DOCSLIB.ORG

Nonequivalent Lethal Equivalents: Models and Inbreeding Metrics for Unbiased Estimation of Inbreeding Load

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nonequivalent Lethal Equivalents: Models and Inbreeding Metrics for Unbiased Estimation of Inbreeding Load Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2019 Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load Nietlisbach, Pirmin ; Muff, Stefanie ; Reid, Jane M ; Whitlock, Michael C ; Keller, LukasF 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. DOI: https://doi.org/10.1111/eva.12713 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-161087 Journal Article Published Version The following work is licensed under a Creative Commons: Attribution 4.0 International (CC BY 4.0) License. Originally published at: Nietlisbach, Pirmin; Muff, Stefanie; Reid, Jane M; Whitlock, Michael C; Keller, Lukas F (2019). Nonequiv- alent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load. Evo- lutionary Applications, 12(2):266-279. DOI: https://doi.org/10.1111/eva.12713 2 Received: 4 February 2018 | Revised: 6 September 2018 | Accepted: 9 September 2018 DOI: 10.1111/eva.12713 ORIGINAL ARTICLE Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load Pirmin Nietlisbach1,2 | Stefanie Muff1 | Jane M. Reid3 | Michael C. Whitlock2 | Lukas F. Keller1,4 1Department of Evolutionary Biology and Environmental Studies, University of Zurich, Abstract Zurich, Switzerland Inbreeding depression, the deterioration in mean trait value in progeny of related 2 Department of Zoology, University of parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant British Columbia, Vancouver, BC, Canada breeding, and conservation biology. The magnitude of inbreeding depression can be 3School of Biological Sciences, University of Aberdeen, Aberdeen, UK quantified by the inbreeding load, typically measured in numbers of lethal equiva‐ 4Zoological Museum, University of Zurich, lents, a population genetic quantity that allows for comparisons between environ‐ Zurich, Switzerland ments, populations or species. However, there is as yet no quantitative assessment of Correspondence which combinations of statistical models and metrics of inbreeding can yield such Pirmin Nietlisbach, Department of Zoology, University of British Columbia, Vancouver, estimates. Here, we review statistical models that have been used to estimate in‐ BC, Canada. breeding load and use population genetic simulations to investigate how unbiased Email: [email protected] estimates can be obtained using genomic and pedigree‐based metrics of inbreeding. Funding information We use simulated binary viability data (i.e., dead versus alive) as our example, but the Forschungskredit of the University of Zurich, Grant/Award Number: FK‐15‐104; Swiss concepts apply to any trait that exhibits inbreeding depression. We show that the National Science Foundation, Grant/Award increasingly popular generalized linear models with logit link do not provide compa‐ Number: P2ZHP3_168447 and 31003A‐ 116794; European Research Council rable 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 over‐ estimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaning‐ fully. 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 equiva‐ lents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum‐like‐ lihood 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. KEYWORDS conservation biology, generalized linear (mixed) models, genomics, inbreeding coefficients, inbreeding depression, pedigree, runs of homozygosity This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2018 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd Evolutionary Applications. 2018;1–14. wileyonlinelibrary.com/journal/eva | 1 2 | NIETLISBACH et al. 1 | INTRODUCTION − loge (y) = A+BF, (2) with individuals pooled into groups of similar F, and where A is the Inbreeding depression, the deterioration in mean trait value in prog‐ intercept and y the expected value of the trait for that level of F. eny of related parents (Crow & Kimura, 1970, chapter 3), is a funda‐ This model is itself rooted in population genetics theory and as‐ mental quantity in genetics, evolutionary biology, animal and plant sumes that effects of different environmental and genetic factors breeding, and conservation biology (Charlesworth & Willis, 2009; act independently and thus have multiplicative effects that trans‐ Hedrick & Kalinowski, 2000; Kristensen & Sorensen, 2005; Wright, late into additive effects only on the logarithmic scale (Charlesworth 1977). Conceptual and practical advances in these disciplines re‐ & Charlesworth, 1987). It is therefore important that a logarithmic quire accurate and