Through sophisticated statistical analyses and advanced computer simulations, researchers are learning more about the genomic patterns of human population structure around the world.
Revealing such patterns provides insights into the history of human evolution, the predominant evolutionary forces that shaped local populations, and the relationships among populations.
"Studying genomic patterns of human population structure also has practical applications in disease-gene mapping," noted Dr. Joshua M. Akey, University of Washington (UW) assistant professor of genome sciences. Akey is senior author of new genomic research findings about the fine-scale structure of diverse human populations. The results will be published May 15 in the American Journal of Human Genetics. The lead authors were Shameek Biswas and Dr. Laura B. Scheinfeldt, both of the UW Department of Genome Sciences.
A statistical method called principle component analysis allows researchers to look through a thick, voluminous fog of genetic data and see significant variations. The UW researchers applied this method to a data set of almost 650,000 SNPs (pronounced "snips").
A single nucleotide polymorphism is a genetic variation in which the DNA code differs by only one "letter" in the same DNA sequence from two individuals of the same species. The data set of 650,000 SNPs came from 944 unrelated persons representing 52 broadly classified populations living in several regions on seven continental groups: Africa, America, Central and South East Asia, East Asia, Europe, Middle East, and Oceania. This global sampling came from The Human Genome Diversity Project - Center for the Study of Human Polymorphisms
Most previous genomic studies of this nature have focused on broad-scale patterns of structure among geographically diverse populations, the UW researchers noted. These studies concluded that 85 to 95 percent of human genetic variation can be attributed to differences among individuals, and 5 to 15 percent is due to differences between populations.
In contrast to these broad-scale patterns, more recently researchers have tried to look at fine-scale population structure. Usually these studies focus on only the two or three top- ranking axes of genetic variation emerging from the statistical analysis. For example, studies of European individuals have shown a strong correlation between the top two axes of genetic variation and the actual geographical location of the sampling.
In their newly published findings, UW researchers demonstrated that substantial information on population structure is hidden more deeply in the genomic data. They were able to identify 18 significant, informative axes of variation. Some of these distinguished particular populations.
The UW researchers also conservatively estimated the set of all of the SNPs, or specific, tiny DNA code differences, matching each of the most informative axes of variation. These variations represent numerous fixed positions on the human genome where different biomarkers can sit and thereby form a "genomic signature" of population structure. They also allow for more detailed inferences, the UW researchers noted, about the evolutionary forces that shape the fine-scaled patterns of human population structure.
"The genome-wide distribution of these markers," Akey believes, "can largely be accounted for by genetic drift." Genetic drift is gradual accumulation of random changes in the gene pool of small populations. Akey added that some of these variations, however, do cluster in regions of the human genome considered to be targets of recent adaptive evolution.
The researchers also observed patterns of human genetic variation that correlated with geography in essentially every continental group. While such geographical patterns have been described in European samples, the researchers think that the extent to which such geographic correlations might be found in other continents may not be fully appreciated.
In mentioning the limitations of his study approach, Akey cautioned that there are still questions about the best way to design human population genetics research in terms of sampling individuals and populations, but that progress is likely.
"Now that we have increasingly dense catalogs of genetic variation," Akey wrote, "the details of human population structure are becoming more tractable. The testing of increasingly refined hypotheses about human population structure should yield new insights into the history and relationships among human genomes."
Funding from the National Institutes of Health, a Sloan Research Fellowship in Computational Biology, and a National Human Genome Research Institute Interdisciplinary Training in Genomic Sciences grant supported this Akey laboratory research project.
Leila Gray | EurekAlert!
The importance of biodiversity in forests could increase due to climate change
17.11.2017 | Deutsches Zentrum für integrative Biodiversitätsforschung (iDiv) Halle-Jena-Leipzig
Win-win strategies for climate and food security
02.10.2017 | International Institute for Applied Systems Analysis (IIASA)
The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.
Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....
The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.
Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...
Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.
That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...
Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.
During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....
The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.
Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...
15.11.2017 | Event News
15.11.2017 | Event News
30.10.2017 | Event News
21.11.2017 | Physics and Astronomy
21.11.2017 | Physics and Astronomy
21.11.2017 | Life Sciences