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 …

A review of long‐branch attraction

J Bergsten - Cladistics, 2005 - Wiley Online Library
The history of long‐branch attraction, and in particular methods suggested to detect and
avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include …

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

N Segata, D Börnigen, XC Morgan… - Nature …, 2013 - nature.com
New microbial genomes are constantly being sequenced, and it is crucial to accurately
determine their taxonomic identities and evolutionary relationships. Here we report …

Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling

S Reddy, RT Kimball, A Pandey, PA Hosner… - Systematic …, 2017 - academic.oup.com
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …

[LIBRO][B] Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

DJ Zwickl - 2006 - search.proquest.com
Phylogenetic trees have a multitude of applications in biology, epidemiology, conservation
and even forensics. However, the inference of phylogenetic trees can be extremely …

Resolution of the early placental mammal radiation using Bayesian phylogenetics

WJ Murphy, E Eizirik, SJ O'Brien, O Madsen, M Scally… - Science, 2001 - science.org
Molecular phylogenetic studies have resolved placental mammals into four major groups,
but have not established the full hierarchy of interordinal relationships, including the position …

[PDF][PDF] An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

APG Ii - Botanical journal of the Linnean Society, 2003 - plantnetwork.org
During the 1990s, reconstruction of flowering plant phylogeny took a great step forward.
Rapidly accumulating DNA sequences, in particular from the plastid gene rbcL (eg Chase et …

Genome-scale approaches to resolving incongruence in molecular phylogenies

A Rokas, BL Williams, N King, SB Carroll - Nature, 2003 - nature.com
One of the most pervasive challenges in molecular phylogenetics is the incongruence
between phylogenies obtained using different data sets, such as individual genes. To …

Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: insights from an eight‐locus plastid phylogeny

TJ Givnish, MHJ Barfuss, B Van Ee… - American journal of …, 2011 - Wiley Online Library
• Premise: Bromeliaceae form a large, ecologically diverse family of angiosperms native to
the New World. We use a bromeliad phylogeny based on eight plastid regions to analyze …

Epstein-Barr virus and cancer

MP Thompson, R Kurzrock - Clinical cancer research, 2004 - AACR
EBV was the first human virus to be directly implicated in carcinogenesis. It infects> 90% of
the world's population. Although most humans coexist with the virus without serious …