Estimating self-fertilization rates from the diploid genotype spectrum
- 1Oregon State University
Abstract
The distribution of self-fertilization across the tree of life remains poorly characterized. Here we present the diploid genotype spectrum (DGS) as a useful genomic data summary for characterizing populations undergoing partial self-fertilization (selfing). This statistic provides a straightforward baseline for estimating selfing rates from population genomic data. At every segregating site across a genome, the diploid genotype configuration records the numbers of homozygous ancestral, heterozygous, and homozygous derived individuals, and the DGS compiles the counts of these configurations across sites. We show that the expected relative frequencies of DGS configurations among segregating sites can be computed under the standard coalescent approximation for partial selfing. We present two methods for doing this, one that is an intuitive recursion through possible states of the model, and one that is a more efficient combinatorial version. We give a worked example, validate the analytical expectations using forward simulations, and introduce a software package that estimates population selfing rates from diploid SNP data. The computations here mechanistically link selfing to observed patterns of diploid genotype configurations.
Related
- Traits and hidden states: is self-fertilization associated with rates of diversification across mating and sexual systems?
- Clinical spectrum and genotype–phenotype correlations of MT-CYB-associated mitochondrial disease: from the m.15045G > A variant to the broader disease landscape
- Estimating de novo mutation rates using parent-offspring pairs
- Estimating age and annual tooth growth rates in narwhals (Monodon monoceros) using computed tomography
- Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process
BibTeX
@misc{mckenzie2026estimating,
title = {{Estimating self-fertilization rates from the diploid genotype spectrum}},
author = {P. F. McKenzie and R. Hopkins and F. L. Wu},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.13.751067},
url = {https://www.biorxiv.org/content/10.64898/2026.10.13.751067v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Estimating self-fertilization rates from the diploid genotype spectrum
AU - P. F. McKenzie
AU - R. Hopkins
AU - F. L. Wu
PY - 2026
DA - 2026/10/13
PB - bioRxiv
DO - 10.64898/2026.10.13.751067
UR - https://www.biorxiv.org/content/10.64898/2026.10.13.751067v1
AB - The distribution of self-fertilization across the tree of life remains poorly characterized. Here we present the diploid genotype spectrum (DGS) as a useful genomic data summary for characterizing populations undergoing partial self-fertilization (selfing). This statistic provides a straightforward baseline for estimating selfing rates from population genomic data. At every segregating site across a genome, the diploid genotype configuration records the numbers of homozygous ancestral, heterozygous, and homozygous derived individuals, and the DGS compiles the counts of these configurations across sites. We show that the expected relative frequencies of DGS configurations among segregating sites can be computed under the standard coalescent approximation for partial selfing. We present two methods for doing this, one that is an intuitive recursion through possible states of the model, and one that is a more efficient combinatorial version. We give a worked example, validate the analytical expectations using forward simulations, and introduce a software package that estimates population selfing rates from diploid SNP data. The computations here mechanistically link selfing to observed patterns of diploid genotype configurations.
ER -