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.

The larva of Andogyrus buqueti (Aube, 1838) is described in all instars. The larva shows characters which are typical for that of Enhydrini and Orectochilini. The closer relationship of Andogyrus Ochs could not be cleared through larval research.

Description of the larva of Andogyrus buqueti (Aubé, 1838) (Coleoptera, Gyrinidae)

Crowsoniella relicta Pace, one of the most obscure and cryptic beetle taxa, was recently transferred from Archostemata to the polyphagan series Cucujiformia. We discuss the arguments in favour of this hypothesis. The placement of the species is evaluated with a cladistic approach and two different morphological data sets: one aiming mainly to clarify the relationships of extinct and extant archostematans, and one aimed at resolving species-level phylogeny for the suborder. The results suggest clearly that a position of Crowsoniella within a polyphagan subgroup is very unlikely, and that a placement in Archostemata is justified and should be maintained. Due to the serious lack of anatomical information, non-destructive µ-CT scanning of enigmatic taxa like Crowsoniella Pace and Sikhotealinia Lafer should have high priority.

Is Crowsoniella relicta really a cucujiform beetle

/pdf/transformation-of-head-structures-during-the-metamorphosis-1b6ql0vipu.pdf

Transformation of head structures during the metamorphosis of Chrysomela populi (Coleoptera: Chrysomelidae).

Distal leg structures of Zoraptera - did the loss of adhesive devices curb the chance of diversification?

Head structures of the leaf mining larva of the chrysomelid species Podagricomela shirahatai are described and illustrated. Internal and external structures were reconstructed three dimensionally based on image stacks obtained with microcomputed tomography. The larval head is characterized by prognathism, a dorsoventrally compressed shape, a flattened maxillolabial complex, a completely reduced coronal suture, and the presence of a deep, V-shaped posterior emargination of the head capsule. Internal structures are not distinctly affected by leaf mining. The cephalic features are compared with conditions found in surface feeding and root feeding alticine larvae and also with characters of chrysomeline larvae of Chrysomela populi Linnaeus. Possible correlations between modifications of the larval head and different feeding behaviors are discussed. Characters are also discussed with respect to possible phylogenetic implications. Some derived features are apparently due to phylogenetic constraints. Apomorphies characterizing alticine larvae with distinctly different life habits are the loss of M. frontoepharyngalis (M. 9), the origin of M. tentoriostipitalis (M. 18) from the head capsule, two insertions of M. tentoriopraementalis inferior (M. 29) and the reduction of stemmata. The study underlines that the anatomical study of chrysomeloid larvae is not only highly desirable in a phylogenetic context, but also crucial for understanding the evolution of different life strategies in this extremely successful group of Coleoptera. J. Morphol. 276:446–457, 2015. © 2014 Wiley Periodicals, Inc.

Rolf G. Beutel

Papers

Description of the larva of Andogyrus buqueti (Aubé, 1838) (Coleoptera, Gyrinidae)

Is Crowsoniella relicta really a cucujiform beetle

Transformation of head structures during the metamorphosis of Chrysomela populi (Coleoptera: Chrysomelidae).

Distal leg structures of Zoraptera - did the loss of adhesive devices curb the chance of diversification?

The larval head structures of Podagricomela shirahatai (Chûjô) (Chrysomelidae, Galerucinae, Alticini) and morphological effects of leaf mining.