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.

It is generally assumed that Cretaceous stem ants were obligately eusocial, because of the presence of wingless adult females, yet the available evidence is ambiguous. Here, we report the syninclusion of a pupa and adult of a stem ant species from Mid-Cretaceous amber. As brood are immobile, the pupa was likely to have been transported by an adult. Therefore, the fossil substantiates the hypothesis that wingless females were cooperators, thus these were true ‘workers’. Re-examination of all described Cretaceous ant species reveals that winged–wingless diphenism – hence a variable dispersal capacity – may have been ancestral to the total clade of the ants, and that highly specialized worker-specific phenotypes evolved in parallel between the stem and crown groups. The soft-tissue preservation of the fossil is exceptional, demonstrating the possibility of analysing the development of the internal anatomy in stem ants. Based on the highest-resolution µ-CT scans of stem ants to date, we describe † Gerontoformica sternorhabda sp. nov. , redescribe † G. gracilis , redefine the species group classification of † Gerontoformica , and provide a key to the species of the genus. Our work clarifies the species boundaries of † Gerontoformica and renders fossils relevant to the discussion of eusocial evolution in a way that has heretofore been intractable.

Evidence for the evolution of eusociality in stem ants and a systematic revision of † Gerontoformica (Hymenoptera: Formicidae)

Burmapseudomorphus planus gen. et sp. nov. – a Late Cretaceous stem group member of the specialized Pseudomorphini (Carabidae, Coleoptera) from northern Myanmar

Phylogenetic methods applied to extinct beetles — the case of † Tunguskagyrus (Gyrinidae or †Triaplidae)

Structural megadiversity in leaf litter predators - the head anatomy of Pselaphus heisei (Pselaphinae, Staphylinidae, Coleoptera)

The adult head morphology of Dascillus (L.) (Dascilloidea: Dascillidae) and Glaresis Erichson (Scarabaeoidea: Glaresidae) and its phylogenetic implications

Rolf G. Beutel

Papers

Evidence for the evolution of eusociality in stem ants and a systematic revision of † Gerontoformica (Hymenoptera: Formicidae)

Burmapseudomorphus planus gen. et sp. nov. – a Late Cretaceous stem group member of the specialized Pseudomorphini (Carabidae, Coleoptera) from northern Myanmar

Phylogenetic methods applied to extinct beetles — the case of † Tunguskagyrus (Gyrinidae or †Triaplidae)

Structural megadiversity in leaf litter predators - the head anatomy of Pselaphus heisei (Pselaphinae, Staphylinidae, Coleoptera)

The adult head morphology of Dascillus (L.) (Dascilloidea: Dascillidae) and Glaresis Erichson (Scarabaeoidea: Glaresidae) and its phylogenetic implications