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

[Emmanuel Paradis]

Hi Marc,

Have you tried model = "N" in dist.dna()?

Best,

Emmanuel

----- Le 4 Mai 20, à 16:44, Marc Domènech Andreu mdomenan using gmail.com a écrit :

> 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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