Wolf-to-dog transition had little to do with humans, ancient skull suggests. I think the headline here is deceptive. This is the important part:

A Canadian researcher who specializes in the biology of ancient dogs co-authored one of the most significant studies of the year in canine science: a paper detailing the world’s earliest evidence of an animal in transition from wild wolf to domesticated dog.

The “extraordinary preservation” of the creature’s 33,000-year-old skull — found in a cave in southern Siberia — has helped show that dog domestication “was, in most cases, entirely natural” and not really a “human accomplishment,” says B.C. evolutionary biologist Susan Crockford.

She was part of a six-member team of researchers from Russia, Britain, the U.S. and the Netherlands that turned the clock back on wolf-dog transformations by thousands of years and showed that the phenomenon probably happened many times in many places around the globe.

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Milk, it does a body good (or not):

I’ve discussed this before earlier this year, when we got our results back (my husband, children, in-laws, parents, siblings… etc have all done genomic scans), two results came back that surprised us but proved true. My mother-in-law and husband were likely lactose intolerant.

When I pointed that out to my mother-in-law she said “no I’m not.” But then she went on to explain that she never drinks more than a glass of milk because it gives her an upset stomach. Bingo. She learned over the decades that she was indeed lactose intolerant, and shifted behavior because of it, but just didn’t put a name to it.

Later, when I looked at my husband’s profile, sure enough “likely lactose intolerant.” His answer was the same as his mother’s, “no I’m not.” Thing was, in the 15 years I’ve known him he’s had regular stomach problems with no solution.

…

He probably didn’t make the connection earlier because his mother is of Danish descent (really? Danes aren’t lactose intolerant?) and often dairy in small amounts wouldn’t do a thing, or some products (like yogurt) would have little effect. The problems seemed ‘sporadic’ but frequent. His doctors never suggested lactose intolerance. We could have done a food elimination test, but that was time consuming and very inconvenient. In hindsight we should have done the slog of eliminating foods from the diet…but you know what they say about hindsight? (Or at least the Phantom Tollbooth). He’s the

This is interesting, because I know several people who went through something similar. The vast majority of Northern Europeans are lactose tolerant, at least judging by phenotype and that particular SNP. But, at least ~5% are not. That’s not a small number in absolute terms, and even proportionally it is common enough that if you know 13 random Northern Europeans, there’s a 50% probability that at least one of them is lactose intolerant.

Note: There are other SNPs which likely confer lactose tolerance. And, it seems likely that environmental factors, such as adaptation of your gut flora, also matter in the final phenotype.

Chinese Scientists Announce the First Complete Sequencing of Mongolian Genome:

In this study, the DNA sample was from a male adult who belongs to the Mongolian “Royal Family” and is the 34th generation descendant of Genghis Khan. “The sample is very valuable for the study with a full record of family pedigree and no background of intermarriage between other ethnic groups.” said Professor Huanmin Zhou, Project Investigator and Director of Science and Technology at IMAU.

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I generated the figure at left from table 9.6 in The Genetics of Human Populations. This book was published in 1971, but I purchased the 1999 edition (which was simply a republication of the original text by Dover) in 2005.* At the time I recall reading the section on inferring the number of genetic loci implicated in the variation in pigmentation with some mild skepticism. The authors, L. L. Cavalli-Sforza and W. F. Bodmer pegged the black-white difference due to ~4 genes. Their data set consisted of individuals of various races in Liverpool; whites, blacks, people with one white parent and one black parent (F1 hybrids), people with three grandparents of one race and one of another (“backcrosses,” where you take an F1 and mate them with one of the parental lines), and finally, F2 individuals who are the product of pairings of F1s.

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With some leisure, I plan to read a bit. Here is my tentative “stack”:

– The Better Angels of Our Nature: Why Violence Has Declined

– Edge of Empire: Lives, Culture, and Conquest in the East, 1750-1850

– Mothers and Others: The Evolutionary Origins of Mutual Understanding

– Mirroring the Past: The Writing And Use of History in Imperial China

– Meditations

– Consolation of Philosophy

I also plan on browsing more of Brian and Deborah Charlesworth’s magisterial Elements of Evolutionary Genetics , and my friend Joel Grus’ Thinking Spreadsheet. I’m skeptical that I would prioritize fiction, but if I manage to read some, I’ll try and finish The Sacred Band, the last in David Anthony Durham’s Acacia trilogy.

What are you reading for the holidays? (and if you aren’t reading for the holidays, why are you spending your marginal time reading this blog!)

It’s a fun fact that there are an order of magnitude more bacterial cells in your body than your own cells. Not only that, it’s well known that we wouldn’t flourish, let alone survive, without our gut “flora,” which digest material which would otherwise pass through out system. Not only are microbes good for us, but they’re also bad for us. The evolutionary flexibility of microbial pathogens is one of the major arguments for why sex exists among multiceullar species: it allows them to adapt to rapidly fluctuating disease pressures. Therefore, obviously the ecology of multicellular organisms’ microbial flora is essential to properly characterize. One element of the project involves genomics. This is not so easy for microbes because we don’t have the reference sequences of most of these organisms. We rely mostly on species which are easy to culture, and that does not include most lineages in the wild. That being said, there are workarounds, such as looking at the 16S rNA sequence, which is strongly constrained in bacterial lineages (i.e., it can serve as a “clock” to measure divergence of very deeply separated lineages).

With that, a new paper, Promiscuity in mice is associated with increased vaginal bacterial diversity:

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As must be obvious, I think now that the spread of Indo-European languages had some demographic impact. It wasn’t analogous to the spread of English to Jamaica, or the existence of French as an official language in Congo-Brazzaville. Because of this, I now believe it is possible in the near future that scientists will reconstruct the genome of the original Indo-Europeans. How?

1) Find the intersection of genetic segments on the chromosomal level which share identity-by-descent between widely separated Indo-European groups. For example, Greeks, Swedes, and Punjabis.

2) Check to see which of these intersecting elements is not found in nearby non-Indo-European groups. For example, Basques, Finns, and non-Brahmin South Indian Dravidian speakers. At least to an appreciable frequency.

My current supposition is that proportionally this component won’t be preponderant in most places, but, it will be significant. By reconstructing an Indo-European genome we may actually have the ability to ascertain the population’s urheimat, as we can compare its genetic distance to extant populations.

In response to the post below I received the above response on twitter. This is an interesting case. The link goes to a paper in the year 2000, Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits:

An analysis of 11 Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43, HS3.23, and HS4.65) has been performed in several NW African (Northern, Western, and Southeastern Moroccans; Saharawi; Algerians; Tunisians) and Iberian (Basques, Catalans, and Andalusians) populations. Genetic distances and principal component analyses show a clear differentiation of NW African and Iberian groups of samples, suggesting a strong genetic barrier matching the geographical Mediterranean Sea barrier. The restriction to gene flow may be attributed to the navigational hazards across the Straits, but cultural factors must also have played a role. Some degree of gene flow from sub-Saharan Africa can be detected in the southern part of North Africa and in Saharawi and Southeastern Moroccans, as a result of a continuous gene flow across the Sahara desert that has created a south-north cline of sub-Saharan Africa influence in North Africa. Iberian samples show a substantial degree of homogeneity and fall within the cluster of European-based genetic diversity.

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The Basque people of northern Spain loom large in any attempt to understand the ethnogenesis of European populations. That is because the speak the only indubitably indigenous non-Indo-European language in Western Europe. By this, I mean that other potential non-Indo-European languages such as the Tartessian or Pictish are either doubtful or uncertain in classification and understanding (Etruscan, or later Arabic in Spain, are not indigenous). As such they may lay claim to be representatives of a deeper pre-Indo-European substratum in the European population. Up until a few years ago the conventional view was that the Basques were the scions of the Paleolithic peoples of Western Europe, who eventually took up farming. Whether by chance or necessity, they alone retained the language of the original Europeans.

That view is now being challenged. It may be that the Basques were the descendants of the first emigres from the Near East, sweeping along the Mediterranean and Atlantic fringe, searching for arable land. This is no new orthodoxy, but if you grant this, then it opens up the likelihood that the European palimpsest is very complicated indeed. Of the public genome blogging projects Dienekes Pontikos has the most extensive database and greatest geographic coverage in the Dodecad Ancestry Project. He has repeatedly found that the Basques, along with the Finns, seem to lack a genetic element present in low amounts in other European populations, more or less, with a modal value in the trans-Caucasian region. The Spanish and the French as a whole exhibit admixture with this element, only their Basque minorities seem to lack it. The inference one can make from this is clear: these indigenous non-Indo-European peoples lack this component because it was introduced by Indo-Europeans! Now Dienekes has looked at the IBS (Spanish) sample from the 1000 Genomes, and the Basque distinctiveness jumps out again:

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At 95 James F. Crow is not only an eminent population geneticist, but he knew the figures who were responsible for the whole field. The journal Genetics has commissioned a series of essays and perspectives in his honor. The first is by Daniel Hartl. I thought this was funny:

Soon after joining the program I asked Professor Crow whether I could join his lab as a graduate student. He thought for a moment and then said, “Yes, Dan, provided you understand that population genetics is a recondite field that will never be of great interest except to a small group of specialists.” I remember this because afterward I hurried to look up “recondite” in the dictionary. His admonition made population genetics seem like some variety of monasticism, which, being an admirer of Gregor Mendel, was all right by me. Little did either of us foresee that genetics would be transformed in our lifetimes by genomic sequencing on a population scale and the development of computer technologies capable of analyzing terabytes of data and that population genetics would become a key approach for understanding human evolutionary history as well as for identifying genetic risk factors for common diseases.

I had the privilege of interviewing Crow in 2006. My email requesting an interview was sent only on the smallest probability of a reply, but he replied immediately! And when I sent my questions again the reply was nearly immediate. My favorite of Crow’s answers: “In my view it is wrong to say that research in this area — assuming it is well done — is out of order. I feel strongly that we should not discourage a line of research because someone might not like a possible outcome.” At his age he’s seen many fashions come and go. But nature abides and persists.