Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens [PDF]
BMC Genomics, 2008 Background Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi.
Carbone Ignazio +4 more
doaj +3 more sources
Lineage-specific gene duplication and loss in human and great ape evolution.
PLoS Biology, 2004 Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone ...
Andrew Fortna +15 more
doaj +4 more sources
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses [PDF]
BMC Bioinformatics, 2011 Background The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding ...
Burleigh Gordon J +2 more
doaj +3 more sources
The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion. [PDF]
PLoS ONE, 2012 Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult.
Matthew A Carrigan +5 more
doaj +4 more sources
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence [PDF]
BMC Bioinformatics, 2012 Background Gene tree - species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree. Gene tree parsimony approaches seek the evolutionary scenario that implies the fewest gene duplications, duplications ...
Chaudhary Ruchi +2 more
doaj +4 more sources
Gene Duplication and Loss of AANAT in Mammals Driven by Rhythmic Adaptations. [PDF]
Mol Biol Evol, 2021 AbstractArylalkylamine N-acetyltransferase (AANAT) plays a crucial role in synchronizing internal biological functions to circadian and circannual changes. Generally speaking, only one copy of AANAT gene has been found in mammals, however, three independent duplications of this gene were detected in several cetartiodactyl lineages (i.e., Suidae ...
Yin D +5 more
europepmc +4 more sources
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models [PDF]
Journal of Mathematical Biology, 2020 AbstractGiven a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms, including—but not limited to—speciation ($${\mathbb {S}}$$S), gene duplication ($${\mathbb {D}}$$D), gene ...
Cedric Chauve +2 more
openaire +5 more sources
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. [PDF]
Bioinformatics, 2020 Abstract Motivation Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome.
Molloy EK, Warnow T.
europepmc +4 more sources
Duplication and Losses of Opsin Genes in Lophotrochozoan Evolution
Molecular Biology and Evolution, 2022 Abstract Opsins are G-coupled receptors playing a key role in metazoan visual processes. While many studies enriched our understanding of opsin diversity in several animal clades, the opsin evolution in Lophotrochozoa, one of the major metazoan groups, remains poorly understood.
Giacinto De Vivo +4 more
openaire +2 more sources
Gene Family Evolution by Duplication, Speciation, and Loss [PDF]
Journal of Computational Biology, 2008 We consider two algorithmic questions related to the evolution of gene families. First, given a gene tree for a gene family, can the evolutionary history of this family be explained with only speciation and duplication events? Such gene trees are called DS-trees.
Cedric, Chauve +2 more
openaire +2 more sources