In September 1941, Hu Chengzhi placed several skulls into two wooden crates. Around him, China was at war with Japan, so he was sending the skulls to the US for safekeeping. They never arrived. Hu was among the last people to see one of the most important palaeontological finds in history. These lost skulls belonged to Homo erectus pekinensis, known as Peking Man.

You can read all of them free online, which include the Maxberg Archaeopteryx, Nixon’s moon rocks, the recipe for Damascus steel and moon trees.

Tumours are bundles of cells that grow and divide uncontrollably, and their genes are deployed in unusual ways. By analysing the genes from different tumour samples, scientists have tried to pin down the chaotic events that lead to cancer. They seem to be making headway. Dozens of papers have reported “gene expression signatures” that predict the risk of dying or surviving from cancer, and new ones come out every month.

These signatures purportedly hint at how healthy cells transform into tumours in the first place. If, for example, the genes in question are involved in wound healing, this tells you that the healing process is somehow involved in a tumour’s progression. These collections of genes reveal deeper truths about the disease they’re associated with.

This idea sounds reasonable, but David Venet from the Université Libre de Bruxelles has thrown a big spanner into the works. He has shown that completely random sets of genes can predict the odds of surviving breast cancer better than published signatures.

Venet found three signatures that are completely unconnected to cancer. Instead, these collections of genes were associated with laughing at jokes after lunch, with the experience of social defeat in mice, and with the positioning of skin cells. All of them were associated with breast cancer outcomes.

Head over to Naturally Selected for the rest, including how long it took to get this study published.

Image by Hakan Dahlstrom

Over at Harappa DNA Zack ran ChromoPainter/fineStructure on his South Asian data set and posted the results. The new method immediately makes a few things clear:

1) The “South Asians” in the HGDP data set that’s been used for so long are rather on the inbred side, and relatively genetically distinct as far as South Asian populations go. It goes to illustrate the importance of finely calibrating geographic coverage, and the consequences of the “Permit Raj.”

2) Some of the Gujarati individuals in the HapMap also shake out as a moderately tight group (the square in the middle of the graphic above). Not too surprising, but rather striking. Another illustration of the importance of selecting representative and informative populations for any given region.

3) In the clustering spreadsheet Zack found that my parents aligned with a Brahmin from trans-Himalaya India and some Indians from Singapore, all notable for clear East Asian ancestry. He labelled the cluster “bit-east asian,” which is appropriately descriptive. One thing that seems to reoccur in these clustering algorithms is that South Asians with elevated East Asian ancestry are often thrown together into one pot, despite very diverse origins. That’s probably because the combination is not too common, and jumps out as rather distinctive. It goes to show the limitations of summarizing individual elements of genetic variation into one statistic or label. On a personal level the ultimate question in regarding my family’s background has to be explored in the future by partitioning up the genome appropriately and then focusing on the history of specific segments. For example, which Southeast Asian groups is this ancestry from? How much Munda do my parents have? Is the close relationship between my parents and various caste groups in South India (e.g., the Naidu and Reddys) due to Bengalis being a compound of these groups with an East Asian group?

Fun times if you have data, a little persistence, and time on your hands.

If your partner is likely to devour you after sex, snapping off your genitals inside her might seem a reasonable reproductive strategy. This game plan is used by males of the orb-web spider Nephilengys malabarensis and, it turns out, continues to work in their favour, regardless of whether they survive the encounter.

Thus begins my new piece for Nature News. Honestly, I can’t believe they let me keep the lede. Here’s more:

Daiqin Li at the National University of Singapore and his colleagues studied the species and found that after the male breaks away his severed organ continues to pump sperm into the female. This allows him to fertilize her remotely, while denying entry to other males. Even though the male cannot regrow his genitals and so renders himself sterile, he increases the odds that he will father the offspring of his one and only mate.

Male spiders deliver their sperm through a pair of structures known as palps, which are found on the sides of their heads. By serving sexual encounters between 25 pairs of virgin N. malabarensis, Li’s group found that every coupling ended with damage to the male’s palp. In 12% of cases it was partially severed; in the rest it snapped off completely.

Li thinks that this bizarre strategy, found in only two spider families so far, evolved to counter the female’s penchant for cannibalism. “The females are very aggressive and 75% of them kill the males during sex,” he explains. “The duration of copulation is also very short, and the females initiate the break-off.”

By dissecting the mated spiders, Li and his co-workers found that the palp has dispensed only about one-third of its sperm by the time the female pushes the male off. But it continues to transfer sperm after it breaks off, and does so at a faster rate.

And head over there for the rest of the story.

(In the picture at the top, the bigger female devours the smaller male while his palp clings on to her underside (in the red box).)

The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins.

The new view is fast supplanting the traditional idea that modern humans triumphantly marched out of Africa about 50,000 years ago, replacing all other types that had gone before.

Instead, the genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.

Their DNA lives on in us even though they are extinct. “In a sense, we are a hybrid species,” Chris Stringer, a paleoanthropologist who is the research leader in human origins at the Natural History Museum in London, said in an interview.

First, for reasons of novelty we are emphasizing the exotic tendrils of the human family tree. Even Chris Stringer, the modern paleontological father of “Out of Africa,” is claiming we’re hybrids! But let’s not forget that non-Africans are the product of a very rapid radiation out of the margins of the Afrotropic ecozone within the last ~50-100,000 years. I am not entirely sure that this is as true of Africans (recall how extremely basal Bushmen are to the rest of humanity; they seem to have diverge well before the “Out of Africa” pulse).

Second, the old model was way easier to write about, even if there were confusions like the idea that mtDNA Eve was our only female ancestor from 200,000 years ago in the past. The new paradigm leaves one with awkward and unhelpful turns of phrase. For example:

But Dr. Reich and his team have determined through the patterns of archaic DNA replications that a small number of half-Neanderthal, half-modern human hybrids walked the earth between 46,000 and 67,000 years ago, he said in an interview. The half-Denisovan, half-modern humans that contributed to our DNA were more recent.

How to make sense of this gibberish? I suspect that the author didn’t have a good idea how to translate a particular population genetic statistic, and its importance to assessing time since admixture, into plainer prose. I have no idea either!

In other news, i09 has an interesting interview up with Rebecca Cann and Mark Stoneking. These two were heavily involved in the mtDNA Eve controversies of the 1980s. Nice capstone to an era. Like Stringer, even they admit the likelihood of a necessity to modify the simple “Out of Africa” with replacement model.

Since 2000, Burmese pythons have been staging an increasingly successful invasion of Florida. No one knows exactly how they got there. They normally live in south-east Asia and were probably carried over by exotic wildlife traders. Once in America, they could have escaped from pet stores or shipping warehouses. Alternatively, overambitious pet owners could have released when they got too large for comfort. Either way, they seem to be thriving.

With an average length of 12 feet (4 metres), the pythons are formidable predators. They suffocate their prey with powerful coils, and they target a wide variety of mammals and birds. The endangered Key Largo woodrat and wood stork are on their menu. So are American alligators (remember this oft-emailed photo?). Conservationists are trying to halt the spread of the giant snakes, out of concern that their booming numbers could spell trouble for local wildlife.

