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.

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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

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.

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.

https://serval.unil.ch/resource/serval:BIB_2A4C7F8DA305.P001/REF.pdf

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves--a clade that encompasses nearly all living bird species--remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades--Columbea and Passerea--were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

https://bioone.org/journals/Proceedings-of-the-Entomological-Society-of-Washington/volume-120/issue-2/0013-8797.120.2.458/Beetles-Insecta-Coleoptera-Associated-with-Dioon-Tomasellii-Cycadales-in-Jalisco/10.4289/0013-8797.120.2.458.pdf

Beetles (Insecta, Coleoptera) Associated with Dioon Tomasellii (Cycadales) in Jalisco, Mexico, with Comments on Others Beetles Found on Cycads

SSe presentan una lista comentada de las especies de hormigas legionarias del estado de Jalisco y occidente de Mexico, asi como claves para la determinacion de soldados y obreras. Este trabajo se baso en muestreos realizados en 17 localidades de 14 municipios de Jalisco, asi como en la revision de especimenes depositados en cuatro colecciones entomologicas nacionales. Se examinaron 21,167 ejemplares de hormigas legionarias, donde 18,344 correspondieron a material depositado en las colecciones. Para cada especie, se elaboro una lamina con los principales caracteres diagnosticos empleados en las claves dicotomicas. Los ejemplares en mejores condiciones, con excepcion de Neivamyrmex pauxillus y N. Pilosus, cuyos esquemas fueron redibujados a partir de fotografias obtenidas del sitio AntWeb (2015), se eligieron para elaborar las laminas. Se incluyen 21 especies, en la clave y la lista comentada, agrupadas en cuatro generos: Eciton, Labidus, Neivamyrmex y Nomamyrmex. Se documentan tres primeros nuevos registros para Jalisco: Neivamyrmex halidaii (Shuckard, 1840), N. Impudens (Mann, 1922) y N. Pauxillus (Wheeler, 1903).

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Las hormigas legionarias de Jalisco (Hymenoptera: Formicidae: Dorylinae): lista comentada y claves

Possible stridulatory organs in oxyporine rove beetles (Coleoptera: Staphylinidae), their biological role and systematic significance

Summary Planning, implementing, and systematic revision of conservation policies are necessary to protect the biodiversity of a territory. This is critical in countries heavily impacted by anthropogenic activities, like El Salvador, where conserving biodiversity remnants must be a priority. Monitoring indicator groups represents a feasible option to review the status of biodiversity and the processes taking place in the country's conservation areas. We evaluated the suitability of Scarabaeidae beetle functional groups as ecological indicators to detect differences in the conservation status of two protected areas in El Salvador. We conducted monthly sampling for one year at each site, using pitfall, aerial, and UV-light traps to capture beetles. We detected differences in species richness, abundance, species composition, and turnover between the two areas. The results suggest the possibility of using this approach to monitor protected areas, to estimate the forest conservation status, and to evaluate the conservation strategies implemented to date. For the future, it is essential to determine if this is possible by replicating studies throughout the territory using standardized methodologies to obtain comparable results. The cost–benefit ratio of using a single indicator group is key in countries like El Salvador, where the economic aspect is a limiting factor for biological prospecting.

Functional-group approach with scarab beetles (Coleoptera: Scarabaeidae): a low-cost alternative for monitoring biodiversity in El Salvador

A new species of Belonuchus Nordmann, 1837 is described based on 118 specimens from Cerro de Garcia, Jalisco, Mexico. Belonuchus cifuentesi Rodriguez & Navarrete-Heredia sp. nov. was primarily collected associated with Agave inaequidens, and is similar to B. arizonicus Casey, 1915 but differs mainly in the structure of the aedeagus and color pattern.

/pdf/a-new-mexican-species-of-belonuchus-nordmann-coleoptera-22f4aeefnn.pdf

José Luis Navarrete-Heredia

Papers

Beetles (Insecta, Coleoptera) Associated with Dioon Tomasellii (Cycadales) in Jalisco, Mexico, with Comments on Others Beetles Found on Cycads

Las hormigas legionarias de Jalisco (Hymenoptera: Formicidae: Dorylinae): lista comentada y claves

Possible stridulatory organs in oxyporine rove beetles (Coleoptera: Staphylinidae), their biological role and systematic significance

Functional-group approach with scarab beetles (Coleoptera: Scarabaeidae): a low-cost alternative for monitoring biodiversity in El Salvador

A new Mexican species of Belonuchus Nordmann (Coleoptera, Staphylinidae).