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Acabei de aprender que em ovelhas, os cordeiros da mesma ninhada geralmente têm pais diferentes, se a ovelha acasalou com machos diferentes. Berry et al. (2020) analisaram rebanhos de ovelhas na Irlanda que usavam mais de um carneiro e:
Dos 539 pares de gêmeos incluídos na análise, 160 (ou seja, 30%) foram gerados por dois carneiros diferentes. Dos 137 conjuntos de trigêmeos incluídos na análise, 73 (ou seja, 53%) foram gerados por mais de um carneiro. Dos nove conjuntos de quádruplos, oito foram gerados por dois carneiros, com o lixo restante sendo monopaterno. A incidência geral de superfecundação heteropaterna entre ninhadas foi, portanto, de 35%. Dado que a incidência de nascimentos múltiplos nesses rebanhos foi de 65%, espera-se que a superfecundação heteropaterna seja relativamente comum em ovinos; isso é especialmente verdadeiro, pois todos, exceto dois dos ninhos, eram poligigóticos.
Eles descobriram isso analisando indivíduos genotipados em chips SNP com dezenas de milhares de SNPs, com cordeiros e genotipados em potencial, para que não haja muita incerteza na tarefa. Você não precisa de tantos marcadores genotipados para obter uma tarefa confiante e eles não têm tantos carneiros para escolher.
Vamos simular uma situação como esta: montamos uma população e um painel de marcadores para genotipagem, dividimos em ovelhas e carneiros e fizemos alguns cordeiros.
library(AlphaSimR) founderpopNow, if we have the genotypes of a lamb and its mother, how do we know the father? In this paper, they use exclusion methods: They compared the genotypes from the offspring with the parents and used inheritance rules to exclude rams that can't be the father because if they were, the offspring couldn't have the genotypes it had. Such breaking of regular inheritance patterns would be a "Mendelian inconsistency". This is the simplest kind of parentage assignment; fancier methods will calculate the probabilities of different genotypes, and allow you to reconstruct unknown relationships.
We can do this in two ways:
- ignore os genótipos da ovelha e procure homozigotos opostos entre cordeiro e carneiro, que são impossíveis independentemente do genótipo da mãe
- use os genótipos da ovelha e do carneiro para ver quais genótipos de cordeiro são possíveis a partir de um cruzamento entre eles; isso adiciona mais alguns casos em que podemos excluir um carneiro, mesmo que o cordeiro seja heterozigoto
Para fazer o primeiro, contamos o número de marcadores homozigotos opostos. Nesse código de genótipo, 0 e 2 são homozigotos e 1 é um marcador heterozigoto.
opposite_homozygotesWhen we include the ewe's genotype, there are a few more possible cases. We could enumerate all of them, but here is some R code to generate them. We first get all possible gametes from each parent, we combine the gametes in all possible combinations, and that gives us the possible lamb genotypes at that marker. If the lamb does, in fact, not have any of those genotypes, we declare the marker inconsistent. Repeat for all markers.
## Generate the possible gametes from a genotype possible_gametes(These functions assume that we have genotypes in vectors. The full code that extracts this information from the simulated data and repeats for all markers is on Gitbhub.)
Here is the outcome for a set of random lambs. The red dots point out the true fathers: because we have perfect genotype data simulated without errors, the true father always has 100% consistent markers.
If we compare how many markers are found inconsistent with the two methods, we get a pattern like this graph. Including the ewe’s genotypes lets us discover a lot more inconsistent markers, but in this case, with plentiful and error-free markers, it doesn’t make a difference.
If I have any complaint with the paper, it’s that the parentage analysis isn’t really described in the methods. This is what it says:
Parentage testing using simple exclusion‐based approaches is determined by the proportion of opposing homozygotes in putative sire–offspring pairs.
/…/
Maternal verification was undertaken using the exclusion method (Double et al . 1997) comparing the genotype of the dam with that of her putative progeny and only validated dam–offspring pairs were retained. Genotypes of the mature rams in the flock were compared with all lambs born in that flock using the exclusion method.
(The reference is related to exclusion methods, but it’s describing how to calculate exclusion probabilities in a certain circumstance. That is, it’s part of a methodological conversation about exclusion methods, but doesn’t actually describe what they did.)
I don’t doubt that they did it well. Still, it would be interesting to know the details, because in the absence of perfect genotype data, they must have had some thresholds for error and some criterion for deciding which ram was right, even if it seemed obvious.
Literature
Berry, D. P., et al. ”Heteropaternal superfecundation frequently occurs in multiple‐bearing mob‐mated sheep.” Animal Genetics (2020).
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