Pan troglodytes

[xin-huang]

• Name: Pan troglodytes
• Common name: Chimpanzee

Description: any other discussion or useful background? (optional)

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).

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.

Demographic information:

• generation time in years: 25 (Langergraber et al. 2012)
• "default" population size: 15000 (de Manuel et al. 2016)

Chromosome structure:

Note: The assembly should be chromosome-level, i.e., not composed of thousands of scaffolds.

• ensembl assembly ID: Pan_tro_3.0

Note: species in Ensembl can be found in one of these lists: vertebrates, "metazoa", plants, fungi, protists, or bacteria.

Recombination rates:

• genetic map of recombination rates (as a hapmap or csv file): Auton et al. 2012
• genome-wide mean recombination rate (which will be used as the default): 0.7e-8 (Stevison et al. 2016)

Mutation rate:

• genome-wide mean mutation rate: 1.20e-8 (Kong et al. 2012)

Demographic model:

• as a list of population sizes, growth rates, migration rates, etcetera. (optional)
• citation:
  • de Manuel et al. 2016
  • Kuhlwilm et al. 2019

Other information:

These are things we don't currently use, but will want to use in the future:

• sex determination system, and which chromosomes are the sex chromosome(s): XY
• ploidy: diploid

[petrelharp]

Looks good - happy to look at a PR for it.

[grahamgower]

Pan troglodytes is in!