theta_estimator {RPANDA}

Compute Watterson genetic diversity (Theta estimator)

Description

This function computes the Theta estimator of genetic diversity (Watterson, 1975) while controlling for the presence of gaps in the alignment (Ferretti et al, 2012), frequent in barcoding datasets.

Usage

theta_estimator(sequences)

Arguments

sequences

a matrix representing the nucleotidic alignment of all the sequences present in the phylogenetic tree.

Value

An estimate of genetic diversity.

Author(s)

Ana C. Afonso Silva & Benoît Perez-Lamarque

References

Watterson GA , On the number of segregating sites in genetical models without recombination, 1975, Theor. Popul. Biol.

Ferretti L, Raineri E, Ramos-Onsins S. 2012. Neutrality tests for sequences with missing data. Genetics 191: 1397–1401.

Perez-Lamarque B, Öpik M, Maliet O, Silva A, Selosse M-A, Martos F, and Morlon H. 2022. Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont, Molecular Ecology, 31:3496–512.

See Also

pi_estimator delineate_phylotypes

Examples

data(woodmouse)

alignment <- as.character(woodmouse) # nucleotidic alignment 

theta_estimator(alignment)