The use of population genetic variability in present-day selection schemes can be improved to red... more The use of population genetic variability in present-day selection schemes can be improved to reduce inbreeding rate and inbreeding depression without impairing genetic progress. We performed an experiment with Drosophila melanogaster to test mate selection, an optimizing method that uses linear programming to maximize the selection differential applied while at the same time respecting a restriction on the increase in inbreeding expected in the next generation. Previous studies about mate selection used computer simulation on simple additive genetic models, and no experiment with a real character in a real population had been carried out. After six selection generations, the optimized lines showed an increase in cumulated phenotypic selection differential of 10.76%, and at the same time, a reduction of 19.91 and 60.47% in inbreeding coefficient mean and variance, respectively. The increased selection pressure would bring greater selection response, and in fact, the observed change in the selected trait was on average 31.03% greater in the optimized lines. These improvements in the selection scheme were not made at the expense of the long-term expectations of genetic variability in the population, as these expectations were very similar for both mate selection and conventionally selected lines in our experiment.
Summary This chapter surveys the different ways in which the diversity we observe within a specie... more Summary This chapter surveys the different ways in which the diversity we observe within a species can be quantified. It will consider:(1) how the diversity we observe in the population of a species can be divided into differences between breeds, or more generally ...
Genomic selection (GS) is now practiced successfully across many species. However, many questions... more Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained on...
Genetic distances: a useful tool to be applied with caution
Journal of Animal Breeding and Genetics, 2008
Genetic differences between populations for a quantitative trait
Journal of Heredity, 1985
ABSTRACT
GENETIC HETEROGENEITY INCREASES VIABILITY IN COMPETING GROUPS OF<i>DROSOPHILA HYDEI</i>
Evolution, Jun 1, 1993
Page 1. Evolution, 47(3), 1993, pp. 977-981 GENETIC HETEROGENEITY INCREASES VIABILITY IN COMPETIN... more Page 1. Evolution, 47(3), 1993, pp. 977-981 GENETIC HETEROGENEITY INCREASES VIABILITY IN COMPETING GROUPS OF DROSOPHILA HYDEI CRISTINA LOPEZ-SUAREZ,&#x27; MIGUEL A. TORO,2 AND CARLOS GARCIA ...
Un eminente evolucionista: John Maynard Smith (1920-2004)
Using two different approaches to infer of the genetic structure of populations with complex relationships: the case of the Avileña-Negra Ibérica
The inference of the genetic structure of domestic animal populations has important implications ... more The inference of the genetic structure of domestic animal populations has important implications in the design of breeding programs. In this paper, we assessed the utility of a graphical clustering algorithm (GCA) to identify the genetic structures of real livestock populations with complex relationships comparing it to a Bayesian clustering algorithm (STRUCTURE). The genetic structure of the Spanish cattle breed Avileña-Negra Ibérica was inferred by the analysis of 13,343 animals from 70 herds genotyped for 17 microsatellites. We compared the results of GCA and STRUCTURE regarding the ability to restore Hardy-Weinberg equilibrium in each subpopulation and the average coancestry within and between subpopulations. Both approaches described a similar structure for the ANI breed, which was found to have three genetic subpopulations and a pool of individuals that cannot be assigned without ambiguity to any of the subpopulations. This structure is coherent with the history of the breed. ...
Altruism and sex ratio
Journal of Theoretical Biology, 1982
Abstract Using precise genetic models, the evolution of the sex ratio in a population in which in... more Abstract Using precise genetic models, the evolution of the sex ratio in a population in which interactions between siblings exist but these interactions are not symmetrical with respect to the sexes has been studied. Some interesting differences between co-operative and aggressive models have emerged.
Background In commercial fish, dominance effects could be exploited by predicting production abil... more Background In commercial fish, dominance effects could be exploited by predicting production abilities of the offspring that would be generated by different mating pairs and choosing those pairs that maximise the average offspring phenotype. Consequently, matings would be performed to reduce inbreeding depression. This can be achieved by applying mate selection (MS) that combines selection and mating decisions in a single step. An alternative strategy to MS would be to apply minimum coancestry mating (MCM) after selection based on estimated breeding values. The objective of this study was to evaluate, by computer simulations, the potential benefits that can be obtained by implementing MS or MCM based on genomic data for exploiting dominance effects when creating commercial fish populations that are derived from a breeding nucleus. Methods The selected trait was determined by a variable number of loci with additive and dominance effects. The population consisted of 50 full-sib famili...
Proceedings of the World Congress on Genetics applied to Livestock Production, 1994
Genetic parameters for piglet weight were estimated using DFREML procedure in two strains of Iber... more Genetic parameters for piglet weight were estimated using DFREML procedure in two strains of Iberian pigs and in records proceeding from a 4 x 4 diallelic design between ancient strains. The model of analysis included four random effects: direct and maternal genetic effects, common environmental effect and residual, and as fixed effects the sex, the farrowing period and the parity of the dam. Inbreeding coefficients of dam and piglet and the parameters of the model were also included as covariables in the analysis of strains and of the diallel cross, respectively.
