nadiv : an R package to create relatedness matrices for estimating non‐additive genetic variances in animal models

1. The Non‐Additive InVerses (nadiv) R software package contains functions to create and use non‐additive genetic relationship matrices in the animal model of quantitative genetics.

[1]  Jarrod D. Hadfield,et al.  MCMC methods for multi-response generalized linear mixed models , 2010 .

[2]  Alastair J. Wilson,et al.  pedantics: an r package for pedigree‐based genetic simulation and pedigree manipulation, characterization and viewing , 2009, Molecular ecology resources.

[3]  K. Meyer,et al.  Likelihood calculations to evaluate experimental designs to estimate genetic variances , 2008, Heredity.

[4]  M. Sillanpää,et al.  Efficient Markov Chain Monte Carlo Implementation of Bayesian Analysis of Additive and Dominance Genetic Variances in Noninbred Pedigrees , 2008, Genetics.

[5]  Otso Ovaskainen,et al.  A Bayesian framework for comparative quantitative genetics , 2008, Proceedings of the Royal Society B: Biological Sciences.

[6]  Karin Meyer,et al.  WOMBAT—A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML) , 2007, Journal of Zhejiang University SCIENCE B.

[7]  B. Charlesworth.  Mutation-selection balance and the evolutionary advantage of sex and recombination. , 2007, Genetical research.

[8]  D. Roff,et al.  The quantitative genetics of sexual dimorphism: assessing the importance of sex-linkage , 2006, Heredity.

[9]  Joachim Hermisson,et al.  The role of epistatic gene interactions in the response to selection and the evolution of evolvability. , 2005, Theoretical population biology.

[10]  N. Barton,et al.  EFFECTS OF GENETIC DRIFT ON VARIANCE COMPONENTS UNDER A GENERAL MODEL OF EPISTASIS , 2004, Evolution; international journal of organic evolution.

[11]  L. Kruuk.  Estimating genetic parameters in natural populations using the "animal model". , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[12]  John J Welch,et al.  ACCUMULATING DOBZHANSKY‐MULLER INCOMPATIBILITIES: RECONCILING THEORY AND DATA , 2004, Evolution; international journal of organic evolution.

[13]  L. Schaeffer.  Computing simplifications for non‐additive genetic models , 2003 .

[14]  G. Wagner,et al.  Epistasis in Polygenic Traits and the Evolution of Genetic Architecture under Stabilizing Selection , 2003, The American Naturalist.

[15]  Robin Thompson,et al.  ASREML user guide release 1.0 , 2002 .

[16]  P. Waldmann.  Additive and non-additive genetic architecture of two different-sized populations of Scabiosa canescens , 2001, Heredity.

[17]  S. Leal.  Genetics and Analysis of Quantitative Traits , 2001 .

[18]  B. Sheldon,et al.  Genetic architecture of fitness and nonfitness traits: empirical patterns and development of ideas , 1999, Heredity.

[19]  D. Roff.  Evolutionary Quantitative Genetics , 1997, Springer US.

[20]  Ignacy Misztal,et al.  Estimation of Variance Components with Large-Scale Dominance Models , 1997 .

[21]  R. Fernando,et al.  Dominance models with method R for stature of Holsteins. , 1997, Journal of dairy science.

[22]  Raphael Mrode,et al.  Linear models for the prediction of animal breeding values , 1996 .

[23]  D. Roff,et al.  Dominance variance: associations with selection and fitness , 1995, Heredity.

[24]  H. A. Orr,et al.  The population genetics of speciation: the evolution of hybrid incompatibilities. , 1995, Genetics.

[25]  Robin Thompson,et al.  Average information REML: An efficient algorithm for variance parameter estimation in linear mixed models , 1995 .

[26]  T. Prout,et al.  Antagonistic Pleiotropy, Reversal of Dominance, and Genetic Polymorphism , 1994, The American Naturalist.

[27]  H. A. Orr,et al.  INCREASED HERITABLE VARIATION FOLLOWING POPULATION BOTTLENECKS: THE ROLE OF DOMINANCE , 1993, Evolution; international journal of organic evolution.

[28]  S. Gavrilets.  Equilibria in an epistatic viability model under arbitrary strength of selection , 1993 .

[29]  I. D. Boer,et al.  Prediction of additive and dominance effects in (un)selected populations with inbreeding. , 1992 .

[30]  J. V. van Arendonk,et al.  Prediction of additive and dominance effects in selected or unselected populations with inbreeding. , 1992, TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.

[31]  I. Hoeschele,et al.  Additive and nonadditive genetic variance in female fertility of Holsteins. , 1991, Journal of dairy science.

[32]  P M VanRaden,et al.  Rapid inversion of dominance relationship matrices for noninbred populations by including sire by dam subclass effects. , 1991, Journal of dairy science.

[33]  E. B. Burnside,et al.  Additive and dominance genetic variation for dairy production traits under an animal model , 1991 .

[34]  B. Charlesworth,et al.  Unravelling the Evolutionary Advantage of Sex : a Commentary on ' Mutation–selection Balance and the Evolutionary Advantage of Sex and Recombination ' , 2022 .

[35]  A Mäki-Tanila,et al.  Genotypic covariance matrices and their inverses for models allowing dominance and inbreeding , 1990, Genetics Selection Evolution.

[36]  C. Goodnight.  EPISTASIS AND THE EFFECT OF FOUNDER EVENTS ON THE ADDITIVE GENETIC VARIANCE , 1988, Evolution; international journal of organic evolution.

[37]  C. Cockerham,et al.  Permanency of response to selection for quantitative characters in finite populations. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[38]  C. R. Henderson.  Applications of linear models in animal breeding , 1984 .

[39]  M. Kimura,et al.  An introduction to population genetics theory , 1971 .

[40]  R. A. Fisher,et al.  The Genetical Theory of Natural Selection , 1931 .

[41]  Sewall Wright,et al.  Fisher's Theory of Dominance , 1929, The American Naturalist.

[42]  W. E. Ritter.  AS TO THE CAUSES OF EVOLUTION. , 1923, Science.