The supermatrix approach to systematics

A de Queiroz, J Gatesy - Trends in ecology & evolution, 2007‏ - cell.com
Recent reviews of the construction of large phylogenies have focused on supertree methods
that involve separate analyses of data sets and subsequent integration of the resulting trees …

The enigmatic roles of Anelloviridae and Redondoviridae in humans

LJ Taylor, EL Keeler, FD Bushman… - Current Opinion in …, 2022‏ - Elsevier
Anelloviridae and Redondoviridae are virus families with small, circular, single-stranded
DNA genomes that are common components of the human virome. Despite their small …

Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria

SM Neuenschwander, R Ghai, J Pernthaler… - The ISME …, 2018‏ - academic.oup.com
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but
there are so far no pure living cultures of these organisms, possibly because of metabolic …

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments

EL Clarke, LJ Taylor, C Zhao, A Connell, JJ Lee, B Fett… - Microbiome, 2019‏ - Springer
Background Analysis of mixed microbial communities using metagenomic sequencing
experiments requires multiple preprocessing and analytical steps to interpret the microbial …

Revised road map to the phylum Firmicutes

W Ludwig, KH Schleifer, WB Whitman - Bergey's Manual® of Systematic …, 2009‏ - Springer
Starting with the Second Edition of Bergey's Manual of Systematic Bacteriology, the
arrangement of content follows a phylogenetic framework or “road map” based largely on …

Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi

M Mehrshad, MM Salcher, Y Okazaki, S Nakano… - Microbiome, 2018‏ - Springer
Background Representatives of the phylum Chloroflexi, though reportedly highly abundant
in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) …

Road map of the phylum Actinobacteria

W Ludwig, J Euzéby, P Schumann, HJ Busse… - Bergey's manual® of …, 2012‏ - Springer
This revised road map and the resulting taxonomic outline update the previous versions of
Garrity and Holt (2001) and Garrity et al.(2005) with the description of additional taxa and …

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves'(LD12)

MM Salcher, J Pernthaler, T Posch - The ISME journal, 2011‏ - academic.oup.com
Alphaproteobacteria are common members of marine bacterioplankton assemblages, but
are believed to be rare in lacustrine systems. However, uncultured Alphaproteobacteria of …

Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR

MC Chiriac, PA Bulzu, AS Andrei, Y Okazaki, S Nakano… - Microbiome, 2022‏ - Springer
Background The increased use of metagenomics and single-cell genomics led to the
discovery of organisms from phyla with no cultivated representatives and proposed new …

A reconsideration of the classification of the spider infraorder Mygalomorphae (Arachnida: Araneae) based on three nuclear genes and morphology

JE Bond, BE Hendrixson, CA Hamilton, M Hedin - PloS one, 2012‏ - journals.plos.org
Background The infraorder Mygalomorphae (ie, trapdoor spiders, tarantulas, funnel web
spiders, etc.) is one of three main lineages of spiders. Comprising 15 families, 325 genera …