PurgeR: inbreeding and purging in pedigreed populations.

Eugenio López-Cortegano, Russell Schwartz

Open Access

https://doi.org/10.1093/bioinformatics/btab599

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Abstract

SummaryInbreeding depression and genetic purging are important processes shaping the survivability and evolution of small populations. However, detecting purging is challenging in practice, in part because there are limited tools dedicated to it. I present a new R package to assist population analyses on detection and quantification of the inbreeding depression and genetic purging of biological fitness in pedigreed populations. It includes a collection of methods to estimate different measurements of inbreeding (Wright’s, partial and ancestral inbreeding coefficients) as well as purging parameters (purged inbreeding, and opportunity of purging coefficients). Additional functions are also included to estimate population parameters, allowing to contextualize inbreeding and purging these results in terms of the population demographic history. purgeR is a valuable tool to gain insight into processes related to inbreeding and purging, and to better understand fitness and inbreeding load evolution in small populations.Availability and implementationpurgeR is an R package available at CRAN, and can be installed via install.packages(“purgeR”). Source code is maintained at a GitLab repository (https://gitlab.com/elcortegano/purgeR).Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

Inbreeding may result in the decline of biological fitness due to the increase in the frequency of homozygote genotypes for deleterious recessive alleles, causing the so-called ‘inbreeding depression’ (Charlesworth and Charlesworth, 1987)
Pedigree information has attracted the attention of genetic purging models, as these allow for direct inferences on single individuals based on their genealogical history, and many conservation programs maintain studbooks with pedigree records
Boakes and Wang (2005) used ancestral inbreeding coefficients (Fa, Ballou, 1997) to measure the consequences of purging on fitness, given the expectation that individuals born from more inbred ancestors are expected to be more fit than individuals with the same level of inbreeding but less inbred ancestors

Summary

Introduction

Inbreeding may result in the decline of biological fitness due to the increase in the frequency of homozygote genotypes for deleterious recessive alleles, causing the so-called ‘inbreeding depression’ (Charlesworth and Charlesworth, 1987). The expectation of population fitness evolution under inbreeding changes with purging, possibly allowing for the survival of small populations (Hedrick and Garcıa-Dorado, 2016). Gulisija and Crow (2007) developed a method to evaluate the potential reduction in the individual inbreeding load (B) using the probability of transmission of highly deleterious recessive alleles under inbreeding. Garcıa-Dorado (2012) defined a purged inbreeding coefficient (g) that measures the expected frequency of recessive deleterious loci in homozygosity, as a function of a purging coefficient (d) that relates to the recessive component of deleterious effects. While many software packages have been developed to compute inbreeding, resources for purging analysis are more limited. No informatic tool is available to compute Gulisija and Crow’s parameters for the opportunity of purging. purgeR computes all these parameters and others, including parameters related to population diversity and demography (e.g. effective population size, Ne), all functions being introduced in tutorials accessible via browseVignettes (“purgeR”)

Input data

Opportunity of purging