Rabbit genome: domestication via soft sweeps

Written by: Stephen Hsu

Primary Source: Information Processing

white bunny

Domestication — genetic change in response to a drastic change in environment — happened via allele frequency changes at many loci. I expect a similar pattern in humans due to, e.g., agriculture.

I don’t know why some researchers find this result surprising — it seemed quite likely to me that “adaptation to domestication” is a complex trait controlled by many loci. Hence a shift in the phenotype is likely to be accomplished through frequency changes at many alleles.

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication (Science DOI: 10.1126/science.1253714)

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

From the paper:

… directional selection events associated with rabbit domestication are consistent with polygenic and soft sweep modes of selection (18) that primarily acted on standing genetic variation in regulatory regions of the genome. This stands in contrast with breed-specific traits in many domesticated animals that often show a simple genetic basis with complete fixation of causative alleles (19). Our finding that many genes affecting brain and neuronal development have been targeted during rabbit domestication is fully consistent with the view that the most critical phenotypic changes during the initial steps of animal domestication probably involved behavioral traits that allowed animals to tolerate humans and the environment humans offered. On the basis of these observations, we propose that the reason for the paucity of specific fixed domestication genes in animals is that no single genetic change is either necessary or sufficient for domestication. Because of the complex genetic background for tame behavior, we propose that domestic animals evolved by means of many mutations of small effect, rather than by critical changes at only a few domestication loci.

I’ll repeat again that simply changing a few hundred allele frequencies in humans could make us much much smarter …

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Stephen Hsu
Stephen Hsu is vice president for Research and Graduate Studies at Michigan State University. He also serves as scientific adviser to BGI (formerly Beijing Genomics Institute) and as a member of its Cognitive Genomics Lab. Hsu’s primary work has been in applications of quantum field theory, particularly to problems in quantum chromodynamics, dark energy, black holes, entropy bounds, and particle physics beyond the standard model. He has also made contributions to genomics and bioinformatics, the theory of modern finance, and in encryption and information security. Founder of two Silicon Valley companies—SafeWeb, a pioneer in SSL VPN (Secure Sockets Layer Virtual Private Networks) appliances, which was acquired by Symantec in 2003, and Robot Genius Inc., which developed anti-malware technologies—Hsu has given invited research seminars and colloquia at leading research universities and laboratories around the world.
Stephen Hsu

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