Benjamin Wipfler
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
- Department of Biology, University of Nevada, Reno, NV 89557
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Alexey M Kozlov
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Institute of Evolutionary Biology and Ecology, University of Bonn, 53121 Bonn, Germany
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg, Germany
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation National Research Collections Australia, Acton, ACT 2601 Canberra, Australia
| | - Alexandros Vasilikopoulos
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907
| | | | - Daniel R Swanson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Diana M Percy
- Department of Life Sciences, Natural History Museum, London, SW7 5BD United Kingdom
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Irene Terry
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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32
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Schwentner M, Richter S, Rogers DC, Giribet G. Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics. Proc Biol Sci 2018; 285:20181524. [PMID: 30135168 PMCID: PMC6125901 DOI: 10.1098/rspb.2018.1524] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/18/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.
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Affiliation(s)
- Martin Schwentner
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Centrum of Natural History, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Stefan Richter
- Allgemeine und Spezielle Zoologie, Universität Rostock, Universitätsplatz 2, 18055 Rostock, Germany
| | - D Christopher Rogers
- Kansas Biological Survey, Kansas University, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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33
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Kuang T, Tornabene L, Li J, Jiang J, Chakrabarty P, Sparks JS, Naylor GJP, Li C. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Mol Phylogenet Evol 2018; 128:192-202. [PMID: 30036699 DOI: 10.1016/j.ympev.2018.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 07/11/2018] [Accepted: 07/17/2018] [Indexed: 11/30/2022]
Abstract
The use of genome-scale data to infer phylogenetic relationships has gained in popularity in recent years due to the progress made in target-gene capture and sequencing techniques. Data filtering, the approach of excluding data inconsistent with the model from analyses, presumably could alleviate problems caused by systematic errors in phylogenetic inference. Different data filtering criteria, such as those based on evolutionary rate and molecular clocklikeness as well as others have been proposed for selecting useful phylogenetic markers, yet few studies have tested these criteria using phylogenomic data. We developed a novel set of single-copy nuclear coding markers to capture thousands of target genes in gobioid fishes, a species-rich lineages of vertebrates, and tested the effects of data-filtering methods based on substitution rate and molecular clocklikeness while attempting to control for the compounding effects of missing data and variation in locus length. We found that molecular clocklikeness was a better predictor than overall substitution rate for phylogenetic usefulness of molecular markers in our study. In addition, when the 100 best ranked loci for our predictors were concatenated and analyzed using maximum likelihood, or combined in a coalescent-based species-tree analysis, the resulting trees showed a well-resolved topology of Gobioidei that mostly agrees with previous studies. However, trees generated from the 100 least clocklike frequently recovered conflicting, and in some cases clearly erroneous topologies with strong support, thus indicating strong systematic biases in those datasets. Collectively these results suggest that data filtering has the potential improve the performance of phylogenetic inference when using both a concatenation approach as well as methods that rely on input from individual gene trees (i.e. coalescent species-tree approaches), which may be preferred in scenarios where incomplete lineage sorting is likely to be an issue.
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Affiliation(s)
- Ting Kuang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jingyan Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China
| | - Prosanta Chakrabarty
- Louisiana State University, Museum of Natural Science, Department of Biological Sciences, Baton Rouge, LA 70803, USA
| | - John S Sparks
- American Museum of Natural History, Central Park West at 79th Street, NY, NY 10024, USA
| | | | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), China.
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34
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Simon S, Blanke A, Meusemann K. Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:328-338. [PMID: 29763650 DOI: 10.1016/j.asd.2018.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
The phylogenetic relationships of the winged insect lineages - mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) - are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Alexander Blanke
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany; Medical and Biological Engineering Research Group, School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Hull, UK
| | - Karen Meusemann
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg (Brsg.), Germany; Center of Molecular Biodiversity Research (ZMB), Zoological Research Museum A. Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany.
