I am working on conservation genetics of some alpine medicinal plants. I have used some dominant markers and co-dominant markers. I am unable to construct network tree by using Splitstree.
Can anybody please help me to construct the input matrix for "Splitstree" or "Neighbournet" using binary data matrix (1,0).
Hi
You can get binary data, such as for dominant markers like AFLP, into splitstree using this format
#NEXUS
BEGIN Taxa;
[&&SPECTRONET SN_BLOCKNAME Taxa_2]
DIMENSIONS NTAX=4;
TAXLABELS tax1 tax2 tax3 tax4;
END;
BEGIN Characters;
[&&SPECTRONET SN_BLOCKNAME Characters_1]
DIMENSIONS NCHAR=10;
FORMAT DATATYPE=STANDARD GAP=- SYMBOLS = "012345";
MATRIX
tax1 01010 01010
tax2 11001 00101
tax3 01110 11001
tax4 10101 10101;
END;
For co-dominant markers, you can code the data as binary data by recording the presence/absence of each allele - but this is not a particularly good approach. If you want to combine dominant and co-dominant markers together it will function.
For co-dominant markers alone, it is generally better to use a population genetic software package to generate a distance matrix for the samples/populations and then get that into Splitstree using the format you can find in the examples folder supplied with the software in the file south.nex. Be careful to use an appropriate genetic distance measure in your population genetic software! My experience would suggest being very wary of models that do not treat all alleles as equally related. Typically the Nei (1972) model is a good start.
I might have the wrong end of the stick here, but Splitstree (at least in my experience) doesn't understand what a dominant or codominant marker is - it just makes a network based on distances between taxa.
Are you hoping to convey something of meaning with regard to dominant or codominant traits using this network? It's a little difficult to understand what you are trying to achieve here.
Further, can you give an example of what you mean by a binary data matrix in this context? The input file for Splitstree is usually an alignment file of some kind.
Hi
You can get binary data, such as for dominant markers like AFLP, into splitstree using this format
#NEXUS
BEGIN Taxa;
[&&SPECTRONET SN_BLOCKNAME Taxa_2]
DIMENSIONS NTAX=4;
TAXLABELS tax1 tax2 tax3 tax4;
END;
BEGIN Characters;
[&&SPECTRONET SN_BLOCKNAME Characters_1]
DIMENSIONS NCHAR=10;
FORMAT DATATYPE=STANDARD GAP=- SYMBOLS = "012345";
MATRIX
tax1 01010 01010
tax2 11001 00101
tax3 01110 11001
tax4 10101 10101;
END;
For co-dominant markers, you can code the data as binary data by recording the presence/absence of each allele - but this is not a particularly good approach. If you want to combine dominant and co-dominant markers together it will function.
For co-dominant markers alone, it is generally better to use a population genetic software package to generate a distance matrix for the samples/populations and then get that into Splitstree using the format you can find in the examples folder supplied with the software in the file south.nex. Be careful to use an appropriate genetic distance measure in your population genetic software! My experience would suggest being very wary of models that do not treat all alleles as equally related. Typically the Nei (1972) model is a good start.
Oops, I meant to delete the text in square brackets in my earlier post, that is not required.
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