add sus scrofa #1312 #1672

AprilYUZhang · 2025-01-26T09:25:47Z

No description provided.

gregorgorjanc · 2025-01-27T16:18:29Z

I will work with @AprilYUZhang on revising this PR (for issue #1312) and the follow-up QC.

gregorgorjanc · 2025-01-27T16:23:54Z

stdpopsim/catalog/SusScr/species.py

+_ZhangEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1016/j.gpb.2022.02.001",
+    year=2022,
+    author="Mingpeng Zhang et al.",


Change to author="Zhang et al.",

gregorgorjanc · 2025-01-27T16:24:16Z

stdpopsim/catalog/SusScr/species.py

+_JohnssonEtAl = stdpopsim.Citation(
+    doi="https://doi.org/10.1186/s12711-021-00643-0",
+    year=2021,
+    author="Martin Johnsson et al.",


Change to author="Johnsson et al.",

gregorgorjanc · 2025-01-27T16:28:12Z

stdpopsim/catalog/SusScr/species.py

+    "16": 1.1407464686635653e-08,
+    "17": 1.3779949516098884e-08,
+    "18": 1.3679923888648167e-08,
+    "X": -1,


We should provide a value for X chromosome too. I appreciate that Johnsson et al. (2021) does not list X-chromosome recombination rate. Hence, I suggest that you calculate average recombination rate across other chromosomes (exclude Y and MT) and replace this for the X-chromosome rec rate value. Make this calculation clear in the code here.

gregorgorjanc · 2025-01-27T16:28:45Z

stdpopsim/catalog/SusScr/species.py

+    # citation is optional and can be deleted if not needed.]
+    citations=[
+        stdpopsim.Citation(
+            author="", year=-1, doi="", reasons={stdpopsim.CiteReason.ASSEMBLY}


@AprilYUZhang provide reference for the pig genome assembly that we use here

gregorgorjanc · 2025-01-27T16:29:34Z

stdpopsim/catalog/SusScr/species.py

+    common_name="Pig",
+    genome=_genome,
+    ploidy=2,
+    # The age at first pregnancy varies in the wild from about 10 to 20 months,


@AprilYUZhang cite the paper here in the comments and point to page/figure/table for there estimates

Sorry, I have no idea; this sentence is from the explanation of generation time. Should I write "the details see in _ZhangEtAl"?

Point to where in the paper is this detail, say page

gregorgorjanc · 2025-01-27T16:29:48Z

stdpopsim/catalog/SusScr/species.py

+    author="Martin Johnsson et al.",
+    reasons={stdpopsim.CiteReason.REC_RATE},
+)
+# [The following are notes for implementers and should be deleted


@AprilYUZhang cite the paper here in the comments and point to page/figure/table for there estimates

gregorgorjanc

@AprilYUZhang I left some comments for you to address. I will then have another look. Thanks for this addition to the stdpopsim catalogue!

gregorgorjanc · 2025-01-27T16:30:18Z

stdpopsim/catalog/SusScr/species.py

+    "MT": 0,
+}
+
+# the de novo mutation rate is inferred by Mingpeng Zhang et al 2022,


@AprilYUZhang point to page/figure/table for there estimates from Zhang et al

…us_scrofa pull remote, becase remote have been updated

codecov · 2025-02-05T18:26:28Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.85%. Comparing base (237d101) to head (65c07e7).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1672   +/-   ##
=======================================
  Coverage   99.85%   99.85%           
=======================================
  Files         136      139    +3     
  Lines        4690     4718   +28     
  Branches      470      470           
=======================================
+ Hits         4683     4711   +28     
  Misses          3        3           
  Partials        4        4

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gregorgorjanc · 2025-02-06T09:16:38Z

I advised @AprilYUZhang offline on this implementation, which is now very complete, and I volunteer to QC it.

I have a question though about recombination rate averaging. The information on the recombination rate for this species comes from a study with an extensive pedigree (so we deem it's very good) and the study reported the recombination rate per Mb of each autosome. To get a value for the X chromosome, @AprilYUZhang has:

summed these recombination rates per Mb for each chromosome and divided by the chromosome length, to get recombination rate per basepair for each autosome
calculated weighted average to get average recombination rate per basepair across the genome
used the value from 2) for the X chromosome.

I think this makes sense, but would like to hear from others here what you have done in such cases. I think that weighted average to represent the recombination rate per basepair for the genome is the right thing to do (average of ratios ...). But is this the right value to use for the X chromosome (in the absence of other information) or should one use the simple (unweighted) average. It's a minor detail, but I thought I would ask here.

Otherwise, I think this looks very good @AprilYUZhang and could soon be merged in by the maintainers. You will have to squash the commits before this happens though!

@AprilYUZhang is also looking at adding the recombination map and demographic models later.

petrelharp · 2025-02-06T13:18:45Z

Weighted average is consistent with what we do elsewhere - sounds good!

petrelharp · 2025-02-06T13:24:56Z

stdpopsim/catalog/SusScr/species.py

+    # which is roughly equivalent to the average age of
+    # the first pregnancy in sows and the beginning of rut in boars
+    # plus the pregnant gestation period of sows."
+    generation_time=3,


Hm - generation time isn't the average age of first pregnancy of an individual, it's the average age of a parent at time of birth of their child, i.e., the thing you'd get by picking a random individual and asking how old their parent was when they were born. For instance, human generation time is 25-30 years (estimates vary).