robust estimates of the magnitude of inbreeding scale is used. depression that can be compared among different traits, among sets When data are only available for mean trait values of known out‐ of individuals of different ages and sexes, and among different en‐ bred (y ) and inbred individuals (y ) with a single known level of F, vironments, populations or species (Armbruster & Reed, 2005; Fox 0 F for example offspring of selfing or full‐sibling mating generated in a & Reed, 2010; Hoeck, Wolak, Switzer, Kuehler, & Lieberman, 2015; breeding design, the inbreeding load can be estimated as Kruuk, Sheldon, & Merilä, 2002; Leroy, 2014; Waller, Dole, & Bersch, 2008). These goals in turn require widespread adoption of a stan‐ B =−loge (yF∕y0)∕F (3) dard estimator of the magnitude of inbreeding depression that is (Charlesworth & Charlesworth, 1987; Lynch & Walsh, 1998, p. 278). unbiased, quantitatively comparable and firmly rooted in population Such breeding designs are hard to impose in wild, free‐living popula‐ genetic theory. tions or captive populations of endangered animals, but comparable One such estimator is the inbreeding load, B, measured as the and unbiased estimates of inbreeding load from such populations are negative slope of a regression of the logarithm of a trait on inbreed‐ key to understanding evolutionary dynamics (Kokko & Ots, 2006) ing coefficient F (Charlesworth & Charlesworth, 1987; Charlesworth and deciding population management strategies (Caballero, Bravo, & & Willis, 2009; Keller & Waller, 2002). Inbreeding load in viability Wang, 2017a,b; Theodorou & Couvet, 2017). Morton et al.’s (1956) (i.e., survival versus mortality) is measured in units of “lethal equiv‐ regression model (equation 2) provides a conceptually elegant and alents,” where one lethal equivalent corresponds to a group of theoretically well‐founded approach for estimating inbreeding load deleterious alleles that would cause one death on average if made that can be applied given a range of naturally occurring F values. homozygous (Morton, Crow,
Load more

Recommended publications
  • The Debate on Plant and Crop Biodiversity and Biotechnology
    The Debate on Plant and Crop Biodiversity and Biotechnology Klaus Ammann, [email protected] Version from December 15, 2017, 480 full text references, 117 pp. ASK-FORCE contribution No. 11 Nearly 470 references on biodiversity and Agriculture need still to be screened and selected. Contents: 1. Summary ........................................................................................................................................................................... 3 2. The needs for biodiversity – the general case ................................................................................................................ 3 3. Relationship between biodiversity and ecological parameters ..................................................................................... 5 4. A new concept of sustainability ....................................................................................................................................... 6 4.1. Revisiting the original Brundtland definition of sustainable development ...............................................................................................................7 4.2. Redefining Sustainability for Agriculture and Technology, see fig. 1 .........................................................................................................................8 5. The Issue: unnecessary stigmatization of GMOs .......................................................................................................... 12 6. Types of Biodiversity ......................................................................................................................................................
    [Show full text]
  • Downloaded from the CSIRO Data Portal [45] and Resampled to the Same Grid As the CHELSA Climate Data
    diversity Article All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala Marlien M. van der Merwe 1,* , Jia-Yee S. Yap 1, Peter D. Wilson 1, Helen T. Murphy 2 and Andrew Ford 2 1 Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, NSW 2000, Australia; [email protected] (J.-Y.S.Y.); [email protected] (P.D.W.) 2 CSIRO Land and Water, Tropical Forest Research Centre, Maunds Road, Atherton, QLD 4883, Australia; [email protected] (H.T.M.); [email protected] (A.F.) * Correspondence: [email protected]; Tel.: +61-292318077 Abstract: Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design Citation: van der Merwe, M.M.; Yap, a collecting strategy for a germplasm conservation collection that optimises genetic diversity.
