Inbreeding effective population size and parentage analysis without parents

Area of Science:

• Population genetics
• Conservation genetics
• Molecular ecology

Background:

• Genetic parentage analysis is crucial for determining offspring counts per parent (k(i)) and effective population size (N(e)).
• Estimating N(e) typically requires knowledge of parental genotypes, which are often unavailable.
• Reconstructing parental genotypes from progeny data is theoretically possible but complex.

Purpose of the Study:

• To develop a method for estimating effective population size (N(e)) without requiring parental genotypes.
• To investigate the impact of 'null' parents (those with no offspring in the sample) on N(e) estimation.
• To provide a novel, single-sample estimator for contemporary N(e) using parentage analysis.

Main Methods:

• Rewriting the standard formula for inbreeding N(e) to depend solely on sample size and the sum of squared offspring counts (∑(k(2)(i))).
• Developing the parentage analysis without parents (PwoP) method.
• Utilizing a matrix of pairwise relationships to construct k(i) values when parental genotypes are absent.

Main Results:

• The standard N(e) formula can be modified to exclude the need for total parent number (N), relying instead on ∑(k(2)(i)).
• Null parents do not influence the N(e) estimate, simplifying calculations.
• The PwoP method provides an unbiased and precise N(e) estimate even with partial progeny data.

Conclusions:

• Parentage analysis without parents (PwoP) offers a viable single-sample estimator for contemporary N(e).
• Accurate determination of pairwise relationships or direct estimation of ∑(k(2)(i)) is key for the PwoP method's success.
• This approach advances population genetics by enabling N(e) estimation in scenarios with limited or no parental genetic data.