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template for requesting addition of a new species
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name: New species | ||
about: Adding a new species to the stdpopsim catalogue. | ||
title: | ||
labels: enhancement | ||
assignees: '' | ||
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--- | ||
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- **Name:** scientific name of the species | ||
- **Common name:** | ||
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**Description:** any other discussion or useful background? (optional) | ||
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*Note: Maybe you don't know a lot of the things below - but, that's OK! | ||
The criteria are that (a) the choice is reasonable, and (b) the rationale is clear. | ||
What we want is a "reasonable estimate" (or, "best guess") - if you were to use a number in a paper, | ||
what would you use and how would you justify it to your collaborators? | ||
For instance, for "generation time", best would be to cite a paper that actually measures | ||
or estimates generation time. But most species don't have this; | ||
next best would be to give a number used in the literature, and provide a citation that used it | ||
(and hopefully the publication gives a justification also). | ||
Lacking this, you might provide a number from a related species (and a citation for this).* | ||
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*Here is the checklist of things that we need to add a species to the catalogue. | ||
Each thing should be provided, with a justification (maybe short) and a citation.* | ||
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**Demographic information:** | ||
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- [] generation time in years | ||
- [] "default" population size | ||
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**Chromosome structure:** | ||
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- [] list of chromosomes with *name* and *length* (in bp) | ||
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**Recombination rates:** | ||
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- [] genetic map (as a .csv) of recombination rates **(optional)** | ||
- [] genome-wide mean recombination rate (which will be used as the default) | ||
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**Mutation rate:** | ||
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- [] genome-wide mean mutation rate | ||
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**Demographic model:** | ||
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- [] as a list of population sizes, growth rates, migration rates, etcetera. **(optional)** | ||
- [] citation | ||
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**Other information:** | ||
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These are things we don't currently use, but will want to use in the future: | ||
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- [] sex determination system, and which chromosomes are the sex chromosome(s) | ||
- [] ploidy |