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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
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Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.
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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Small population sizes put a species at extreme risk of extinction due to a lack of variation, and a consequent decrease in adaptability. This weakens the chances of survival under pressures such as climate change, competition from other species, or new diseases. Large populations are more likely to survive pressures such as these, as such populations are more likely to harbor individuals that have genetic variants that are adaptive under new stresses. Small populations are much less...
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Frequency and Distribution of Crossovers in Caenorhabditis elegans Meiosis by SNP Genotyping using Real-time PCR
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Exploring population size changes using SNP frequency spectra.

Xiaoming Liu1, Yun-Xin Fu2

  • 1Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA.

Nature Genetics
|April 8, 2015
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Summary
This summary is machine-generated.

We developed Stairway Plot, a novel method to infer population size changes over time using genetic data. This tool reveals historical human population fluctuations, particularly recent shifts, offering insights into demographic history.

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Area of Science:

  • Population Genetics
  • Genomics
  • Evolutionary Biology

Background:

  • Inferring demographic history is crucial in population genetics.
  • Existing methods often rely on simplified models, limiting exploratory analysis.

Purpose of the Study:

  • To develop a novel, model-flexible method for inferring population size changes over time.
  • To enable exploratory analysis of demographic history using genome-wide data.

Main Methods:

  • Developed the Stairway Plot method, which utilizes SNP frequency spectra.
  • Applied the method to whole-genome sequences from hundreds of individuals.
  • Validated using extensive simulations.

Main Results:

  • Stairway Plot effectively infers demographic history, especially recent population size changes.
  • Analysis of 1000 Genomes Project data revealed population fluctuations from 10,000 to 200,000 years ago.

Conclusions:

  • The Stairway Plot method provides a powerful tool for demographic inference.
  • The study highlights significant past fluctuations in human population sizes.