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

[Emmanuel Paradis]

----- Le 5 Mai 20, à 0:36, Marc Domènech Andreu <mdomenan using gmail.com> a écrit : 

> Hi,
> Yes I tried it. Most of the results are very similar but some change. Do you
> know the difference between those two methods?

model = "N" is the Hamming distance (absolute number of differences between two sequences) 

model = "raw" is the Hamming distance divided by the sequence length (aka uncorrected distance, or p-distance) 

About the use of 'pairwise.deletion' in dist.dna(): in fact there is no simple/unique solution for this option. It depends very much on the data at hand and the distribution of "missing data", especially gaps. You need to check their distribution, for example with image(x) of image(x, what = "-") where 'x' is the DNA data. You may get nonsensical results leaving the default pairwise.deletion = FALSE if there are long gaps. Even a small number of gaps may be problematic if there are in a column (site) which is polymorphic. 

Best, 

Emmanuel 

> Thanks,
> Marc

> On Mon, May 4, 2020 at 2:44 PM Emmanuel Paradis < [
> mailto:emmanuel.paradis using ird.fr | emmanuel.paradis using ird.fr ] > wrote:

>> Hi Marc,

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

>> Best,

>> Emmanuel

>> ----- Le 4 Mai 20, à 16:44, Marc Domènech Andreu [ mailto:mdomenan using gmail.com |
>> 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 < [ mailto:zkamvar using gmail.com |
>> > 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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> --
> Marc Domènech Andreu
> PhD student at University of Barcelona.
> Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.

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