Gene linkage, in depth

A recurring Excellence "discuss" comparing how linked and unlinked genes behave differently during meiosis — genuinely different mechanisms, not a restatement of independent assortment.

The full comparison

UNLINKED genes sit on DIFFERENT chromosomes (or far apart on the same one), so INDEPENDENT ASSORTMENT during metaphase I randomly shuffles which allele of each gene ends up in each gamete — producing all four combinations roughly equally.
LINKED genes sit CLOSE TOGETHER on the SAME chromosome, so they tend to be inherited TOGETHER — the chromosome carrying them moves as one unit during independent assortment, meaning linked genes do NOT independently assort.
CROSSING OVER during prophase I can still separate linked genes occasionally, by physically swapping a segment of chromosome between homologous pairs — producing a small proportion of "recombinant" offspring that show a new combination.
The closer together two genes are on a chromosome, the LESS likely crossing over is to separate them — so linked genes deviate from the standard 9:3:3:1 dihybrid ratio, showing far more of the parental combinations and only a few recombinants.

Worked example Explaining a 7:1:1:7 ratio instead of 9:3:3:1 A dihybrid cross gives a 7:1:1:7 ratio instead of the expected 9:3:3:1. Explain why, using linked and unlinked genes. IDENTIFY: a ratio this skewed towards two large groups (7 and 7) and two small groups (1 and 1) indicates the two genes are LINKED on the same chromosome, not independently assorting. PARENTAL TYPES: the two large groups (7:7) are the "parental" combinations — the allele combinations that travelled together on the same chromosome from each parent, largely undisturbed. RECOMBINANT TYPES: the two small groups (1:1) are "recombinant" offspring, produced when CROSSING OVER in prophase I physically swapped a segment between the homologous chromosomes, separating the linked alleles in a minority of gametes. CONCLUSION: because crossing over is a physical, position-dependent event, it separates linked genes only OCCASIONALLY — which is exactly why parental types vastly outnumber recombinant types in the ratio. ✓ Naming BOTH why the majority follow the parental pattern (linkage) AND why a minority do not (crossing over) is what distinguishes an Excellence answer from a Merit one that explains only linkage. ✕

Saying linked genes "never" separate

Linked genes are inherited together MOST of the time, but crossing over can still separate them in a minority of gametes — describing linkage as absolute ("linked genes always inherit together") contradicts the very mechanism (crossing over) the question is usually also asking about.

Ratio pattern	What it tells you
9:3:3:1	Genes are unlinked — full independent assortment
Two large + two small groups (e.g. 7:1:1:7)	Genes are linked; large = parental, small = recombinant (crossing over)
Roughly equal parental/recombinant proportions	Genes are far apart on the same chromosome — crossing over happens often

Practice for this standard covers the whole topic — flashcards and quiz.