I am not a biology student and therefore, need clarification if crossover rate and recombination rate are the same thing. So if the text says 'recombination rate per base pair per generation' or 'cross over rate per locus per generation', is it the same thing? And if not then what is the difference? Also, is 'per base pair' and 'per locus' the same thing?
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Let's start with the second question.
Is 'per base pair' and 'per locus' the same thing?
No, not necessarily. A locus (plur. loci) is a location in the genome. It can be of any size. A locus can be a single base pair or it can be 10 base pairs, or a whole gene or anything you want.
'recombination rate per base pair per generation' or 'cross over rate per locus per generation', is it the same thing?
Recombination rate and crossover rate are not exactly the same thing!
Let's define two loci. Here is a drawing of two haplotypes (the maternal one and the paternal one). Let's represent the loci on the maternal haplotype with capitalized letters and the loci on the paternal haplotype with lower case letters
---A---------B---
---a---------b---
Let's Let's say that between these two loci there are on average 0.2 crossover per reproduction. The crossover rate is therefore 0.2.
Let's draw the two haplotypes after crossover(s) in a case with...
... 0 crossover
---A---------B---
---a---------b---
... 1 crossover
---A---------b---
---a---------B---
... 2 crossovers
---A---------B---
---a---------b---
... 3 crossovers
---A---------b---
---a---------B---
... 4 crossovers
---A---------B---
---a---------b---
You might see a pattern here! If the number of crossovers is even (including 0), then the association between the two loci is unchanged. If the number of crossovers is odd (including 1), then the association between the two loci is changed.
The recombination rate is the rate at which the association between the two loci is changed. Let $P(n)$, be the probability that there are $n$ crossovers between our two loci. The recombination rate is therefore $P(1) + P(3) + P(5) + P(7) + P(9) + P(11) + ...$.
To make a long story short, the recombination rate is the rate at which the number of crossovers is odd.
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$\begingroup$ Thank you for such a detailed answer. It makes a lot more sense now. $\endgroup$ Jan 15, 2019 at 12:00