    [Show full text]
  • An Evolutionary Perspective on Contemporary Genetic Load In
    An evolutionary perspective on contemporary genetic load in threatened species to inform future conservation efforts Samarth Mathur1, John Tomeˇcek2, Luis Tarango-Ar´ambula3, Robert Perez4, and Andrew DeWoody1 1Purdue University 2Texas A&M University 3Colegio de Postgraduados Campus San Luis Potosi 4Texas Parks and Wildlife Department June 29, 2021 Abstract In theory, genomic erosion can be reduced in fragile “recipient” populations by translocating individuals from genetically diverse “donor” populations. However, recent simulation studies have argued that such translocations can, in principle, serve as a conduit for new deleterious mutations to enter recipient populations. A reduction in evolutionary fitness is associated with a higher load of deleterious mutations and thus, a better understanding of evolutionary processes driving the empirical distribution of deleterious mutations is crucial. Here, we show that genetic load is evolutionarily dynamic in nature and that demographic history greatly influences the distribution of deleterious mutations over time. Our analyses, based on both demographically explicit simulations as well as whole genome sequences of potential donor-recipient pairs of Montezuma Quail (Cyrtonyx montezumae) populations, indicate that all populations tend to lose deleterious mutations during bottlenecks, but that genetic purging is pronounced in smaller populations with stronger bottlenecks. Despite carrying relatively fewer deleterious mutations, we demonstrate how small, isolated populations are more likely to suffer inbreeding depression as deleterious mutations that escape purging are homogenized due to drift, inbreeding, and ineffective purifying selection. We apply a population genomics framework to showcase how the phylogeography and historical demography of a given species can enlighten genetic rescue efforts. Our data suggest that small, inbred populations should benefit the most when assisted gene flow stems from genetically diverse donor populations that have the lowest proportion of deleterious mutations.
    [Show full text]
  • Reviewing the Consequences of Genetic Purging on the Success of Rescue 3 Programs
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452459; this version posted July 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Authors: Noelia Pérez-Pereiraa, Armando Caballeroa and Aurora García-Doradob 2 Article title: Reviewing the consequences of genetic purging on the success of rescue 3 programs 4 5 6 a Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, 36310 Vigo, 7 Spain. 8 9 b Departamento de Genética, Fisiología y Microbiología, Universidad Complutense, Facultad 10 de Biología, 28040 Madrid, Spain. 11 12 13 Corresponding author: Aurora García-Dorado. Departamento de Genética, Fisiología y 14 Microbiología, Universidad Complutense, Facultad de Biología, 28040 Madrid, Spain. 15 Email address: [email protected] 16 17 ORCID CODES: 18 Noelia Pérez-Pereira: 0000-0002-4731-3712 19 Armando Caballero: 0000-0001-7391-6974 20 Aurora García-Dorado: 0000-0003-1253-2787 21 22 23 24 25 26 27 28 29 30 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452459; this version posted July 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 31 DECLARATIONS: 32 Funding: This work was funded by Agencia Estatal de Investigación (AEI) (PGC2018- 33 095810-B-I00 and PID2020-114426GB-C21), Xunta de Galicia (GRC, ED431C 2020-05) 34 and Centro singular de investigación de Galicia accreditation 2019-2022, and the European 35 Union (European Regional Development Fund - ERDF), Fondos Feder “Unha maneira de 36 facer Europa”.
    [Show full text]
  • Detection of Genetic Purging and Predictive Value of Purging Parameters Estimated in Pedigreed Populations
    Heredity (2018) 121:38–51 https://doi.org/10.1038/s41437-017-0045-y ARTICLE Detection of genetic purging and predictive value of purging parameters estimated in pedigreed populations 1 1 2 1 Eugenio López-Cortegano ● Diego Bersabé ● Jinliang Wang ● Aurora García-Dorado Received: 24 July 2017 / Revised: 7 December 2017 / Accepted: 9 December 2017 / Published online: 13 February 2018 © The Genetics Society 2018 Abstract The consequences of inbreeding for fitness are important in evolutionary and conservation biology, but can critically depend on genetic purging. However, estimating purging has proven elusive. Using PURGd software, we assess the performance of the Inbreeding–Purging (IP) model and of ancestral inbreeding (Fa) models to detect purging in simulated pedigreed populations, and to estimate parameters that allow reliably predicting the evolution of fitness under inbreeding. The power to detect purging in a single small population of size N is low for both models during the first few generations of inbreeding (t ≈ N/2), but increases for longer periods of slower inbreeding and is, on average, larger for the IP model. The ancestral inbreeding approach overestimates the rate of inbreeding depression during long inbreeding periods, and produces joint fi 1234567890();,: estimates of the effects of inbreeding and purging that lead to unreliable predictions for the evolution of tness. The IP estimates of the rate of inbreeding depression become downwardly biased when obtained from long inbreeding processes. However, the effect of this bias is canceled out by a coupled downward bias in the estimate of the purging coefficient so that, unless the population is very small, the joint estimate of these two IP parameters yields good predictions of the evolution of mean fitness in populations of different sizes during periods of different lengths.
