genetic destances

[Iliana Papantonaki]

hi all

i need to calculate mean intra- and inter- specific genetic distances for my sequences?

can anyone help me how to do it?

I have 88 sequences/7 species

thankss

[Koeng]

In what units? Base pairs? nm? Length hypothetically should be pretty easy.

Or do you mean sequence differences? Then just blast it.

-Koeng

[Iliana Papantonaki]

My teacher gave me a paper to use as guide and that says
"To estimate genetic distances, we selected the best fit model of evolution for each data set using JMODELTEST 0.1.1 (Guindon & Gascuel 2003; Posada 2008) with the Akaike Information Criterion (AIC; Akaike 1974). We calculated intra- and interspecific genetic distances using MEGA 4.0 (Tamura et al. 2007) for species that were represented by several individuals.
To assess the presence of barcoding gap (i.e. the gap between intra- and interspecific genetic variation), minimum interspecific distances were plotted against maximum intraspecific distances .
We also calcu-lated variability of each of the seven barcodes as the number and percentage of variable characters using MEGA 4.0."

[SC]

Hi Iliana,

 

I assume you want pairwise distances in order to make a phylogenetic tree.  Is that right?

Can you clarify:  you have 88 sequences for *each* of 7 species, or 88 sequences total that were taken from 7 species?

 

Stacy

[Iliana Papantonaki]

Hi Koeng
I hane a total of 88 sequences, that were taken from 7 species.

:)

[SC]

Emailing with Iliana, but I will also post here so others can find the information if they want to.

 

Iliana,

How many sequence types do you have that are common to all species?

 

You will have to align them.  You can do this either individually by sequence type, or make a concatamer.  I'd suggest you do both and see what the results look like.  (Note:  don't just dump all the sequences and align together.)

 

You can use this NCBI page to make the alignments:

 

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=blast2seq

 

Note that the box "align two or more sequences" must be checked.

 

Afterwards you can make the tree with your alignments using a variety of different types of software, for example:

 

http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/

 

Try different options and see what they look like.

 

Note:  missing data for a species for a sequence type means you can't use that species in either a single-sequence tree or a concatamer tree.  Don't just leave a blank in the concatamer  :)

[Nathan McCorkle]

On Tue, Feb 17, 2015 at 3:18 PM, Iliana Papantonaki
<iliana...@gmail.com> wrote:
> My teacher gave me a paper to use as guide and that says
> "To estimate genetic distances, we selected the best fit model of evolution
> for each data set using JMODELTEST 0.1.1 (Guindon & Gascuel 2003; Posada
> 2008) with the Akaike Information Criterion (AIC; Akaike 1974). We
> calculated intra- and interspecific genetic distances using MEGA 4.0 (Tamura
> et al. 2007) for species that were represented by several individuals.
> To assess the presence of barcoding gap (i.e. the gap between intra- and
> interspecific genetic variation), minimum interspecific distances were
> plotted against maximum intraspecific distances .
> We also calcu-lated variability of each of the seven barcodes as the number
> and percentage of variable characters using MEGA 4.0."
>

Did you search the references given in that text? Do you know about
Google Scholar?

MEGA 4.0 seems outdated, as the authors have released a few more
MEGA[number] papers since then... for example here's MEGA6:
http://mbe.oxfordjournals.org/content/30/12/2725.full

(here's MEGA4)
http://www.researchgate.net/profile/Koichiro_Tamura/publication/6342202_MEGA4_Molecular_Evolutionary_Genetics_Analysis_(MEGA)_software_version_4.0/links/00b7d52e6272878b8d000000.pdf