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vanOosterhoutLab / HybridCheck

HybridCheck, an R package for quickly scripting scans of sequence data for recombination regions.
http://vanOosterhoutLab.github.io/HybridCheck/
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How to read dating results？ #30

Open BioGeorge opened 4 years ago

BioGeorge commented 4 years ago

Hi, I followed your manual in R and get the dating results. But when I look into the results, there are three types of age, 0.05_Age, 0.5_Age and 0.95_Age. I've read your paper and learned about the function of age inferring. But sorry for my lack knowledge of mathematics, I am still confused about the 5-95%CI and median results of dating. Why do we need these three types of age?

Besides, does the Age mean generations or years? And how can I figure out the speciation time and coalescence time to prove the introgression?

Thanks in advance and wish you all the best.

TransGirlCodes commented 4 years ago

Hi @BioGeorge The three values define the 95% CI of the age estimate, so the true value of the age is expected to lie somewhere in that range. The age is in terms of generations. To demonstrate a block detected by HybridCheck is the result of introgression using the dates you can use either known speciation dates from the literature, and point out how early that block of sequence coalesces vs that time, or sometimes I calculate the average coalescence time for the entire chromosome/genome and use that as a comparison. To make conversions to years, again in projects we've used HybridCheck for in the past, we've used known generation times from the literature to make our estimates in terms of real-time like years.