Author
Rolf G. Beutel
Other affiliations: Schiller International University, Massachusetts Institute of Technology, RWTH Aachen University ...read more
Bio: Rolf G. Beutel is an academic researcher from University of Jena. The author has contributed to research in topics: Monophyly & Myxophaga. The author has an hindex of 51, co-authored 305 publications receiving 10832 citations. Previous affiliations of Rolf G. Beutel include Schiller International University & Massachusetts Institute of Technology.
Topics: Monophyly, Myxophaga, Sister group, Autapomorphy, Strepsiptera
Papers published on a yearly basis
Papers
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Commonwealth Scientific and Industrial Research Organisation1, Rutgers University2, Heidelberg Institute for Theoretical Studies3, University of Jena4, University of Bonn5, Naturhistorisches Museum6, University of Vienna7, University of Tsukuba8, Landcare Research9, Johns Hopkins University10, University of Hamburg11, Ehime University12, Florida Museum of Natural History13, Staatliches Museum für Naturkunde Stuttgart14, Macquarie University15, National Evolutionary Synthesis Center16, Australian National University17, American Museum of Natural History18, University of Memphis19, University of Guadalajara20, Bavarian Academy of Sciences and Humanities21, Natural History Museum22, Karlsruhe Institute of Technology23, California Academy of Sciences24, South China Agricultural University25, North Carolina State University26, Hokkaido University27
TL;DR: The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
1,998 citations
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TL;DR: The analysis demonstrates, that similar structures (arolium, euplantulae, hairy tarsomeres) have evolved independently in several lineages, and some of them support monophyletic groups (e.g. Embioptera + Dermaptera; Dictyoptera + Phasmatodea; Hymenoptera+ Mecopterida; Neuropterida + Strepsiptera + Coleoptera).
Abstract: Attachment devices of representatives of most higher taxa of hexapods were examined. Short descriptions of tibial, tarsal and pretarsal adhesive structures for each order are presented. In their evolution, hexapods have developed two distinctly different mechanisms to attach themselves to a variety of substrates: hairy surfaces and smooth flexible pads. The flexible properties of pad material guarantees a maximal contact with surfaces, regardless of the microsculpture. These highly specialized structures are not restricted to one particular area of the leg. They may be located on different parts, such as claws, derivatives of the pretarsus, tarsal apex, tarsomeres, or tibia. The 10 characters of the two alternative designs of attachment devices – smooth and hairy – were coded and analysed together with a data matrix containing 105 additional morphological characters of different stages and body parts. The analysis demonstrates, that similar structures (arolium, euplantulae, hairy tarsomeres) have evolved independently in several lineages. Nevertheless, some of them support monophyletic groups (e.g. Embioptera + Dermaptera; Dictyoptera + Phasmatodea + Grylloblattodea + Orthoptera; Dictyoptera + Phasmatodea; Hymenoptera + Mecopterida; Neuropterida + Strepsiptera + Coleoptera). Other structures such as claw pads (Ephemeroptera), balloon-shaped eversible pads (Thysanoptera), or fossulae spongiosae (Reduviidae) are unique for larger or smaller monophyletic units. It is plausible to assume that the evolution of flight and the correlated necessity to cling to vegetation or other substrates was a major trigger for the evolution of adhesive structures. Groups with a potential to evolve a great variety of designs of adhesive pads are Hemiptera and Diptera. Even though characters of the adhesive pads are strongly subject to selection, they can provide phylogenetic information. The results of the cladistic analyses are largely congruent with current hypotheses of hexapod phylogeny. A sistergroup relationship between Diplura and Insecta and between Zygentoma (excl. Tricholepidion) and Pterygota is confirmed. Plecoptera are probably the sistergroup of the remaining Neoptera. Dermaptera are the sistergroup of Embioptera and Dictyoptera the sistergroup of Phasmatodea. Paurometabola excl. Dermaptera + Embioptera are monophyletic. A sistergroup relationship between Zoraptera and a clade comprising Paraneoptera + Endopterygota is only supported by weak evidence. Coleoptera + Strepsiptera are the sistergroup of Neuropterida and Hymenoptera the sistergroup of Mecopterida.