Michael Dorcas from Davidson College thinks they are right to be concerned. In the first systematic assessment of the pythons’ impact, Dorcas has found that many of Florida’s mammals have plummeted in numbers in places where the snakes now live.

Raccoons, for example, used to be one of the most frequently seen animals in Florida’s Everglades National Park. Between 1996 and 1997, you’d see one every 35 kilometres on the local roadsides. That’s no longer the case. In the last few years, Dorcas and his team have driven over 57,000 kilometres of Everglades tracks, counting animals as they went. They worked between sunset and sunrise on 313 separate nights. Their roadside census showed that since 2003, when the python populations really took off, raccoon sightings have fallen by 99.3 per cent. Opossum numbers have fallen by 98.9 per cent. There are 87.5 per cent fewer bobcats. They didn’t see a single rabbit.

This could, of course, be coincidence, but the numbers fit in both time and space. The mammal populations have suffered the greatest losses at the southern end of the park where the pythons first staged their invasion. At the further corners, where the snakes have only been recently found, the mammals’ numbers haven’t fallen quite as far. And mammal sightings were even more common in two areas outside the park, where pythons have never been seen.

It’s possible that some other factor has simultaneously triggered the decline of these mammals, but it’s hard to think what that might be. There’s no evidence that they’ve been hit by a new disease, and they all hail from diverse groups, which makes the possibility of a shared infection less likely. Hunting is unlikely too. It’s banned in the Everglades National Park. While some inevitably happens, it’s hard to imagine that it would occur at the scale necessary to bring about the falls that Dorcas saw, especially in the park’s remote southern area.

This is probably just the tip of the iceberg. Raccoons and opossums are easy to spot; there may be dozens of other species, including local birds, which are also being affected in less detectable ways. But beyond Dorcas’ hard statistics, it’s difficult to predict what impact the pythons would have. They could eat some species to extinction. They could outcompete other predators for food. They could allow mid-tier animals to boom in numbers, by getting rid of predators.

Regardless, Dorcas’ results should give added urgency to attempts to control the invasive pythons. We’re actually in a fortunate position of having identified a problem a mere decade or so after it began. Other parts of the world haven’t been so fortunate.

Shortly after World War II, the brown tree snake was introduced to the Pacific island of Guam. It slowly went about exterminating the native species. It took more than 30 years to work out what the snake was up to, and by then it was too late for many species. Thanks to the snake, the Guam rail and Micronesian kingfisher only survive in zoos. The Guam flycatcher has disappeared. The rufous fantail is no more. Hopefully, the Everglades will avoid the same fate.

Reference: Dorcas, Wilson, Reed, Snow, Rochford, Miller, Meshaka, Andreadis, Mazzotti, Romagosa & Hart. 2011. Severe mammal declines coincide with proliferation of invasive Burmese pythons in Everglades National Park. PNAS http://dx.doi.org/10.1073/pnas.1115226109

Image by Bobosh_t

More on pythons and other giant snakes:

• Snakes know when to stop squeezing because they sense the heartbeats of their prey
• Meet the Agta, a tribe where a quarter of men have been attacked by giant snakes
• A recipe for growing bigger hearts, found in the blood of pythons
• Titanoboa – thirteen metres, one tonne, largest snake ever.
• Snake proteins have gone through massive evolutionary redesign

The independent cross-government advisory group was set up in response to the 2009 House of Lords report on genomic medicine. It draws on expertise from across Government and research institutes and makes six recommendations to Government:

The recommendations are:

• to develop a cross-cutting strategic document, to set out the direction on genomic technology adoption in the NHS;

• to develop a national central genomic data storage facility;

• that the NHS Commissioning Board should lead on developing genomic technology adoption;

• to work to develop a service delivery model for genomic technologies;

• that the NHS should continue to develop genomics education and training; and

• to raise public awareness of genomic technology and its benefits.

Many researchers believe that personal genomics will really not hit the biomedical sweet spot until you have on the order of a million people sequenced. But even then in the American system how to get a hold of all that information is going to be problematic, since it will likely be decentralized. In contrast in Britain tens of millions of people have one primary healthcare provider, their national government.

You can read the full report online (PDF). Like the “rise of China,” the “rise of genomics,” was one of those futurist predictions. Until now. It’s ridiculous to talk about the rise of something which has risen. Now it’s about maturity and ripening.

According to the reader survey >50 percent of you don’t know how to interpret PCA or model-based (e.g., ADMIXTURE) genetic plots, so I am a little hesitant to point to this new paper in PLoS Genetics, Inference of Population Structure using Dense Haplotype Data, as it extends the results of those earlier methods. But it’s an important paper, and at some point I’ll starting using their software. The “big picture” is that earlier methods left “some information on the table.” That’s partly due to the fact that they were developed (or in the case of PCA leveraged, as it’s a very general technique) in an era where very dense marker data sets were not available (today we’re shifting to full genome sequences in many cases!). The information left on the table would be haplotype structure. Genetic variation in a concrete form manifests as sequences along a line, many of them physically connected. These correlations of nearby variant markers represent haplotypes of great interest, because they are excellent clues to admixture or divergence events across populations. In contrast the older methods, were looking at variation from marker to marker, each in turn independently, which collapses some of the important genomic structure that we can now inspect (in fact, linkage disequilibrium due to these correlations can distort some of the results in the older methods, so you want to “thin” your marker set).

Let me make this concrete for you. On 23andMe you can see where your friends shake out on a PCA plot using the HGDP data set as a reference. What this means is that the HGDP data set is used to generate independent dimensions of genetic variation. As is the usual case in these analyses the largest dimension separates Africans from everyone else, and the second largest dimension separates Asians from Europeans and Africans. 23andMe customers are then projected upon this variation, so you can get a sense where you are positioned in the clusters. To the left is a zoom in on the section for Central/South Asians. You can see that one of my friends, highlighted with a green color, falls almost perfectly in the Uygur cluster. According to ancestry estimates my friend is 50 percent Asian and 50 percent European. The “representative” Uygur in the 23andMe chromosome painting gives about the same results. But these are total genome estimates. The historical nature of my friend’s admixture and that of the Uygur woman is very different, as one can see in the below figure.

My friend is to the right, and the Uygur woman is to the left. Why the big difference? My friend has an East Asian parent an a European parent. The Uygur woman is the product of a marriage between Uygurs, a population which is due to admixture betwen East Asians and Europeans one to two thousand years ago. Recombination has broken apart the perfect linkage between European and East Asian regions among the Uygurs. Obviously this isn’t the case with my friend, as recombination has had no time to generate alternative sequences of ancestry. This is critical information which genome-wide estimates displayed on PCA or ADMIXTURE will miss out on.

