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 …

Molecular phylogenetics: principles and practice

Z Yang, B Rannala - Nature reviews genetics, 2012 - nature.com
Phylogenies are important for addressing various biological questions such as relationships
among species or genes, the origin and spread of viral infection and the demographic …

[HTML][HTML] The integrative future of taxonomy

JM Padial, A Miralles, I De la Riva, M Vences - Frontiers in zoology, 2010 - Springer
Background Taxonomy is the biological discipline that identifies, describes, classifies and
names extant and extinct species and other taxa. Nowadays, species taxonomy is …

[HTML][HTML] Supergene origin and maintenance in Atlantic cod

M Matschiner, JMI Barth, OK Tørresen, B Star… - Nature Ecology & …, 2022 - nature.com
Supergenes are sets of genes that are inherited as a single marker and encode complex
phenotypes through their joint action. They are identified in an increasing number of …

[HTML][HTML] Evolution of the immune system influences speciation rates in teleost fishes

M Malmstrøm, M Matschiner, OK Tørresen, B Star… - Nature Genetics, 2016 - nature.com
Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic
and phenotypic variation, including diverse immune defense strategies. The genomic basis …

[HTML][HTML] Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

A Bissett, A Fitzgerald, T Meintjes, PM Mele, F Reith… - GigaScience, 2016 - Springer
Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …

Clarification of generic and species boundaries for Metarhizium and related fungi through multigene phylogenetics

RM Kepler, RA Humber, JF Bischoff, SA Rehner - Mycologia, 2014 - Taylor & Francis
The genus Metarhizium historically refers to green-spored asexual insect pathogenic fungi.
Through culturing and molecular methods, Metarhizium has been linked to Metacordyceps …

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae: Diplostephium)

OM Vargas, EM Ortiz, BB Simpson - New Phytologist, 2017 - Wiley Online Library
High‐throughput sequencing is helping biologists to overcome the difficulties of inferring the
phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of …

[图书][B] Molecular evolution: a statistical approach

Z Yang - 2014 - books.google.com
Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

V Hampl, L Hug, JW Leigh, JB Dacks… - Proceedings of the …, 2009 - National Acad Sciences
Nearly all of eukaryotic diversity has been classified into 6 suprakingdom-level groups
(supergroups) based on molecular and morphological/cell-biological evidence; these are …