Add Bos Indicus and Taurus model from Rossi et al. (2024)

[gregorgorjanc]

• Name: Bos Indicus and Bos Taurus
• Common name: Indian (humped) cattle and European (non-humped) cattle

Description:

We already have a Bos Taurus species and one specific breed model https://github.com/popsim-consortium/stdpopsim/tree/main/stdpopsim/catalog/BosTau, but the recent study by Rossi et al. (2024) has added considerable knowledge about the history of the modern cattle (Bos Taurus and Bos Indicus):

The genomic natural history of the aurochs
https://www.nature.com/articles/s41586-024-08112-6

I am about to e-mail authors for specific data used …

any other discussion or useful background? (optional)

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 - available in the current implementation and the above citation
• [] "default" population size - available in the current implementation and the above citation

Chromosome structure:

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

• [] ensembl assembly ID or, if the assembly is not in Ensembl, a list of chromosomes with name and length (in bp) available in the current implementation and the above citation

Recombination rates:

• [] genetic map of recombination rates (as a hapmap or csv file) - TODO
• [] genome-wide mean recombination rate (which will be used as the default) - available in the current implementation and the above citation

Mutation rate:

• [] genome-wide mean mutation rate - available in the current implementation and the above citation

Demographic model:

• [] as a list of population sizes, growth rates, migration rates, etcetera. (optional) - available in the current implementation and the above citation

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): simple since cattle are mammals
• [] ploidy: 2