Almond Species

[jorgemasgomez]

• ** Prunus dulcis ** scientific name of the species
• Almond:

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:

• [10] generation time in years
• [200] "default" population size

Chromosome structure:

"assembly_accession": "GSE254853",
"assembly_name": "Texas v.3.0",
"chromosomes": {
    "1": {"length":50452767 , "synonyms": []},
    "2": {"length": 30972344, "synonyms": []},
    "3": {"length": 30498384, "synonyms": []},
    "4": {"length": 28068711, "synonyms": []},
    "5": {"length": 22241271, "synonyms": []},
    "6": {"length": 32371708, "synonyms": []},
    "7": {"length": 24859559, "synonyms": []},
    "8": {"length": 27108964, "synonyms": []},
    "MT": {"length": 444092, "synonyms": []},
    "Pt": {"length": 157783, "synonyms": []}

Recombination rates:

_recombination_rate = {"1": 1.97036e-8, "2": 1.51361e-8, "3": 1.886e-8,
"4": 2.22347e-8,
"5":2.54212e-8,
"6": 1.9829e-8,
"7": 2.61388e-8,
"8": 2.11591e-8,
"MT": 0,
"Pt": 0}

• [] genome-wide mean recombination rate (which will be used as the default)

Mutation rate:

genome-wide mean mutation rate:
_overall_rate = 10e-8 # per generation, from Velasco et al. 2016

Demographic model:

• [] as a list of population sizes, growth rates, migration rates, etcetera
  times = np.array(
  [14440, 22074, 26655, 29949, 32601, 34771, 36700, 38307, 41120, 43611, 45861, 47950, 49959, 51888]
  )
  sizes = np.array(
  [216523, 219758, 110605, 65380, 49918, 45483, 44353, 47616, 57496, 69583, 83878, 98724, 116879, 133409]
  )
• [] citation
  stdpopsim.Citation(
  author="Velasco et al.",
  year=2016,
  doi="https://doi.org/10.1534/g3.116.032672",
  reasons={stdpopsim.CiteReason.DEM_MODEL},

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)

Sex determination system: Hermaphroditic (no separate sex chromosomes)
Sex chromosome(s): None identified; no heteromorphic sex chromosomes in almond (Prunus dulcis)

• [diploid] ploidy

[gregorgorjanc]

PR for this implementation is at #1729

QC issue is at #1731

[gregorgorjanc]

Noticed this publication

Insights Into the Almond Domestication History https://doi.org/10.1111/eva.70150

They have a neat demographic model in Figure 4.

This work is based on 23 microsatelites tho.

@jorgemasgomez let's work on the Velasco et al. (2016) study for now