Patterns of gene evolution following duplications and speciations in vertebrates

PeerJ

article

Kyle T. David¹  Jamie R. Oaks¹  Kenneth M. Halanych¹ 

[1] Department of Biological Sciences, Auburn University

关键词: Ortholog;    Paralog;    Gene duplication;    dN/dS;   

DOI  :  10.7717/peerj.8813

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. Methods To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. Results Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.

【 授权许可】

CC BY