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AADavin / Zombi

Evolution simulator with extinct lineages

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Genome-wise rates

BenoitMorel opened this issue · comments

commented

Hello,

I have a question about duplication rates when generating genomes.
The wiki (here) says that

The rates are genome-wise. For instance, a duplication rate of 3 means 3 duplication events per genome per unit of time.

I am not sure how I should understand "genome" in this context. Is it the set of all genes from all all families for a given species at a given time? In practice:

  • Let's assume that I have 10 families, and a duplication rate of 3. Will I get on average 3 duplication events per unit of time per family, or 3 duplication events for the whole set of families?
  • Now if I have one family, and if after some time I have 5 genes in my genome (because I got 4 duplication events). Does a duplication rate of 3 mean that I will have 3 duplication event per unit of time per gene, or for the whole set of these 5 genes?

Also: your tool is super useful and easy to use, thanks a lot ;-)

Best,
Benoit

commented

Hello,

Let's assume that I have 10 families, and a duplication rate of 3. Will I get on average 3 duplication events per unit of time per family, or 3 duplication events for the whole set of families?

The 'genome' here represents the collection of gene families that have been simulated.
You will have a mean of 3 duplication events per unit of time for the complete genome.
For a fix rate, like Duplication, Transfers, Loss, ... whether you have 10 or 1000 gene families in your genome, you will always have the same mean number of events per unit of time across the GENOME.
The number of events is linked to the event rate and the length of your species tree (the number of units of time composing it) and not the number of gene families.

Now if I have one family, and if after some time I have 5 genes in my genome (because I got 4 duplication events). Does a duplication rate of 3 mean that I will have 3 duplication event per unit of time per gene, or for the whole set of these 5 genes?

I'm not sure I understand the question.
In Zombi duplication events don't generate new gene family. At the end of the genome simulation, if you choose to simulate a genome with only 1 family and with a duplication rate of 3, you will have, in this genome of 1 gene family, a mean of 3 events per unit of time.

Theo

commented

Hello Theo,

thanks a lot, you answered both the questions.

Benoit