As for this particular paper and method, I want to point you to figure 5. The darker/bluish colors indicate higher conancestry estimates, and yellower colors lower ones. Red is in the middle. The diagonal tends to be blue/red because that represents populations’ correlations with themselves, which one would expect to be high. You can’t really read the labels, but  I wanted to highlight the Italian and Sardinian blocks. Explanation below.

You can see an ADMIXTURE plot underneath the heat-map. What’s going on? Sardinians exhibit the hallmarks of an isolated population with smaller effective population which has undergone more genetic drift than Italians over the same amount of time. This is naturally one reason that they “break out” rather quickly in ADMIXTURE and PCA. You see this in South Asia with the Kalash, who often emerge as their own cluster rather quickly, and separate out in a PCA as well. This is simply a function of their isolation and lower effective population size. Most of the people who use ADMIXTURE and PCA know this, but those reading these plots do not. Without that knowledge one can make incorrect inferences. The methods outlined here in the paper allow one to visually observe immediately these trends, while keeping in place broader wold-wide correlations across populations in mind. This is a big step forward not only in data analysis, but result visualization.

If you are more interested in this topic, the first author has a comparison of the various tools up. Both Dienekes and Eurogenes are using the new software. Get the software at PaintMyChromosomes.com!

Citation: Lawson DJ, Hellenthal G, Myers S, Falush D (2012) Inference of Population Structure using Dense Haplotype Data. PLoS Genet 8(1): e1002453. doi:10.1371/journal.pgen.1002453

The study focuses on the Hadza, a hunter-gatherer population of Tanzania. Their language seems to be an isolate, though there have been suggestions of a connection to Khoisan. Additionally the genetic evidences tells us that like the Bushmen and Pygmies the Hadza do descend from populations which are basal to other human lineages, and were likely resident in their homeland before the arrival of farmers. And it is critical to also note that the Hadza are probably uninterrupted hunter-gatherers in terms of the history of their lifestyle, as agriculture likely arrived in Tanzania on the order of two thousand years ago, and their genetic distinctiveness indicates a separation from groups like Bantus far deeper in time. When it comes to Paleolithic model populations the Hadza are relatively “uncontaminated.”

So how does 2a matter? It shows a sharp discontinuity in cooperation across Hadza camps, all things controlled. There have been debates about the level of analysis necessary to explain human cooperation, with reductionists focused on the individual, arguing that dynamics such as kin selection and reciprocal altruism can explain the complexity we see around us simply through extension (e.g., universalist religious ideologies and philosophies usually appeal to fictive kinship or the golden rule). These data instead given some support to models which posit that group-level cultural dynamics must also be taken into account. Remember though that these more complicated systems don’t deny the importance of kin selection and reciprocal altruism; they only posit that there are other forces which can’t easily be reduced to these two.

The peculiarity of figure 2a illustrates the difference between transmission of culture, memes, and biology, genes. The Hadza are a small population, and genetically rather homogeneous in relation to their neighbors (to my knowledge they don’t exhibit much population substructure). It is difficult for between group variance to develop between human populations with adjacent residence patterns because even small amounts of migration rapidly equilibrate gene frequencies. This is why biologists have traditionally been skeptical of selection across groups. If the two entities are nearly clonal (because the groups do not differ much) then evolution by natural selection can not operate across the groups (remember, being clonal at the scale of the group does not mean there isn’t variation within groups, so selection still operates, just at a “lower” scale). But human culture is very different. Novel groups with their own distinctive cues can emerge very rapidly, and generate horizontal networks of affinity. Sometimes, as with accents, it is rather difficult for outsiders to a group to mimic and deceive because of a biologically “critical period” of enculturation (this might also be the role that radical body modification plays in a functional sense; it’s a difficult-to-fake identity marker, often irreversible).

That’s the theory. The main problem with these group-level models is that there’s always a lot of talk (theory), but a lot less empirical data. Hopefully that will change. The paper used a lot of experimental methods, and these are probably the way to go. Obviously you can’t put people in life or death situations, but you can at least discern general and specific patterns cross-culturally. And are these canned “games” any less valid than surveys to the WEIRD set?

Citation: Social networks and cooperation in hunter-gatherers, doi:10.1038/nature10736

Image credit: Wikipedia

Many years back, a young researcher called Brian Hare was listening to the Harvard anthropologist Richard Wrangham expound on this bizarre constellation of traits. “He was talking about how bonobos are an evolutionary puzzle,” recalls Hare. “They have all these weird traits relative to chimps and we have no idea how to explain them.”

But Hare had an idea. “I said, ‘Oh that’s like the silver foxes!’ Richard turned around and said, ‘What silver foxes?’”

Hare meant these silver foxes.

They were the work of Russian geneticist Dmitri Belyaev. In the 1950s, Belyaev managed to breed domesticated foxes in a startlingly short amount of time. He simply selected for the nicest individuals, breeding those who were least aggressive towards their human handlers. Twenty generations later, and foxes that would once have snarled at human handlers would wag their tails instead.

But it wasn’t just the foxes’ temperaments that changed. The domestication process also warped their bodies. They ears became floppier, their tails curlier, their canines shorter, and their skulls smaller. They developed white patches on their fur. Their physiology changed too: they became less sensitive to stress and more sensitive to social cues.

They developed a suite of features known as the “domestication syndrome”, which you can see in domesticated animals from dogs to guinea pigs. This set of traits, both physical and psychological, seem to appear as a package. And it’s the same set that Hare recognised in the bonobo.

Now, in a new review, Hare puts forward the hypothesis that bonobos are “self-domesticated” apes. By naturally selecting for a ‘nicer’, less competitive ape, evolution has forged an animal with the same cluster of traits that humans have pushed onto other species.

I’ve written about Hare’s idea at Scientific American, so head over there for the full story, including why and how exactly this would have happened. For now, I want to highlight two bits of the work.

First, a nice quote from Greger Larsen – a domestication researcher – who sums up why Hare’s idea is interesting: “People have been thinking about domestication as a human-centered thing: purposeful, directed, something we do to animals. But what Brian says is that this process, which we imbue with all this human-centric meaning, is something that takes place in nature. That’s super cool.”

Second, Hare was refreshingly candid about the fact that this is a hypothesis, and open to criticisms (and you’ll find some from Frans de Waal at the SciAm piece). He himself identified three to me. First, it’s not clear if the ancestor of chimps and bonobos was more chimp-like than bonobo-like. Second, he’s making educated guesses about how the self-domestication happened because we know very little about the bonobo’s environment, both current and ancient. And third, you’d ideally want to test the self-domestication hypothesis in other species too, rather than just bonobos and chimps.

Still, it’s a fascinating idea and one that will no doubt be tested in the future. As Hare says: “The goal of the paper is to generate a lot of enthusiasm and excitement about studying bonobos,” he says.  “Even scientists don’t even know they exist and that’s horrible.”

