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Alexander Böhm

Bio: Alexander Böhm is an academic researcher from University of Vienna. The author has contributed to research in topics: Phylogenomics & Monophyly. The author has an hindex of 8, co-authored 10 publications receiving 1790 citations.

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Journal ArticleDOI
Bernhard Misof, Shanlin Liu, Karen Meusemann1, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen2, Jessica L. Ware2, Tomas Flouri3, Rolf G. Beutel4, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco3, Torsten Wappler5, Jes Rust5, Andre J. Aberer3, Ulrike Aspöck6, Ulrike Aspöck7, Horst Aspöck6, Daniela Bartel6, Alexander Blanke8, Simon Berger3, Alexander Böhm6, Thomas R. Buckley9, Brett Calcott10, Junqing Chen, Frank Friedrich11, Makiko Fukui12, Mari Fujita8, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin1, Akito Y. Kawahara13, Lars Krogmann14, Martin Kubiak11, Robert Lanfear15, Robert Lanfear16, Robert Lanfear17, Harald Letsch6, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida8, Yuta Mashimo8, Pashalia Kapli3, Pashalia Kapli18, Duane D. McKenna19, Guanliang Meng, Yasutaka Nakagaki8, José Luis Navarrete-Heredia20, Michael Ott21, Yanxiang Ou, Günther Pass6, Lars Podsiadlowski5, Hans Pohl4, Björn M. von Reumont22, Kai Schütte11, Kaoru Sekiya8, Shota Shimizu8, Adam Slipinski1, Alexandros Stamatakis3, Alexandros Stamatakis23, Wenhui Song, Xu Su, Nikolaus U. Szucsich6, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler6, Shigekazu Tomizuka8, Michelle D. Trautwein24, Xiaoli Tong25, Toshiki Uchifune8, Manfred Walzl6, Brian M. Wiegmann26, Jeanne Wilbrandt, Benjamin Wipfler4, Thomas K. F. Wong1, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates1, Kazunori Yoshizawa27, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer2, Xin Zhou 
07 Nov 2014-Science
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

Journal ArticleDOI
TL;DR: An 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, and provide new insights into the timing of diversification of neuropterida.
Abstract: 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. 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. 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.

56 citations

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica L. Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas R. Buckley, Brett Calcott, Junqing Chen, Frank Friedrich, Makiko Fukui, Mari Fujita, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin, Akito Y. Kawahara, Lars Krogmann, Martin Kubiak, Robert Lanfear, Harald Letsch, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida, Yuta Mashimo, Pashalia Kapli, Duane D. McKenna, Guanliang Meng, Yasutaka Nakagaki, José Luis Navarrete-Heredia, Michael Ott, Yanxiang Ou, Günther Pass, Lars Podsiadlowski, Hans Pohl, Björn M. von Reumont, Kai Schütte, Kaoru Sekiya, Shota Shimizu, Adam Slipinski, Alexandros Stamatakis, Wenhui Song, Xu Su, Nikolaus U. Szucsich, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler, Shigekazu Tomizuka, Michelle D. Trautwein, Xiaoli Tong, Toshiki Uchifune, Manfred Walzl, Brian M. Wiegmann, Jeanne Wilbrandt, Benjamin Wipfler, Thomas K. F. Wong, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates, Kazunori Yoshizawa, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer, Xin Zhou 
01 Jan 2014
TL;DR: A phylogenetic analysis of protein-coding genes from all major insect orders and close relatives was performed by Misof et al. as discussed by the authors, who used this resolved phylogenetic tree together with fossil analysis to date the origin of insects to ~479 million years ago and to resolve longcontroversial subjects in insect phylogeny.
Abstract: Toward an insect evolution resolution Insects are the most diverse group of animals, with the largest number of species. However, many of the evolutionary relationships between insect species have been controversial and difficult to resolve. Misof et al. performed a phylogenomic analysis of protein-coding genes from all major insect orders and close relatives, resolving the placement of taxa. The authors used this resolved phylogenetic tree together with fossil analysis to date the origin of insects to ~479 million years ago and to resolve long-controversial subjects in insect phylogeny. Science, this issue p. 763 The phylogeny of all major insect lineages reveals how and when insects diversified. 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.

52 citations

01 Jan 2011
TL;DR: A non-destructive DNA extraction method is applied and subsequently confocal autofluorescence imaging is used to analyse and document cuticular characters of the same specimens to overcome the problem of species determination in certain minute arthropods.
Abstract: In certain minute arthropods, such as Protura, species determination cannot be performed unambiguously without clearing and slide mounting of specimens. This causes an awkward dilemma for scientists conducting molecular research, since conventional DNA extraction entails destruction of the whole specimen. Thus, single individuals can be used either to obtain molecular data or for determination purposes. Such molecular datasets are thus dependent on determination of co-habitant specimens, and entries in GenBank are highly prone to misidentification. To overcome this problem, we applied a non-destructive DNA extraction method and subsequently used confocal autofluorescence imaging to analyse and document cuticular characters of the same specimens. Alternatively the preparations can be examined by conventional microscopy. Our results show that the used non-destructive extraction method results in completely clear cuticular remains and does not significantly affect autofluorescence or shape. The acquired confocal image stacks and resulting volume renderings are useful to visualise, reconstruct and quantify structures for taxonomic purposes but also for morphological investigation of special cuticular structures such as the head endoskeleton of hexapods.

20 citations

Journal ArticleDOI
TL;DR: In this paper, the brain structures of Campodea augens and Catajapyx aquilonaris were analyzed using a 3D reconstruction of the major neuropils and tracts from semi-thin section series.
Abstract: In the past decade neuroanatomy has proved to be a valuable source of character systems that provide insights into arthropod relationships. Since the most detailed description of dipluran brain anatomy dates back to Hanstrom (1940) we re-investigated the brains of Campodea augens and Catajapyx aquilonaris with modern neuroanatomical techniques. The analyses are based on antibody staining and 3D reconstruction of the major neuropils and tracts from semi-thin section series. Remarkable features of the investigated dipluran brains are a large central body, which is organized in nine columns and three layers, and well developed mushroom bodies with calyces receiving input from spheroidal olfactory glomeruli in the deutocerebrum. Antibody staining against a catalytic subunit of protein kinase A (DC0) was used to further characterize the mushroom bodies. The japygid Catajapyx aquilonaris possesses mushroom bodies which are connected across the midline, a unique condition within hexapods. Mushroom body and central body structure shows a high correspondence between japygids and campodeids. Some unique features indicate that neuroanatomy further supports the monophyly of Diplura. In a broader phylogenetic context, however, the polarization of brain characters becomes ambiguous. The mushroom bodies and the central body of Diplura in several aspects resemble those of Dicondylia, suggesting homology. In contrast, Archaeognatha completely lack mushroom bodies and exhibit a central body organization reminiscent of certain malacostracan crustaceans. Several hypotheses of brain evolution at the base of the hexapod tree are discussed.

15 citations


Cited by
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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

Journal ArticleDOI

3,734 citations

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
TL;DR: This work presents BUSCO v3 with example analyses that highlight the wide‐ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.
Abstract: Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.

1,575 citations