All Outputs (14)

Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome (2023)
Journal Article

Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangeno... Read More about Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.

Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome (2021)
Journal Article

A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of... Read More about Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.

Coinfinder: Detecting significant associations and dissociations in pangenomes (2020)
Journal Article

© 2020 The Authors. The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whet... Read More about Coinfinder: Detecting significant associations and dissociations in pangenomes.

Eukaryote genes are more likely than prokaryote genes to be composites (2019)
Journal Article

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, howeve... Read More about Eukaryote genes are more likely than prokaryote genes to be composites.

Reply to ‘The population genetics of pangenomes’ (2017)
Journal Article

Function-related replacement of bacterial siderophore pathways (2017)
Journal Article

© The Author(s) 2018. Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis o... Read More about Function-related replacement of bacterial siderophore pathways.

Why prokaryotes have pangenomes (2017)
Journal Article

The existence of large amounts of within-species genome content variability is puzzling. Population genetics tells us that fitness effects of new variants—either deleterious, neutral or advantageous—combined with the long-term effective population si... Read More about Why prokaryotes have pangenomes.

“Every gene is everywhere but the environment selects”: Global geolocalization of gene sharing in environmental samples through network analysis (2016)
Journal Article

© The Author(s) 2016. The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused... Read More about “Every gene is everywhere but the environment selects”: Global geolocalization of gene sharing in environmental samples through network analysis.

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis (2015)
Journal Article

© 2015 The Author(s) Published by the Royal Society. All rights reserved. The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic or... Read More about Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.

Endosymbiotic origin and differential loss of eukaryotic genes (2015)
Journal Article

Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory... Read More about Endosymbiotic origin and differential loss of eukaryotic genes.

Origins of major archaeal clades correspond to gene acquisitions from bacteria (2014)
Journal Article

The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paire... Read More about Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears (2014)
Journal Article

Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyperlipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown... Read More about Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

Heterogeneous models place the root of the placental mammal phylogeny (2013)
Journal Article

Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene-and lineage-specific variation in amino acid substitution rates and... Read More about Heterogeneous models place the root of the placental mammal phylogeny.

GCUA: General codon usage analysis (1998)
Journal Article

The program General Codon Usage Analysis (GCUA) has been developed for analysing codon and amino acid usage patterns. Availability: ftp://ftp.nhm.ac.uk/pub/gcua. Freely available for acedemic use, commercial users should contact the author. Contact:... Read More about GCUA: General codon usage analysis.