When integration fails: Prokaryote phylogeny and the tree of life

MA O'Malley - Studies in History and Philosophy of Science Part C …, 2013 - Elsevier
Much is being written these days about integration, its desirability and even its necessity
when complex research problems are to be addressed. Seldom, however, do we hear much …

Genetic exchange across a species boundary in the archaeal genus Ferroplasma

JM Eppley, GW Tyson, WM Getz, JF Banfield - Genetics, 2007 - academic.oup.com
Speciation as the result of barriers to genetic exchange is the foundation for the general
biological species concept. However, the relevance of genetic exchange for defining …

Introgression in the genus Campylobacter: generation and spread of mosaic alleles

SK Sheppard, ND McCarthy, KA Jolley… - …, 2011 - microbiologyresearch.org
Horizontal genetic exchange strongly influences the evolution of many bacteria,
substantially contributing to difficulties in defining their position in taxonomic groups. In …

The Inadequacy of Morphology for Species and Genus Delineation in Microbial Eukaryotes: An Example from the Parabasalian Termite Symbiont Coronympha

JT Harper, GH Gile, ER James, KJ Carpenter… - PLoS …, 2009 - journals.plos.org
Background For the majority of microbial eukaryotes (protists, algae), there is no clearly
superior species concept that is consistently applied. In the absence of a practical biological …

The modern synthesis in the light of microbial genomics

A Booth, C Mariscal, WF Doolittle - Annual review of …, 2016 - annualreviews.org
We review the theoretical implications of findings in genomics for evolutionary biology since
the Modern Synthesis. We examine the ways in which microbial genomics has influenced …

Duplication is more common among laterally transferred genes than among indigenous genes

SD Hooper, OG Berg - Genome biology, 2003 - Springer
Background Recent developments in the understanding of paralogous evolution have
prompted a focus not only on obviously advantageous genes, but also on genes that can be …

Comparative Genomic Analysis of the Genus Nocardiopsis Provides New Insights into Its Genetic Mechanisms of Environmental Adaptability

HW Li, XY Zhi, JC Yao, Y Zhou, SK Tang, HP Klenk… - PLoS …, 2013 - journals.plos.org
The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much
attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array …

Betaproteobacteria are predominant in drinking water: are there reasons for concern?

P Ferro, I Vaz-Moreira, CM Manaia - Critical reviews in …, 2019 - Taylor & Francis
Betaproteobacteria include some of the most abundant and ubiquitous bacterial genera that
can be found in drinking water, including mineral water. The combination of physiology and …

Introduction to genome biology and diversity

N Youssef, A Budd, JP Bielawski - Evolutionary Genomics: Statistical and …, 2019 - Springer
Organisms display astonishing levels of cell and molecular diversity, including genome size,
shape, and architecture. In this chapter, we review how the genome can be viewed as both a …

Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement

D MacLeod, RL Charlebois, F Doolittle… - BMC evolutionary …, 2005 - Springer
Background When organismal phylogenies based on sequences of single marker genes are
poorly resolved, a logical approach is to add more markers, on the assumption that weak but …