Reference: Hare, Wobber & Wrangham. 2011. The self-domestication hypothesis: evolution of bonobo psychology is due to selection against aggression. Animal Behaviour  http://dx.doi.org/10.1016/j.anbehav.2011.12.007

Images by Pierre Fidenci and Ikiwaner; silver fox from Cornell

We are no longer talking just about African mtDNA Eve and her husband Y chromosomal Adam. I’m going to consciously avoid the term “revolutionize,” because the broad outlines of the old story certainly hold. Rather, as we are wont to do it seems that we became a bit too bold with some of our brush strokes, and elided fascinating and subtle elements of the landscape on the margins. There were Crebs, and other assorted Oogas and Boogas. And the painting is not completed yet. As such we can’t really draw any conclusions as to “what it all means,” aside from the fact that it’s fascinating.

Addendum: Someone in the comments observes in relation to a depiction of Eve in the story that “She’s awfully pale for an East African.” This is true on the merits, but the logic is kind of dumb. Why exactly do we think that people ~150,000 years ago looked anything like modern East Africans? It is very likely that Europeans ~35,000 years ago did not look like Daryl Hannah.

Several companies provide tests that can confirm whether adoptees are related to individuals they already know. Others cast a wider net by plugging DNA results into databases that contain tens of thousands of genetic samples, provided mostly by people searching for their ancestral roots. The tests detect genetic markers that reveal whether people share a common ancestor or relative.

Some experts on adoption and genetics have criticized ancestry and genealogy testing companies, saying they are, at times, connecting people whose genetic links are tenuous — in effect stretching the definition of a relative. Nevertheless, the growing popularity of the tests, combined with social media sites that connect people day to day, has given some adoptees a sense of family that feels tangible, intimate and immediate.

I think that these tenuous connections and slivers of information are better than nothing. This isn’t rocket science. And naturally many adopted people also could care less. This is a deeply personal issue, and the valence is going to be private. I suspect that those of us who aren’t adopted, and take for granted knowledge of our own family background have a hard time imagining the value which even a 3rd or 4th cousin could give someone.

Additionally, though finding very close relatives is not that common (first cousins, let alone first order relatives), knowledge of more distant relations can still help you triangulate aspects of family history if you begin with nothing. To give a personal example I know someone whose paternal grandparents were immigrants from Germany. The maternal side is much more mixed, and some of the genealogical records hit dead-ends in the mid 19th century in the USA. It turns out that one of the individuals that this person is closest to on 23andMe is an African American (both maternal and paternal lineages are clearly African). What does this mean? The lead hasn’t been followed up, but combining family histories might be very informative in this case.

CeCe Moore and Blaine Bettinger have covered this story in detail, so I won’t go much further in this specific case. But as more and more people get typed and sequenced I suspect that genetic material is going to be more and more “actionable.” What long term effects will this have? Will criminals start taking precautions?

Another interesting aspect to this phenomenon is that it looks like the three populations respond to adaptive pressures differently. Their physiological response varies. And the more recent work in genomics implies that though there are similarities between the Asian and American populations, there are also differences. This illustrates the evolutionary principle of convergence, where different populations approach the same phenotypic optimum, though by somewhat different means. To my knowledge there has not been as much investigation of the African example. Until now. A new provisional paper in Genome Biology is out, Genetic adaptation to high altitude in the Ethiopian highlands:

We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia.

The main shortcoming about this paper for me is that it does not highlight the evolutionary history of this adaptation. In the paper the authors compared the Amhara (a highland population) to nearby lowland populations. But did not explore the nature of the population structure and how it might have influenced the arc of adaptation. Are these very ancient adaptations? Or new ones? It seems that hominins have been resident in Ethiopian for millions of years. If this is so presumably there have been adaptations to higher elevations from time immemorial. But what if these adaptations are new?

More pointedly the Ethiopians can be modeled as a compound of an Arabian population with an indigenous East African one. If this is a genuine recent admixture event, then one might be able to ascertain via haplotype structure whether the adaptive variants derive from ancient African genetic variation, or whether they’re novel mutations. It seems that this paper is a good first step, but there’s a lot more to see here….

Citation: Genome Biology, doi:10.1186/gb-2012-13-1-r1

Image credit: Wikipedia

It’s been a while since I’ve gone looking for genotypes of particular ethnic groups. The results were rather good for the Tutsi and Malagasy. So I thought I’d venture out again, despite being a bit busy. Here’s what I want: the genotype of an Afrikaner (or several). A few years ago South African geneticist J. M. Greeff did an analysis of his own pedigree, and estimated that he had ~6 percent non-European ancestry (he did validate this with some genetic markers; e.g., his father’s mtDNA is of the M haplogroup, which is almost always Indian). This is in line with other genealogists who have estimated, about 5 percent non-European heritage. How much should we trust these non-biological studies? The genomic estimates of African American ancestry being ~20 percent European were anticipated by analyses of family histories from text records, so we certainly shouldn’t dismiss them (in fact, it seems possible that these analyses will underestimate non-European ancestry because of cryptic individuals in the pedigrees).

And we have plenty of records of people of non-European ancestry contributing to the Afrikaner population in any case. Greeff found the records for his own pedigree, but the first Governor of the Dutch Cape Colony was himself of mixed-race (his mother was Eurasian). The question is is a matter of degree. Are Afrikaners like American whites, with hardly any non-European ancestry (~1 percent or less), or like Latin American whites, with significant non-European ancestry (~5 to 20 percent)? My own bet is that they’ll be in the middle. The proportion of non-European ancestry is low enough that individuals such as Sandra Laing are very rare indeed. But if the 5 percent estimate is valid, and almost of all these ancestors were women, then a larger proportion of the mtDNA is going to be non-European.

So how do we do this? Well, I need an autosomal genotype. I’ll take it anyway I can get it. But, if you don’t have one, but are willing to let me analyze your own genotype, and, are of 100 percent known Afrikaner descent, then we can probably figure out a way to purchase you a kit.

Why does this matter? I guess you could ask why any science matters. I’m a little confused as to why no one has done this before. There’s plenty of work on the cultural cousins of the Afrikaners, the Cape Coloureds. My working assumption is that except for the initial decades of the Cape Colony, when women were in severe shortage and the color line was not as strict, most of the non-European gene flow into the Afrikaners is going to be from the Cape Coloureds. This means that like the Cape Coloureds the Afrikaners carry within them the genetic variation of a huge swath of the world’s population. The non-European ancestry of the Afrikaners is naturally part African. Bantu and Khoisan. But there is also considerable Asian, from South and East Asia. Though this leaves out the Middle East and the New World, you have here most of extant genetic variation in human populations.

There are approximately 3 million Afrikaners in South Africa. What if these were the only human beings left on earth? At 5 percent that’s 150,000 non-Europeans, with a mix of Southeast Asians, Chinese, Indians, Khoisan, and Bantu. Because of diminishing returns you’ll actually have enough variation in just a few thousand individuals of any given ethnic group to capture most of its genetic character. In other words you could in theory reconstitute the Chinese and Khoisan from these Afrikaners.

Addendum: The paper, Complete Khoisan and Bantu genomes from southern Africa, has one “South African European.” But I suspect that this individual is author Vanessa M Hayes, and she is not an Afrikaner to my knowledge.