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35
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Evangelista D, Thouzé F, Kohli MK, Lopez P, Legendre F. Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny. Mol Phylogenet Evol 2018; 128:112-122. [PMID: 29969656 DOI: 10.1016/j.ympev.2018.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 11/18/2022]
Abstract
Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree's relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.
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Affiliation(s)
- Dominic Evangelista
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - France Thouzé
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - Manpreet Kaur Kohli
- Department of Biological Sciences, Rutgers, The State University of New Jersey, 195 University Ave., Newark, NJ 07102, United States.
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - Frédéric Legendre
- Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
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36
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Godwin RL, Opatova V, Garrison NL, Hamilton CA, Bond JE. Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901. Mol Phylogenet Evol 2018; 126:303-313. [PMID: 29656103 DOI: 10.1016/j.ympev.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/08/2018] [Accepted: 04/06/2018] [Indexed: 02/08/2023]
Abstract
The mygalomorph family Ctenizidae has a world-wide distribution and currently contains nine genera and 135 species. However, the monophyly of this group has long been questioned on both morphological and molecular grounds. Here, we use Anchored Hybrid Enrichment (AHE) to gather hundreds of loci from across the genome for reconstructing the phylogenetic relationships among the nine genera and test the monophyly of the family. We also reconstruct the possible ancestral ranges of the most inclusive clade recovered. Using AHE, we generate a supermatrix of 565 loci and 115,209 bp for 27 individuals. For the first time, analyses using all nine genera produce results definitively establishing the non-monophyly of Ctenizidae. A lineage formed exclusively by representatives of South African Stasimopus was placed as the sister group to the remaining taxa in the tree, and the Mediterranean Cteniza and Cyrtocarenum were recovered with high support as sister to exemplars of Euctenizidae, Migidae, and Idiopidae. All the remaining genera-Bothriocyrtum, Conothele, Cyclocosmia, Hebestatis, Latouchia, and Ummidia-share a common ancestor. Based on these results, we formally elevate this clade to the level of family. Our results definitively establish both the non-monophyly of the Ctenizidae and non-validity of the subfamilies Ummidiinae and Ctenizinae. In order to establish the placement of the remaining three ctenizid genera, Cteniza, Cyrtocarenum, and Stasimopus, thorough analyses within the context of a complete mygalomorph phylogenetic framework are needed. We formally describe the family Halonoproctidae Pocock 1901 and infer that the family's most recent common ancestor was likely distributed in western North America and Asia.
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Affiliation(s)
- Rebecca L Godwin
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Vera Opatova
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Nicole L Garrison
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Chris A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Jason E Bond
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
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37
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Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 2018. [PMID: 29077904 DOI: 10.5281/zenodo.854445] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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Affiliation(s)
- Diep Thi Hoang
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Olga Chernomor
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria
| | - Le Sy Vinh
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
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38
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Klopfstein S, Massingham T, Goldman N. More on the Best Evolutionary Rate for Phylogenetic Analysis. Syst Biol 2018; 66:769-785. [PMID: 28595363 PMCID: PMC5790136 DOI: 10.1093/sysbio/syx051] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/24/2017] [Indexed: 11/13/2022] Open
Abstract
The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability. We here use simulations to infer optimal rates in a set of realistic phylogenetic scenarios with varying tree sizes, numbers of terminals, and tree shapes. Furthermore, we study the relationship between the optimal rate and rate variation among sites and among lineages. Finally, we examine how well the predictions made by a range of experimental design methods correlate with the observed performance in our simulations.We find that the optimal level of divergence is surprisingly robust to differences in taxon sampling and even to among-site and among-lineage rate variation as often encountered in empirical data sets. This finding encourages the use of methods that rely on a single optimal rate to predict a gene's utility. Focusing on correct recovery either of the most basal node in the phylogeny or of the entire topology, the optimal rate is about 0.45 substitutions from root to tip in average Yule trees and about 0.2 in difficult trees with short basal and long-apical branches, but all rates leading to divergence levels between about 0.1 and 0.5 perform reasonably well.Testing the performance of six methods that can be used to predict a gene's utility against our simulation results, we find that the probability of resolution, signal-noise analysis, and Fisher information are good predictors of phylogenetic informativeness, but they require specification of at least part of a model tree. Likelihood quartet mapping also shows very good performance but only requires sequence alignments and is thus applicable without making assumptions about the phylogeny. Despite them being the most commonly used methods for experimental design, geometric quartet mapping and the integration of phylogenetic informativeness curves perform rather poorly in our comparison. Instead of derived predictors of phylogenetic informativeness, we suggest that the number of sites in a gene that evolve at near-optimal rates (as inferred here) could be used directly to prioritize genes for phylogenetic inference. In combination with measures of model fit, especially with respect to compositional biases and among-site and among-lineage rate variation, such an approach has the potential to greatly improve marker choice and should be tested on empirical data.
