An evaluation of allowing for mismatches as a way to manage genotyping errors in parentage assignment by exclusion

Vandeputte, Marc; Mauger, Stéphane; Dupont‐Nivet, Mathilde

doi:10.1111/j.1471-8286.2005.01167.x

Cited by 121 publications

(105 citation statements)

References 15 publications

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“…It is also possible that some of the assigned embryos could be the product of type I error (false assignment) (Kalinowski et al, 2007;Oddou-Muratorio et al, 2003;Vandeputte et al, 2006); however, the set of embryos used for the mode of inheritance analyses were the same used in paternity analysis, thus it is unlikely that false assignment has a significant contribution. The number of unassigned embryos/female parent varied between 2 (Family 25) and 14 (Families 3, 39, and 40), this could be a function of female receptivity timing with outside pollen and/or the lack of informative nature of the embryos' genotypes (Tab.…”

Section: Paternity Analysismentioning

confidence: 99%

“…The remaining unassigned 121 (22%) could be either the product of gene flow from the neighbouring orchard or their genotypes were not informative enough for assignment to any of the orchard's 41 parents (i.e., type II error (false exclusion) (Kalinowski et al, 2007;Oddou-Muratorio et al, 2003;Vandeputte et al, 2006)) or a combination of the two. It is also possible that some of the assigned embryos could be the product of type I error (false assignment) (Kalinowski et al, 2007;Oddou-Muratorio et al, 2003;Vandeputte et al, 2006); however, the set of embryos used for the mode of inheritance analyses were the same used in paternity analysis, thus it is unlikely that false assignment has a significant contribution.…”

Section: Paternity Analysismentioning

confidence: 99%

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Pedigree and mating system analyses in a western larch (Larix occidentalis Nutt.) experimental population

et al. 2008

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. Pedigree and mating system analyses in a western larch (Larix occidentalis Nutt.) experimental population. Annals of Forest Science, Springer Verlag/EDP Sciences, 2008, 65 (7), pp.1. Ann. For. Sci. 65 (2008) Abstract•The mating pattern and gene flow in a western larch (Larix occidentalis Nutt.) experimental population was studied with the aid of microsatellite markers and a combination of paternity-mating system analysis. The commonly difficult to assess, male gametic contribution was determined with 95% confidence and its impact on genetic gain and diversity was determined.• Male fertility success rate ranged between 0 and 11%. Male reproductive output parental imbalance was observed with 50% of the pollen being produced by the top 5% of males while the lower 39% males only produced 10% of the pollen.• A significant difference was observed between male effective population size (genetic diversity) estimates from paternity assignment compared to those based on population's census number (21 vs. 41); however, this difference did not affect estimates of genetic gain.• A total of 221 full-fib families were identified (sample size range: 1-8) and were nested among the studied 14 seed-donors.• A combination of paternity-mating system analysis is recommended to provide a better insight into seed orchards' mating dynamics. While pollen flow tends to inflate mating system's outcrossing rate, the paternity analysis effectively determined the rate and magnitude of contamination across receptive females. • Le taux de succès reproductif mâle était compris entre 0 et 11 %. Un déséquilibre dans la contribution des parents mâles a été observé avec la production de 50 % du pollen par 5 % des pères alors que 39 % d'entre eux ne contribuaient que pour seulement 10 % du pollen. Mots-clés• Une différence significative a été observée entre la taille efficace de la population mâle (diversité génétique) estimée par la recherche de paternité et celle basée sur les effectifs recensés de la population (21 vs. 41) ; cependant, cette différence n'affecte pas l'estimation du gain génétique.• 221 familles de plein-frères ont été identifiées (effectifs entre 1 et 8), regroupées parmi les 14 arbresmères étudiés.• La combinaison d'une analyse de paternité et du système de reproduction est recommandée pour étudier de manière approfondie la dynamique de croisement en vergers à graines. Tandis que les flux de pollen tendent à augmenter le taux d'inter-croisements, l'analyse de paternité détermine de manière effective le taux et l'amplitude de contamination des arbres-mères.

