December 22, 2005

Natural selection in the last 50,000 years

Gene Expression alerts me to a new paper on natural selection in Homo sapiens. Researchers have identified almost 2,000 genes which have been targeted by natural selection in modern humans of the last 50,000 years, i.e., since the emergence of behaviorally modern humanity and its spread around the world.

I will post more from the paper once it becomes "live". For the moment, from ScienceNow:
The genes belong to several biologically important categories, including genes important in defense against disease, controlling the cell cycle, protein metabolism, and nervous system functioning, the researchers report online this week in Proceedings of the National Academy of Sciences.
The New Scientist also covers this paper:
One way to look for genes that have recently been changed by natural selection is to study mutations called single-nucleotide polymorphisms (SNPs) – single-letter differences in the genetic code. The trick is to look for pairs of SNPs that occur together more often than would be expected from the chance genetic reshuffling that inevitably happens down the generations.

Such correlations are known as linkage disequilibrium, and can occur when natural selection favours a particular variant of a gene, causing the SNPs nearby to be selected as well.


Moyzis speculates that we may have similarly “domesticated” ourselves with the emergence of modern civilisation.

“One of the major things that has happened in the last 50,000 years is the development of culture,” he says. “By so radically and rapidly changing our environment through our culture, we’ve put new kinds of selection [pressures] on ourselves.”

Genes that aid protein metabolism – perhaps related to a change in diet with the dawn of agriculture – turn up unusually often in Moyzis’s list of recently selected genes. So do genes involved in resisting infections, which would be important in a species settling into more densely populated villages where diseases would spread more easily. Other selected genes include those involved in brain function, which could be important in the development of culture.
You might also want to read my older post on Human domestication reconsidered, which reports on anthropological changes which are also evidence of human domestication:
Helen Leach is proposing that the Late Pleistocene and early Holocene (archaeologically Neolithic) humans underwent changes similar to those of animals that underwent the domestication process. So, she argues that if we apply terminology consistently, we must also entertain the possibility that humans themselves are a domesticated species.


Here is the abstract and link to the open-access article. With "Darwinian" in the title and "Darwin's fingerprint" in one of the figures, I think that someone is having fun sticking it in to the creationism/ID crowd.

Proc. Natl. Acad. Sci. USA. (published online)

Global landscape of recent inferred Darwinian selection for Homo sapiens

Eric T. Wang et al.

By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The {approx}1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.

Link (open access)

No comments: