There are dark sheep and light sheep. The dark sheep are bigger, and bigger sheep tend to have higher fitness (survival and reproductive success)...but their frequency has gone down over the past 20 years. what gives? - their findings suggest "a negative genetic correlation between size and fitness in the vicinity of TYRP1" due to either pleiotropy or LD with surrounding loci for which they give some candidate genes that have been found to have the relevant effects in mice: neonatal size via VLDLR and "brown-associated fitness" via PTPRD. This gene, TYRP1, is very convenient for this study because it has been shown to control most of the variation in sheep coat color.
The implications here are important but, I think we also need to ask why we find the specific combinations of pleiotropic effects or the patterns of LD that we find. For example why is tameness apparently genetically linked to coat color in foxes (here, here)?
A Localized Negative Genetic Correlation Constrains Microevolution of Coat Color in Wild Sheep
J. Gratten, A. J. Wilson, A. F. McRae, D. Beraldi, P. M. Visscher, J. M. Pemberton, J. Slate
Science 18 January 2008: Vol. 319. no. 5861, pp. 318 - 320
The evolutionary changes that occur over a small number of generations in natural populations often run counter to what is expected on the basis of the heritability of traits and the selective forces acting upon them. In Soay sheep, dark coat color is associated with large size, which is heritable and positively correlated with fitness, yet the frequency of dark sheep has decreased. This unexpected microevolutionary trend is explained by genetic linkage between the causal mutation underlying the color polymorphism and quantitative trait loci with antagonistic effects on size and fitness. As a consequence, homozygous dark sheep are large, but have reduced fitness relative to phenotypically indistinguishable dark heterozygotes and light sheep. This result demonstrates the importance of understanding the genetic basis of fitness variation when making predictions about the microevolutionary consequences of selection.