Proceedings of the World Congress on Genetics Applied to Livestock Production, 2018
Effective population size (N e ) is a key parameter in conservation genetics. In the management o... more Effective population size (N e ) is a key parameter in conservation genetics. In the management of conservation programs there is a consensus that the optimal method for maximizing effective population size is to calculate the contribution of each potential parent (the number of offspring that each individual leaves to the next generation) by minimizing the global coancestry between potential parents weighted by their contributions. When using genomic data the optimal method for managing genetic diversity will remain the same but now the molecular coancestry calculated from markers will substitute the genealogical coancestry However, in this situation, the concept of effective population size loses its meaning because when optimal molecular management starts, genetic diversity increases and therefore effective population size takes negative values. Furthermore, in the long term the molecular effective population size does not attain an asymptotic value but it increases continuously.
A new method that allows use of part of the dominance effects in a closed population is proposed.... more A new method that allows use of part of the dominance effects in a closed population is proposed. In the framework of a progeny test selection scheme, the method basically consists of performing 2 types of matings: a) minimum coancestry matings in order to obtain the progenies that will constitute the commercial population and that will also be utilized for testing purposes, and b) maximum coancestry matings from which the population will be propagated. The performance of the new method has been checked by computer simulation and results show a superiority over the standard progeny test in all cases where unfavourable alleles are recessive, especially when they are at low frequency. artificial selection / dominance variance / mating strategy / computer simulation R.ésumé -Une nouvelle méthode visant à utiliser la variance de dominance dans des populations fermées en sélection. Une nouvelle méthode est proposée pour utiliser les effets de dominance dans des populations fermées. Dans le cadre d'un schéma de sélection sur descendance, la méthode consiste à réaliser 2 types d'accouplements: a) accouplements avec parenté minimale afin d'obtenir les descendants qui constituent la population commer- ciale et qui en même temps servent à l'épreuve de descendance, et 6) accouplements avec parenté maximale servant à propager la population. La valeur de la nouvelle méthode a été vérifiée par simulation sur ordinateur, et les résultats montrent qu'elle est supérieure à l'épreuve de descendance classique dans tous les cas où les allèles défavorables sont récessifs, et surtout si leurs fréquences sont faibles. sélection artificielle / variance de dominance / système d'accouplement / simulation sur ordinateur
The use of prior information in the estimation of the heritability by parent-offspring regression... more The use of prior information in the estimation of the heritability by parent-offspring regression is discussed within a bayesian context. The a posteriori distribution is obtained by combining the a priori distribution (uniform between 0 and 1), to that obtained from the data. Hence, a bayesian estimator h *2 is proposed and its performance compared with those obtained by the least squares and constrained maximum likelihood methods and also with two different bayesian estimators (Nicnnt et al., 1979), using Monte Carlo simulation techniques. It is concluded that the estimate h *2 should be preferred to the others, particularly for small sets of data.
BackgroundThe availability of genome-wide marker data allows estimation of inbreeding coefficient... more BackgroundThe availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computingFand ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1andFLH2), VanRaden (FVR1andFVR2), Yang and colleagues (FYA1andFYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD).ResultsIf the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated withFIBDand provide accurate estimates o...
ABSTRACT. Darwin's attempt to analyze human culture and behavior from a naturalistic point o... more ABSTRACT. Darwin's attempt to analyze human culture and behavior from a naturalistic point of view was not well received by most of the thinkers responsible for the foundations of the standard model in social sciences. However, in the last years the Darwinian proposal has been ...
Background: In commercial fish, dominance effects could be exploited by predicting production abi... more Background: In commercial fish, dominance effects could be exploited by predicting production abilities of the offspring that would be generated by different mating pairs and choosing those pairs that maximise the average offspring phenotype. Consequently, matings would be performed to reduce inbreeding depression. This can be achieved by applying mate selection (MS) that combines selection and mating decisions in a single step. An alternative strategy to MS would be to apply minimum coancestry mating (MCM) after selection based on estimated breeding values. The objective of this study was to evaluate, by computer simulations, the potential benefits that can be obtained by implementing MS or MCM based on genomic data for exploiting dominance effects when creating commercial fish populations that are derived from a breeding nucleus. The selected trait was determined by a variable number of loci with additive and dominance effects. The population consisted of 50 full-sib families with 30 offspring each. Males and females with the highest estimated genomic breeding values were selected in the nucleus and paired using the MCM strategy. Both MCM and MS were used to create the commercial population. Results: For a moderate number of SNPs, equal or even higher mean phenotypic values are obtained by selecting on genomic breeding values and then applying MCM than by using MS when the trait exhibited substantial inbreeding depression. This could be because MCM leads to high levels of heterozygosity across the whole genome, even for loci affecting the trait that are in linkage equilibrium with the SNPs. In contrast, MS specifically promotes heterozygosity for SNPs for which a dominance effect has been detected. In most scenarios, for the management of aquaculture breeding programs it seems advisable to follow the MCM strategy when creating the commercial population, especially for traits with large inbreeding depression. Moreover, MCM has the appealing property of reducing inbreeding levels, with a corresponding reduction in inbreeding depression for traits beyond those included in the selection objective.
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Papers by Miguel Toro