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Genomics In The Journals: Aug 25, 2011

NEW YORK (GenomeWeb News) – In Nature Communications, an international research group describes how it used ancient DNA to explore the lack of genetic diversity found in modern stallions. The researchers used Roche 454 GS FLX sequencing to sequence about 4,000 bases on the horse Y chromosome using ancient DNA from eight wild horse samples found in Siberia and North America estimated to be between 15,000 and 47,000 years old and from a 2,800-year-old domesticated horse sample. By comparing these sequences with Y chromosome data on dozens of modern horses from 15 domestic breeds and a single living wild horse population, the researchers concluded that the lack of genetic diversity in stallions is likely a long-term consequence of domestication, since wild horse samples displayed significant genetic diversity on the Y chromosome.

"We found substantial genetic diversity among ancient horse Y chromosomal sequences, demonstrating that wild horses exhibited Y chromosomal diversity before domestication," senior author Michael Hofreiter, from the Max Planck Institute for Evolutionary Anthropology and the University of York, and co-authors wrote.

Using Y chromosome data for men from the R-M269 haplogroup, the major Y chromosome haplogroup in Europe, researchers found genetic patterns hinting that European men are descended from early hunter-gatherer groups on the continent rather than from farming populations moving into the area from the Near East, as recently proposed. As they report in Proceedings of the Royal Society, the team analyzed data on more than 4,500 R-M269 Y chromosomes from men sampled throughout Europe and in western Asia and the Near East. The group said the frequency distribution and variation patterns for the Y chromosome markers they assessed do not support a model in which the main European Y chromosome lineage was introduced by farming populations from the east.

A University of Oxford-led team reports in Neuron that it has come up with a transcriptomic atlas for six layers of the neocortical region of the mouse brain. Based on their RNA-sequencing data, generated with the Illumina GAIIx, the researchers found 66 non-coding RNA sequences and more than 5,800 protein-coding genes showing different expression patterns depending on the brain layer tested. The gene expression resource is expected to serve as a resource for a wide range of future studies including comparisons involving humans and other primates.

"Knowing the detailed pattern of expression of all genes in the cortex and how this fits into the overall brain architecture will help us understand how genes act together to sustain the cells and circuits that underlie behavior and disease," lead author T. Grant Belgard of the University of Oxford and the National Human Genome Institute, said in a statement.

A study in the early, online edition of Science suggests the human immune system contains genetic contributions from archaic humans. An international team looked at patterns for a highly variable group of genes in the human leukocyte antigen class I region in the Denisovan and Neandertal genomes, comparing these with HLA class I patterns in modern human populations sampled through the HapMap project. The team found that many HLA class I variants, including HLA-B*73 and HLA-A*11, apparently entered the human genome through breeding between modern and archaic humans outside of Africa.

"Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations," corresponding author Peter Parham, a structural biology, microbiology, and immunology researcher at Stanford University, and co-authors wrote. "These alleles … now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.