scholarly journals The nonrandom evolution of gene families

2018 ◽  
Vol 106 (1) ◽  
pp. 14-17
Author(s):  
Claudio Casola ◽  
A. Michelle Lawing
Keyword(s):  
Gene Families ◽  
Evolution Of Gene Families

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

scholarly journals Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates

2017 ◽  
Vol 114 (48) ◽  
pp. 12779-12784 ◽  
Author(s):  
Arbel Harpak ◽  
Xun Lan ◽  
Ziyue Gao ◽  
Jonathan K. Pritchard
Keyword(s):  
Gene Conversion ◽  
Genetic Diseases ◽  
Sequence Divergence ◽  
Duplicate Gene ◽  
Gene Families ◽  
Sequence Evolution ◽  
Donor Region ◽  
Order Of Magnitude ◽  
Evolution Of Gene Families ◽  
Gene Duplicates

Gene conversion is the copying of a genetic sequence from a “donor” region to an “acceptor.” In nonallelic gene conversion (NAGC), the donor and the acceptor are at distinct genetic loci. Despite the role NAGC plays in various genetic diseases and the concerted evolution of gene families, the parameters that govern NAGC are not well characterized. Here, we survey duplicate gene families and identify converted tracts in 46% of them. These conversions reflect a large GC bias of NAGC. We develop a sequence evolution model that leverages substantially more information in duplicate sequences than used by previous methods and use it to estimate the parameters that govern NAGC in humans: a mean converted tract length of 250 bp and a probability of 2.5×10−7 per generation for a nucleotide to be converted (an order of magnitude higher than the point mutation rate). Despite this high baseline rate, we show that NAGC slows down as duplicate sequences diverge—until an eventual “escape” of the sequences from its influence. As a result, NAGC has a small average effect on the sequence divergence of duplicates. This work improves our understanding of the NAGC mechanism and the role that it plays in the evolution of gene duplicates.

Dosage sensitivity and the evolution of gene families in yeast

Nature ◽  
2003 ◽  
Vol 424 (6945) ◽  
pp. 194-197 ◽  
Author(s):  
Balázs Papp ◽  
Csaba Pál ◽  
Laurence D. Hurst
Keyword(s):  
Gene Families ◽  
Evolution Of Gene Families ◽  
Dosage Sensitivity
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