DOCSLIB.ORG

On the Consequences of Ignoring Purging on Genetic Recommendations for Minimum Viable Population Rules

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read 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, for example, in the elaboration of for fitness inbreeding depression be obtained using an effective purging coeffi- the International Union for the Conservation cient that applies to the overall inbreeding of Nature Red List criteria for threatened W t ¼ W 0Exp½ÀBFt ; ð1Þ load (García-Dorado, 2012); however, it is convenient to separately consider the conse- species, states that the effective population where W and F stand, respectively, for the t t quences of purging upon the inbreeding load size (Ne) should be at least 50 to prevent the average fitness and Wright’s inbreeding coef- dramatic consequences from inbreeding ascribed to true recessive lethal alleles (B , ficient at generation t,andtheinbreeding L depression in the short term, whereas a larger with purging coefficient d ≈0.5) from those load (B) is the rate of inbreeding depression. L value (N ⩾ 500) would be needed to preserve ascribed to non-lethal alleles (B with e This expression assumes that the homozygo- NL, adaptive potential in the long term (Franklin, effective purging coefficient d ). This gives sis for (partially) recessive deleterious alleles NL 1980; Jamieson and Allendorf, 2012). As it Âà increases with inbreeding at the same rate as ¼ À À : ð Þ is well known, these N values imply W t W 0Exp BLgLt BNLgNLt 2 e that for neutral alleles and, using B = 6, it considerably larger censuses. predicts that N = 50 would cause the In addition, the inbreeding load of the However, it has been recently proposed e expected fitness to decline to 75% of its initial reduced population ascribed to deleterious that these figures should be doubled value in just five generations and to 0.2% in alleles segregating in the original population (Frankham et al., 2014), a recommendation the long term. can also be predicted as that could have important consequences on However, as inbreeding promotes the ÀÁ resource allocation but may be based ¼ þ ðÞÀ = ; ð Þ expression of the recessive component of Bt BLgLt BNLgNLt 1 Ft Ft 3 on exceedingly simplifying assumptions deleterious effects, it not only causes inbreed- although the actual inbreeding load will be (Franklin et al.,2014). ing depression but also leads to an increase of larger in the long term due to new deleterious Frankham et al.’s proposal that N should e the efficiency of natural selection, known as mutation. For d = d = 0, Equations (2) and be at least 100 to prevent extinction risk from L NL genetic purging. Here I discuss the conse- (3) produce the corresponding classical inbreeding depression, was prompted by quences of purging on Frankham et al.’s neutral predictions. a bulk of recent estimates of the inbreeding recommendation using the inbreeding– To date, the only empirical estimate of the load in the wild that are much larger than purging approach (García-Dorado, 2012), intensity of purging in the fraction of B not those previously obtained in captive condi- where the evolution of fitness is approxi- due to recessive lethal alleles, obtained in the tions. Thus, a meta-analysis by O’Grady et al. mated by replacing F with a purged inbreed- lab for a partial measure of fitness in (2006) on wild mammalian and avian species, t ing coefficient (g ⩽ F ) that determines the Drosophila (Bersabé and García‐Dorado, corroborated by additional reports (Kruuk t t increase in homozygosis for the alleles that 2013), suggests 0.02od o0.08. However, it et al., 2002; Liberg et al., 2005; Walling et al., NL are being purged. This parameter can be is reasonable to assume that, as B estimates in computed as a function of Ne and of the the wild are about four times those for captive A García-Dorado is at Departamento de Genética, intensity of purging, which is measured by a and laboratory populations, dNL in the wild Facultad de Biología, Universidad Complutense, Madrid, fi o o Spain purging coef cient (d) that represents the should behave similarly (0.08 dNL 0.32). To E-mail: [email protected] magnitude of the deleterious effects concealed be conservative, I will illustrate the possible News and Commentary 186 consequences of purging in the wild consider- populations, leading to reduced asymptotic has not been detected in several experiments, ing dNL = 0.05 or dNL = 0.15. fitness values. In fact, simulation results have but it has been observed in other instances, Figure 1 (upper panels) gives the evolution shown that purging becomes inefficient for mainly under slow inbreeding (Crnokrak and fi of the tness average of a previously large Neo1/d, due to genetic drift. As the appro- Barrett, 2002; Leberg and Firmin, 2008). population after a reduction in size to priate Ne in this respect is the drift-effective However, purging can pass undetected in Ne = 25, Ne = 50 and Ne = 100, as predicted population size, some inbreeding due to non- experimentation, even for populations where by the classical neutral model or by the panmictic mating in moderate to large popu- it should be relevant in the medium term. inbreeding–purging theory. As in O’Grady lations could produce situations particularly The main reason is that, as shown by the et al. (2006), I assume that the inbreeding favorable for genetic purging, in agreement inbreeding–purging predictions, either load (B = 6) consists of a fraction BL = 2.5 with theoretical and experimental results experimental inbreeding increases too fast to ascribed to recessive lethal alleles (purging (Glémin, 2003; Ávila et al., 2010). allow efficient purging or inbreeding is slow coefficient dL = 0.5) and another fraction Figure 1 (lower panels) also gives an enough but the number of generations ana- BNL = 3.5 due to non-lethal alleles undergoing approximation for the evolution of the lyzed is too small (Hedrick, 1994; Frankham purging (dNL = 0.05 or dNL = 0.15) or not inbreeding load ascribed to deleterious alleles et al., 2001; Kennedy et al., 2014). Further- (dNL = 0). Figure 1 shows that: (i) the con- segregating in the original population, which more, experimental detection is often sequences of purging on fitness decline only drops much faster in the presence of purging obscured by many factors, such as concurrent become apparent after some inbreeding has than under drift alone (dL = dNL = 0). It adaptation, genetic management or uncer- fi accumulated, usually leading to a later tness clearly shows that the reduction of B caused tainty regarding B or Ne values, and few rebound; (ii) the larger the effective popula- bypurgingduringthefirst generations can experiments have addressed the evaluation tion size, the more generations are needed for be mainly ascribed to lethal alleles, whereas of purging in the wild. Thus, the experimental purging consequences to become relevant, that caused by less intense purge is delayed. support for the claim that purging is modest but this occurs at lower inbreeding levels Frankham et al. (2014) argued that classical is, at least, controversial. and, therefore, after smaller fitness declines; neutral predictions for the reduction of mean O’Grady et al. (2006) performed viability (iii) the efficiency of purging in reducing fitness are appropriate because purging has analyses assuming B = 6 for a range of mam- fitness depression is lower for the smaller been shown to be modest. In fact, purging mal and avian species, concluding that the Figure 1 Average fitness predicted for B = 6 using the inbreeding–purging approach (W, upper panels) together with the corresponding inbreeding load ascribed to deleterious alleles in the original population (B, lower panels), computed from Equations 2 and 3. Black Dotted lines: classical prediction (dL = 0; dNL = 0); magenta solid lines: purging acts only against recessive lethals (BL = 2.5, with dL = 0.5; BNL = 3.5, with dNL = 0), as assumed by O’Grady et al. (2006); blue dashed lines: purging acts against recessive lethals (BL = 2.5, with dL = 0.5) and against the remaining inbreeding load (BNL = 3.5, with dNL = 0.05); green dotted-dashed lines: purging acts against recessive lethals (BL = 2.5, with dL = 0.5) and against the remaining inbreeding load (BNL = 3.5, with dNL = 0.15).
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]
  • 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.
    [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]