Confusion in DNA barcoding results !!!

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Permalink Reply by C. Haris Saslis-Lagoudakis on January 12, 2011 at 6:13pm

Hi Ashutosh,

 

It seems like rbcL and matK are telling you they are all the same species. Regarding the SNP for one of the samples of population C, I would firstly go back to the raw sequence data to check that it hasn't been miscalled. Even if it is an SNP, not sure you can make a case that it is a different species. It could also be that in your plant group there is not enough variation in these markers. What group of plants is it? Success rates with rbcL+matK are not 100%.

 

In theory, I would discard the information from rpoC1, as it has been shown that its discriminatory power is one of the lowest of all proposed markers. (See CBOL Plants working group, Hollingsworth et al. 2009. PNAS). As you describe it though, it seems that it gives you 3 different taxa. Do these 3 groups of populations correspond to different species? 

 

Also, the taxonomist might have got it "wrong", meaning that they observed the morphological or maybe ecological variation correctly, but they are actually all infraspecific units.

 

I have to say that I am by no means an expert, so please seek more opinions on this. The PNAS paper I am citing above is a good starting point. 

 

Hope this helps

Haris

 

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Permalink Reply by Ashutosh sharma on January 23, 2011 at 1:17pm

Hi Dr. haris,

 

Thanks for your beautiful explanation.

 

Ashu

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Permalink Reply by Prasad Kesanakurti on January 14, 2011 at 11:26am

Hi Ashutosh,

 

There is some confusion in your statement. You mean to say "genus" in place of "gender" to which all these 7 populations belong. Also, you said 6 samples were collected for each population which means are you looking for variation with in the population!!!!! If so, I wouldn't be surprised if barcodes (rbcL+matK) didn't show any difference in these samples.

 

As Haris mentioned all these 7 populations may have been one single species at least at genome level, if not at morphological level. This could be possible if these samples belong to recent speciation event. If you collected these samples from hot humid parts of Mexico (which represent tropical climate), your results are not uncommon. Because tropics are rich in biodiversity.

 

Finally, I wouldn't make any conclusions based on rpoC1 because of its lower resolution power.

 

Best wishes

Prasad.

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Permalink Reply by Ashutosh sharma on January 23, 2011 at 1:13pm

Hi Dr. Prasad,

I like your comment of the second paragraph.

And I think my question is clear, I am not looking variations within the population but in a mixture of 7 populations which represent 4 different species.

Thanks

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Permalink Reply by Isaac Chow on January 18, 2011 at 10:25am

Hi Ashutosh,

 

Simply repeat the experiment with trnH-psbA spacer sequencing and would probably give you more information. Remember, avoid contamination and always wash or soak your plant sample before DNA extraction.

 

Isaac

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