What was the research project? hypothesis or discovery science?
Through carbon dating and genomic testing of a male femur found off of a river in Siberia, a team of scientists were able to uncover the oldest modern human outside of the Middle East and Africa to-date. The fossil was aptly named Ust'-Ishim after the location of his discovery. The Ust'-Ishim femur has increased our knowledge of human history by providing a unique genomic sequence that, when compared with both current and ancient human genomes, has provided new insights into early human migrations. This research was not conducted to test a hypothesis, but to analyze a piece of history that had been discovered.
What genomic technology was used in the project?
The first genomic technology used was Illumina HiSeq platform to sequence the DNA of Ust'-Ishim. After the Ust'-Ishim genome was sequenced, it was compared against other current genomes using the Human Reference Genome. The team of scientists were able to reaffirm the approximate age of Ust'-Ishims' bone by comparing his level of mutations with nine other ancient genomes. Principal Component Analysis was also used to compare the Ust'-Ishim genome with nearly 1,000 modern individual genotypes in varying populations. As visible in Figure 1 below, the Ust'-Ishim genotype is more similar to non-Africans than Africans. This result is further supported when the scientists performed D statistics to determine whether the Ust'-Ishim genome is closer in allele's to one population versus another. A Pairwise Sequentially Markovian Coalescent method was used to compare the Ust'-Ishim genome with 25 modern individuals to estimate previous changes in population size. Finally, a phlogeny was estimated to compare a section of the Ust'-Ishim Y-Chromosome to the same section on 23 modern male genomes to infer mutation rate differences.
What is the take home message?
Genomic comparison between Ust'-Ishim and modern day genomes lead to the conclusion that Ust'-Ishim was part of one of the early populations migrating out of Africa. Ust'-Ishim also had comparatively longer conserved DNA segments from Neanderthals than those of current human genomes. This indicates that Ust'-Ishim lived in a population close in time to an admixture of populations. Sequencing the Ust'-Ishum femur not only supported previous hypotheses about initial human migration and an "out of Africa model", but also provided researchers with a new and entirely unique population of human and therefor more information about the evolution of the human genome.
What is your evaluation of the project?
I thought the project was very thorough. I really liked how the scientists contributed a variety of calculations and methods to compare the Ust'-Ishim genome with modern humans. Not only did the scientists look for differences within genome populations, but they also analyzed mutation rates. Beyond general sequencing comparison of the Ust'-Ishim and current day genomes, the scientists compared Y-Chromosomes in male genomes to Ust'-Ishum which provides an entirely different aspect of comparison. I thought it was incredibly smart to carbon date the femur and then use this as a control when determining the age of the femur through genome analysis. The variety calculations conducted were incredibly well explained and very clear when visually assembled in figures. Although this was a discovery science and did not test a hypothesis, the amount of results and conclusions they were able to gain through comparing genomes was quite incredible. Not only is this discovery incredibly exciting for the age of the femur itself, but through genomic testing, our history as humans has become even more clear.
Fu, Qiaomei et. al.10/22/2014.Genome sequence of a 45,000-year-old modern human from western Siberia. Nature [Internet]. [cited 24 Jan 2016]. Available from: http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html#author-information
Callaway, Ewen. 10/22/2014. Oldest-known Human Genome Sequenced. Nature [Internet]. [cited 24 Jan 2016]. Available from: http://www.nature.com/news/oldest-known-human-genome-sequenced-1.16194