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The Inference of Gene Trees with Species Trees

Gergely J. Szöllősi, Eric Tannier, Vincent Daubin and Bastien Boussau.

in Systematic Biology

January 2015; p ublished online July 2014 .

Journal Article. Subjects: Biological Sciences. 15904 words.

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models...

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Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors

Chi Zhang, Bruce Rannala and Ziheng Yang.

in Systematic Biology

November 2014; p ublished online August 2014 .

Journal Article. Subjects: Biological Sciences. 6774 words.

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Phylogenetics and the Human Microbiome

Frederick A. Matsen.

in Systematic Biology

January 2015; p ublished online August 2014 .

Journal Article. Subjects: Biological Sciences. 11525 words.

The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than...

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Concatabominations: Identifying Unstable Taxa in Morphological Phylogenetics using a Heuristic Extension to Safe Taxonomic Reduction

Karen Siu-Ting, Davide Pisani, Christopher J. Creevey and Mark Wilkinson.

in Systematic Biology

January 2015; p ublished online September 2014 .

Journal Article. Subjects: Biological Sciences. 3808 words.

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From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus <i>Viola</i> (Violaceae)

Thomas Marcussen, Lise Heier, Anne K. Brysting, Bengt Oxelman and Kjetill S. Jakobsen.

in Systematic Biology

January 2015; p ublished online October 2014 .

Journal Article. Subjects: Biological Sciences. 12483 words.

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and...

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How Much Information is Needed to Infer Reticulate Evolutionary Histories?

Katharina T. Huber, Leo Van Iersel, Vincent Moulton and Taoyang Wu.

in Systematic Biology

January 2015; p ublished online September 2014 .

Journal Article. Subjects: Biological Sciences. 6790 words.

Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in...

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Genomic Repeat Abundances Contain Phylogenetic Signal

Steven Dodsworth, Mark W. Chase, Laura J. Kelly, Ilia J. Leitch, Jiří Macas, Petr Novák, Mathieu Piednoël, Hanna Weiss-Schneeweiss and Andrew R. Leitch.

in Systematic Biology

January 2015; p ublished online September 2014 .

Journal Article. Subjects: Biological Sciences. 9467 words.

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of...

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Cancer Evolution: Mathematical Models and Computational Inference

Niko Beerenwinkel, Roland F. Schwarz, Moritz Gerstung and Florian Markowetz.

in Systematic Biology

January 2015; p ublished online October 2014 .

Journal Article. Subjects: Biological Sciences. 16463 words.

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance...

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The Phylogenetic Likelihood Library

T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. Von Haeseler and A. Stamatakis.

in Systematic Biology

March 2015; p ublished online October 2014 .

Journal Article. Subjects: Biological Sciences. 3943 words.

We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis...

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Integrating Fossils, Phylogenies, and Niche Models into Biogeography to Reveal Ancient Evolutionary History: The Case of <i>Hypericum</i> (Hypericaceae)

Andrea S. Meseguer, Jorge M. Lobo, Richard Ree, David J. Beerling and Isabel Sanmartín.

in Systematic Biology

March 2015; p ublished online November 2014 .

Journal Article. Subjects: Biological Sciences. 11633 words.

In disciplines such as macroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that...

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