Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load
Abstract Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typi...
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doaj-cc18aa084edc4da79cfab380e11667b82020-11-25T03:32:08ZengWileyEvolutionary Applications1752-45712019-02-0112226627910.1111/eva.12713Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding loadPirmin Nietlisbach0Stefanie Muff1Jane M. Reid2Michael C. Whitlock3Lukas F. Keller4Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich SwitzerlandDepartment of Evolutionary Biology and Environmental Studies University of Zurich Zurich SwitzerlandSchool of Biological Sciences University of Aberdeen Aberdeen UKDepartment of Zoology University of British Columbia Vancouver BC CanadaDepartment of Evolutionary Biology and Environmental Studies University of Zurich Zurich SwitzerlandAbstract Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree‐based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum‐likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.https://doi.org/10.1111/eva.12713conservation biologygeneralized linear (mixed) modelsgenomicsinbreeding coefficientsinbreeding depressionpedigree |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Pirmin Nietlisbach Stefanie Muff Jane M. Reid Michael C. Whitlock Lukas F. Keller |
spellingShingle |
Pirmin Nietlisbach Stefanie Muff Jane M. Reid Michael C. Whitlock Lukas F. Keller Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load Evolutionary Applications conservation biology generalized linear (mixed) models genomics inbreeding coefficients inbreeding depression pedigree |
author_facet |
Pirmin Nietlisbach Stefanie Muff Jane M. Reid Michael C. Whitlock Lukas F. Keller |
author_sort |
Pirmin Nietlisbach |
title |
Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load |
title_short |
Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load |
title_full |
Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load |
title_fullStr |
Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load |
title_full_unstemmed |
Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load |
title_sort |
nonequivalent lethal equivalents: models and inbreeding metrics for unbiased estimation of inbreeding load |
publisher |
Wiley |
series |
Evolutionary Applications |
issn |
1752-4571 |
publishDate |
2019-02-01 |
description |
Abstract Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree‐based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum‐likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available. |
topic |
conservation biology generalized linear (mixed) models genomics inbreeding coefficients inbreeding depression pedigree |
url |
https://doi.org/10.1111/eva.12713 |
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