Description
- 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