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A phenotype is an observable characteristic of an organism, arising from its genotype, environment and other influences. Seed shape is a phenotype; $Aa$ is a genotype. The distinction prevents appearance from being mistaken for a complete inherited description. See NHGRI: phenotype.

For a specified binary phenotype $T$, let its penetrance in genotype $g$ be $r_g=P(T\mid g)$. The law of total probability gives $P(T)={\sum }_g{r}_{g}P(g)$. Thus the ideal $Aa\times Aa$ example has $P(T)=r_{AA}/4+r_{Aa}/2+r_{aa}/4$: the familiar $3/4$ follows only when these penetrances are $1,1,0$. A pedigree likelihood keeps inheritance and the conditional phenotype model as separate factors.

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.

For full siblings in an outbred pedigree, condition on both being affected under multiplicative diallelic penetrance and on residual disease outcomes being independent given their genotypes. The usual Mendelian IBD sharing of full siblings probabilities $(1/4,1/2,1/4)$ are weighted by $p^2{\alpha }^4,p^2{\alpha }^2\beta ,p^2{\beta }^2$, respectively, giving the displayed conditional sharing probabilities. Since $\beta -{\alpha }^2=\varphi (1-\varphi )(\theta -1{)}^2\ge 0$, $z_1\le 1/2$, strictly for a polymorphic locus with a nontrivial effect.

A species can encompass many biological populations. A biological population specifies a set of organisms in a place and time; a biological strain identifies a maintained variant or lineage, often in a laboratory. A species name, a local census and a biological strain designation therefore describe different things. Multiple independently maintained cultures can also share the same biological strain designation.

For example, a culture identified as Escherichia coli K-12 MG1655 specifies more than the species alone. Two flasks inoculated from that culture are separate experimental biological populations; the separate containers do not establish two species or two different biological strains. This is an original experimental bookkeeping example, not a claim that every biological strain name encodes a complete genotype.

A biological strain is a maintained variant or lineage within a species. Naming the species alone does not specify a laboratory genotype or its genetic background.