The reviewers describe some of the many techniques that are available for inferring details about the process of domestication--including measuring allele frequencies, looking for extended homozygous genomic regions, estimating ancestral population sizes and looking for bottlenecks, and identifying "introgression," or hybridization, between breeds.
(Female Belgian blue cow. These animals are so large that human intervention is often needed during the birthing process. This individuals bears the scars of a C-section that was required to remove her hefty calf.)
Animals raised for food products are often genetically manipulated to produce more food, sooner. Over the past 100 years, for instance, Belgian blue cattle (Bos taurus) have gone from "conventional" morphologies to a "double muscling" phenotype, which is now nearly fixed in the population. This was driven by selection on growth differentiation factor 8 (GDF-8), which impacts muscle conformation. During the 18th and 19th centuries, many British pig (Sus scrofa domesticus) farmers cross-bred their stock with Asian animals in order to introduce genes to increase fattening and speed up maturation. Asian traits can still be found today in breeds like the Berkshire and Middle White--the latter of which also bears the "squashed face" morphology of its Eastern ancestors.
Pigs are also a good example of another process that may occur once animals are domesticated--relaxation of selection pressures that were quite strong in the wild. Wild boar tend to have camouflaging coats, a result of "purifying selection" on the melanocortin 1 receptor (MC1R), which impacts coat color; animals whose pelts were too obvious often did not survive long enough to breed. Since domestic pigs don't need to hide, this pressure has been relaxed, paving the way for the variegated coats we see in many domestic pigs today. In China, however, pigs were exposed to a new selective pressure--one that produced a higher number of black-coated pigs, which were preferred for sacrificial purposes.
(Spotted pigs--common in domestication, rare in the wild)
Morphological changes may be both aesthetic and functional, as in the case of domestic dogs (Canis lupus familiaris). In a study of 79 dog breeds, for example, the genetic loci that had most obviously been manipulated during domestication were body size, skull and scout shape, coat characteristics, and ear type. Although some of these traits were doubtless deliberately shaped--for instance, in pursuit of a dog small enough to fit into a badger hole, or with jaws strong enough to win a fight against a bear--some of them were likely also side effects of selection for other traits. This has been one of the major discoveries of the Novosibirsk, Siberia "farm-fox" experiment, in which a population of wild foxes was selectively bred to produce increasingly tame animals. Although the experimenters only used behavioral characteristics to choose which animals they would breed to produce the next generation, they ended up with animals that were not only human-tolerant, but also displayed a number of other traits familiar from domestic dogs--tail wagging, licking, floppy ears, curly tails, and shortened snouts.
Indeed, studies in other animals have shown that behavioral and morphological traits are often linked, such that selection on the latter may influence the former, or vice versa. The PMEL17 gene, which encodes plumage color in chickens (Gallus gallus domesticus), is also associated with vocalizations, fear of humans, aggression, sociality, and exploratory behaviors. It is not yet clear whether these diverse traits co-exist because of pleiotropy, the process by which a single gene impacts multiple traits, or because genes for these characteristics are so closely positioned on chromosomes that they are inadvertently selected for en masse. It is known, however, that other suites of characteristics--including composite personality traits such as "playfulness," "curiosity," "sociability," and "aggressiveness"--have been very important in the formation of pet breeds; a study of 31 types of dog found that the most popular pets were those with higher sociability and playfulness scores.
By examining the genomes of domestic animals, researchers can also begin to get an idea of how large the animals' original populations were, how long ago they may have been domesticated, and whether current domestic selection pressures are sustainable. An investigation of domestic taurine cattle (B. taurus, or those without a hump) found that the animals have recently undergone a "severe" bottleneck--evidence of breed formation and modern husbandry techniques such as artificial insemination. In general, domestication has been associated with bottlenecks for many species; domestic dogs have gone through 2--the first during the initial domestication process, and the second during breed formation.
As a result, many of today's domesticated animals are lacking the genetic diversity possessed by their ancestors; some researchers have estimated that domestication has wiped out as many as 50% of the original alleles. Despite this, genetic variation is still higher in many domestics than you might guess. Cattle--especially Bos indicus breeds (those with a hump) have particularly high nucleotide diversity, as do pigs (probably because of sustained gene flow from wild boars). Domestic chickens are also quite diverse, thanks to their large and variegated ancestral population. A few breeds, though--Chillingham cattle and Cavalier King Charles Spaniels, for example--do suffer from homozygosity as a result of low initial population sizes, which caused inbreeding and, therefore, a higher incidence of inherited disease.
(A Cavalier King Charles Spaniel. Because of inbreeding, these animals are particularly susceptible to syringomyelia, a disorder in which a cyst or cavity forms in the spinal cord.)
Although modern techniques have provided a wealth of information about the process of domestication--and its genetic consequences--there are still some questions that remain unanswered. It can still be difficult to distinguish whether some genomic properties are a result of active selection (human or otherwise) or some other chance event in the environment that happened to impact the way in which animals bred with each other. Current techniques are inadequate for assaying the role of selection on quantitative traits such as milk yield. Perhaps most intriguingly, there are differences in fox and rat (Rattus norvegicus) genetic maps associated with tameness, suggesting that there are multiple evolutionary/genetic ways in which animals can be made tolerant of, and comfortable with, humans. By studying the process of domestication in other species, and mapping genes at multiple stages along the way, we can doubtless learn much more about this process by which we humans
have bent evolution to our will. This information can, in turn, be used to improve our husbandry practices, ensuring that we can maintain healthy and productive domestic stocks for years to come.
Wiener, P. and Wilkinson, S. 2011. Deciphering the genetic basis of animal domestication. Proceedings of the Royal Society B 278:3161-3170.
Thanks to the following websites for providing the images used in this post: