Gene flow stops at Gibraltar (mostly)

By Razib Khan | April 14, 2011 1:35 pm


Rock of Gibraltar

In The Humans Who Went Extinct the author makes much of the fact that Neandertals obviously lacked skill at crossing the water, insofar as their range was constricted by barriers to their south in Iberia. This sort of issue is kind of confusing to me, insofar as it seems probable that very ancient humans did make water crossings of a more arduous nature in Southeast Asia, if the Hobbits finds are valid.

I don’t really know what to think about the general issue of water crossings, but it does seem that the short distance between North Africa and Iberia has had a big impact. Bodies of water tend to serve as a major check on conventional gene flow between adjacent populations, because they limit “casual encounters.” An analogy can be made with the inbreeding coefficients in the mountainous regions of southern Italy. They were rather high until modern transportation made travel between isolated regions much easier, because the typical peasant simply wasn’t likely to venture far, or have a social network which would span valleys (rather, often the minimal transit avenues tended to lead back to a central entrepot in a hub & spoke fashion). Bodies of water can facilitate bulk trade and cultural diffusion, as well as “leap frog” population movements, but even trivial distances tend to be major barriers in an “isolation-by-distance” model.

With that in find, I ran ADMIXTURE up to K = 6 for a range of European and North Africa populations. I merged data from Behar et al. and the HGDP. I wanted illustrate the genetic distance between North Africans despite their geographic proximity. I first ran 300,000 markers, but pruned it down to 120,000 markers after confirming that the estimates were congruent between the two runs. Because of non-trivial Sub-Saharan admixture among many populations in the Maghreb I also ran a preliminary run with a Central African population and pulled out individuals who seemed to be outliers in their population for Sub-Saharan African admixture.

Below is the ADMIXTURE plot divided by population. I’ve also plotted the genetic distance (Fst) relationships between the different color components, labeling them by their modal population (e.g., light blue is modal in Lithuanians, so I’ve labeled it “Lithuanian”).



Genetic distance by inferred ancestral population

Georgian Sardinian Mozabite Lithuanian Saudi Basque
Georgian 0 0.048 0.071 0.039 0.059 0.049
Sardinian 0.048 0 0.073 0.041 0.061 0.046
Mozabite 0.071 0.073 0 0.069 0.077 0.077
Lithuanian 0.039 0.041 0.069 0 0.059 0.04
Saudi 0.059 0.061 0.077 0.059 0 0.067
Basque 0.049 0.046 0.077 0.04 0.067 0


I also ran a plot with the North African Henn et al. samples, but only 36,000 SNPs:

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: Genetics, Genomics
  • Arseny

    Hi!
    First of all, thank you very much for your books page!
    http://www.razib.com/books/

    And secondly, please, note, that the 1st book on this page (the one about Neanderthals) does not actually link to the review for this book:
    http://blogs.discovermagazine.com/gnxp/2011/03/pruning-the-family-tree-chance-inevitability/
    The word “Review” actually links to Amazon, in the same way as the cover does, which is probably a mark-up typo.

    Arseny

  • Angus

    From a purely pragmatic point of view, there are some very scary currents and stuff in the Strait of Gibraltar that aren’t an issue in more wide-open island groups. The Strait is constantly flowing out of the Med into the Atlantic, and there are eddies that would seriously impede the progress of a canoe-type thing or even a bigger boat. Just a thought.

  • Eze

    This is in agreement with the haplogroup frequencies observed in the Maghreb and Southern Europe, which tend to be quite different.

  • Pingback: Laura’s Psychology Blog » readings in psychology for april 15th 2011()

  • http://abugblog.blogspot.com Blackbird

    The issue of the arrival of H. floresiensis to Flores island was recently hypothesized by the discovery team as the result of a tsunami possibly from Sulawesi, not a voluntary crossing.
    “Given these circumstances, the arrival of hominins by 880 ka was probably the result of an extremely rare event, such as a tsunami. In such a scenario, a small colonizing group could have accidentally crossed to the island while clinging to a natural raft of vegetation or an up-rooted tree washed out to sea”
    (http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WJS-4XP220M-2&_user=10&_coverDate=11%2F30%2F2009&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_searchStrId=1719936016&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=17be9da788d9a24ea13ee05f48ae9601&searchtype=a)

  • http://dioegenesartemis.blogspot.com/ Diogenes

    I think “Mozabite” and “Saudi” are being somewhat artificially pushed too much apart by more West African-like and East-African-like influences here.
    I agree there seems to be a distinct component to Mozabites, but its also present in Egyptians and Ethiopians in smaller amounts in my runs. I can’t imagine it would have sprung from the desert, so either there’s a Green Sahara continuum, or the “Nile core” was quite a bit diverse along the valley, and Mozabites and Saudis have influence from different subsets of it… Thing is places like Cyprus tend to have small “Mozabite” elements as well…

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    I think “Mozabite” and “Saudi” are being somewhat artificially pushed too much apart by more West African-like and East-African-like influences here.

    just to be clear, i removed the people with sub-saharan african admixture from these runs. that being said, there might be basal admixture from these two sources subsumed into the mozabite and saudi clusters via deep time events.

  • Will

    Hi, could you post the exact percentages of each run ?
    Thanks,
    By the way, that’s an intersting run. Contrary to Dodecad here appears a basque cluster, whereas at Dodecad the Basques are about half Sardinian/ half north-european

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    #8, it doesn’t contradict dodecad. at a different K it looks just like dodecad. i simply selected the one where the populations overlapped cleanly with different clusters.

  • AP

    Sardinians are too inbred for AdMIXTURE and STRUCTURE and always skew the results. Just remove them and you will get more realistic results

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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