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As Naraoia points out, that was the old genome sequence. The new version has 30x coverage over the "mappable genome".
Written by another member of the same series, I note.
All analyses that made comparisons to modern humans used alignments to the chimpanzee genome, to avoid introducing population-specific biases.
The current news is about the public release of a new version of the genome, not about a paper; they say they'll write a paper on it eventually.
Based on the amount of news coverage the Denisovan and Neandertal papers have gotten, many people do seem to care about our history as a species. Presumably the new genome will permit much better estimates of Denisovan diversity, of the size and distribution of Denisovan genetic variation contributed to modern humans, and of the possible role of positive selection in the preservation of some of that variation. Probably other things that I can't think (see above re relative intelligence).
Is there a reason they cannot move to hg19?
I still don't get the fascination, especially not at the genetic level.
Again, I don't get why anyone outside the research area cares.
Can you expand on this? Which phenotypic traits could be considered?
The series of office-mates who are smarter than I am. (Heng Li, in this case.)
Oh, you mean the build. No clue -- I can ask.
Lots of people have vague notions about Neanderthals, and the discovery that many of us are partly descended from them is fascinating on a pretty basic level, the level that cares about genealogy. Likewise, the discovery that there were relatives of Neandertals that that we didn't know about until this bone was found, and that we're descended from them too is also interesting.
It wouldn't be looking for phenotypes, but for haplotype chunks that have increased in frequency unusually quickly.
Please do. I'd be interested in the answer. Maybe I can take their data do a UCSC liftover and republish
Not getting that mate. There's not enough Deniosovan material to determine any kind of frequency, best you could do would be qualitative presence/absence, at which point my question would be which ethnic hapmap would you compare to? Once you have done that, how do you assign function? We can barely (or perhaps not even) do that with GWAS now.
Simple answer: it's not hg18, it's hg19.Please do. I'd be interested in the answer. Maybe I can take their data do a UCSC liftover and republish
I just mean the kind of analysis done in [URL="http://www.citeulike.org/group/3378/article/9707766]this paper[/URL]. The identification of loci that have been under positive selection is independent of the origin of the haplotypes, and usually doesn't depend on knowledge of phenotype, but on things like long haplotypes or skewed allele frequency distributions. What you can use the Denisova genome for is to see whether archaic haplotypes were positively selected for once they entered the modern human genome.
Assuming a very small number of matings produced the admixture (which seems likely), then we know that the frequency would have started out very low in the modern human population.
They did. Check the page at the MPI.
We get that you don't get it. Can we move on?
Why am I interested in cosmology when I'm a biologist and I haven't done physics since I was 16? Why is anyone interested in anything? Don't know. Don't care. It just happens.
"Useful" doesn't necessarily equal "interesting" for everyone
A substantial chunk of chromosome is not going to be the result of incomplete lineage sorting; it would long since have been broken down by recombination. Substantial chunks that are present at high frequency only in populations with a Denisovan component and absent in Africa are also quite unlikely to be inherited via African Homo sapiens.
Your paper disagrees with you (about phenotype). HLA in general is a special case, and B*73 is extra special in particular, a case we have known about for decade or two. It's also not fair to refer to them as "haplotypes". and it is strongly linked to phenotype, which I'd like to hope is how it made it into Science (good paper by the way, unlike the rubbish from Cell that just crossed my desk).
I remain skeptical (partly about whether they will find any, but mostly whether they will have enough tie in to phenotype to make a decent paper), but await the analysis.
I didn't mean a repetition of that exact analysis, and I wasn't referring to haplotypes because of that paper. We know of many likely instances of positive selection in the human genome, and in the majority of cases, we know about them because a particular stretch of haplotype has increased in frequency rapidly, and we know nothing about the phenotype which was involved in the selection. Eventually the phenotype can sometimes be worked out, but that effort is independent of determining whether the selected allele came from Denisovans or not.
