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.

10.4. Protocucujidae Crowson, 1954

[This corrects the article DOI: 10.1371/journal.pntd.0009098.].

/pdf/correction-comparative-dissection-of-the-peripheral-20hu04xh.pdf

Correction: Comparative dissection of the peripheral olfactory system of the Chagas disease vectors Rhodnius prolixus and Rhodnius brethesi

4. Traditional and modern techniques in insect morphology

Abstract. Since the description of Ptilophorus dufourii (Latreille, 1818), the unknown immature stages and biology of Ptilophorinae is one of the longest persisting gap in the research of the wedge-shaped beetles (Ripiphoridae). Here we describe the primary larva of P. dufourii based on SEM and CLSM images. Its modified mouthparts unsuitable to grasp prey rule out predaceous habits and also processing any solid substrates (e.g., wood or other fresh plant tissues). In contrast, the weakly sclerotized and very small body, the enlargement of the sensorial appendage of the antennae, and simplified mouthparts strongly suggest parasitism and consumption of liquid food. We provide a comparison with the only known larva of Pelecotominae, another possible basal lineage of Ripiphoridae, and discuss potential synapomorphies and differences between larvae of both subfamilies. A sistergroup relationship between Ptilophorinae and Pelecotominae is suggested by the presence of only two stemmata, spatulate femoral setae, a scale-like lateral cranial surface, and an enlarged antennal sensorial appendage, and a clade Ripidiini + Ripiphorinae by a characteristic boat-shape of the primary larvae. The host of P. dufourii remains unknown. We reviewed published host records, but none of them is based on traceable evidence and none of them appears credible. Observations of adult behaviour of P. dufourii are documented. Taxonomy and systematics of Ptilophorus and Ptilophorinae are discussed. The Cretaceous Spinotoma ruicheni Hsiao et Huang, 2017 is transferred from Pelecotominae to Ptilophorinae in accordance with diagnostic characters given in the original description and current definitions of both subfamilies.

Rolf G. Beutel

Papers

10.4. Protocucujidae Crowson, 1954

Correction: Comparative dissection of the peripheral olfactory system of the Chagas disease vectors Rhodnius prolixus and Rhodnius brethesi

4. Traditional and modern techniques in insect morphology

Systematic Position of Ptilophorus dufourii Inferred from Its Primary Larva, with Notes on Ptilophorinae (Coleoptera: Ripiphoridae)

Catching prey with the antennae - The larval head of Corethrella appendiculata (Diptera: Corethrellidae).