Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

Abstract

Whole genome duplications (WGDs) followed by massive gene loss occurred in the evolutionary history of many groups. WGDs are usually inferred from the age distribution of paralogs (Ks-based methods) or from gene collinearity data (synteny). However, Ks-based methods are restricted to detect the recent WGDs due to saturation effects and the difficulty to date old duplicates, and synteny is difficult to reconstruct for distantly related species. Recently, Jiao et al. (Jiao Y, Wickett N, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473:97-100) introduced an empirical method that aims to detect a peak in duplication ages among nodes selected from a previous phylogenetic analysis. In this context, we present here two rigorous methods based on data from multiple gene families and on a new probabilistic model. Our model assumes that all gene lineages are instantaneously duplicated at the WGD event with a possible almost-immediate loss of some extra copies. Our reconciliation method relies on aligned molecular sequences, whereas our gene count method relies only on gene count data across species. We show, using extensive simulations, that both methods have a good detection power. Surprisingly, the gene count method enjoys no loss of power compared with the reconciliation method, despite the fact that sequence information is not used. We finally illustrate the performance of our methods on a benchmark yeast data set. Both methods are able to detect the well-known WGD in the Saccharomyces cerevisiae clade and agree on a small retention rate at the WGD, as established by synteny-based methods.

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

“…The precise phylogenetic position of this putative duplication remains unresolved until additional members of subtribe Fragariinae (including Alchemilla and Aphanes ) are sampled, and statistical methods to detect whole genome duplications are applied (e.g. Jiao et al ., ; Rabier et al ., ; Huang et al ., ; Tiley et al ., ).…”

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

“…Therefore, we simulated gene family copy number evolution along the 37 species tree, using a probabilistic model in which SSD is modeled as a random birth-death (BD) process (Bailey, 1964) and that takes into account known WGD events by assuming an instantaneous doubling (or triplication) of all genes, as by Rabier et al (2014) (see Methods). Using this model as a null hypothesis and using realistic rates of small-scale gene duplication and loss, l, sampled from a normal distribution with mean m = 0.53 and SD s = 0.156 duplications/losses per evolutionary time unit (see Methods), we generated gene counts at the leaves of the species tree for 9178 3 1000 = 9,178,000 simulated gene families.…”

“…Since WGDs violate the assumption of independency of duplication events in Bailey's BD model (Bailey, 1964), we placed these events as separate nodes on the branches of the species tree, similar to the strategy employed by Rabier et al (2014). At WGD nodes, all gene family members are instantaneously duplicated (or triplicated, depending on the nature of the polyploidy event).…”

“…At WGD nodes, all gene family members are instantaneously duplicated (or triplicated, depending on the nature of the polyploidy event). As in the model of Rabier et al (2014), we assume that a given fraction of duplicates is lost very quickly after WGD, represented by an immediate loss rate parameter q in our model. The remaining WGD duplicates are lost over time at a loss rate l, the same as for SSD duplicates.…”

Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives

“…After duplication, the paralogous gene (copy of the original gene) can co-exist with the original copy and complement its function (subfunctionalization) or diverge and develop a new function (neofunctionalization) [8,9]. However, WGDs are typically followed by massive gene loss, and in most cases only a single copy of the duplicated genes will be maintained [10].…”