Mesquite: a modular system for evolutionary analysis. Version 2.6

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.

https://bioinformatics.cs.vt.edu/~easychair/HusonBryant_MBE_2006.pdf

Application of Phylogenetic Networks in Evolutionary Studies

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.

/pdf/bayesian-coalescent-inference-of-past-population-dynamics-4unp68r4jo.pdf

Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. We present q2-feature-classifier (
 https://github.com/qiime2/q2-feature-classifier
 ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data. The naive-Bayes, BLAST+-based, and VSEARCH-based classifiers implemented in QIIME 2 meet or exceed the species-level accuracy of other commonly used methods designed for classification of marker gene sequences that were evaluated in this work. These evaluations, based on 19 mock communities and error-free sequence simulations, including classification of simulated “novel” marker-gene sequences, are available in our extensible benchmarking framework, tax-credit (
 https://github.com/caporaso-lab/tax-credit-data
 ). Our results illustrate the importance of parameter tuning for optimizing classifier performance, and we make recommendations regarding parameter choices for these classifiers under a range of standard operating conditions. q2-feature-classifier and tax-credit are both free, open-source, BSD-licensed packages available on GitHub.

/pdf/optimizing-taxonomic-classification-of-marker-gene-amplicon-3n7ay68e4j.pdf

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

Hepatitis C virus (HCV) is a leading worldwide cause of liver disease. Here, we use a new model of HCV spread to investigate the epidemic behavior of the virus and to estimate its basic reproductive number from gene sequence data. We find significant differences in epidemic behavior among HCV subtypes and suggest that these differences are largely the result of subtype-specific transmission patterns. Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease.

https://science.sciencemag.org/content/sci/292/5525/2323.full.pdf

The epidemic behavior of the hepatitis C virus.

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem.

The association between two or more lineages over evolutionary time is a recurrent theme spanning several different fields within biology, from molecular evolution to coevolution and biogeography. In each `historical association', one lineage is associated with another, and can be thought of as tracking the other over evolutionary time with a greater or lesser degree of fidelity. Examples include genes tracking organisms, parasites tracking hosts and organisms tracking geological and geographical changes. Parallels among these problems raise the tantalizing prospect that each is a special case of a more general problem, and that a single analytical tool can be applied to all three kinds of association.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(98)01438-4.pdf

Trees within trees: phylogeny and historical associations

The problem of finding least-cost reconstructions of past host/parasite associations, given the phylogenetic histories of a set of host taxa and of their associated parasites, is known to be complex. I provide in this article a new method of implicitly listing all the potentially optimal solutions to the problem, by considering each hypothesised past association individually, in a structure I have termed a Jungle. These structures are demonstrated to enable fast acquisition of globally optimal solutions under general weighting schemes, including minimisation of total number of postulated events and maximization of postulated cospeciation events. A simple example is given, and the pocket gopher/chewing louse system investigated by Hafner and Nadler [Hafner and Nadler, Nature 332 (1988) 258] is re-examined.

Jungles: a new solution to the host/parasite phylogeny reconciliation problem

Primate lentiviruses (PLV) from closely related primate species have been observed to be more closely related to each other than to PLV from more distantly related primate species. The current explanation for this observation is the codivergence hypothesis; that is, the divergence of a virus lineage results from the divergence of the host lineage. We show that, alternatively, frequent cross-species transmission of PLV, coupled with a tendency for more closely related primate species to exchange viruses "successfully," can result in apparent codivergence. This host-switching hypothesis reconciles several puzzling observations related to the evolution of PLV.

Michael A. Charleston

Papers

The epidemic behavior of the hepatitis C virus.

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem.

Trees within trees: phylogeny and historical associations

Jungles: a new solution to the host/parasite phylogeny reconciliation problem

Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny.