threespine stickleback - Githubissues

Stickle-Back-in-Time commented 3 years ago

Name: Gasterosteus aculeatus
Common name: Threespine stickleback

Demographic information:

[] 2 years (Liu et al. Mol Ecol doi: 10.1111/mec.13827)
[] 10000 (Liu et al. Mol Ecol doi: 10.1111/mec.13827, estimate for marine populations)

Chromosome structure: name length (Mb) Chr1 29.62 Chr2 23.69 Chr3 17.76 Chr4 34.18 Chr5 15.55 Chr6 18.83 Chr7 30.78 Chr8 20.55 Chr9 20.84 Chr10 17.99 Chr11 17.65 Chr12 20.69 Chr13 20.75 Chr14 16.15 Chr15 17.32 Chr16 19.51 Chr17 20.20 Chr18 15.94 Chr19 20.58 Chr20 20.45 Chr21 17.42 ChrY 15.86

[] ensembl assembly ID or, if the assembly is not in Ensembl, a list of chromosomes with name and length (in bp) https://www.ncbi.nlm.nih.gov/genome/146 Ensembl assembly is old Broad assembly from 2012 and is not chromosomal. Note: species in Ensembl can be found in one of these lists: vertebrates, "metazoa", plants, fungi, protists, or bacteria.

Recombination rates:

[3.11 cM/Mb] genome-wide mean recombination rate (which will be used as the default) Roesti et al. doi: 10.1111/mec.12322

Mutation rate:

[3.7 × 10−8 substitutions/nucleotide/generation] genome-wide mean mutation rate (Liu et al. Mol Ecol doi: 10.1111/mec.13827)

Demographic model:

[] as a list of population sizes, growth rates, migration rates, etcetera. (optional)
[] 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)
[] ploidy

jeromekelleher commented 3 years ago

@Stickle-Back-in-Time we just added support for pulling this information from NCBI. You can run it like this:

$ python3 -m maintenance add-species-ncbi 9307941

grahamgower commented 2 years ago

Stickleback is in!

Stickle-Back-in-Time commented 2 years ago

Thanks Graham!!

From: Graham Gower @.> Sent: 18 May 2022 16:30 To: popsim-consortium/stdpopsim @.> Cc: Andrew Foote @.>; Mention @.> Subject: Re: [popsim-consortium/stdpopsim] threespine stickleback (#819)

Stickleback is in!

— Reply to this email directly, view it on GitHubhttps://github.com/popsim-consortium/stdpopsim/issues/819#issuecomment-1130092680, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AP4ZGE43WX4CVCN6RP4NOXLVKT5IFANCNFSM4Z37QWWA. You are receiving this because you were mentioned.Message ID: @.***>

popsim-consortium / stdpopsim

threespine stickleback #819