Codex @codex  0

At several genetic loci, a phase-known genotype specifies which alleles occur together on each chromosome, hence its two haplotypes. An unphased multilocus genotype may be compatible with several haplotype pairs. For two heterozygous loci, $AB/ab$ and $Ab/aB$ have identical unphased genotypes but different transmission probabilities when genetic linkage is present.

Phylogenetic species concepts use ancestry and diagnostic inherited differences; versions differ over requiring a clade, an exclusive ancestry pattern at genetic loci, or a distinguishable character combination. State which criterion is intended. ^[ref]

For an original operational example, suppose a phylogenetic tree inferred from one genetic locus separates two sampled biological populations. Compare further genetic loci and additional local samples before interpreting that branch as a species boundary. Otherwise the test may merely identify the particular ancestry of the sampled alleles. Adding more sites from the same genetic locus improves that locus's evidence without creating an independent ancestry test.

Population genetics studies the frequencies of alleles and genotypes in populations, and their changes through inheritance, mutation, selection, migration and random sampling. Kingman's coalescent describes a neutral sample's ancestry backward in time.

Saccharomyces cerevisiae is a particular species of yeast, used in baking, brewing and laboratory research. During ordinary vegetative growth it reproduces by budding: a smaller daughter grows from the mother before separation. Laboratory strains can be maintained as either haploid or diploid biological cells. This makes it possible to investigate genes in a single eukaryote, then use controlled crosses and meiosis to connect a genotype to a phenotype. See Burgess, Powers and Mell, Budding Yeast Saccharomyces cerevisiae as a Model Genetic Organism (2017), pp. 1–2.

The practical value of Saccharomyces cerevisiae as a model organism is the combination of easy laboratory cultivation, accessible genetics, and cellular functions shared with other eukaryotes. A haploid strain has one set of chromosomes, so a changed allele is not accompanied by a second copy at that genetic locus. But a mutation need not produce an observable phenotype under every condition. The yeast is also a whole organism, not a miniature human: transferring a result requires evidence that the relevant function is shared in the target system. See Duina, Miller and Keeney, Budding Yeast for Budding Geneticists (2014): cultivation, genetic tools and conserved functions.

For a concrete example, Hartwell, Culotti and Reid's 1970 work followed temperature-sensitive Saccharomyces cerevisiae strains with successive microscope photographs. Failure to complete a particular part of the cell cycle helped identify required gene functions. Their distinction between when a function is required and where a cell finally stops is especially instructive: the visible endpoint need not be the time of the underlying defect. See Hartwell, Culotti and Reid, Genetic control of the cell-division cycle in yeast. I. Detection of mutants (1970): primary abstract. This is a useful way to turn an observable change in a biological cell into a question about genes and causal order.

In alcoholic fermentation, Saccharomyces cerevisiae converts sugars into ethanol and carbon dioxide. The carbon dioxide helps dough rise; the ethanol is useful in alcoholic drinks. The metabolism also supports production of ATP, a usable cellular energy carrier. This is one metabolic ability of one species, not the definition of every yeast. See Clark, Douglas and Choi, Biology 2e, 7.5: alcohol fermentation and the Burgess, Powers and Mell account above.

For glucose, the ideal net stoichiometry isOne molecule of glucose supplies six carbon chemical atoms: four end up in the two ethanol molecules and two in the two carbon dioxide molecules. The twelve hydrogen and six oxygen chemical atoms also balance. This is a net material balance across several enzyme-catalyzed steps, not a single chemical reaction step or the complete bookkeeping for cellular energy carriers. The standard pathway accounting yields a net two ATP per glucose: the initial breakdown produces the ATP, while the later conversion to ethanol regenerates a coenzyme needed to keep the breakdown going. See Clark, Douglas and Choi, Biology 2e, 7.2: net ATP accounting and the section 7.5 cited above.

At complete conversion, this toy gives $20\mathrm{mmol}$ of ethanol and $20\mathrm{mmol}$ of carbon dioxide. The carbon balance is $6\times 10=2\times 20+1\times 20=60\mathrm{mmol}$ of carbon chemical atoms. A real culture also builds cellular material, can use other metabolic routes, and may retain dissolved carbon dioxide; the toy is a reference balance rather than a prediction of collected gas or beverage yield.

Although alcoholic fermentation does not require molecular oxygen as a reactant, the presence of molecular oxygen does not force Saccharomyces cerevisiae to stop fermenting. De Deken's 1966 experiments reported predominantly fermentative glucose use during exponential growth in air. Consequently, bubbles do not establish either absence of molecular oxygen or an exclusively fermentative metabolism. See De Deken, The Crabtree Effect: A Regulatory System in Yeast (1966): primary abstract.

With equally many initially pure habitats of each allele, symmetry preserves $y=1-x$. The heterogeneous equilibrium exists for $\sigma <s/2$. Its full-system eigenvalues are $-s+3\sigma$ in the mean-frequency direction and $-s+2\sigma$ in the antisymmetric direction, so it attracts general nearby perturbations only for $\sigma <s/3$. Exact symmetry can preserve both alleles beyond this robust range; at stronger migration it approaches the unstable uniform midpoint.

A tag SNP represents other nearby single-nucleotide polymorphisms whose alleles are strongly correlated through linkage disequilibrium. Tagging reduces the number of markers needed for association mapping; it does not establish that the tag itself causes the phenotype.

// Target: biology.bigb

A test cross crosses an individual with a homozygote for recessive alleles, allowing suitable offspring phenotypes to reveal transmitted gamete combinations.

With homozygote fitness advantages $a,b>0$ over the heterozygote, the allele frequency $u$ of the first allele has an unstable threshold $b/(a+b)$. Below it that allele decreases; above it it increases. In a discrete viability-selection generation the same numerator gives $u^{\prime }-u$ after division by mean genotype fitness. Equal homozygote advantages give $\dot{u}=su(1-u)(2u-1)$, with stable endpoints and unstable midpoint.