Razib Khan One-stop-shopping for all of my content

October 8, 2012

Dienekes and ADMIXTOOLS

Filed under: ADMIXTOOLS,Personal genomics — Razib Khan @ 6:55 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.

September 13, 2012

ADMIXTOOLS is out

Filed under: ADMIXTOOLS,Genetics,Genomics — Razib Khan @ 7:58 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.

September 7, 2012

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

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. ...

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