    [Show full text]
  • Inbreeding Depression in the Speke's Gazelle Captive Breeding Program
    Contributed Papers Inbreeding Depression in the Speke’s Gazelle Captive Breeding Program STEVEN T. KALINOWSKI,*‡ PHILIP W. HEDRICK,* AND PHILIP S. MILLER† *Department of Biology, Arizona State University, Tempe, AZ 85287–1501, U.S.A. †Conservation Breeding Specialist Group, 12101 Johnny Cake Ridge Road, Apple Valley, MN 55124–8151, U.S.A. Abstract: The Speke’s gazelle (Gazella spekei) captive breeding program has been presented as one of the few examples of selection reducing the genetic load of a population and as a potential model for the captive breeding of endangered species founded from a small number of individuals. In this breeding program, three generations of mate selection apparently increased the viability of inbred individuals. We reanalyzed the Speke’s gazelle studbook and examined potential causes for the reduction of inbreeding depression. Our analysis indicates that the decrease in inbreeding depression is not consistent with any model of genetic im- provement in the herd. Instead, we found that the effect of inbreeding decreased from severe to moderate dur- ing the first generation of inbreeding, and that this change is responsible for almost all of the decline in in- breeding depression observed during the breeding program. This eliminates selection as a potential explanation for the decrease in inbreeding depression and suggests that inbreeding depression may be more sensitive to environmental influences than is usually thought. Depresión por Intracruza en el Programa de Reproducción en Cautiverio para la Gacela de Speke Resumen: El programa de reproducción en cautiverio para la gacela de Speke (Gazella spekei) ha sido pre- sentado como uno de los pocos ejemplos de selección que reducen la carga genética de una población y un modelo potencial para la reproducción en cautiverio de especies en peligro fundado a partir de un número pequeño de individuos.
    [Show full text]
  • 00 Alfabetizaciones (Prel.)
    BIBLIOGRAFÍA WEB AgrAwAl , A. F. y M. C. w hitloCk (2012). Mutation load: the fitness of individuals in popu - lations where deleterious alleles are abundant. Annual review of Ecology, Evolution, and Systematics, 43: 115-135. AndErSSon l. y l. g EorgES (2004). domestic-animal genomics: deciphering the genetics of complex traits . nature reviews genetics, 5: 202-212. ÁlvArEz -C AStro , J. M., A. l E rouziC y o. C Arlborg (2008). how to perform meaningful estimates of genetic effects. PloS genetics, 5: e1000062. AMAdor , C., A. g ArCíA -d orAdo , d. b ErSAbé y C. l óPEz -F AnJul (2010). regeneration of the variance of metric traits by spontaneous mutation in a drosophila population. genetics research, 92: 91-102. AMAdor , C., J. F ErnÁndEz y t. h. E. MEuwiSSEn (2013). Advantages of using molecular coancestry in the removal of introgressed genetic material. genetics, Selection, Evolution, 45(1): 13. AllEndorF , F. w., g. l uikArt y S. n. A itkEn (2013). Conservation and the Genetics of Pop - ulations (2ª ed.) wiley-blackwell, oxford, reino unido. ArMbruStEr , P. y P. h. r EEd (2005). inbreeding in benign and stressful environments. heredity, 95: 235-242. Arnold , S. J. y M. J. w AdE (1984a). on the measurement of natural and sexual selection: theory. Evolution, 38: 709-719. — (1984b). on the measurement of natural and sexual selection: Applications. Evolution, 38: 720-734. Auton , A. et al., 1000 genomes Project Consortium (2015). A global reference for human genetic variation. nature, 526: 68-74. ÁvilA v., A. P érEz -F iguEroA , A. C AbAllEro , w. g.