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Section: Paternity Analysismentioning

confidence: 99%

Section: Paternity Analysismentioning

confidence: 99%

Pedigree and mating system analyses in a western larch (Larix occidentalis Nutt.) experimental population

et al. 2008

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“…Nestlings with a positive trio LOD score that mismatched their social father's genotype at maximally one locus were classified as WPO. Mismatches at only one locus are most likely due to null alleles, mutations, spurious alleles or genotyping errors [42,43]. We determined the paternity status (WPO or EPO) of 464 offspring originating from 157 broods.…”

Section: Methodsmentioning

confidence: 99%

When mothers make sons sexy: maternal effects contribute to the increased sexual attractiveness of extra-pair offspring

et al. 2011

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Quality differences between offspring sired by the social and by an extra-pair partner are usually assumed to have a genetic basis, reflecting genetic benefits of female extra-pair mate choice. In the zebra finch ( Taeniopygia guttata ), we identified a colour ornament that is under sexual selection and appears to have a heritable basis. Hence, by engaging in extra-pair copulations with highly ornamented males, females could, in theory, obtain genes for increased offspring attractiveness. Indeed, sons sired by extra-pair partners had larger ornaments, seemingly supporting the genetic benefit hypothesis. Yet, when comparing ornament size of the social and extra-pair partners, there was no difference. Hence, the observed differences most likely had an environmental basis, mediated, for example, via differential maternal investment of resources into the eggs fertilized by extra-pair and social partners. Such maternal effects may (at least partly) be mediated by egg size, which we found to be associated with mean ornament expression in sons. Our results are consistent with the idea that maternal effects can shape sexual selection by altering the genotype–phenotype relationship for ornamentation. They also caution against automatically attributing greater offspring attractiveness or viability to an extra-pair mate's superior genetic quality, as without controlling for differential maternal investment we may significantly overestimate the role of genetic benefits in the evolution of extra-pair mating behaviour.

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“…(Cercueil et al 2002) No S. trutta application found but see Vandeputte et al 2006PEDAGREE (Coombs et al 2010 No S. trutta application found but see EasyPOP (Balloux 2001) No S. trutta application found but see Castric et al 2002;Gomez-Uchida et al 2008;Whiteley et al 2010FPG (Hey 2004 No salmonid application found SFS-CODE (Hernandez 2008) No salmonid application found Coalescent simulation models MS (Hudson 2002) No salmonid application found SEQ-GEN (Rambaut & Grassly 1997) Cortey et al 2009 SIMCOAL (Excoffier et al 2000;Laval & Excoffier 2004) No salmonid application found DIY ABC (Cornuet et al 2008) No S. trutta application found but see Nikolic et al 2009 Quantitative genetics: animal model MCMCglmm R package (Hadfield 2010) Serbezov et al 2010bVCE (Groeneveld 1994 No S. trutta application found but see Martyniuk et al 2003;Wilson & Rannala 2003;Norris 2004;Perry et al 2004, 2005 DFREML (replaced by WOMBAT) (Meyer 1988(Meyer , 2007 No S. trutta application found but see Hard et al 1999;Rogers et al 2002;Garant et al 2003;Araneda et al 2005;Paez et al 2010 (Ortigosa et al 2000) No salmonid application found HABSCORE (Milner et al 1993) Barnard et al 1995 Habitat-hydraulic models e.g., 'What are the habitat preferences of a fish population in relation to stream discharge?' (Parasiewicz 2001(Parasiewicz , 2007 No salmonid application found EVHA (Ginot 1995;P...…”

Section: Population Dynamics Modelsmentioning

confidence: 99%

A review of ecological models for brown trout: towards a new demogenetic model

Frank

Piccolo

Baret

2011

Ecology of Freshwater Fish

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-Ecological models for stream fish range in scale from individual fish to entire populations. They have been used to assess habitat quality and to predict the demographic and genetic responses to management or disturbance. In this paper, we conduct the first comprehensive review and synthesis of the vast body of modelling literature on the brown trout, Salmo trutta L., with the aim of developing the framework for a demogenetic model, i.e., a model integrating both population dynamics and genetics. We use a bibliometric literature review to identify two main categories of models: population ecology (including population dynamics and population genetics) and population distribution (including habitat-hydraulic and spatial distribution). We assess how these models have previously been applied to stream fish, particularly brown trout, and how recent models have begun to integrate them to address two key management and conservation questions: (i) How can we predict fish population responses to management intervention? and (ii) How is the genetic structure of fish populations influenced by landscape characteristics? Because salmonid populations tend to show watershed scale variation in both demographic and genetic traits, we propose that models combining demographic, genetic and spatial data are promising tools for improving their management and conservation. We conclude with a framework for an individual-based, spatially explicit demogenetic model that we will apply to stream-dwelling brown trout populations in the near future.

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An evaluation of allowing for mismatches as a way to manage genotyping errors in parentage assignment by exclusion

Cited by 121 publications

References 15 publications

Pedigree and mating system analyses in a western larch (Larix occidentalis Nutt.) experimental population

Pedigree and mating system analyses in a western larch (Larix occidentalis Nutt.) experimental population

When mothers make sons sexy: maternal effects contribute to the increased sexual attractiveness of extra-pair offspring

A review of ecological models for brown trout: towards a new demogenetic model

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