The following is an extract from an article by:Dr. Sara Via, PhD
Professor, University of Maryland. Owner, Meadowlark Farm Alpacas. IAC Genetics Editor

Problem: In order to breed alpacas with better and better fleece traits, we want to choose
superior alpacas for our herds. But how do we identify a “superior” alpaca? Genetic
superiority cannot be reliably estimated just by measuring an animal’s fleece traits or even
by pedigree!
• Measurements of an alpaca’s fleece do not reliably indicate the quality of its
progeny’s fleeces. This is because an animal’s phenotype (what it looks like) for a
given trait, such as its mean fiber diameter, is influenced not only by its genotype
(i.e. genes for fiber thickness that it passes on to progeny), but also by effects that
aspects of its environment (i.e. diet, stress etc.) may have on its fiber.
So, looking at an animal in a pasture, or tracking its success in the show ring is not
a foolproof method for picking good breeding stock. An animal that wins many
ribbons may not have progeny with equally wonderful fleece.
• How about knowing an animal’s pedigree? Again, this provides only a rough guide
to its possible value as a breeding animal. Only half of a famous alpaca’s genes
will be passed on to a son or daughter, and a famous grandparent’s genes only
make up 1/4 of an individuals genotype. Even with prepotent males, prediction of
the phenotype of progeny from pedigree information is not perfectly accurate
because of the unknown genetic influences from the other relatives.
• Together, using the phenotype and the pedigree only provide about 60%
accuracy in making breeding decisions. That means, 40% of the time, the
progeny won’t be what you expect if you limit yourself to these tools.
• To improve accuracy, we need an estimate of each individual’s genetic value for
the key fleece traits, and this cannot be obtained either by measurements of its
fleece or by its pedigree.

Dr Via's full article can be found here