Population genetics

The logarithm of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the product of the contributions from each of its loci.
Drosophila melanogaster
Gene flow is the transfer of alleles from one population to another population through immigration of individuals. In this example, one of the birds from population A immigrates to population B, which has fewer of the dominant alleles, and through mating incorporates its alleles into the other population.
The Great Wall of China is an obstacle to gene flow of some terrestrial species.
Current tree of life showing vertical and horizontal gene transfers.

Subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology.

- Population genetics
The logarithm of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the product of the contributions from each of its loci.

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Wright in 1954

Sewall Wright

American geneticist known for his influential work on evolutionary theory and also for his work on path analysis.

American geneticist known for his influential work on evolutionary theory and also for his work on path analysis.

Wright in 1954
Visualization of a fitness landscape. The X and Y axes represent continuous phenotypic traits, and the height at each point represents the corresponding organism's fitness. The arrows represent various mutational paths that the population could follow while evolving on the fitness landscape.

He was a founder of population genetics alongside Ronald Fisher and J. B. S. Haldane, which was a major step in the development of the modern synthesis combining genetics with evolution.

The logarithm of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the product of the contributions from each of its loci.

Linkage disequilibrium

The logarithm of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the product of the contributions from each of its loci.

In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population.

Fisher in 1913

Ronald Fisher

British polymath who was active as a mathematician, statistician, biologist, geneticist, and academic.

British polymath who was active as a mathematician, statistician, biologist, geneticist, and academic.

Fisher in 1913
As a child
Inverforth House, North End Way NW3, where Fisher lived from 1896 to 1904
On graduating from Cambridge University, 1912
The peacock tail in flight, the classic example of a Fisherian runaway
Rothamsted Research
Memorial plaque over his remains, lectern-side aisle of St Peter's Cathedral, Adelaide
Stained glass window (now removed) in the dining hall of Caius College, in Cambridge, commemorating Ronald Fisher and representing a Latin square, discussed by him in The Design of Experiments
As a steward at the First International Eugenics Conference, 1912

Together with J. B. S. Haldane and Sewall Wright, Fisher is known as one of the three principal founders of population genetics.

Gregor Mendel, the Moravian Augustinian monk who founded the modern science of genetics

Mendelian inheritance

Type of biological inheritance that follows the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 by Hugo de Vries and Carl Correns, and popularized by William Bateson.

Type of biological inheritance that follows the principles originally proposed by Gregor Mendel in 1865 and 1866, re-discovered in 1900 by Hugo de Vries and Carl Correns, and popularized by William Bateson.

Gregor Mendel, the Moravian Augustinian monk who founded the modern science of genetics
Characteristics Mendel used in his experiments
P-Generation and F1-Generation: The dominant allele for purple-red flower hides the phenotypic effect of the recessive allele for white flowers. F2-Generation: The recessive trait from the P-Generation phenotypically reappears in the individuals that are homozygous with the recessive genetic trait.
Myosotis: Colour and distribution of colours are inherited independently.
F1 generation: All individuals have the same genotype and same phenotype expressing the dominant trait ( red ).
F2 generation: The phenotypes in the second generation show a 3 : 1 ratio.
In the genotype 25 % are homozygous with the dominant trait, 50 % are heterozygous genetic carriers of the recessive trait, 25 % are homozygous with the recessive genetic trait and expressing the recessive character.
In Mirabilis jalapa and Antirrhinum majus are examples for intermediate inheritance. As seen in the F1-generation, heterozygous plants have " light pink " flowers—a mix of " red " and "white". The F2-generation shows a 1:2:1 ratio of red : light pink : white
A Punnett square for one of Mendel's pea plant experiments – self-fertilization of the F1 generation
Segregation and independent assortment are consistent with the chromosome theory of inheritance.
When the parents are homozygous for two different genetic traits (llSS and LL sP sP), their children in the F1 generation are heterozygous at both loci and only show the dominant phenotypes (Ll S sP). P-Generation: Each parent possesses one dominant and one recessive trait purebred (homozygous). In this example, solid coat color is indicated by S (dominant), Piebald spotting by sP (recessive), while fur length is indicated by L (short, dominant) or l (long, recessive). All individuals are equal in genotype and phenotype. In the F2 generation all combinations of coat color and fur length occur: 9 are short haired with solid colour, 3 are short haired with spotting, 3 are long haired with solid colour and 1 is long haired with spotting. The traits are inherited independently, so that new combinations can occur. Average number ratio of phenotypes 9:3:3:1
For example 3 pairs of homologous chromosomes allow 8 possible combinations, all equally likely to move into the gamete during meiosis. This is the main reason for independent assortment. The equation to determine the number of possible combinations given the number of homologous pairs = 2x (x = number of homologous pairs)

Ronald Fisher combined these ideas with the theory of natural selection in his 1930 book The Genetical Theory of Natural Selection, putting evolution onto a mathematical footing and forming the basis for population genetics within the modern evolutionary synthesis.

Figure A: Line graph example. The birth rate in Brazil (2010–2016); Figure B: Bar chart example. The birth rate in Brazil for the December months from 2010 to 2016; Figure C: Example of Box Plot: number of glycines in the proteome of eight different organisms (A-H); Figure D: Example of a scatter plot.

Biostatistics

Biostatistics (also known as biometry) are the development and application of statistical methods to a wide range of topics in biology.

Biostatistics (also known as biometry) are the development and application of statistical methods to a wide range of topics in biology.

Figure A: Line graph example. The birth rate in Brazil (2010–2016); Figure B: Bar chart example. The birth rate in Brazil for the December months from 2010 to 2016; Figure C: Example of Box Plot: number of glycines in the proteome of eight different organisms (A-H); Figure D: Example of a scatter plot.
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Scatter diagram that demonstrates the Pearson correlation for different values of ρ.

