Does Nature Play Dice with Genomes?

HERMAN DOPAZO; VERONICA BECHER; FRANÇOIS SERRA

Barcelona

Jornada; XI Jornadas de Bioinformática; 2012

Is there a common rule governing species abundance and diversity (SAD) in ecology and genomics? Even, in the case that such rule exists, it is the same for functional and non- functional components of genomes? It is the same for small and large genomes? To what extent SAD reflects adaptive or stochastic outcomes?Species diversity and their relative abundance have always intriguing ecologists. Ecological models of SAD are descriptive (statistical-based) or mechanistic (niche-based or neutrals). Most mechanistic models assume niche differences as the main cause driving community composition. Neutral models however, consider niche differences among species irrelevant. The unified neutral theory of biodiversity and biogeography (UNTB) [1] is a neutral- stochastic theory originally inspired in neutral population genetic models. UNTB assumes interactions among tropically similar species equivalent on an individual ?per capita? basis. This provocative assumption means that these individuals, regardless of the species, appear to be controlled by similar birth, death, dispersal, and speciation rates. Since each species follows a random walk, biodiversity composition emerges randomly in the community [2]. Here, taking advantage of UNTB formulation and the general framework posed by ecological genomics [3, 4] we ask for the relative SAD of genetic elements in genomes.Ensembl database was used to obtain complete functional and non-functional elements of ~500 chromosomes in 30 eukaryote genomes. UNTB+[5] was used to test neutrality and to fit by maximum likelihood UNTB parameters.Ideal models for ecological genomics would consider all diversity of elements populating genomes: satellites sequences, DNA-transposons, LTR-retrotransposons, LINES, SINES, mi-RNA, scRNA, rRNA, tRNA, genes, and pseudogenes among many other functional and non-functional elements. After ML adjustment of UNTB parameters we found that most chromosomes follow relative SAD according to the expected by UNTB. Functional and non-functional genome elements showed equivalent SAD describing neutral dynamics in chromosomes. While ecologists found natural selection an irrelevant component to explain relative SAD in forests [1,2], we found that the same simple neutral model fits SAD of genetic elements in genomes. Nature seems to play forest and genomes with same dice.