    [Show full text]
  • Nonequivalent Lethal Equivalents: Models and Inbreeding Metrics for Unbiased Estimation of Inbreeding Load
    Received: 4 February 2018 | Revised: 6 September 2018 | Accepted: 9 September 2018 DOI: 10.1111/eva.12713 ORIGINAL ARTICLE Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load Pirmin Nietlisbach1,2 | Stefanie Muff1 | Jane M. Reid3 | Michael C. Whitlock2 | Lukas F. Keller1,4 1Department of Evolutionary Biology and Environmental Studies, University of Zurich, Abstract Zurich, Switzerland Inbreeding depression, the deterioration in mean trait value in progeny of related 2 Department of Zoology, University of parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant British Columbia, Vancouver, BC, Canada breeding, and conservation biology. The magnitude of inbreeding depression can be 3School of Biological Sciences, University of Aberdeen, Aberdeen, UK quantified by the inbreeding load, typically measured in numbers of lethal equiva‐ 4Zoological Museum, University of Zurich, lents, a population genetic quantity that allows for comparisons between environ‐ Zurich, Switzerland ments, populations or species. However, there is as yet no quantitative assessment of Correspondence which combinations of statistical models and metrics of inbreeding can yield such Pirmin Nietlisbach, Department of Zoology, University of British Columbia, Vancouver, estimates. Here, we review statistical models that have been used to estimate in‐ BC, Canada. breeding load and use population genetic simulations to investigate how unbiased Email: [email protected] estimates can be obtained using genomic and pedigree‐based metrics of inbreeding. Funding information We use simulated binary viability data (i.e., dead versus alive) as our example, but the Forschungskredit of the University of Zurich, Grant/Award Number: FK‐15‐104; Swiss concepts apply to any trait that exhibits inbreeding depression.
    [Show full text]
  • Origin and Evolution of Deleterious Mutations in Horses
    G C A T T A C G G C A T genes Article Origin and Evolution of Deleterious Mutations in Horses Ludovic Orlando 1,2 and Pablo Librado 1,2,* 1 Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France 2 Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1350K Copenhagen, Denmark * Correspondence: [email protected]; Tel.: +33-0561145505 Received: 23 July 2019; Accepted: 26 August 2019; Published: 28 August 2019 Abstract: Domestication has changed the natural evolutionary trajectory of horses by favoring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago. To identify the factors underlying this trajectory, we gather an extensive dataset consisting of 175 modern and 153 ancient genomes previously published, and carry out the most comprehensive characterization of deleterious mutations in horses. We confirm that deleterious variants segregated at low frequencies during the last 3500 years, and only spread and incremented their occurrence in the homozygous state during modern times, owing to inbreeding. This independently happened in multiple breeds, following both the development of closed studs and purebred lines, and the deprecation of horsepower in the 20th century, which brought many draft breeds close to extinction. Our work illustrates the paradoxical effect of some conservation and improvement programs, which reduced the overall genomic fitness and viability.
    [Show full text]
  • Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations
    G3: Genes|Genomes|Genetics Early Online, published on September 7, 2016 as doi:10.1534/g3.116.032425 1 Predictive model and software for inbreeding-purging analysis of pedigreed populations 2 3 AURORA GARCÍA-DORADO*, JINLIANG WANG† and EUGENIO LÓPEZ-CORTEGANO* 4 5 * Departamento de Genética, Universidad Complutense, Madrid 28040, Spain 6 † Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom 7 © The Author(s) 2013. Published by 1the Genetics Society of America. 8 Running title: Purging in pedigreed data 9 10 Key words: 11 - Inbreeding depression 12 - purging coefficient 13 - rate of inbreeding depression 14 - inbreeding load 15 - logarithmic fitness 16 17 Corresponding author: 18 Aurora García-Dorado 19 Departamento de Genética, Facultad de Biología, Universidad Complutense, Ciudad 20 Universitaria, Madrid 28040, Spain 21 Phone number: 0034 3944975 22 Email address: [email protected] 23 24 2 25 Abstract 26 The inbreeding depression of fitness traits can be a major threat for the survival of 27 populations experiencing inbreeding. However, its accurate prediction requires taking into 28 account the genetic purging induced by inbreeding, which can be achieved using a “purged 29 inbreeding coefficient”. We have developed a method to compute purged inbreeding at the 30 individual level in pedigreed populations with overlapping generations. Furthermore, we derive 31 the inbreeding depression slope for individual logarithmic fitness, which is larger than that for 32 the logarithm of the population fitness average. In addition, we provide a new software PURGd 33 based on these theoretical results that allows analyzing pedigree data to detect purging and to 34 estimate the purging coefficient, which is the parameter necessary to predict the joint 35 consequences of inbreeding and purging.
