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

[Emmanuel Paradis]

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 < [
> mailto:emmanuel.paradis using ird.fr | emmanuel.paradis using ird.fr ] > wrote:

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


>>>> >> _______________________________________________
>>>> >> R-sig-genetics mailing list
>>>> >> [ mailto:R-sig-genetics using r-project.org | R-sig-genetics using r-project.org ]
>>>>>> [ https://stat.ethz.ch/mailman/listinfo/r-sig-genetics |
>>>> >> 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.

>>>> > [[alternative HTML version deleted]]

>>>> > _______________________________________________
>>>> > R-sig-genetics mailing list
>>>> > [ mailto:R-sig-genetics using r-project.org | R-sig-genetics using r-project.org ]
>>>>> [ https://stat.ethz.ch/mailman/listinfo/r-sig-genetics |
>>>> > 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.

	[[alternative HTML version deleted]]