theta_estimator function

Compute Watterson genetic diversity (Theta estimator)

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.

theta_estimator(sequences)

Arguments

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

Returns

An estimate of genetic diversity.

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.

Author(s)

Ana C. Afonso Silva & Benoît Perez-Lamarque

See Also

pi_estimator

delineate_phylotypes

Examples

data(woodmouse)

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

theta_estimator(alignment)