422 citations
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University of Memphis1, Harvard University2, University of Arizona3, University of Texas at Austin4, Oregon State University5, California Department of Food and Agriculture6, University of Jena7, Clemson University8, University of California, Riverside9, Montana State University10, Wichita State University11, Landcare Research12, National University of La Plata13, University of Georgia14, Field Museum of Natural History15, Brigham Young University16, Commonwealth Scientific and Industrial Research Organisation17
TL;DR: A phylogeny of beetles based on DNA sequence data from eight nuclear genes, including six single‐copy nuclear protein‐coding genes, for 367 species representing 172 of 183 extant families provides a uniquely well‐resolved temporal and phylogenetic framework for studying patterns of innovation and diversification in Coleoptera.
Abstract: © 2015 The Authors. Systematic Entomology published by John Wiley & Sons Ltd on behalf of Royal Entomological Society
This is an open access article under the terms of the Creative Commons AttributionߚNonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
419 citations
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TL;DR: Beetles diversity appears to have resulted from multiple factors, including low extinction rates over a long evolutionary history, codiversification with angiosperms, and adaptive radiations of specialized herbivorous beetles following convergent horizontal transfers of microbial genes encoding PCWDEs.
Abstract: The order Coleoptera (beetles) is arguably the most speciose group of animals, but the evolutionary history of beetles, including the impacts of plant feeding (herbivory) on beetle diversification, remain poorly understood. We inferred the phylogeny of beetles using 4,818 genes for 146 species, estimated timing and rates of beetle diversification using 89 genes for 521 species representing all major lineages and traced the evolution of beetle genes enabling symbiont-independent digestion of lignocellulose using 154 genomes or transcriptomes. Phylogenomic analyses of these uniquely comprehensive datasets resolved previously controversial beetle relationships, dated the origin of Coleoptera to the Carboniferous, and supported the codiversification of beetles and angiosperms. Moreover, plant cell wall-degrading enzymes (PCWDEs) obtained from bacteria and fungi via horizontal gene transfers may have been key to the Mesozoic diversification of herbivorous beetles—remarkably, both major independent origins of specialized herbivory in beetles coincide with the first appearances of an arsenal of PCWDEs encoded in their genomes. Furthermore, corresponding (Jurassic) diversification rate increases suggest that these novel genes triggered adaptive radiations that resulted in nearly half of all living beetle species. We propose that PCWDEs enabled efficient digestion of plant tissues, including lignocellulose in cell walls, facilitating the evolution of uniquely specialized plant-feeding habits, such as leaf mining and stem and wood boring. Beetle diversity thus appears to have resulted from multiple factors, including low extinction rates over a long evolutionary history, codiversification with angiosperms, and adaptive radiations of specialized herbivorous beetles following convergent horizontal transfers of microbial genes encoding PCWDEs.
326 citations
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TL;DR: A review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence.
Abstract: Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).
224 citations
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TL;DR: Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release of ape.
Abstract: Summary After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users The release of version 50 has marked a leap towards a modern software for evolutionary analyses Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity Availability and implementation ape is distributed through the Comprehensive R Archive Network: http://cranr-projectorg/package=ape Further information may be found at http://ape-packageirdfr/
4,303 citations
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TL;DR: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses that includes the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, and new output formats to facilitate interoperability with downstream software.
Abstract: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.
3,445 citations
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Commonwealth Scientific and Industrial Research Organisation1, Rutgers University2, Heidelberg Institute for Theoretical Studies3, University of Jena4, University of Bonn5, Naturhistorisches Museum6, University of Vienna7, University of Tsukuba8, Landcare Research9, Johns Hopkins University10, University of Hamburg11, Ehime University12, Florida Museum of Natural History13, Staatliches Museum für Naturkunde Stuttgart14, National Evolutionary Synthesis Center15, Australian National University16, Macquarie University17, American Museum of Natural History18, University of Memphis19, University of Guadalajara20, Bavarian Academy of Sciences and Humanities21, Natural History Museum22, Karlsruhe Institute of Technology23, California Academy of Sciences24, South China Agricultural University25, North Carolina State University26, Hokkaido University27
TL;DR: The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
1,998 citations
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TL;DR: RAxML-NG is presented, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML, which offers improved accuracy, flexibility, speed, scalability, and usability compared with RAx ML/ exaML.
Abstract: MOTIVATION Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets. RESULTS We present RAxML-NG, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML-NG offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and the recently introduced transfer bootstrap support metric. AVAILABILITY AND IMPLEMENTATION The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng. RAxML-NG web service (maintained by Vital-IT) is available at https://raxml-ng.vital-it.ch/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
1,765 citations