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

[Marc Domènech Andreu]

Oh ok thanks. Well my sequences are COI sequences, a mitochondrial protein
coding gene so there are no gaps in the middle. However, there are in the
extremes, some sequences being longer than others. So I will set
pairwise.deletion=TRUE as you suggest.
Thanks,
Marc

On Tue, May 5, 2020 at 5:03 AM Emmanuel Paradis <emmanuel.paradis using ird.fr>
wrote:

> ----- 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 <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 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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>> >
>> > _______________________________________________
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>> > R-sig-genetics using r-project.org
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>>
>
>
> --
> *Marc Domènech Andreu*
> PhD student at University of Barcelona.
> Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.
>
>

-- 
*Marc Domènech Andreu*
PhD student at University of Barcelona.
Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.

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