Image credit: Wikipedia

This is an

Right from its entrance, Disneyland is designed to cast an illusion upon its visitors. The first area –  Main Street – seems to stretch for miles towards the towering castle in the distance. All of this relies on visual trickery. The castle’s upper bricks and the upper levels of Main Street’s buildings are much smaller than their ground-level counterparts, making everything seem taller. The buildings are also angled towards the castle, which makes Main Street seem longer, building the anticipation of guests.

These techniques are examples of forced perspective, a trick of the eye that makes objects seem bigger or smaller, further or closer than they actually are. These illusions were used by classical architects to make their buildings seem grander, by filmmakers to make humans look like hobbits, and by photographers to create amusing shots. But humans aren’t the only animals to use forced perspective. In the forests of Australia, the male great bowerbird uses the same effect to woo his mate.

Bowerbirds are relatives of crows and jays that live in Australian and New Guinea. There are 20 or so species. In most of them, the male attracts mates by building an intricate structure called a bower, which he decorates with specially chosen objects. Some species favour blue trinkets; others collect a  mishmash of flowers, fruits, insect shells and more. Surrounded by these knick-knacks, the artistic male performs an elaborate display. The females judge him on his skill as a performer, builder and decorator.

The great bowerbird’s taste for interior design seems quite Spartan compared to his relatives. He creates an avenue of sticks, around 60 centimetres long, leading up to a courtyard. The courts are decorated with gesso – a collection of gray and white objects including shells, bones and pebbles.

The male performs in this messy courtyard. He struts. He sings. He tosses brightly coloured objects about. All the while, the female watches from the lined avenue. Her point of view is fixed and narrow, and according to John Endler, the male knows how to exploit that.

In 2010, Endler showed that the males place the largest objects towards the rear of the courtyard and the smallest objects in the front near the avenue. This creates forced perspective. From the female’s point of view, it looks like the bigger objects, which are further away, are the same size as the smaller objects, which are close by. If bowerbird vision is anything like humans, the courtyard as a whole looks smaller to a watching female. It’s the opposite effect to the one that Disney visitors experience.

By analysing 19 different bowers across Queensland, Endler showed that the arrangement of objects in the courtyards were far from random. When he messed up the careful gradients by reversing the large and small trinkets, the males were quick to put things right. Within three days, the illusions had been restored.

Now, Endler has shown why the bowerbirds are so fussy. With his colleague Laura Kelley, he has found that the males who create the strongest illusions get the most mates. From the female’s point of view, the courts with the strongest forced perspective and the most even patterns earned their owners the most sex. “To my knowledge no other animals make constructions which produce perspective,” says Endler.

Perspective has been a familiar element of Western art since the Renaissance, and Endler describes the great bowerbird’s courtyards as “bowerbird art”. Others would agree. In this clip David Attenborough compares the work of a Macgregor’s bowerbird to a sculpture by British artist Andy Goldsworthy and asks why one might be considered art and the other not. Defining art is a tricky business, but Endler thinks of it as one individual creating a visual pattern in the outside world to influence the behaviour of others. “Influencing behaviour can range from attraction to and voluntary viewing of the art by others to viewers mating with the artist, which is what bowerbirds do,” he says.

The bowers might be art, but are they actually illusions? It’s not clear. Despite Kelley and Endler’s new study, we’re no closer to knowing exactly why the bower gradients work. Perhaps more regular pattern on the court, as seen from the avenue, could make the male more conspicuous or easier to see. The same applies to the object that he waves about – perhaps it stands out more against such a regular background, or seems bigger.

Endler notes that from the female’s perspective, the male’s display items are often slightly larger than the ones in the gesso. This could trigger the ‘Ebbinghaus illusion’, where objects seem bigger if they’re next to smaller ones than next to larger ones.

But there are explanations that could account for the male’s habits without having to invoke any illusions. Perhaps it’s simply that the female likes a more uniform texture. Maybe she recognises that males who can produce regular patterns might be mentally sharper, better at stealing the right objects from other bowerbirds, better at resisting such acts of thievery, or better at choosing building sites with lots of varied objects to choose from.

In a related editorial, Barton Anderson from the University of Sydney writes that we still don’t know if the bowerbirds are actually crafting illusions for their mates. He says, “Kelley and Endler’s data suggest that male bowerbirds appear to consider the viewpoint of their potential mates when constructing their bower courtyards, and the ones who do this best are rewarded with a higher rate of mating success. Just what matters, and why it matters, remain open and intriguing questions.”

There’s plenty of time to answer them. After all, the bowerbird’s behaviour has only just been discovered. Back in 2010, Endler says that he still needs to do the “critical experiments” to see how much brainpower the birds need to pull off their illusions. That’s still the case in 2012.

The most extreme explanation is that they have a sense of perspective (insert joke about humans here) and know that they should put small objects near the avenue and bigger objects further away. But Endler says, “The very simplest hypothesis is that the birds make the gradients by trial and error.” They spend around 80% of their time at the bower on moving objects within the courts, checking the view from the avenue, and moving things again.

“They could just be doing that until the view of the court from inside the avenue looks ‘good’,” says Endler.  “A slightly more complex behaviour might be needed if they had an inherited or learned decision rule which made them put smaller objects closer to the avenue entrance and increasingly larger objects further away.”  Neither technique would be unexpected, given that bowerbirds are closely related to some of the smartest of all birds – crows, ravens, jays and their kin.

References: Kelley & Endler. 2012. Illusions Promote Mating Success in Great Bowerbirds. Science http://dx.doi.org/10.1126/science.1212443

Endler, Endler & Doerr. 2010. Great Bowerbirds Create Theaters with Forced Perspective When Seen by Their Audience. Current Biology http://dx.doi.org/10.1016/j.cub.2010.08.033

Credits: Photos by Endler; videos by Keller

The main lacunae in the above analysis is that it does not cover results from autosomal studies. Some of that has been performed by Dienekes, but more is necessary for a region characterized by as much ethnographic diversity and density as the Caucasus. One peculiarity that emerges in analyses of autosomal data sets is that the Caucasus looms relatively large in a wide array of dispersed populations. For example, there is a genetic signature which ties Indo-Aryan and Caucasian populations together, and others which seem to connect the latter to some Balkan groups.

These are possible hints that the Caucasus is the “mother of nations,” and that the old idea of the “Caucasian race” may have some reality to it. But I would bet on something else: the Caucasus is not the mother of nations, but the repository of forgotten peoples. The Ossetes themselves are presumed to be just such a population. I offer up the hypothesis that one reason that disparate Caucasian populations have diverse and wide-ranging connections has less to do with outward expansion, and more to do with the fact that on the margins of the Caucasus a great range of historic genetic diversity erased by later demographic events (e.g., the Slavic and Turkic expansions from two directions in on the North Iranian peoples) is preserved, as the defeated take refuge.

