Fully Bayesian tests of neutrality using genealogical summary statistics

Abstract

Background: Many data summary statistics have been developed to detect departures from neutral expectations of evolutionary models. However questions about the neutrality of the evolution of genetic loci within natural populations remain difficult to assess. One critical cause of this difficulty is that most methods for testing neutrality make simplifying assumptions simultaneously about the mutational model and the population size model. Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome.

The Comparative Genomics of Human Respiratory Syncytial Virus Subgroups A and B: Genetic Variability and Molecular Evolutionary Dynamics

“…This was similar to the situation observed with the RSV-A data set (48). Although it would be useful to explore other genealogical test statistics in the posterior predictive simulation, such as a recently proposed temporal clustering statistic (74), which may prove more sensitive in detection of departures from neutrality, it is clear that population turnover is not as pervasive and selection driven as that observed for human influenza A virus (62) and norovirus GII.4 (61). Neutrality was, however, rejected for the completegenome RSV-B data set, but since this focuses on a smaller time scale that accommodates one of bottleneck events observed over longer time scales (Fig.…”

“…A genealogical test based on posterior predictive simulation was conducted in order to determine whether the posterior phylogenetic tree shapes deviated from neutral expectations (61). In short, the tree shapes estimated by the Bayesian coalescent analysis were summarized with the genealogic Fu and Li statistic (D F ), which compares the length of the terminal branches to the total length of the coalescent genealogy and returns negative values for long terminal branch lengths.…”

Evidence of balancing selection in multiple indigenous chicken populations

“…In addition, increasing numbers of studies have focused on identifying the effect of positive selection on the genomes of different species (Sabeti et al, 2007;Drummond and Suchard, 2008;Huard-Chauveau et al, 2013). Under this type of directional selection, advantageous alleles accumulate in an ongoing manner due to the high survival rate; however, dominant/recessive alleles will eventually become fixed (Molles and Cahill, 1999).…”

Genomic Analysis of Viral Outbreaks

“…The basic principle behind these methods is that selective pressure on a population leaves a distinct mark on overall genetic diversity and tree symmetry (89, 111, 112). Statistics that test for selection, or non-neutrality, using these principles include Tajima’s D, Fu and Li’s D, and tree-imbalance metrics (113). …”