Tag: ADMIXTOOLS

Dienekes and ADMIXTOOLS

By Razib Khan | October 8, 2012 7:55 pm

Less than a month ago I pointed to the release of ADMIXTOOLS. Unfortunately, though I have a desktop at home devoted purely to my personal genomic hobbies I haven’t been able to free up the time on weekends to start doing my own analysis. This is pretty pathetic, and sometimes I get a little depressed at how little usage there is of all the great scientific software released into the public domain. But in case you haven’t seen it, I want to point you to Dienekes Pontikos’ posts using ADMIXTOOLS. Frankly, my personal experience with this sort of thing tells me to hold off on any judgement until I’ve used the software package and gotten a feel for its tendencies. But until those of us with aspirations manage to get some blocks of time together Dienekes has the field all to himself.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: ADMIXTOOLS

ADMIXTOOLS is out

By Razib Khan | September 13, 2012 8:58 pm

The time for commentary uninformed by DIY exploratory analysis is fast coming to a close. The alpha version of ADMIXTOOLS is out. It’s a moderately large download, 166 MB in compressed format. Do note that most of this consists of data files, not the program itself. I uploaded a zip of the README files if you are hesitant. Dienekes has a preview. I probably won’t poking around until this weekend.

If you are confused as to why this is a big deal, please see my post. We’re nearing Adam-biting-the-apple territory for regular people on the street willing to devote some computing time to exploring questions.

Update: From the comments:

For future googlers, the only thing you need to do to compile on a mac (Mac OS X 10.6.8) is add a single line to the Makefile. Replace:

libnick.a: dirs tables $(OBJ)
ar -r libnick.a $(OBJ)

with

libnick.a: dirs tables $(OBJ)
ar -r libnick.a $(OBJ)
ranlib libnick.a

then make clean and make all. Should compile fine.

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: ADMIXTOOLS

Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian

By Razib Khan | September 7, 2012 12:11 pm

The Pith: You’re Asian. Yes, you!

A conclusion to an important paper, Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich:

In particular, we have presented evidence suggesting that the genetic history of Europe from around 5000 B.C. includes:

1. The arrival of Neolithic farmers probably from the Middle East.

2. Nearly complete replacement of the indigenous Mesolithic southern European populations by Neolithic migrants, and admixture between the Neolithic farmers and the indigenous Europeans in the north.

3. Substantial population movement into Spain occurring around the same time as the archaeologically attested Bell-Beaker phenomenon (HARRISON, 1980).

4. Subsequent mating between peoples of neighboring regions, resulting in isolation-by-distance (LAO et al., 2008; NOVEMBRE et al., 2008). This tended to smooth out population structure that existed 4,000 years ago.

Further, the populations of Sardinia and the Basque country today have been substantially less influenced by these events.

 

It’s in Genetics, Ancient Admixture in Human History. Reading through it I can see why it wasn’t published in Nature or Science: methods are of the essence. The authors review five population genetic statistics of phylogenetic and evolutionary genetic import, before moving onto the novel results. These statistics, which measure the possibility of admixture, the extent of admixture, and the date of admixture, are often presented, but nested into supplements, in previous papers by the same group. On the one hand this removes from view the engines which are driving the science. On the other hand I have always appreciated that a benefit of this injustice to the methods which make insight possible is that those without academic access can actually bite into the meat of the researcher’s mode of thought.

I did read through the methods. Twice. I’ve encountered all the statistics before, and I’ve read how they were generated, but I’ll be honest and admit that I haven’t internalized them. That has to end now, because the authors have finally released a software package which implements the statistics, ADMIXTOOLS. I plan to use it in the near future, and it is generally best if you understand the underlying mechanisms of a software package if you are at the bleeding end of analytics. I will review the technical points in more detail in future posts, more for my own edification than yours. But for the moment I’ll be a bit more cursory. Four of the tests use comparisons of allele frequencies along explicit phylogenetic trees. That’s so general as to be uninformative as a description, but I think it’s accurate to the best of my knowledge. In the basics the tests are seeing if a model fits the data (as opposed to TreeMix, which finds the best model out of a range to fit the data). The last method, rolloff, infers the timing of an admixture event based upon the decay of linkage disequilibrium. In short, admixture between two very distinct populations has the concrete result of producing striking genomic correlations. Over time these correlations dissipate due to recombination. The magnitude of dissipation can allow one to gauge the time in the past when the original admixture occurred.

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CATEGORIZED UNDER: Human Genetics, Human Genomics
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