A constricting snake like a boa or a python kills its prey by suffocation. It uses the momentum of its strike to throw coils around its victim’s body. Then, it squeezes. Every time the prey exhales, the snake squeezes a little more tightly. Soon, the victim can breathe no more.

We’ve known this for centuries but amazingly, no one has worked out how the snakes can tell when to stop constricting. Scott Boback from Dickinson College has the answer. Through its thick coils, a boa can sense the tiny heartbeats of its prey. When the heart stops, the snake starts to relax.

It would be virtually impossible to measure the heartbeat of a live rat while it was being crushed by a snake, so Boback opted for a macabre alternative. He fitted the bodies of dead rats with artificial hearts – two tiny water-filled bulbs connected to a pump – and pressure sensors to measure the snake’s squeezes. In this way, he could isolate the influence of the heartbeats; he didn’t have to worry about other movements that might confuse the results, such as struggling muscles or panicked breaths.

Boback clearly showed that boas finely adjust their coils to the beats of their prey. If the artificial hearts were beating, the boas constricted the rats for twice as long and with twice as much pressure as when the hearts were still. And all the while, they kept on tightening, bit by bit. If Boback stopped the hearts after 10 minutes, the pythons stopped constricting a few minutes later.

Some of Boback’s boas had been caught in the wild, but others had been reared in captivity and had always lived on a diet of dead rats. They had never killed a victim with an actual heartbeat before, but they responded to the artificial beats in the same way as the wild snakes. They did, however, use less pressure than the wild ones. This suggests that constrictors have an innate ability to react to a victim’s heart, but experience tells them how strongly they should do so.

Squeezing the breath out of an animal takes a lot of energy. The snake’s metabolism can shoot up by seven times, and all the while, it’s vulnerable to attack. It would seem to make sense for the snake to precisely detect when its prey has breathed its last.

But there’s something about this logic that doesn’t quite add up. Birds and mammals need a lot of oxygen to fuel their burning metabolisms, and a constrictor should be able to kill them in just a few minutes. Is it really worth being able to sense a victim’s heart if all that does is save a few seconds of effort?

Boback thinks so. He speculates that the earliest snakes from the late Cretaceous period would have often fed on cold-blooded prey, which can cope for much longer without any oxygen. For example, a lizard like an iguana can slow its heart to just one beat every 5 minutes, and stay underwater for up to 4.5 hours. For such animals, the line between still and dead is much subtler, and constrictors would need more acute senses to be able to confirm the time of death.

There’s an alternative explanation. Perhaps the ability to sense the ground beneath their limbless bodies made it easier for early snakes to detect the life signs of their prey. A constrictor’s sensitive side may have evolved from sensitive sides.

Reference: Boback, Hall, McCann, Hayes, Forrester & Zwemer. 2011. Snake modulates constriction in response to prey’s heartbeat. Biology Letters http://dx.doi.org/10.1098/rsbl.2011.1105

Photo by Christian Mehlführer

More on constrictors:

• Meet the Agta, a tribe where a quarter of men have been attacked by giant snakes
• A recipe for growing bigger hearts, found in the blood of pythons
• ‘Wasabi protein’ responsible for the heat-seeking sixth sense of rattlesnakes
• Titanoboa – thirteen metres, one tonne, largest snake ever.
• Snake proteins have gone through massive evolutionary redesign

These two body plans might look radically different, but looks can be deceiving. Chengcheng Ji and Liang Wu from the China Agricultural University have found that starfish have hidden bilateral tendencies, which reveal themselves under times of stress.

Starfish belong to a group of animals called echinoderms, which also include sea urchins, sea cucumbers, brittlestars. As adults, most of the group have five-sided symmetry. As larvae, they’re very different. A baby starfish looks entirely unlike a star and rather like an alien spacecraft, with tentacle-like prongs sticking out from a central bell. The whole structure has a head and is very clearly bilateral. Their five-sided symmetry only emerges when they grow up, but Ji and Wu think that starfish never forget their two-sided beginnings.

The duo studied over a thousand starfish, and exposed them to various challenges to see how they would react. First, they dropped the animals in a new tank of water, waited for them to crawl away, and noted which arms they led with. Next, they turned the animals over. An upside-down starfish pushes two arms against the ground for support and stamps down with the opposite one to flip itself back up. Ji and Wu recorded which arms they led with. Finally, they put the starfish in a shallow tank and dropped an irritating liquid on their backs. Again, as the animals fled, Ji and Wu noted the arms that led the way.

These three challenges revealed that starfish have a hidden bilateral symmetry, and move in a preferred direction. That’s especially obvious when they face stressful situations, such as fleeing or having to turn themselves over.

They tend to lead with the fifth arm. There are many ways of numbering the arms, but here’s what Ji and Wu used. Starfish have a small wart-like valve called a madreporite, which allows water into their bodies. It sits in the central disc, but off to one side. The arm opposite the madreporite is arm number 1, and the rest are numbered clockwise. And it’s the fifth one that usually leads the way. It’s as close to a head as the starfish has.

Ji and Wu think that this hint of bilateral symmetry is a faint vestige of the body that starfish have as larvae. If they have a preferred direction, they could potentially make faster decisions in times of danger.

Ji and Wu now want to see if other aspects of a starfish’s body also conform to this hidden symmetry. For example, the starfish’s brain is spread throughout its body. It has a ring of nerves in its central disc, with spokes branching off into each of the arms. Perhaps these nerves are slightly more concentrated towards the fifth arm, just as our nerves are more concentrated inside our skulls.

Reference: Ji, C., Wu, L., Zhao, W., Wang, S., & Lv, J. (2012). Echinoderms Have Bilateral Tendencies PLoS ONE, 7 (1) DOI: 10.1371/journal.pone.0028978

Photos by Nick Hobgood and authors.

More on echinoderms:

• Fishing bans protect coral reefs from devastating predatory starfish
• Sand dollars avoid predators by cloning themselves
• Sea urchins use their entire body as an eye
• Pocket Science: Stealth mode in the sea

The idea of a “folk wandering” was once a well accepted idea in history, in particular for the phase of the Late Roman Empire, and the subsequent fall of the Western Empire. It’s a rather simple concept: the collapse of the Pax Romana occurred simultaneous with a mass ethnic reordering of Europe, primarily via the migration of Germanic peoples across its frontiers and beyond. The most extreme depictions of this can be found in the works of the British cleric Gildas: German hordes literally drove the British into the sea, until they only retained their redoubts around the “Celtic Fringe.”

This was an extreme understanding of the dynamics of post-Roman Europe. It was, and has been, succeeded by another extreme model: that the ethnic change in the post-Roman world was more illusion than substance, a manner of shifting nomenclature, than lineage. For example, I have commonly read in this literature that the Germanic tribes which crystallized as “federates” to the Romans, or on occasion as antagonists (or vassals to hostile powers such as the Huns) were ad hoc collections of mercenaries who created an identity de novo.  In some cases it is posited that masses of Romans simply assimilated to the identity of a small cadre of warriors whose demographic impact was trivial. This is the scenario that is posited for the transformation of Celtic Britain into Germanic England. But let’s shift away from that extreme case, and look at another one: the 5th and early 6th century kingdom of the Vandals in Norh Africa.