@petrelharp your are totally right, but this is verbatim text from the paper that we are following, so I guess we stick to their 3 years, which is an OK value.

Um, I guess? I mean, according to the stated rationale, that explanation is an underestimate, probably by a good factor, unless most pigs die after one litter.

This paper used 5 years, which the paper you're citing cites several other papers as using? Hm, that's "based on a studbook"; I wonder what the method is?

However, googling suggests that a mean life span is like 4-8 years; so 3 can't be too far off (maybe just a factor of 2). If you do want to use this one, then make sure you document that it is not the actual generation time.

@petrelharp you are completely right here! Darn, I should know this (generation interval is a key quantity in the breeder's equation) :( I guess I was too fixated on following the publication. Indeed, looking now at this, 3 years is indeed low. @AprilYUZhang best if you follow https://link.springer.com/article/10.1186/s12711-016-0204-2 for the generation interval statistic. This will be a "fun" discrepancy when dealing with demographic models:(

I wonder if part of the discrepancy is that for the breeder's equation the relevant "generation time" is "how fast can we get these pigs to breed" which is more like the minimum value, not the average-in-the-wild value?

No, your definition still stands! Generation interval is the average age of parents at the age of their progeny. Having said this, to increase response to selection, breeders aim to reduce this average by replacing parents as soon as possible.

petrelharp · 2025-02-06T13:26:29Z

Looks good! Just a thing about the generation time.

AprilYUZhang · 2025-02-10T10:07:12Z

Thank you for your suggestions @gregorgorjanc @petrelharp! I will follow these comments. I still have a question: do we need to change other parameters? Because now there are mainly two sets of pig demography paramsters. One is sourced from "Analyses of pig genomes provide insight into porcine demography and evolution" where the generation interval is 5 years and the mutation rate is $2.5 × 10^{-8}$. Another is "Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree" where the generation interval is 3 years and the mutation rate is $3.6 × 10^{-9}$. There is a quite big difference between these two papers.

petrelharp · 2025-02-10T20:33:34Z

That is a good question. I think that (a) for the "species" parameters, choose what you judge to be the "best". However, for just this sort of reason, demographic models can specify their own mutation rate (and I think generation time?) that overrides the species parameters, so things are self-consistent. If you run into problems, let me know?

gregorgorjanc · 2025-02-11T07:31:40Z

@AprilYUZhang That 2.5x10^-8 is from human studies (at least that's what https://pmc.ncbi.nlm.nih.gov/articles/PMC3566564/ and https://pmc.ncbi.nlm.nih.gov/articles/PMC4053821/ state, and https://link.springer.com/article/10.1186/s12711-016-0204-2 cites these two papers as a source).

The one you started with (3.6x10^-9) has an independent estimate from de-novo mutations in a pedigree, so it should be better, but it's an order of magnitude lower than the human one (which might be ok) and the recombination rate (which makes me wonder).

Annoyingly, this new demographic model preprint https://www.biorxiv.org/content/10.1101/2025.02.05.636574v1 also used 5 years for generation interval and 2.5x10^-8 mutation rate (citing https://link.springer.com/article/10.1186/s12711-016-0204-2), so these values keep propagating because everyone uses them:(

Chrissy has done work in this space (https://icqg6.org/wp-content/uploads/2020/11/ICQG6_2020_Abstract_Book.pdf#page=85, https://link.springer.com/article/10.1186/s12864-023-09296-3) so talk to her - she will be able to guide you to the best current estimate for mutation rate.

But for the generation interval, I do think that 3 years could indeed be low, particularly for a wild population, which would correspond to most of the period that we would simulate here! I reckon that 5 years is a better estimate, however I am now starting to wonder if the value of 5 is propagated through literature similarly as the human mutation rate!? Can you please check the average age at first litter for sows and for boars and their average lifespan and a reference that looked into this without plucking a value from the air?

AprilYUZhang added 2 commits January 26, 2025 09:24

add sus scrofa popsim-consortium#1312

9ddb015

update species file #popsim-consortium#1312

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gregorgorjanc reviewed Jan 27, 2025

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gregorgorjanc suggested changes Jan 27, 2025

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AprilYUZhang and others added 7 commits January 28, 2025 17:18

fix species file

d370206

update the describe of generation time

dea86c6

update the describe to add pages and tables in detail

b8c0d34

Merge branch 'popsim-consortium:main' into Sus_scrofa

3de5c62

rewrite species.py popsim-consortium#1312

9180b9d

Merge branch 'Sus_scrofa' of github.com:AprilYUZhang/stdpopsim into S…

072e4bf

…us_scrofa pull remote, becase remote have been updated

debug 'TestSpeciesData' object has no attribute 'genome'

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gregorgorjanc mentioned this pull request Feb 6, 2025

Add recombination map for SusScr (pig) #1677

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