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

[Marc Domènech Andreu]

Hello,
Thanks for the tip. I tried that in several species and it looks like it
does have an effect. The values with pairwise.deletion=TRUE are most of the
times a bit higher than with pairwise.deletion=FALSE, and sometimes equal.
Would you suggest using pairwise.deletion=TRUE then?
I also tried to find if the very negative values in AMOVA results (like
-0,25) were due to very low values of genetic distances, but there doesn't
seem to be a relation.
Thanks for your help,
Marc

On Thu, May 7, 2020 at 5:53 AM Emmanuel Paradis <emmanuel.paradis using ird.fr>
wrote:

> To see if this has an impact, you can do this:
>
> d0 <- dist.dna(x, "N")
> d1 <- dist.dna(x, "N", pairwise.deletion = TRUE)
> plot(d0, d1)
> abline(0, 1, lty = 3) # draw x = y line
>
> Best,
>
> Emmanuel
>
> ----- Le 6 Mai 20, à 21:35, Marc Domènech Andreu <mdomenan using gmail.com> a
> écrit :
>
> 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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>>> >> R-sig-genetics using r-project.org
>>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
>>> >>
>>> >
>>> >
>>> > --
>>> > *Marc Domènech Andreu*
>>> > PhD student at University of Barcelona.
>>> > Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals.
>>> >
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>>> >
>>> > _______________________________________________
>>> > R-sig-genetics mailing list
>>> > R-sig-genetics using r-project.org
>>> > https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
>>>
>>
>>
>> --
>> *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.
>
>

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

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