A new study published in the journal Nature Genetics revealed a novel population genetics model that could clarify the reason why the Finnish population has a genetic composition that differs from other European populations. The study is entitled “Exploring population size changes using SNP frequency spectra” and was performed by two researchers at the University of Texas Health Science Center at Houston (UTHealth).
Understanding demographic history is important in the context of population genetics. In order to study population genetics, researchers can either predefine a demographic model, suitable to test hypotheses, or set a model-flexible more suitable for exploratory analysis.
In the study, researchers developed a new model-flexible method called the stairway plot, capable of determining changes in population size over time by modeling the frequency of single nucleotide polymorphisms (SNPs; correspond to a difference in a single nucleotide in the DNA molecule) in the whole-genome sequence of hundreds of individuals. SNPs are the most common DNA variations in genomes.
The research team employed this new model in whole-genome sequence data of nine populations, including European, Asian and African ancestries, from the 1000 Genomes Project, a comprehensive detailed catalog on human genetic variation with samples from institutes around the world.
Through extensive simulation, researchers show that this is a valid method for inferring demographic history, particularly recent changes in population size. Researchers reported the finding of a pattern of fluctuations in human populations represented by bottlenecks, defined as a time period when the population size is significantly reduced and then recovers. The team found a previously unknown bottleneck that most likely occurred 10,000 to 20,000 years ago in the Finnish population but not in other European populations. After a bottleneck, the number of individuals is decreased and consequently, the population’s progeny have less genetic differences, as is the case of the population in Finland. Environmental factors, migration, disease and war can all cause bottleneck events, but the cause of this particular Finnish bottleneck is still unclear. The team also confirmed a previously reported bottleneck 100,000 to 200,000 years ago in the African population, which might be linked to the origin of modern humans.
“Inferring human history from population size is an important question in population genetics. There are some methods out there to determine population size, but this new model can provide a more detailed picture,” concluded the study’s lead author Dr. Xiaoming Liu in the news release.