Starbeast3 with phased nuclear and mitochondrial dna

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Dylan O'Hearn

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Nov 14, 2022, 6:58:51 PM11/14/22
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Hello,

I'm currently phasing diploid nuclear sequences to be used in Starbeast3, and will probably be combining them with mtdna also.  Am I correct that, after phasing, nuclear loci should have their ploidy set to 1 while mtdna should stay at 0.5? 

Dylan

Alexei Drummond

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Nov 16, 2022, 4:02:24 PM11/16/22
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I believe that If you are including both parental copies (or one from a random parent) of the diploid sequences in your analysis then the total population of such sequences is 4 times that of the mitochondrial genome. The mitochondrial genome only has one copy that can be transmitted from half the population (1*0.5 = 0.5), whereas nuclear genes have two possible copies that can be transmitted from every individual (2*1 = 2).

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