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/

/pdf/ape-5-0-an-environment-for-modern-phylogenetics-and-mon2ib4h2c.pdf

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.

Evolution of Protein Molecules

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.

/pdf/partitionfinder-2-new-methods-for-selecting-partitioned-3pmxb5gg72.pdf

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

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.

https://science.sciencemag.org/content/sci/346/6210/763.full.pdf

Phylogenomics resolves the timing and pattern of insect evolution

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.

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.

Friedemann K., Wipfler B., Bradler S. and Beutel R.G. 2011. On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta). —Acta Zoologica (Stockholm) 00: 1–16.



External and internal head structures of Phyllium siccifolium are described in detail. The findings are compared with conditions found in other phasmatodeans and members of other neopteran lineages. The compiled 125 characters were analysed cladistically. A clade Eukinolabia (Phasmatodea + Embioptera) was confirmed. Synapomorphies of these two taxa are the shift of the origin of M. tentorioparaglossalis to the hind margin of the prementum, the presence of M. tentorioscapalis medialis, and antennal muscles that originate exclusively on the anterior tentorial arms. Within Eukinolabia, the position of Timema remains somewhat ambiguous because of missing anatomical data. However, it was confirmed as sister group of Euphasmatodea in a monophyletic Phasmatodea. Apomorphic groundplan features of Euphasmatodea are salivary ducts with separate external openings, apically rounded glossae, the presence of the galealobulus, and the reduction of the antennifer. The monophyly of Neophasmatidae was confirmed. Autapomorphies are the loss of M. frontobuccalis posterior, the anteriorly or dorsally directed maxillary palps, and the reduction of the mandibular incisivi. The analysis of characters of the head yielded three new autapomorphies of Phylliinae, the presence of a protuberance on the attachment site of the dorsal tentorial arms, dorsoventrally flattened maxillary- and labial palps, and possibly the narrow and U-shaped field of trichomes on the apical part of the galea.

On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta)

The use of new technologies, especially computer-based three dimensional reconstructions and micro-computer tomo-graphy (µ-CT) have greatly improved and facilitated the detailed investigation of insect anatomy. Optimal results in morphological work aiming at phylogenetic reconstruction can be obtained with a combined application of different techniques such as histology, scanning electron microscopy, and µ-CT. The use of µ-CT greatly enhances the efficiency of the acquisition of detailed anatomical data and allows a br oad taxon sampling in phylogenetic studies partly or entirely based on morphological characters. A disadvantage of phase contrasted µ-CT images is the poor differentiation of differ-ent tissue types. This problem can be overcome by the use of stable low energy photon beams as available at the beam-line BW2 of the Deutsches Elektronen-Synchrotron in Hamburg (DESY). Synchrotron-radiation-based µ-Ct data (SR µ-CT) obtained with this approach are an ideal basis for highl y efficient three dimensional reconstructions of high quality.

Micro-computer tomography and a renaissance of insect morphology

Various characters of adult and larval members of Adephaga and Cupedidae were analyzed, and suggest that Gyrinidae are the sister-group of the remaining Adephaga, and are not closely related to the remaining aquatic Adephaga. The aquatic families Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae seem to form a well founded monophyletic unit. The following characters are considered as synapomorphies of Adephaga excluding Gyrinidae: bifurcate condition of the muscle (= M.) tentoriopraementalis inferior, reduction of hypopharynx, strongly developed prosternal process, reduction in size and specialized modification of the ventral sclerite of the mesothorax, strongly developed mesofurcal arms, a high mesopleural ridge, globular mesocoxae restricted to rotatory movements, invaginated sternum VIII (coxostemum), the strongly curved base of the median lobe of the aedeagus, which articulates with the parameres, the rotated position of the aedeagus in repose, fusion of the larval clypeolabrum with the frons and reduction of the larval lacinia. Mesal shifting of M. episterno-coxalis prothoracis, and the fusion of the apical portions of the malpighian tubules of either side are considered as synapomorphies of Adephaga excluding Rhysodidae and Gyrinidae. Lateral reduction of the meta “sternal” transverse ridge and the presence of the subcubital setal binding patch of the hind wing are considered as synapomorphic characters of Trachypachidae, Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae. We postulate that the metacoxal fusion occurred independently in gyrmids and the common ancestor of Trachypachidae, Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae. Consequently we consider this character state as another synapomorphy of Trachypachidae and Hydradephaga excluding Haliplidae and Gyrinidae. The following characters are considered as synapomorphies of Noteridae, Amphizoidae, Hygrobiidae and Dytiscidae: Loss of tactile setae on the head capsule, metafurcal origin on the intercoxal wall, expansion of the intercoxal wall, elongation of the subcubital setal binding patch, loss of Mm. furca-coxale anterior and posterior, reduction of the larval abdominal segments IX and X, and the shifting of the uropmphi onto the ventral side of segment VIII. Presence of M. tentorio-mandibularis and M. stipitopalpalis intemus are certainly primitive features of adult gyrinids but the distribution of these character states among most members of Adephaga is yet unclear. Chemical defence gland constituents point towards a very isolated position of Gyrinidae. The old age of the group, documented by a larva found in upper Permian deposits, may support the hypothesis of a sister-group relation-ship between Gyrinidae and the remainder of Adephaga.

On the systematic position of the family Gyrinidae (Coleoptera: Adephaga)

Glossary of morphological terms.

https://www.zin.ru/animalia/coleoptera/pdf/ptinella.pdf

Morphology of the minute larva of Ptinella tenella, with special reference to effects of miniaturisation and the systematic position of Ptiliidae (Coleoptera: Staphylinoidea).

Rolf G. Beutel

Papers

On the head morphology of Phyllium and the phylogenetic relationships of Phasmatodea (Insecta)

Micro-computer tomography and a renaissance of insect morphology

On the systematic position of the family Gyrinidae (Coleoptera: Adephaga)

Glossary of morphological terms.

Morphology of the minute larva of Ptinella tenella, with special reference to effects of miniaturisation and the systematic position of Ptiliidae (Coleoptera: Staphylinoidea).