pop_Nancestors: Population founders and ancestors

In purgeR: Inbreeding-Purging Estimation in Pedigreed Populations

Population founders and ancestors

Description

Estimate the total and effective number of founders and ancestors in a pedigree, as well as the number of founder genome equivalents (see details on these parameters below). Note that a reference population (RP) must be defined, so that founders and ancestors are referred to the set of individuals belonging to that RP. This is set by means of a boolean vector passed as argument.

Usage

pop_Nancestors(ped, reference, nboot = 10000L, seed = NULL, skip_Ng = FALSE)

Arguments

ped	A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.
reference	A string naming a column indicating whether individuals belong to the reference population or not. Column must be boolean or coercible to boolean type.
nboot	Number of bootstrap iterations (for computing Ng).
seed	Sets a seed for the random number generator.
skip_Ng	Skip Ng computation or not (FALSE by default).

Details

The total number of founders (Nf) and ancestors (Na) are calculated simply as the count of founders and ancestors of individuals belonging to the reference population (RP). Founders here are defined as individuals with both parentals unknown.

The effective number of founders (Nfe) is the number of equally contributing founders, that would account for observed genetic diversity in the RP, while the effective number of ancestors (Nae) is defined as the minimum number of ancestors, founders or not, required to account for the genetic diversity observed in the RP. These parameters are computed from the probability of gene origin, following methods in Tahmoorespur and Sheikhloo (2011).

While the previous parameters account for diversity loss due to bottlenecks at the level of founders or ancestors, other sources of random loss of alleles (such as drift) can be accounted by means of the number of founder genome equivalents (Ng, Caballero and Toro 2000). This parameter is estimated via Monte Carlo simulation of allele segregation, following Boichard et al. (1997).

Value

A dataframe containing population size estimates for founders and ancestors:

• Nr - Total number of individuals in the RP

• Nf - Total number of founders

• Nfe - Effective number of founders

• Na - Total number of ancestors

• Nae - Effective number of ancestors

• Ng - Number of founder genome equivalents

• se_Ng - Standard error of Ng

If some of the auxiliary functions is used (e.g. pop_Nr), only the corresponding numerical estimate will be returned. In the case of pop_Ng, a list object is returned, with the number of founder genome equivalents (Ng) and its standard error (se_Ng).

References

• Boichard D, Maignel L, Verrier E. 1997. The value of using probabilities of gene origin to measure genetic variability in a population. Genet. Sel. Evol. 29: 5-23.

• Caballero A, Toro M. 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet. Res. 75: 331-343.

• Tahmoorespur M, Sheikhloo M. 2011. Pedigree analysis of the closed nucleus of Iranian Baluchi sheep. Small Rumin. Res. 99: 1-6.

Examples

data(arrui)
pop_Nancestors(arrui, reference = "target", skip_Ng = TRUE)

purgeR documentation built on Aug. 16, 2023, 9:07 a.m.