ModelFinder: fast model selection for accurate phylogenetic estimates

S Kalyaanamoorthy, BQ Minh, TKF Wong… - Nature …, 2017 - nature.com
Abstract Model-based molecular phylogenetics plays an important role in comparisons of
genomic data, and model selection is a key step in all such analyses. We present …

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

RJE Alves, BQ Minh, T Urich, A von Haeseler… - Nature …, 2018 - nature.com
Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major
role in nitrogen cycling. AOA have been studied intensively based on the amoA gene …

Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels

A Rozenberg, I Kaczmarczyk, D Matzov… - Nature structural & …, 2022 - nature.com
Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal
chromophore. Here we report the discovery, structure and biophysical characterization of …

Revised Phylogeny of the Cellulose Synthase Gene Superfamily: Insights into Cell Wall Evolution

A Little, JG Schwerdt, NJ Shirley, SF Khor… - Plant …, 2018 - academic.oup.com
Cell walls are crucial for the integrity and function of all land plants and are of central
importance in human health, livestock production, and as a source of renewable bioenergy …

Phylogenomics

JSL Patané, J Martins, JC Setubal - Comparative Genomics: Methods and …, 2018 - Springer
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into
account whole genomes or large fractions of genomes. The abundance of genomic data for …

Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons

MP Simmons - Journal of Systematics and Evolution, 2017 - Wiley Online Library
Both traditional as well as 10 more recent methods of coding characters from exons of
protein‐coding genes are reviewed. The more recent methods collectively blur the …

Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats

LR Yohe, M Fabbri, D Lee, KTJ Davies, TP Yohe… - …, 2022 - academic.oup.com
Although evolvability of genes and traits may promote specialization during species
diversification, how ecology subsequently restricts such variation remains unclear …

Ungulate malaria parasites

TJ Templeton, M Asada, M Jiratanh, SA Ishikawa… - Scientific Reports, 2016 - nature.com
Haemosporida parasites of even-toed ungulates are diverse and globally distributed, but
since their discovery in 1913 their characterization has relied exclusively on microscopy …

Relative model fit does not predict topological accuracy in single-gene protein phylogenetics

SJ Spielman - Molecular biology and evolution, 2020 - academic.oup.com
It is regarded as best practice in phylogenetic reconstruction to perform relative model
selection to determine an appropriate evolutionary model for the data. This procedure ranks …

Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change

LR Yohe, M Fabbri, M Hanson, BAS Bhullar - Current Zoology, 2020 - academic.oup.com
Chemosensation is the most ubiquitous sense in animals, enacted by the products of
complex gene families that detect environmental chemical cues and larger-scale sensory …