Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Statistics and truth in phylogenomics

S Kumar, AJ Filipski, FU Battistuzzi… - Molecular biology …, 2012 - academic.oup.com
Phylogenomics refers to the inference of historical relationships among species using
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …

Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation

NS Upham, JA Esselstyn, W Jetz - PLoS biology, 2019 - journals.plos.org
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …

Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae …

M Adeolu, S Alnajar, S Naushad… - … journal of systematic …, 2016 - microbiologyresearch.org
Understanding of the phylogeny and interrelationships of the genera within the order
'Enterobacteriales' has proven difficult using the 16S rRNA gene and other single-gene or …

Revisiting metazoan phylogeny with genomic sampling of all phyla

CE Laumer, R Fernández, S Lemer… - … of the royal …, 2019 - royalsocietypublishing.org
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of
key taxa—or fail when such key taxa are not sampled. In this light, we here present the first …

Terrace aware data structure for phylogenomic inference from supermatrices

O Chernomor, A Von Haeseler, BQ Minh - Systematic biology, 2016 - academic.oup.com
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix,
is commonly accompanied by the assumption of partition models. Under such models each …

[图书][B] Computational molecular evolution

Z Yang - 2006 - books.google.com
The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

[PDF][PDF] Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria

JM Padial, T Grant, DR Frost - Zootaxa, 2014 - mapress.com
Alkatib, S., Scharff, LB, Rogalski, M., Fleischmann, TT, Matthes, A., Seeger, S., Schöttler, MA,
Ruf, S. & Bock, R.(2012) The contributions of wobbling and superwobbling to the reading of …

A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error

JA Ballesteros, PP Sharma - Systematic Biology, 2019 - academic.oup.com
Horseshoe crabs (Xiphosura) are traditionally regarded as sister group to the clade of
terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent …

Taxon sampling and the accuracy of phylogenetic analyses

TA Heath, SM Hedtke, DM Hillis - Journal of systematics and evolution, 2008 - jse.ac.cn
Appropriate and extensive taxon sampling is one of the most important determinants of
accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary …