Population genomics

Population genomics is the large-scale comparison of DNA sequences of populations. Population genomics is a neologism that is associated with population genetics. Population genomics studies genome wide effects to improve our understanding of microevolution so that we may learn the phylogenetic history and demography of a population.

Population genomics has been of interest to scientists since Darwin. Some of the first methods used for studying genetic variability at multiple loci included gel electrophoresis and restriction enzyme mapping. Previously genomics was restricted to only the study of a low amount of loci. However recent advancements in sequencing and computer storage and power have allowed for the study of hundreds of thousands of loci from populations. Analysis of this data requires identification of non-neutral or outlier loci that indicate selection in that region of the genome. This will allow the researcher to remove these loci to study genome wide effects or to focus on these loci if they are of interest.

In the study of S. pombe (more commonly known as fission yeast), a popular model organism, population genomics has been used to understand the reason for the phenotypic variation within a species. However, since the genetic variation within this species was previously poorly understood due to technological restrictions, population genomics allows us to learn about the species' genetic differences. In the human population, population genomics has been used to study the genetic change since humans began to migrate away from Africa approximately 50,000-100,000 years ago. It has been shown that not only were genes related to fertility and reproduction highly selected for, but also that the further humans moved away from Africa, the greater the presence of lactase.

A 2007 study done by Begun et al. compared the whole genome sequence of multiple lines of Drosophila simulans to the assembly of D. melanogaster and D. yakuba. This was done by aligning DNA from whole genome shotgun sequences of D. simulans to a standard reference sequence before carrying out whole genome analysis of polymorphism and divergence. This revealed a large number of proteins that had experienced directional selection. They discovered previously unknown, large scale fluctuations in both polymorphism and divergence along chromosome arms. They found that the X chromosome had faster divergence and significantly less polymorphism than previously expected. They also found regions of the genome (e.g. UTRs) that signaled adaptive evolution.

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