Anthropology.net

Two similar papers published the latest issues of Nature and Genome Research do high-resolution analyses of the structure of the human genome. They differ in methodology, but have some cool conclusions. The Nature paper, “Mapping and sequencing of structural variation from eight human genomes,” created libraries of 4 African, 2 Asian, and 2 European genomes. From these libraries they created thousands of clones to figure out if there are structural variations in genomes of these eight individuals from diverse geographic ancestry.

The Genome Research paper, “Scanning the human genome at kilobase resolution,” used ditag genome scanning (DGS) to analyze the human genome in high resolution. This method is really similar to serial analysis of gene expression (SAGE), in that genome is fragmented, each tag is ligated with a marker, and a sequencing technique (454 in this particular study) is used ultimately to determine the origin of the fragment in genome. The authors of this paper report that their method was strong enough to provides a kilobase resolution for studying genome structure. DGS is also highly specific and can cover a lot of the genome. Downstream applications of DGS are to validate assembled genomes but also to compare genome similarity and variation in normal populations.

Both methods are able to identify genomic abnormalities like insertions, inversions, deletions, and translocations, much better than current technologies. But why is this all important to anthropology? The Nature paper shows how they were able to find 525 new insertion sequences that are not present in the human reference genome. These new insertion sequences are shown to be variable in copy number between individuals, which ultimately make for 525 new ancestry inherited markers. Furthermore, when the authors of the Nature paper sequenced their clones they were able to find an additional 261 structural variants which reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome.

One last point, most ancestry inherited markers have been SNPs, but more recent research on the human genome has shown, however, that larger-scale differences like the copy number variations (CNVs) and others screened in these two papers, may account for a great deal of genetic variation among individuals.

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Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F., Haugen, E., Zerr, T., Yamada, N.A., Tsang, P., Newman, T.L., Tüzün, E., Cheng, Z., Ebling, H.M., Tusneem, N., David, R., Gillett, W., Phelps, K.A., Weaver, M., Saranga, D., Brand, A., Tao, W., Gustafson, E., McKernan, K., Chen, L., Malig, M., Smith, J.D., Korn, J.M., McCarroll, S.A., Altshuler, D.A., Peiffer, D.A., Dorschner, M., Stamatoyannopoulos, J., Schwartz, D., Nickerson, D.A., Mullikin, J.C., Wilson, R.K., Bruhn, L., Olson, M.V., Kaul, R., Smith, D.R., Eichler, E.E. (2008). Mapping and sequencing of structural variation from eight human genomes. Nature, 453(7191), 56-64. DOI: 10.1038/nature06862

Chen, J., Kim, Y.C., Jung, Y., Xuan, Z., Dworkin, G., Zhang, Y., Zhang, M.Q., Wang, S.M. (2008). Scanning the human genome at kilobase resolution. Genome Research DOI: 10.1101/gr.068304.107

Robert Stainton at the University of Western Ontario and Jessica de Villiers of The University of British Columbia have recently conducted a study which aims to measure and define pragmatic capabilities of autism patients, specifically those with Autism Spectrum Disorder, or ASD. Previously, one of the defining features of ASD patients was the deficiency or absence of pragmatic systems, particularly the ability to understand and use language appropriately by societal standards. ASD interferes with the ability to utilize language in practice, interfering with systems such as Entailment, Deixis, Implicature, and Presupposition. As a result, ASD patients have difficulty understanding sarcasm, irony, and abstract language.

According to Stainton, some ASD patients have shown no difficulty in understanding and using literal pragmatic systems, such as reference to specific media in nondescript terms. Although these patients are unable to grasp abstract systems such as metaphors, they show potential in literal pragmatics.

These researchers do not contest the well-established claim that people with ASD have difficulty with non-literal pragmatics, such as metaphors (“Juliet is the sun”) or irony/sarcasm (“Boy, is that a good idea”). They have, however, found that many speakers with ASD do not show the same difficulty with literal pragmatics. An example is the phrase, “I took the subway north” from a transcript of a conversation with a research participant with ASD. The use of the word “the” could indicate there is only one subway in existence going north. “The subway” could also be referring to a subway car, a subway system or a subway tunnel. Taking account of the context and the listener’s expectations, however, the individual using the phrase was able to convey the specific meaning he intended. That is, he used pragmatics effectively.

As autism is one of the most difficult neurological disorders to understand, Stainton’s research provides an important benchmark to its scientific comprehension. The breakthrough in noting ASD patient understanding of literal pragmatics has lead to the development of a rating scale of pragmatic abilities which can be used for clinical assessment. Considering the mysterious nature of autism, multidiciplanary approaches such as Stainton’s may become the standard for research in the field.