[R-sig-genetics] Pegas vs Arlequin, and negative AMOVA values

[Marc Domènech Andreu]

Thanks for your answer. For computing the distance matrix I am using the
dist.dna function in Ape package, with the model set to "raw"
and pairwise.deletion = FALSE. However I don't know exactly the equation or
formula pegas uses for AMOVA.
I am working with a mitochondrial marker so it would be haploid.
Marc

On Wed, Apr 29, 2020 at 5:26 PM Zhian N. Kamvar <zkamvar using gmail.com> wrote:

> This highly depends on the distance function you are using for pegas:
>
> 1. How does it treat missing data? I believe Arlequin treats missing
> data by dropping them from the denominator.
>
> 2. If you have a diploid species, does it calculate distance for
> haplotypes?
>
> Both of these can affect the resulting Phi values. You might also try
> poppr.amova() with the method = "pegas" function to automate the process.
>
> Best,
>
> Zhian
>
> On 4/29/20 3:04 AM, Marc Domènech Andreu wrote:
> > Hello everyone,
> > I would like to ask for help with two questions regarding AMOVA and the
> > Pegas package.
> > 1. Do you know which is the formula or equation that Pegas and Arlequin
> use
> > for performing AMOVA? I only get to obtain almost identical results when
> I
> > set "is.squared = FALSE" in pegas and "Locus by locus AMOVA" in Arlequin.
> > 2. I'm doing the analyses for several species, and for some of them I
> > obtained negative AMOVA results. I know slightly negative results are not
> > uncommon and as far as I know they should be treated as 0, but in some
> > cases they are very negative, such as -25%. Why can this be? Maybe
> because
> > I have too few sequences for those species?
> > Thanks in advance,
> > Marc
> >
>
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-- 
*Marc Domènech Andreu*
PhD student at University of Barcelona.
Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.

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