Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

MITOS: Improved de novo metazoan mitochondrial genome annotation

In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and Mayden, 1997). Despite this influence, a well-justi? fied, uniformly applied method of treating gaps is lacking in sequence-based phyloge? netic studies. Treatment of gaps varies widely from secondarily mapping gaps onto the tree inferred from base characters

/pdf/gaps-as-characters-in-sequence-based-phylogenetic-analyses-4hdlrw0k0r.pdf

Gaps as Characters in Sequence-Based Phylogenetic Analyses

https://www.ruhr-uni-bochum.de/imperia/md/content/geobot/2007/hibbett_2007-a_higher-level-phylogenetic.pdf

A higher-level phylogenetic classification of the Fungi

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

Our understanding of insect development and evolution has increased greatly due to recent advances in the comparative developmental approach. Modern developmental biology techniques such as in situ hybridization and molecular analysis of developmentally important genes and gene families have greatly facilitated these advances. The role of the comparative developmental approach in insect systematics is explored in this paper and we suggest two important applications of the approach to insect systematics--character dissection and morphological landmarking. Existing morphological characters can be dissected into their genetic and molecular components in some cases and this will lead to more and richer character information in systematic studies. Character landmarking will he essential to systematic studies for clarifying structures such as shapes or convergences, which are previously hard to analyze anatomical regions. Both approaches will aid greatly in expanding our understanding of homology in particular, and insect development in general.

/pdf/crossroads-milestones-and-landmarks-in-insect-development-wg9fufbfep.pdf

Crossroads, milestones and landmarks in insect development and evolution: implications for systematics.

Sun et al. (2006) recently published an analysis of phylogenetic relationships of the major lineages of maysies (Ephemeroptera). Their study used partial 18S rDNA sequences (583 nucleotides), which were analyzed via parsimony to obtain a molecular phylogenetic hypothesis. Their study included 23 maysy species, representing 20 families. They aligned the DNA sequences via default settings in Clustal and reconstructed a tree by using parsimony in PAUP*. However, this tree was not presented in the article, nor have they made the topology or alignment available despite multiple requests. This molecular tree was compared with previous hypotheses based on morphological data to “test” (but see below) which morphology-based relationships were not signiÞcantly different from the molecular topology. Although molecular data can help shed light on many of the fundamental questions in insect phylogenetics, it is important to perform analyses correctly and to accurately report results in a way that allows subsequent validation. Sun et al. (2006) provided an adequate review of the major traditional hypotheses concerning higher level classiÞcation and relationships among maysies. Some of these hypotheses are based on cladistic analysis of morphology, but others are intuitive phylogenies that were not derived from any formal repeatable and objective analysis. These authors failed to report previously published molecular hypotheses that shed light on maysy phylogeny, many of which disagree with their results. For example, there have been previously published molecular studies investigating higher level relationships among maysies and relatives

/pdf/pisciforma-setisura-and-furcatergalia-order-ephemeroptera-3p9yt7nfuw.pdf

Pisciforma, Setisura, and Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based on 18S rDNA Sequences: A Response to Sun et al. (2006)

A brief survey of invertebrates in caves of Peninsular Malaysia

This study was presented at the International Conference on Ephemeroptera and Plecoptera held in Aracruz, Brazil from June 3–8, 2018. Higher-level relationships among major mayfly lineages remains controversial and previous molecular and morphological data do not robustly support the current classification scheme and many of the proposed branching orders (Ogden et al. 2009a). This project represents the largest phylogenetic analysis for mayflies to date. Over 440 targeted genomic protein coding regions (exons) were generated using a novel hybrid enrichment probes set. The dataset, analyzed as amino acids, allowed testing for the monophyly of many of the proposed higher-level groupings. The results from this work were congruent with the lineages Carapacea, Caenoidea, and Ephemerelloidea, but the other higher-level lineages were not supported as monophyletic. This study was an initial evaluation of the anchored hybrid enrichment dataset for uses in deep level mayfly systematics, and a more comprehensive analysis is forthcoming. Still, this study supports the conclusion that more taxa and data, especially phylogenomic data, should result in more robust trees for future studies in mayfly phylogenetics and systematics.

Michael F. Whiting

Papers

Crossroads, milestones and landmarks in insect development and evolution: implications for systematics.

Pisciforma, Setisura, and Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based on 18S rDNA Sequences: A Response to Sun et al. (2006)

A brief survey of invertebrates in caves of Peninsular Malaysia

Mayfly Phylogenomics: Initial Evaluation of Anchored Hybrid Enrichment Data for the order Ephemeroptera

Evidence from Mitochondrial Genomics on Interordinal Relationships