Population Genomics
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Population genomics is the large-scale comparison of
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
sequences of populations. Population genomics is a
neologism In linguistics, a neologism (; also known as a coinage) is any newly formed word, term, or phrase that has achieved popular or institutional recognition and is becoming accepted into mainstream language. Most definitively, a word can be considered ...
that is associated with
population genetics Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...
. Population genomics studies
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
-wide effects to improve our understanding of
microevolution Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection ( natural and artificial), gene flow and genetic drift. This change happens over ...
so that we may learn the
phylogenetic In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...
history and
demography Demography () is the statistical study of human populations: their size, composition (e.g., ethnic group, age), and how they change through the interplay of fertility (births), mortality (deaths), and migration. Demographic analysis examine ...
of a population.Luikart, G.; England, P. R.; Tallmon, D.; Jordan S.; Taberlet P. (2003). "The Power and Promise of Population Genomics: From Genotyping to Genome Typing". ''Nature Reviews'' (4): 981-994


History

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 Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...
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.


Research applications

In the study of ''
Schizosaccharomyces pombe ''Schizosaccharomyces pombe'', also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically meas ...
'' (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 ''Drosophila simulans'' is a species of fly closely related to '' D. melanogaster'', belonging to the same ''melanogaster'' species subgroup. Its closest relatives are ''D. mauritiana'' and ''D. sechellia''. Taxonomy This species was discover ...
'' 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. In 2014 Jacquot ''et al.'' studied the diversification and epidemiology of endemic bacterial pathogens by using the ''
Borrelia burgdorferi ''Borrelia burgdorferi'' is a bacterial species of the spirochete class in the genus '' Borrelia'', and is one of the causative agents of Lyme disease in humans. Along with a few similar genospecies, some of which also cause Lyme disease, it m ...
'' species complex (the bacteria responsible for Lyme disease) as a model. They also wished to compare the genetic structure between ''B. burgdorferi'' and the closely related species '' B. garinii'' and '' B. afzelii''. They began by sequencing samples from a culture and then mapping the raw read onto reference sequences. SNP based and phylogenetic analyses were used on both intraspecific and interspecific levels. When looking at the degree of genetic isolation, they found that intraspecific recombination rate was ~50 times higher than the interspecific rate. They also found that by using most of the genome conspecific strains didn’t cluster in clades, raising questions about previous strategies used when investigating pathogen epidemiology. Moore ''et al'' conducted a study in 2014 in which a group of
Atlantic Salmon The Atlantic salmon (''Salmo salar'') is a species of ray-finned fish in the family Salmonidae. It is the third largest of the Salmonidae, behind Hucho taimen, Siberian taimen and Pacific Chinook salmon, growing up to a meter in length. Atlan ...
populations which were previously analyzed with traditional population genetic analyses ( microsatellites, SNP-array genotyping, BayeScan (which uses the Dirichlet-multinomial distribution)) to place them into defined conservational units. This genomic assessment mostly agreed with previous results, but did identify more differences between regionally and genetically discrete groups, suggesting there were potentially even greater number of conservation units of salmon in those regions. These results verified the usefulness of genome-wide analysis in order to improve the accuracy of future designation of conservation units. In highly migratory marine species, traditional population genetic analyses often fail to identify population structure. In tunas, traditional markers such as short-range PCR products, microsatellites and SNP-arrays have struggled to distinguish
fish stocks Fish stocks are population, subpopulations of a particular species of fish, for which intrinsic parameters (growth, recruitment, mortality and fishing mortality) are traditionally regarded as the significant factors determining the Population ...
from separate ocean basins. However, population genomic research using RAD sequencing in
yellowfin tuna The yellowfin tuna (''Thunnus albacares'') is a species of tuna found in pelagic waters of tropical and subtropical oceans worldwide. Yellowfin is often marketed as ahi, from the Hawaiian , a name also used there for the closely related bigeye ...
and albacore has been able to distinguish populations from different ocean basins and reveal fine-scale population structure. These studies identify putatively adaptive loci that reveal strong population structure, even though these sites represent a relatively small proportion of the overall DNA sequence data. In contrast, the majority of sequenced loci that are presumed to be selectively neutral do not reveal patterns of population differentiation, matching results for traditional DNA markers. The same pattern of putatively adaptive loci and RAD sequencing revealing population structure, compared to limited insight provided by traditional DNA markers is also observed for other marine fishes, including striped marlin and lingcod.


Mathematical models

Understanding and analyzing the vast data that comes from population genomics studies requires various mathematical models. One method of analyzing this vast data is through QTL mapping. QTL mapping has been used to help find the genes that are responsible for adaptive phenotypes. To quantify the genetic diversity within a population a value known as the
fixation index The fixation index (FST) is a measure of population differentiation due to genetic structure. It is frequently estimated from Polymorphism (biology), genetic polymorphism data, such as single-nucleotide polymorphisms (SNP) or Microsatellite (genet ...
, or FST is used. When used with Tajima's D, FST has been used to show how selection acts upon a population. The McDonald–Kreitman test (or MK test) is also favored when looking for selection because it is not as sensitive to changes in a species' demography that would throw off other selection tests.


Future developments

Most developments within population genomics have to do with increases in the sequencing technology. For example, restriction-site associated DNA sequencing, or RADSeq is a relatively new technology that sequences at a lower complexity and delivers higher resolution at a reasonable cost. High-throughput sequencing technologies are also a rapidly growing field that allows for more information to be gathered on genomic divergence during speciation. High-throughput sequencing is also very useful for SNP detection, which plays a key role in personalized medicine. Another relatively new approach is reduced-representation library (RRL) sequencing which discovers and genotypes SNPs and also doesn't require reference genomes.


See also

* Cognitive genomics * Landscape genomics * Personal genomics * Population groups in biomedicine * Sociogenomics


Notes


External links


Population Genomics
from ''Nature Education''
The Simple Fool’s Guide to Population Genomics via RNA-Seq

Drosophila Population Genomics Project


References


Population genomics: a bridge from evolutionary history to genetic medicine
*
The Power and Promise of Population Genomics: From Genotyping to Genome Typing
* {{Population genetics Genomics Population genetics