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Affiliation(s)
- Seraina Klopfstein
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastr. 15, CH-3005 Bern, Switzerland.,University of Bern, Institute of Ecology and Evolution, Baltzerstr. 6, CH-3012 Bern, Switzerland
| | - Tim Massingham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
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Abstract
With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.
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Affiliation(s)
- Andrew Edward Z Short
- Department of Ecology and Evolutionary Biology; and Division of Entomology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA;
| | - Torsten Dikow
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA;
| | - Corrie S Moreau
- Department of Science and Education, Field Museum of Natural History, Chicago, Illinois 60605, USA;
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40
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Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development of many computer programs implementing the associated methods. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil
| | - Joaquim Martins
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil.
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41
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Wang YH, Wu HY, Rédei D, Xie Q, Chen Y, Chen PP, Dong ZE, Dang K, Damgaard J, Štys P, Wu YZ, Luo JY, Sun XY, Hartung V, Kuechler SM, Liu Y, Liu HX, Bu WJ. When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera-Heteroptera. Cladistics 2017; 35:42-66. [DOI: 10.1111/cla.12232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yan-Hui Wang
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hao-Yang Wu
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Yan Chen
- Chinese Academy of Inspection and Quarantine; No. A3, Gaobeidian Bei Lu Chaoyang District Beijing 100123 China
| | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis; 2300 RA Leiden Netherlands
| | - Zhuo-Er Dong
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Kai Dang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jakob Damgaard
- Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Pavel Štys
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-128 44 Praha 2 Czech Republic
| | - Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Viktor Hartung
- Staatliches Museum für Naturkunde Karslruhe; Erbprinzenstrasse 13 76133 Karlsruhe Germany
- Museum für Naturkunde - Leibniz-Institute for Research on Evolution and Biodiversity; Invalidenstrasse 43 10115 Berlin Germany
| | - Stefan M. Kuechler
- Department of Animal Ecology II; University of Bayreuth; Universitaetsstrasse 30 95440 Bayreuth Germany
| | - Yang Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hua-Xi Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
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42
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Lemer S, González VL, Bieler R, Giribet G. Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach. Proc Biol Sci 2017; 283:rspb.2016.0857. [PMID: 27358369 PMCID: PMC4936043 DOI: 10.1098/rspb.2016.0857] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/03/2016] [Indexed: 11/12/2022] Open
Abstract
Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix (Matrix 3: 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.
