**GENEALOGY-DNA-L Archives**

From:"Ken Nordtvedt" <>Subject:Re: [DNA] Percentages of males and females who reproduce-compare to the "one third rule"Date:Sun, 14 Mar 2010 20:20:16 -0600References:<SNT115-W31A2CB4A7320E1EEF018E8CC2E0@phx.gbl>,<013e01cac3d5$9509ac90$5e82af48@Ken1><SNT115-W12454C9DC087C61A25CB31CC2E0@phx.gbl>----- Original Message -----

From: "Steven Bird" <>

If so, then you are also saying (and please correct me if I am mistaken)

that population history is irrelevant when calculating a coalescent? That

would suggest that the germ line mutation rate is in fact correct for

estimating the time to the coalescent and there is no need to be concerned

about reduced diversity due to founder's effects. This is assuming of

course that the germ line rate is in fact correctly estimated for each locus

of the Y.

>

>

>

> This is helpful, thanks for your response.

There are three kinds of variances floating around in in use by different

people.

1. Interclade variance between two separate clade haplotype sample

populations whose common ancestry is at an earlier node. (you will use this

interclade variance to estimate the age back to that early node ancestral to

both clades).

2. Variance of a clade sample population of haplotypes measured from

assumed founding haplotype.

3. Self variance (Coalescence) of a clade sample population of haplotypes.

The first two variances have expected values UNaffected by tree structure

(bottlenecks, subclades, variation of growth rate, etc). Those variance

expected values are only a function of generations to the TMRCA.

The third variance expected value is influenced by all the details of the

tree structure complications (bottlenecks, subclades, variation of growth

rate, etc), because it is an average of the haplotype pair-wise TMRCAs which

is necessarily less than the overall TMRCA. That's why special names of

coalescence age or expansion age are used for what it estimates; it is

something other than TMRCA.

The shape of the distribution of the variance values you will get for all

the three cases, this shape determining the statistical confidence interval

of the age estimates, is definately determined by the population history,

i.e. tree structure in all its gory details.

The final caveat is that you are always estimating the ages of the pruned

tree for the sample of the haplotypes you use. This is not the tree of the

whole population that was sampled. If one's sampling was of quality and

sufficient size, your estimated ages for the tree for the haplotype samples

will be close to the age for the tree of the whole population.

**This thread:**

- [DNA] Percentages of males and females who reproduce - compare tothe "one third rule" by Steven Bird <>
- Re: [DNA] Percentages of males and females who reproduce - compareto the "one third rule" by "Ken Nordtvedt" <>