This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nu...

The egg-recognition processes underlying egg rejection are assumed to be based on an imprinting-like process (a female learning the aspect of her own eggs during her first breeding attempt). The imprinting-like process and the misimprinting costs have been the objective of many theoretical models and frequently have a leading role in papers published on brood parasitism; however, an experiment ...

Plant breeding is a key mechanism for adaptation of cropping systems to climate change. Much discussion of breeding for climate change focuses on genes with large effects on heat and drought tolerance, but phenology and stress tolerance are highly polygenic. Adaptation will therefore mainly result from continually adjusting allele frequencies at many loci through rapid-cycle breeding that deliv...

The objective of the breeding herd is the predictable and consistent production of high quality pigs. To achieve this objective, an appropriate number of females need to be mated in each breeding week and they should maintain their pregnancy and deliver large litters. Many factors can impact achievement of optimal sow productivity, particularly breeding management. Most matings will involve art...

This article presents a holistic framework for understanding the science of plant breeding, as an alternative to the common objectivist and constructivist approaches in studies of science. It applies this approach to understanding disagreements about how to deal with yield stability. Two contrasting definitions of yield stability are described, and concomitant differences in the understanding a...

Commercial plant breeders improve economically important traits by selectively mating individuals from a given breeding population. Potential pairings are evaluated before the growing season using Monte Carlo simulation, and a mating design is created to allocate a fixed breeding budget across the parent pairs to achieve desired population outcomes. We introduce a novel objective function for t...

Intuition is a poor guide for evaluating the effects of human disturbance on wildlife. Using the endangered Yellow-eyed penguin, Megadyptes antipodes, as an example, we show that heart rate responses provide an objective tool to evaluate human disturbance stimuli and encourage the wider use of this simple and low-impact approach. Yellow-eyed penguins are a flagship species for New Zealand's wil...

BACKGROUND Cavalier King Charles Spaniels (CKCS) are predisposed to myxomatous mitral valve disease (MMVD). Studies have indicated a strong genetic background. OBJECTIVE The aim of this study was to evaluate the effect of a breeding scheme involving auscultation and echocardiography. ANIMALS In the Danish Kennel Club mandatory breeding scheme, 997 purebred CKCS were examined during the peri...

An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. E...