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Mol Biol Evol. 2019 Dec 17. pii: msz302. doi: 10.1093/molbev/msz302. [Epub ahead of print]

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach.

Author information

1
Dept. of Evolutionary Biology, University of Haifa, Israel.
2
Faculty of Technology, Bielefeld University, Germany.
3
School of Mathematics and Statistics, University of Canterbury, NZ.

Abstract

The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systematic resolution, the standard markers are too crude to provide a phylogenetic signal. Nevertheless, among prokaryotes, genome dynamics in the form of horizontal gene transfer (HGT) between organisms and gene loss seem to provide far richer information by affecting both gene order and gene content. The synteny index (SI) between a pair of genomes combines these latter two factors, allowing comparison of genomes with unequal gene content, together with order considerations of their common genes. Although this approach is useful for classifying close relatives, no rigorous statistical modelling for it has been suggested. Such modelling is valuable, as it allows observed measures to be transformed into estimates of time periods during evolution, yielding the additivity of the measure. To the best of our knowledge, there is no other additivity proof for other gene order/content measures under HGT. Here we provide a first statistical model and analysis for the synteny index measure. We model the gene neighbourhood as a birth-death-immigration process affected by the HGT activity over the genome, and analytically relate the HGT rate and time to the expected SI. This model is asymptotic and thus provides accurate results, assuming infinite size genomes. Therefore, we also developed a heuristic model following an exponential decay function, accounting for biologically realistic values, which performed well in simulations. Applying this model to 1133 prokaryotes partitioned to 39 clusters by the rank of genus, yields that the average number of genome dynamics events per gene in the phylogenetic depth of genus, is around half with significant variability between genera. This result extends and confirms similar results obtained for individual genera in different manners.

KEYWORDS:

Gene Order; Horizontal Gene Transfer; Markovian Processes; Phylogenetics

PMID:
31845962
DOI:
10.1093/molbev/msz302

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