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

Publisher Summary
This chapter discusses the Siphonaptera, laterally compressed wingless holometabolous insects. The order contains approximately 2575 species. All species are parasitic in the adult stage and possess mouthparts modified for piercing and sucking, highly modified combs and setae on their body and legs, and legs that are modified for jumping. Some species are vectors of disease, and current research is providing important insights into flea phylogeny and evolution. Most flea species require a blood meal prior to oogenesis and spermatogenesis. With the exception of some species whose reproductive cycle is synchronized with that of their host, there are few studies on the nutritional requirements of adult fleas. Although the larvae of several fleas have been noted to burrow into dead host tissues, those of Uropsylla tasmanica are the only truly parasitic flea larvae that burrow into and feed on the tissues of their live hosts. Some larvae have been documented to feed directly on fresh blood as it is excreted from the anus of feeding adult fleas, but most scavenge on the dried blood residues or animal dandruff and excreta. A few species are predaceous on other small organisms within the nest.

Chapter 236 – Siphonaptera: (Fleas)

Wilkinson (1991) suggests that the problems of polarity decisions and homoplasy in a cladistic analysis may be solved if cladists simply accept plesiomorphy as a reliable indicator of monophyly. Here we argue that: (1) Wilkinson's argument is based on misapprehension of synapomorphy and the problem of homoplasy; (2) His proposed methodology fails to consider the full ramifications of rooting, polarity, and parsimony; and (3) His method does not solve the problems he raises. We demonstrate the limitations of this methodology by using Wilkinson's practical example. We find no justification for the assertion that plesiomorphy may reliably delimit monophyly and recommend against Wilkinson's suggested methodological revisions.

Synamorphy, monophyly, and cladistic analysis: A reply to Wilkinson

Nycteridopsylla iae Beaucournu and Kock, 1992 and Nycteridopsylla quadrispina Lu and Wu, 2003 have heretofore been known only by the male and female sexes, respectively. The morphological differences in these two species are striking; however, a recent collection of male N. iae and female N. quadrispina from a single host individual of the Great Evening Bat (I. io Thomas), led us to suspect that N. iae and N. quadrispina represented the same species. Morphological similarities were noted and male and female exemplars were sequenced using five genes (18S, 28S, 16S, 12S, and COII). Across the five sequenced genes from both specimens (male and female), sequence identity was 100%. Considering morphological characteristics and DNA analysis, N. quadrispina is indisputably a junior synonym of N. iae. Myanmar is a new country record for N. iae, Harpiocephalus harpia (Temminck) is a new host record for N. iae and the preferred host is the Great Evening Bat, I. io.

Nycteridopsylla quadrispina LU and WU, a junior synonym of nycteridopsylla IAE Beaucournu and Kock (Siphonaptera: Ischnopsyllidae) as determined by morphological and DNA analyses

Michael F. Whiting

Papers

Chapter 236 – Siphonaptera: (Fleas)

Synamorphy, monophyly, and cladistic analysis: A reply to Wilkinson

Nycteridopsylla quadrispina LU and WU, a junior synonym of nycteridopsylla IAE Beaucournu and Kock (Siphonaptera: Ischnopsyllidae) as determined by morphological and DNA analyses