title: Comparing alternative definitions of the contemporary group effect in Avilena Negra Iberica beef cattle using classical and Bayesian criteria.
abstract: Data on weaning weight from 12,740 animals were used to compare different definitions of contemporary groups (CG) for the genetic evaluation of the Avilena Negra Iberica beef cattle breed. Six alternative definitions for the CG effect were considered: herd-year-season of calving (HYS), with seasons defined according to the four natural seasons; herd-year-month of calving (HYM); herd clusters of 30 d (HC30-30) or 90 d (HC90-90); and adaptive herd clusters with two time limits, 30 and 90 d (HC30-90), and 30 and 180 d (HC30-180). A minimum of five observations in each CG class was required. This rendered substantial differences in loss of information, ranging from 0.7% of the total number of records for HC30-180 to 14% for HYM. Several classical statistics and Bayesian criteria for statistical model comparison were used. The use of classical criteria, such as the between- and within-CG variation and the accuracy of prediction, can be controversial because of their dependency on the unknown variance components. Residual variance decreased with the decrease in time span associated with the definition of CG. This was expected in this population because environmental conditions are highly variable throughout the year. However, estimates of the additive genetic variance for direct effects, which should not be affected by the definition of CG, were substantially larger for definitions involving larger time periods (HYS, HC90-90). When parameters used in the current evaluation procedure were used with all data sets, CG involving 30 d (HYM and HC30-30) were optimal in terms of providing the lowest/largest within-/between-CG variation. On the other hand, CG involving 90 d (HYS and HC90-90) yielded the poorest within-/between CG variation, with only a slight improvement of accuracy of prediction of direct genetic values over the other definitions. Bayes factors and cross-validation predictive densities allowed for improved discrimination among models. Models including CG spanning 30 d were more plausible and showed better predicting ability than models spanning 90 d. Adaptive CG showed intermediate results. Overall, it seems that average time span rendered by the different definitions had a major effect on the ranking of models. However, from the breeder's point of view, the loss of information associated with definitions involving shorter periods of time, such as HYM or HC30-30, might be unacceptable.
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, Spain. mjc@inia.es
authors.forename: M J
authors.initials: MJ
authors.lastname: Carabaño
authors.forename: A
authors.initials: A
authors.lastname: Moreno
authors.forename: P
authors.initials: P
authors.lastname: López-Romero
authors.forename: C
authors.initials: C
authors.lastname: Díaz
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001835:Body Weight; D001947:Breeding; D002417:Cattle / Q000235:genetics* / Q000254:growth & development; D014644:Genetic Variation; D008957:Models, Genetic; D012621:Seasons; D014886:Weaning