To examine evolutionary relationships among piroplasmids, we conducted phylogenetic analyses of 192 18S r DNA sequences from the genera .Our analyses revealed eight clades potentially representing distinct genera, and we distinguish the Duncani Group and Microti Group as genetically distinct groups of species requiring detailed analysis of morphology and life-history to allow formal generic description.To source the newest code at any point, use these functions: # Online (you can also download each and source locally) library(devtools,httr) devtools::source_gist(id="https://gist.github.com/nmatzke/b2dbf78532eca734881a", filename="sourceall_git.R") sources = sourceall_git(repo="nmatzke/BEASTmaste R") I have improved the treatment of the "use" columns in the "OTUs", "taxa", and "data" worksheets of the Excel settings file.The purpose of "BEASTmaste R" is to convert NEXUS data file(s) (DNA, amino acids, discrete morphological characters, and/or continuous traits), plus an Excel settings file, into Beast2 XML format. The Birth-Death-Skyline-Serial-Sampling tree model is used (or the Sampled-Ancestors variant), enabling different birth, death, and sampling rates through time. Of course, identified bugs I will always try to fix or post work-arounds. BEASTmaste R is primarily aimed at enabling tip-dating analyses using fossils as dated terminal taxa. If you want any serious help/feature additions with BEASTmaste R, for me, given my current commitments, that feels more like a coauthorship-type situation than a generic-free-help situation.Subsequent divergences are characterized by long internodes followed by short bursts of speciation extending from an initial episode of divergence in the Early and Middle Miocene (19–17 Mya) to a second episode during the Pliocene and Pleistocene (3.6 Mya – recent).Estimates of divergence dates overlap significantly with periods of global warming, during which upwelling intensity – and related high primary productivity in upwelling regions – decreased markedly.
► As many as eight clades potentially corresponding to distinct genera were recovered.
The order Piroplasmida consists of several genera of tick-borne parasites that infect mammals, and to a lesser extent birds, and are therefore of medical and economic importance.
Despite their importance, considerable confusion exists concerning the relationship among piroplasmid species, specifically concerning the number of genera and the intergeneric relationships.
However, it may be useful for setting up molecular-only analyses (particularly automated variants), for learning Beast2 XML (since the BEASTmaste R XML output is annotated and much easier for human reading than the BEAUTi output), or for automating such analyses. And, feature additions can be suggested, and questions asked, and I will get to these when I can.
BEASTmaste R also contains functions for parsing Beast2 output, e.g. All such matters are best posted to the BEASTmaste R Google Group.