It is not yet 7 a.m. and I’ve already been flooded with hot new anthropology related publications. There are so many that I don’t know where to start. I’ve got papers on human genetic variation and human genome evolution, comparisons of human versus Neandertal dental development, and the lack of archaeological evidence during mega droughts in Africa. I’ll start on the human genetic variation and genome evolution papers in this post. If I find more time, we’ll talk about the dental anthropolog and the archeology paper later today.
First things first, a couple weeks ago an interesting paper was published in Science, “Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome,” which announced a new technique to study the differences between the structures in the human genome. The authors found out that the number of structural variations among genomes of the humans they sampled is much larger than initially hypothesized. The authors extended the hypothesis that structural variations do far more to human genetic variation and diversity than single nucleotide polymorphisms. The pressed loved this. They went crazy over it, but that hypothesis isn’t breaking news. Actually in February 2006, Nature Reviews Genetics, ran this paper, “Structural variation in the human genome,” where they wrote,
“The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term ‘structural variation’ in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants — collectively termed copy-number variants or copy-number polymorphisms — as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.”
That being said Nature Genetics published a paper two days ago, “Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution,” which studies these structural variations in a evolutionary context. Specifically they asked which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates? The authors were able to figure out the ancestral origin of more than two thirds of these long DNA duplications.
The authors figure that specific regions of the human genome experienced elevated rates of duplication activity at different times in our recent genomic history. This contrasts with most models of genomic duplication which suggest a continuous model for recent duplications. They also figure that a large fraction of the recent duplication architecture centers around a rather small subset of “core duplicons” — short segments of DNA that come together to form segmental duplications. These cores are focal points of human gene/transcript innovations. They found 14 different duplicons where not all of the duplications in the human genome were selected equally.
Which leads me to these two papers from Human Molecular Genetics, “Challenges in human genetic diversity: demographic history and adaptation,” and “The genetic architecture of normal variation in human pigmentation: an evolutionary perspective and model.” The first of these two is an open access paper which investigates the causality of demographic history, and selective effects on human genetic diversity. The authors investigate the role of pathogen, climatic, dietary and cognitive genetic adaptation, on human genetic diversity. Maybe those 14 duplicons I mentioned above are areas where the genome responds to these external elements?
And last but not least, in the pursuit of understanding why we’re so different in skin color comes the second, closed access publication, where the authors,
“review recent progress in identifying the genes controlling this variation with a particular focus on the trait’s evolutionary past and the potential role of testing for signatures of selection in aiding the discovery of functionally important genes.”
Unlike the author two papers which studied big changes, big structural variations, these guys analyzed SNP data from the International HapMap project. They took 77 pigmentation candidate genes and built a three-population model (West Africa, East Asia and North Europe) to screen out the evolutionary–genetic architecture of human pigmentation. The results suggest a complex evolutionary history, with selection acting on different gene targets at different times and places in the human past. Some of the candidate genes may have been selected in the ancestral human population, others in the ‘out of Africa’ proto European-Asian population, whereas most appear to have selectively evolved solely in either Europeans or East Asians separately despite the pigmentation similarities between these two populations.
The conclude that selection signatures can provide important clues to aid gene discovery. The big but is that these should be viewed as complements, rather than replacements of, functional studies including linkage and association analyses, which can directly refine our understanding of the trait.
Anyways I gotta get ready for my day.