The Vandals were a German tribe with a rather unsavory reputation (perhaps undeserved, but it is what it is). Originally after breaking into the Roman Empire they were junior partners in Spain to a confederation of Iranian tribes, the Alans. But in a series of conflicts the Spanish Alans were reduced to a shadow of their former selves by Romans or Roman federates (e.g., Visigoths), and they allowed themselves to be assimilated into the Vandal power structure. When the Vandals moved into North Africa, they took the Alans with them. And just as the monarchs of England were monarchs of Scotland distinctly, in the 17th century, so the king of the Vandals was separately a king of the Alans.

What does this have to do with genetics? Easy. A few years ago the historian Peter Heather came out with a book, Empires and Barbarians, where he attempted to resurrect the idea of a folk wandering. Instead of the idea of post-Roman Europe being dominated by the rapid emergence of ethnic identities from a small platoon of warriors, he posits that there were general transfers of the freeborn caste of whole Germanic tribes across Northern Europe. The women and children moved with the men. Heather’s thesis is more modest than that of Gildas. He does not suggest there was total, or even wholesale, replacement. Rather, the Franks, Visigoths, Anglo-Saxons, etc., were not rapid social constructions on a chaotic cultural landscape, but peoples which were organic developments out of a broader Germanic cultural milieu who were transplanted in toto across the post-Roman world. The kludge of a dual monarchy in the case of the king of the Vandals and Alans does not make much sense if ethnic identity was so fluid as to be purely instrumental in a proximate sense. Rather, even in extremis the Alans insisted upon retaining their identity as a people in the face of the more practical option of total assimilation into the Vandal horde. If ethnic identities are purely ephemeral labels given to political coalitions of mercenaries this behavior makes no sense. On the other hand if these identities carry with them the weight of history, of cultural memory, then these actions and baroque compromises are rendered understandable.

The Vandal kingdom of North Africa in some ways is probably the most least plausible case for a folk wandering, in that the wandering was quite extensive, and the Vandal kingdom seems to have been the least culturally robust its long term impact (suggesting perhaps a superficiality of their hegemony). And I have read scholarly literature which does argue that the concept of “Vandal” and “Alan” were simply constructs, which post-Roman elites easily took upon when the circumstances suited them. There is something to the idea that individuals can acculturate, but I think what the idea of radical social constructionism in post-Roman Europe misses is that you need a culture to assimilate to, and that culture can only exist in the first place due to a critical mass. Could a small number of German and Iranian warriors, without any women or other elements of their freeborn population replicate their tribal culture over thousands of miles? I think not. Single elements of culture are replicable, but whole cultural systems often exhibit more integrity and contingency than is obvious from the outside.

To explore the possibility of Germanic ancestry in North Africa I decided to use the Henn et al. data set. I merged it with the Utah white sample from the HapMap. I then had 188,000 markers. My goal was to find runs where Southern and Northern Europeans were distinct. Below are two sets of runs where Northern and Southern Europeans were distinct. The first are supervised, and the second unsupervised.

[Show as slideshow]

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K = 8, unsupervised

K = 8, Algerians, Andalucians, N. Moroccans unsupervised

K = 8, supervised

K = 8, Algerians, Andalucians, N. Moroccans supervised

I don’t really see any good evidence of the impact of specifically a German element in this. The Vandals seem to fail the test of long term demographic impact in these samples. To really explore this issue I’d have to look at the ancestry at the chromosomal level, and look for matching haplotypes and segments identical-by-descent. Perhaps I will in the future.

Image credit: Wikipedia

It probably went a bit like this. A single cell split into two and rather than going their separate ways, they stayed together. This happened again and again. Eventually, the groups of individual cells became individuals of grouped cells, evolving as a unit. It’s the story of how I became we, and how we became I again.

In an elegant new experiment, William Ratcliff from the University of Minnesota has shown that this story could have been a surprisingly quick one. In his laboratory, he successfully nudged single-celled brewer’s yeast into multicellular clusters, within just a few months. The clumps of cells evolved as one. They even developed a primitive division of labour, with some of them deliberately dying so that the others could grow and reproduce.

I’ve written about this discovery for Nature News, so head over there to read the full take.

Over here, I want to emphasise that Ratcliff’s work isn’t meant to directly recap how multicellularity evolved in any particular group. It’s meant to look at the general principles that govern this transition. Richard Lenski, another evolutionary biologist famous for his work on bacteria, adds, “They’re not saying that it happened in nature the way it happened in their experiments. The point of experimental evolution is to test hypotheses and watch evolution in action, not to replicate a specific event from some point in the distant past.”

Ratcliff’s work shows that this transition, from one cell to many, could have happened much more quickly than anyone expected. To set his yeast along that path, all he had to do was to let them sink. In a tube of liquid, clumps of yeast will settle faster than single cells. By picking and growing the cells that sunk quickest, Ratcliff selected for those that tend to stick together.

Many single-celled microbes clump together to create multicellular entities, from predatory bacteria like Mxyococcus to slime moulds like Dictyostelium. Yeast cells sometimes do this too – they form clumps called ‘flocs’. Ratcliff says, “My original guess was that we flocculation would evolve, but that’s not what we saw.”

Within 60 days, the yeast had evolved clusters of many cells, radiating out into microscopic ‘snowflakes’. Unlike flocs, these flakes weren’t clumps of unrelated cells. They were formed by genetically identical cells that grew and divided, but never separated. That’s similar to what happens in our own bodies. A single cell – a fertilised egg – grows and divides into trillions of cells that all stay together.

Many other studies have shown that sticking together would have provided benefits for single cells. “We can be fairly confident that, early on, large size was beneficial”, says Ratcliff. In a cluster, single cells are better at absorbing nutrients from their environment, surviving through rough conditions, or escaping predators.

But these studies only hint at the conditions that encourage cells to stay in groups. Ratcliff’s experiments speak to something subtler and more important: the transition from groups of distinct cells to true multicellular individuals. That’s what his snowflakes were. As I write in the Nature piece:

The snowflakes behaved like true multicellular organisms. They had a simple life cycle with a juvenile stage, when they grew unimpeded, and an adult one, when they reached a certain size and split into a large parent flake and a smaller, daughter flake.

Ratcliff could even tune these stages. If he cultivated only those snowflakes that settled faster, he ended up with larger ones that grew bigger before splitting. This confirmed that natural selection was acting on the entire flake, rather than on the individual cells within it. “They survive as a whole, or they die as a whole. Selection shifts to the multicellular level,” says Ratcliff.

The snowflakes split because some of their component cells sacrifice themselves, allowing pieces to snap off. These individual cells die for the good of the whole, allowing the parent flake to continue growing and produce many offspring.

