Release Of Forensic Dna Results For Sierra Kills Sample

[southernyahoo]

Not sure what you mean, SY?.

I was referring to Ketchum's prophetic statement made in private to you, of what you would find in the results. I think it is a confusing matter in DNA analysis where you can take segments of sequences and find identical matches to other animals in the same locations. This fact would make it easy to confuse a layman, and it wouldn't necessarily mean you had chimp DNA for instance if humans and chimps were identical at that location while looking at a human genome.

Best policy, use a locus known to distinguish species and have large data sets across mammals. I know you feel that was done in your testing, and you may be right about sample 26, but the nuclear genomes does not seem to be appropriate in all places for species ID. Does that make sense?

[Guest Tyler H]

I was referring to Ketchum's prophetic statement made in private to you, of what you would find in the results. I think it is a confusing matter in DNA analysis where you can take segments of sequences and find identical matches to other animals in the same locations. This fact would make it easy to confuse a layman, and it wouldn't necessarily mean you had chimp DNA for instance if humans and chimps were identical at that location while looking at a human genome.

Best policy, use a locus known to distinguish species and have large data sets across mammals. I know you feel that was done in your testing, and you may be right about sample 26, but the nuclear genomes does not seem to be appropriate in all places for species ID. Does that make sense?

NOt sure that I completely follow what you are asking.

Yes, DNA has conserved areas (areas that different species have in common) and then they have variable (hyper-variable) regions which differentiate to a great degree.

Testing the conserved areas makes no sense for species identification... so, yes, you are right, not all areas of a 'nuclear genome' would be appropriate for species identification.

But as for "Ketchum's prophetic statement made in private to you, of what you would find in the results"... there are several things you could be referring to here, so I'm not quite following that aspect.

[southernyahoo]

I think I read that she had told you that the sierra sample would give human and known animal results. True or not, this is a logical occurance since all species share sequences that are identical somewhere in the genome, chimps are in the order of 100% identical in 30% of the genome. I have no idea whether one could pick a genome from say a wolf, then ask your software to show you sequences that are identical to a hyena, but it seems likely you would find some.

Does that make sense?

ETA: If chromosome 11 in sample 26 had for instance two different copies of the same sequence representing both human and bear where there should just be one or the other, then that would be proof the data is bear and human stiched together, but I've not read it intimated in that that way from other analystis. Perhaps I missed it. perhaps the claims of the contigs addressed it, and your PDF visual addresses it , but not well intimated.

Edited March 8, 2013 by southernyahoo

[Guest Tyler H]

I think I read that she had told you that the sierra sample would give human and known animal results. True or not, this is a logical occurance since all species share sequences that are identical somewhere in the genome, chimps are in the order of 100% identical in 30% of the genome. I have no idea whether one could pick a genome from say a wolf, then ask your software to show you sequences that are identical to a hyena, but it seems likely you would find some.

Does that make sense?

ETA: If chromosome 11 in sample 26 had for instance two different copies of the same sequence representing both human and bear where there should just be one or the other, then that would be proof the data is bear and human stiched together, but I've not read it intimated in that that way from other analystis. Perhaps I missed it. perhaps the claims of the contigs addressed it, and your PDF visual addresses it , but not well intimated.

Yes, this makes sense, and I believe this is what I was referring to above, re: conserved areas - areas in the genome that are shared by more than one species. But no, it does not 'make sense' as a means for species identification. The labs target variable regions which are not shared across species...

So, for that reason, I would have to say that Melba's suggestion that 'other labs will only get human, and regular animals' would either have to be incompetently uninformed, or a deliberate misrepresentation of something that anyone familiar with genetics would understand.

[southernyahoo]

Actually Tyler, the CO1 gene in the mitochondira is a conserved gene and is used in species ID. Some scientists feel it would detect new species but they also acknowledge it's pitfalls dealing with hybridized species. I've been leery of it because of all the human results coming from the mtDNA and it uses around 600 base pairs, but it makes a case for conserved genes being used as a evolutionary clock. The New species recognition threshold using this method has been recommended to be 10 times the variation within a species. This is out there as an option, and probably appealing to those that think there is no human mtDNA in bigfoot.

http://www.biotechlearn.org.nz/themes/barcoding_life/the_ideal_barcoding_gene.

Close enough but not too close

For DNA barcoding of animals, the CO1 gene can be used to identify individuals belonging to the same species, as well as to distinguish between individuals from different species. This is because the rate that the gene sequence changes over time is slow enough so that it’s likely to be identical in the same species, but fast enough so that it’s different between species.

[Guest Tyler H]

This is because the rate that the gene sequence changes over time is slow enough so that it’s likely to be identical in the same species, but fast enough so that it’s different between species.

To me, that states that it is different between species

[southernyahoo]

Yes, small differences between species recently diverged, and greater differences between species with common ancestors further back. It won't work so well on hybrids who carry the mitochondria of another closely related species though. Disotell mentioned in a recent interview that there are species of primate with the mito of another.

You might find this an interesting read as they use the gene for primate delineation.

http://www.genemetrix.net/pdf/Hajibabaei_et_al_2006_Benchmarking_DNA_barcodes.pdf

[Guest Tyler H]

microsatellite tests can distinquish one pack of wolves from another, one pod of whales from another. The science is there to distinguish hybrids and nearly any such situation one can dream up.

Thanks for the link - look forward to reading it.