The three leading figures in the establishment of population genetics and this synthesis all relied on statistics and developed its use in biology.

Gene effects and Phenotype values.

Quantitative genetics

Quantitative genetics deals with phenotypes that vary continuously (in characters such as height or mass)—as opposed to discretely identifiable phenotypes and gene-products (such as eye-colour, or the presence of a particular biochemical).

Quantitative genetics deals with phenotypes that vary continuously (in characters such as height or mass)—as opposed to discretely identifiable phenotypes and gene-products (such as eye-colour, or the presence of a particular biochemical).

Gene effects and Phenotype values.
Analysis of Sexual reproduction.
Population mean across all values of p, for various d effects.
Genetic Drift example analysis.
Random fertilization compared to Cross-fertilization
Spatial fertilization patterns
Analysis of Allele Substitution
Components of Genotypic variance using the gene-model effects.
Components of Genotypic variance using the allele-substitution effects.
Connection between the inbreeding and co-ancestry coefficients.
Illustrative pedigree.
Cross-multiplication rules.
Inbreeding in sibling relationships
Inbreeding from Full-sib and Half-sib crossing, and from Selfing.
Self fertilization inbreeding
Pedigree analysis First cousins
Pedigree analysis Second cousins
Inbreeding from several levels of cousin crossing.
Pedigree analysis: Backcrossing
Backcrossing: basic inbreeding levels
Genetic advance and Selection pressure repeated
Changes arising from repeated selection
Selection differential and the Normal Distribution
Reproductive coefficients of determination and Inbreeding
Path analysis of sexual reproduction.
Sources of attribute correlation.

While population genetics can focus on particular genes and their subsequent metabolic products, quantitative genetics focuses more on the outward phenotypes, and makes summaries only of the underlying genetics.

An example of epistasis is the interaction between hair colour and baldness. A gene for total baldness would be epistatic to one for blond hair or red hair. The hair-colour genes are hypostatic to the baldness gene. The baldness phenotype supersedes genes for hair colour, and so the effects are non-additive.

Epistasis

Phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes.

Phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes.

An example of epistasis is the interaction between hair colour and baldness. A gene for total baldness would be epistatic to one for blond hair or red hair. The hair-colour genes are hypostatic to the baldness gene. The baldness phenotype supersedes genes for hair colour, and so the effects are non-additive.
Example of epistasis in coat colour genetics: If no pigments can be produced the other coat colour genes have no effect on the phenotype, no matter if they are dominant or if the individual is homozygous. Here the genotype "c c" for no pigmentation is epistatic over the other genes.
Quantitative trait values after two mutations either alone (Ab and aB) or in combination (AB). Bars contained in the grey box indicate the combined trait value under different circumstances of epistasis. Upper panel indicates epistasis between beneficial mutations (blue). Lower panel indicates epistasis between deleterious mutations (red).
Since, on average, mutations are deleterious, random mutations to an organism cause a decline in fitness. If all mutations are additive, fitness will fall proportionally to mutation number (black line). When deleterious mutations display negative (synergistic) epistasis, they are more deleterious in combination than individually and so fitness falls with the number of mutations at an increasing rate (upper, red line). When mutations display positive (antagonistic) epistasis, effects of mutations are less severe in combination than individually and so fitness falls at a decreasing rate (lower, blue line).
The top row indicates interactions between two genes that show either (a) additive effects, (b) positive epistasis or (c) reciprocal sign epistasis. Below are fitness landscapes which display greater and greater levels of global epistasis between large numbers of genes. Purely additive interactions lead to a single smooth peak (d); as increasing numbers of genes exhibit epistasis, the landscape becomes more rugged (e), and when all genes interact epistatically the landscape becomes so rugged that mutations have seemingly random effects (f).

Some introductory courses still teach population genetics this way.

Haldane in 1914

J. B. S. Haldane

British scientist who worked in physiology, genetics, evolutionary biology, and mathematics.

British scientist who worked in physiology, genetics, evolutionary biology, and mathematics.

Haldane in 1914
Marcello Siniscalco (standing) and Haldane in Andhra Pradesh, India, 1964
J.B.S. Haldane Avenue in Kolkata, the busy connecting road from Eastern Metropolitan Bypass to Park Circus area containing Science City
A Low cartoon featuring Haldane – "Prophesies for 1949"
Lysenko speaking at the Kremlin in 1935. Behind him are (left to right) Stanislav Kosior, Anastas Mikoyan, Andrei Andreev and Joseph Stalin.
Oxford University Museum of Natural History display dedicated to Haldane and his reply when asked to comment on the mind of the Creator.

Subsequent works established a unification of Mendelian genetics and Darwinian evolution by natural selection whilst laying the groundwork for modern evolutionary synthesis and thus helped to create population genetics.

Genetic diversity

Total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species.

Total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species.

A graphical representation of the typical human karyotype.
Varieties of maize in the office of the Russian plant geneticist Nikolai Vavilov
Photomontage of planktonic organisms.
A Tanzanian cheetah.

The academic field of population genetics includes several hypotheses and theories regarding genetic diversity.

Gene flow is the transfer of alleles from one population to another population through immigration of individuals.

Gene flow

Gene flow is the transfer of alleles from one population to another population through immigration of individuals.
Examples of speciation affecting gene flow.
Marine iguana of the Galapagos Islands evolved via allopatric speciation, through limited gene flow and geographic isolation.

In population genetics, gene flow (also known as gene migration or geneflow and allele flow) is the transfer of genetic material from one population to another.