    [Show full text]
  • On the Consequences of Ignoring Purging on Genetic Recommendations for Minimum Viable Population Rules
    Heredity (2015) 115, 185–187 & 2015 Macmillan Publishers Limited All rights reserved 0018-067X/15 www.nature.com/hdy NEWS AND COMMENTARY Purging and MVP rules On the consequences of ignoring purging on genetic recommendations for minimum viable population rules A García-Dorado Heredity (2015) 115, 185–187; doi:10.1038/hdy.2015.28; published online 15 April 2015 nconservationpractice,preliminaryassess- 2011; Kennedy et al., 2014), concluded that in the heterozygous condition. For each Iments of extinction risk as well as emer- the inbreeding load for overall fitness in the particular deleterious allele, d depends both gency decisions are often based on scarce wild is on the average B≈6 haploid-recessive on the selection coefficient against homozy- information. Thus, a simple 50/500 rule of lethal equivalents, that is, about fourfold the gous (s) and on the degree of dominance (h) thumb has been applied for a long time as estimate obtained in a meta analysis for (d = s(1–2h)/2; note that, for any given d a guidance to determine when genetic threats captive conditions (Ralls et al., 1988) that value, the intensity of purging does not become relevant to conservation, and to settle had been widely used as a default value (Lacy, depend of the underlying s and h coeffi- the genetic threshold to the minimum size for 1993). To derive this new Ne = 100 rule, cients). It has been shown that good approx- population viability (the so-called MVP). This Frankham et al. used the classical equation imations for fitness inbreeding depression can rule, used,
    [Show full text]
  • Detection of Genetic Purging and Predictive Value of Purging
    1 2 3 4 Detection of genetic purging and predictive value of purging 5 parameters estimated in pedigreed populations 6 Eugenio López-Cortegano1, Diego Bersabé1, Jinliang Wang2, and Aurora 7 García-Dorado1* 8 9 10 1 Departamento de Gen´etica. Facultad de Biolog´ıa. Universidad 11 Complutense. 28040, Madrid. Spain. 12 2 Institute of Zoology. Zoological Society of London. Regent’s Park, London 13 NW1 4RY. United Kingdom. 14 * Corresponding author 15 16 Running title: purging analysis of pedigreed data 17 18 Key words: Inbreeding depression; Inbreeding-Purging model; ancestral 19 inbreeding; PURGd software; Simulation. 20 21 22 1 23 ABSTRACT 24 The consequences of inbreeding for fitness are important in evolutionary and 25 conservation biology, but can critically depend on genetic purging. However, estimating 26 purging has proven elusive. Using PURGd software, we assess the performance of the 27 Inbreeding-Purging (IP) model and of ancestral inbreeding (Fa) models to detect purging in 28 simulated pedigreed populations, and to estimate parameters that allow reliably predicting 29 the evolution of fitness under inbreeding. The power to detect purging in a single small 30 population of size N is low for both models during the first few generations of inbreeding (t 31 ≈ N/2), but increases for longer periods of slower inbreeding and is, on average, larger for 32 the IP model. The ancestral inbreeding approach overestimates the rate of inbreeding 33 depression during long inbreeding periods, and produces joint estimates of the effects of 34 inbreeding and purging that lead to unreliable predictions for the evolution of fitness. The IP 35 estimates of the rate of inbreeding depression become downwardly biased when obtained 36 from long inbreeding processes.
    [Show full text]