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Affiliation(s)
- Sarah Lemer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Vanessa L González
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Rüdiger Bieler
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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43
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Bank S, Sann M, Mayer C, Meusemann K, Donath A, Podsiadlowski L, Kozlov A, Petersen M, Krogmann L, Meier R, Rosa P, Schmitt T, Wurdack M, Liu S, Zhou X, Misof B, Peters RS, Niehuis O. Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae). Mol Phylogenet Evol 2017; 116:213-226. [DOI: 10.1016/j.ympev.2017.08.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
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44
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Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Mol Phylogenet Evol 2017; 115:16-26. [DOI: 10.1016/j.ympev.2017.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/31/2017] [Accepted: 07/13/2017] [Indexed: 01/31/2023]
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45
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Faddeeva-Vakhrusheva A, Kraaijeveld K, Derks MFL, Anvar SY, Agamennone V, Suring W, Kampfraath AA, Ellers J, Le Ngoc G, van Gestel CAM, Mariën J, Smit S, van Straalen NM, Roelofs D. Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida. BMC Genomics 2017; 18:493. [PMID: 28659179 PMCID: PMC5490193 DOI: 10.1186/s12864-017-3852-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Background Folsomia candida is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of Wolbachia, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle. Results We applied Pacific Bioscience sequencing and assembly to generate a reference genome for F. candida of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont Wolbachia, was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The Hox gene cluster of F. candida showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster. Conclusions The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3852-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ken Kraaijeveld
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martijn F L Derks
- Department of Animal Sciences, Animal Breeding and Genetics, Wageningen University, Wageningen, The Netherlands
| | - Seyed Yahya Anvar
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Valeria Agamennone
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wouter Suring
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andries A Kampfraath
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jacintha Ellers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Giang Le Ngoc
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Janine Mariën
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sandra Smit
- Department of Plant Sciences, Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Nico M van Straalen
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dick Roelofs
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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46
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Schwentner M, Combosch DJ, Pakes Nelson J, Giribet G. A Phylogenomic Solution to the Origin of Insects by Resolving Crustacean-Hexapod Relationships. Curr Biol 2017; 27:1818-1824.e5. [DOI: 10.1016/j.cub.2017.05.040] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/10/2017] [Accepted: 05/10/2017] [Indexed: 12/11/2022]
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47
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Peters RS, Krogmann L, Mayer C, Donath A, Gunkel S, Meusemann K, Kozlov A, Podsiadlowski L, Petersen M, Lanfear R, Diez PA, Heraty J, Kjer KM, Klopfstein S, Meier R, Polidori C, Schmitt T, Liu S, Zhou X, Wappler T, Rust J, Misof B, Niehuis O. Evolutionary History of the Hymenoptera. Curr Biol 2017; 27:1013-1018. [DOI: 10.1016/j.cub.2017.01.027] [Citation(s) in RCA: 340] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/13/2016] [Accepted: 01/16/2017] [Indexed: 10/24/2022]
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48
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Zhao L, Li X, Zhang N, Zhang SD, Yi TS, Ma H, Guo ZH, Li DZ. Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids. Mol Phylogenet Evol 2016; 105:166-176. [DOI: 10.1016/j.ympev.2016.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 06/06/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022]
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49
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Kjer K, Borowiec ML, Frandsen PB, Ware J, Wiegmann BM. Advances using molecular data in insect systematics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:40-47. [PMID: 27939709 DOI: 10.1016/j.cois.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.
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Affiliation(s)
- Karl Kjer
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Marek L Borowiec
- University of Rochester, 226 Hutchison Hall, Rochester, NY 14627, USA
| | - Paul B Frandsen
- Smithsonian Institution, Office of Research Information Services, Office of the Chief Information Officer, Washington, D.C. 20024, USA
| | - Jessica Ware
- Rutgers University, Department of Biological Sciences, 415 Boyden Hall, Newark, NJ 07012, USA
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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Hamilton CA, Lemmon AR, Lemmon EM, Bond JE. Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life. BMC Evol Biol 2016; 16:212. [PMID: 27733110 PMCID: PMC5062932 DOI: 10.1186/s12862-016-0769-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 09/28/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae. RESULTS Our aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma. CONCLUSIONS The Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.
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Affiliation(s)
- Chris A. Hamilton
- Department of Biological Sciences, Auburn University & Auburn University Museum of Natural History, Auburn, AL USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL USA
| | | | - Jason E. Bond
- Department of Biological Sciences, Auburn University & Auburn University Museum of Natural History, Auburn, AL USA
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