lizard recomb rate estimate

[andrewkern]

recombination rate estimate for AnoCar from a linkage map for the common lizard, Zootoca vivipara, from this paper: https://doi.org/10.1093/gbe/evaa161

closes #1365

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[petrelharp]

Hm - what do you think about this estimate, actually from Anolis carolinensis? This paper says it's 0.52e-8 based on

which comes from this paper; however, the latter paper points out it's just in a male, and females often have higher recombination rates?

[andrewkern]

I prefer the linkage map data I found above for a few reasons, I think.

Linkage map data is still the gold standard for estimating genome-wide rates for our uses I reckon, as they incorporate recombination in a number of individuals over generations. The immuno-histological / microscopy approach of the original paper here is good and I know people have shown they are correlated with linkage maps, but I get nervous about a sample of N=2 males (for instance we know the female map will be longer).

OTOH the paper I found was a different species, but their linkage map was really dense and sampling seems excellent - 205 half-sib progeny collected from 20 wild caught dams.

[petrelharp]

Hm - I still would guess the rougher estimate from the taxon in question is probably closer to the truth than this estimate (which differs threefold) in distant species? True that we expect females to be higher, but judging from the 'common lizard', not a ton higher (nothing approaching threefold).

[andrewkern]

that's fine by me- we can use this other estimate if you prefer