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.

Myxophaga are a small group of beetles, but phylogenetically crucial as one of the four coleopteran suborders. The monogeneric Sphaeriusidae, one of four myxophagan families, comprise about 20 species, most of them living in moist substrate at river edges. The morphology of the minute hemispherical adult is very insufficiently known. Consequently, we document external and internal head structures using scanning electron microscopy, microtome sections and three‐dimensional reconstructions. The results are discussed with respect to effects of miniaturization and also functional aspects, especially microphagous feeding habits. The head of Sphaerius is less affected by size reduction compared with other beetles of the same size class (e.g. larger Ptiliidae, Corylophidae). Features related to very small size are the absence of externally visible ridges and a partial shift of the brain into the prothorax. The cephalic musculature is apparently not affected. The feeding apparatus is similar to what is found in microphagous species of Polyphaga, especially in Scirtoidea and Staphyliniformia. However, in contrast to polyphagans with similar feeding habits, the hypopharyngeal longitudinal ridge (or process) of Sphaerius is strongly reduced and a fimbriate galea is lacking. The observed features are also evaluated in a cladistic analysis of larval and adult characters. The results are distinctly in conflict with branching patterns suggested by analyses of molecular data, but in agreement with previous morphological studies. In contrast to a pattern obtained in a recent molecular study – (Hydroscaphidae + (Torridincolidae + (Sphaeriusidae + Lepiceridae))) – our analyses yielded Lepiceridae as sister to the remaining Myxophaga (branch support 9), and Sphaerius as sister taxon of Hydroscaphidae (branch support 5). The monophyletic origin of the latter two taxa is supported by unusual synapomorphies of adults and larvae. Sphaerius is characterized by numerous autapomorphies of the head: a labro‐mandibular locking device, a bipartite M. frontoepipharyngalis (M9) with subcomponents oriented in the opposite direction, a deep antennal furrow, an intercalary antennomere with a structure resembling a sucking disc, a strongly elongated flagellomere 1, a compact three‐segmented antennal club, strong bundles of M. tentorioscapalis (M4) originating on the posterior head capsule, a concave anterior side of maxillary palpomere 2, and an elongated second pair of tormae posteriorly connected with a process of the hypopharyngeal suspensorium.

Cephalic anatomy of Sphaeriusidae and a morphology-based phylogeny of the suborder Myxophaga (Coleoptera)

Clavigeritae is a group of obligate myrmecophiles of the rove beetle subfamily Pselaphinae (Staphylinidae). Some are blind and wingless, and all are believed to depend on ant hosts through feeding by trophallaxis. Phylogenetic hypotheses suggest that their ancestors, as are most pselaphines today, were free-living predators. Morphological alterations required to transform such beetles into extreme myrmecophiles were poorly understood. By studying the cephalic morphology of Claviger testaceus, we demonstrate that profound changes in all mouthpart components took place during this process, with a highly unusual connection of the maxillae to the hypopharynx, and formation of a uniquely transformed labium with a vestigial prementum. The primary sensory function of the modified maxillary and labial palps is reduced, and the ventral mouthparts transformed into a licking/'sponging' device. Many muscles have been reduced, in relation to the coleopteran groundplan or other staphylinoids. The head capsule contains voluminous glands whose appeasement secretions are crucial for the beetle survival in ant colonies. The brain, in turn, has been shifted into the neck region. The prepharyngeal dilator is composed of an entire series of bundles. However, the pharynx does not show any peculiar adaptations to taking up liquid food. We demonstrate that far-reaching cephalic modifications characterize C. testaceus, and that the development of appeasement glands and adaptation of the mouthparts to trophallaxis determine the head architecture of this extreme myrmecophile.

Profound head modifications in Claviger testaceus (Pselaphinae, Staphylinidae, Coleoptera) facilitate integration into communities of ants

Insects have invaded marine habitats only rarely and secondarily. Recently, we discovered a flightless dipteran species skating rapidly on the surface of seawater ponds at the Pacific coast of eastern China. Morphological analyses initially suggested an isolated position of the non‐biting midge, suggesting the erection of a new genus within Chironomini (Diptera: Chironomidae). However, an analysis of molecular data revealed that the marine species is in fact nested within the species‐rich genus Dicrotendipes. The apparent conflict between molecular and morphological data can be easily explained. It is likely that the new species has evolved a series of autapomorphic adaptations. These traits clearly distinguish the taxon from other species of the genus but do not justify the erection of a new supraspecific taxon, which would render Dicrotendipes paraphyletic. The switch to marine environments was likely a trigger for various morphological modifications resulting from increased selective pressure. Molecular data suggest that the potential speciation event occurred around 19–29 Ma, linked with a migration from freshwater to seawater ponds along the Pacific Ocean. Considering the results of our analysis, we place the flightless marine skater in the genus Dicrotendipes. All life stages of Dicrotendipes sinicus Qi & Lin sp. n. are described and illustrated, associated with larvae obtained by rearing or confirmed through association with DNA barcodes. The biology and ecology of the species are outlined based on collection data and in situ observations. Evolutionary patterns linked with repeated invasions of marine habitats are discussed.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/zsc.12331

Rolf G. Beutel

Papers

Cephalic anatomy of Sphaeriusidae and a morphology-based phylogeny of the suborder Myxophaga (Coleoptera)

Profound head modifications in Claviger testaceus (Pselaphinae, Staphylinidae, Coleoptera) facilitate integration into communities of ants

A new surface gliding species of Chironomidae: An independent invasion of marine environments and its evolutionary implications

New findings on the enigmatic beetle family Lepiceridae (Coleoptera: Myxophaga)

Evolution of the male genitalia in the genus Limnebius Leach, 1815 (Coleoptera, Hydraenidae)