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.

Giant stick insects reveal unique ontogenetic changes in biological attachment devices.

The skeletomuscular system of the larva of Drosophila melanogaster (Drosophilidae, Diptera): a contribution to the morphology of a model organism.

Functional morphology and evolution of specialized mouthparts of Cephenniini (Insecta, Coleoptera, Staphylinidae, Scydmaeninae)

Internal and external features of larvae of Nosodendron fasciculare were examined and compared to character states found in other groups of Derodontoidea and Bostrichoidea. Synapomorphic larval features indicate a sistergroup relationship between Nosodendridae and Derodontidae: tubercular surface structure, body compressed dorsoventrally, tergites with lateral projections, spiracles located on tubular processus. These families share three derived character states with Jacobsoniidae in one of two equally parsimonious trees. However, the monophyletic origin of Nosodendridae + Derodontidae + Jacobsoniidae is not sufficiently established at present. The monophyly of Bostrichoidea (Dermestidae + Bostrichidae + Anobiidae + Ptinidae) is suggested by hypognathism. Larvae of these families are characterized by the absence of the mandibular mola and a robust apical part of the mandible. The monophyly of Bostrichidae + Anobiidae + Ptinidae is indicated by a C-shaped, grub like body and the abdominal apex formed by an enlarged and rounded segment IX. Bostrychiformia are probably paraphyletic. A closer relationship between Bostrichoidea with Cucujiformia is suggested by the possession of cryptonephric malpighian tubules in adults. The specific type of cryptonephridism in Bostrichoidea is probably derived from this condition and is considered autapomorphic. The monophyly of Nosodendridae (Nosodendron) is supported by several autapomorphies. The assignment of the supposed larva of Nosodendron ovatum remains unclear. An inclusion of the dermestid genus Orphilus in Nosodendridae is rejected. Muscular features of larvae of Nosodendron (and Derodontus) are largely plesiomorphic.

Rolf G. Beutel

Papers

Giant stick insects reveal unique ontogenetic changes in biological attachment devices.

The skeletomuscular system of the larva of Drosophila melanogaster (Drosophilidae, Diptera): a contribution to the morphology of a model organism.

Functional morphology and evolution of specialized mouthparts of Cephenniini (Insecta, Coleoptera, Staphylinidae, Scydmaeninae)

Study of the larva of Nosodendron fasciculare (Olivier 1790) (Coleoptera: Nosodendridae) with implications for the phylogeny of Bostrichiformia

The morphology and evolution of the adult head of Adephaga (Insecta: Coleoptera)