This mirrors a critical division in other multicellular creatures, such as us, between two groups of cells – the soma (body) and the germline. Lenski explains the difference well: “The vast majority of cells in our bodies are soma, and those cells won’t live beyond our individual mortal existence.  But the germline cells produce the sperm and eggs. Through reproduction, these privileged cells are, in some sense, immortal. Their lineages can go on and on, even after we die, so long as the bodies they build from fertilized eggs survive to reproduce in each generation.” The same is true for the yeast snowflakes. The dying cells are like the soma, and the surviving ones are like the germline.

Reference: Ratcliff, Denison, Borrello & Travisano. 2011. Experimental evolution of multicellularity. PNAS http://dx.doi.org/10.1073/pnas.1115323109

Images and video by Will Ratcliff

I was holding my 1-year-old, ambling about downtown with some friends. White friends. She must have thought my boy belonged to one of them.

There’s a simple explanation: I’m black but my son, Ashe, is white. At least he looks it.

But things are more complicated than that.

I’m actually half black and half white. It should come as no surprise, though, that even as sophisticated as we’ve become about people of mixed parentage, I’m pigeonholed as black. If someone asks and I don’t have time to go deeper, that’s what I call myself.

Ashe is mixed too. His mother, my wife, Vanashree, is half white and half South Asian, with roots in India. She has olive skin, and Ashe is slightly lighter than she is.

This surprised us. When Ashe was born, one of the first things I said to Vanashree was, “Honey, he’s so light!” We chuckled, poking fun at our assumptions.*

Let’s get the sociological aspect out of the way. Is this really that surprising? Folk-biology has always had the concept of a “throwback,” which really distills the reality of Mendelian inheritance (as opposed to simple blending processes). In societies such as Brazil or India where there is a fair amount of segregation of polymorphisms which control skin color it isn’t that unheard of for a child to be darker or lighter in tone than both parents. And more frankly, this is not unknown within the African American community, where there is a range of skin tone due to ~20% European admixture. I suspect many African American would have these “assumptions,” because of an intuitive understanding of the unpredictable nature of the inheritance of this trait.

Second, the author of the piece is half black and half white in social terms, but there is no chance he is 50 percent African in ancestry. Barack H. Obama is 50 percent African in ancestry, but African Americans almost always have some admixture. I’ve analyzed ~150 African Americans in terms of their ancestry, and they always have some European ancestry. In fact the few Africans in my data set jump out because they lack this component. In other words, the author’s child is somewhat more than 50 percent European in ancestry.

Finally, what’s the science behind this? This isn’t that  hard to actually understand, because the genetic architecture of pigmentation has been well elucidated. Only a few genes control most of the variation across populations (the difference we see between Africans and Europeans, South Asians and East Asians). Because we know the parents’ ancestry we can make a few educated guess.es The largest effect size upon of a gene pigmentation in a given individual is probably from SLC24A5. The father is likely  a heterozygote on this at the SNP in question, with a “light” European copy, and a “dark” African one. The mother is most likely, though not inevitably, a homozygote; the frequency of the “light” copy is well north of 50 percent in South Asians (I’m a homozygote, as are both my parents). So the child has a 50 percent chance of being a heterozygote or a “light” homozygote. That’s some of the answer right there. Because the child does not have blue eyes we know that they are unlikely to be homozygote for the combination of markers which is correlated with blue eyes (probably due to a regulator element on the HERC2 locus). This is also associated with lighter complexion and hair color. But there is another locus which I think would be especially important: SLC45A2. There is a “light” variant here which is highly localized to Europeans. Its frequency is 95 percent in Northern Europe, and 15 percent in Northern India (85 percent in Northern Italy, 65 percent in Turkey, etc.). It is not found in East Asia or Africa, except in cases of clear admixture with Europeans. Europeans who are homozygote for the “dark” variant tend to be olive skinned (this genotype is relatively rare, though not unheard of in Southern Europe as per the frequencies above). Both the parents in this case would almost certainly be heterozygotes. This means that their son had a 25 percent chance of exhibiting the Northern European genotype. That is a straightforward explanation for why he might be lighter than either parent. Of course there are a few other genes of some importance, but I suspect that SLC45A2 is where most of the work is done in this case because of the backgrounds of the parents (i.e., I’m pretty sure they’re heterozygotes).

I understand that the point of the article was not the genomics of pigmentation. But to talk about social matters it sometimes pays to get the science nailed down. Like it or not this is a time in the United States where people of mixed ancestry are going to be more common. I rarely get the “Where are you from?” question anymore (because I’m not black or white), but I wonder if the “What are you?” (asked of mixed-race individuals) is going to persist a little longer.

* I think lurking within the subtext of the article is the salience of African ancestry, and the idea that it is particularly potent. The author’s wife’s background is mentioned almost in passing, before moving back to the main attraction of the child of an African American no longer appearing visibly African American. Many of the ideas of white nationalist thinkers such as Madison Grant may no longer be in vogue, but their idea that African ancestry was particular powerful in swamping out all other ancestry remains an unspoken assumption in American society.

Lactase persistence is a dominant trait. That means any individual with at least one copy of the T allele is persistent. As Maju noted a peculiarity here is that the genotypes are not in Hardy-Weinberg Equilibrium. Specifically, there are an excess of homozygotes. Using the SJAPL location as a potentially random mating scenario you should expect ~7 T/C genotypes, not 2. Interestingly the persistent individual in the Longar location also a homozygote.

HWE makes a few assumptions. For example, no selection, migration, mutation, or assortative mating. Deviation from HWE is suggestive of one of these dynamics. The sample size here is small, but the deviation is not to be dismissed. Recall that lactase persistence has dominant inheritance patterns. If the trait was being positively selected for you would only need one copy. The enrichment of homozygotes is unexpected if selection in situ is occurring here. It can not be ruled out that one is observing the admixture of two distinct populations. One generation of random mating would generate HWE, but when populations hybridize in realistic scenarios this is not always a plausible assumption. Rather, assortative mating often persists over the generations, slowing down the diminishing of population substructure.

Stepping back from speculation in this case what can we say? First, the LCT locus has a large mutational target. The trait of lactase persistence has arisen multiple times via different mutational events across the Old World. But, there does seem to be one particular variant which is found from Spain to Northern India. There is some circumstantial evidence that the allele had its origin somewhere in Central Eurasia, but currently its modal frequency is in Northern Europe, Scandinavia and Germany. The region in the genome around this mutation is characterized by a very long haplotype. It is one of the most definitive loci as a candidate for natural selection in the human genome. There is now a fair amount of ancient DNA evidence that lactase persistence in Europe is a feature of the last ~5,000 years or so. Among the modern Basques the frequency of the allele is 66 percent.

For me the key issue is teasing apart the role of migration and selection in each specific case. It does not seem to be correct that the frequency of the -13910T LCT allele in Basques and Punjabis is reflective of the frequency of recent common ancestry. That implies that natural selection is at work at this locus. On the other hand, the haplotype which is present in both the Basque and Punjabis is likely to be descended from a common set of individuals, implying that there is a genealogical chain connecting these two very distinct and distant Eurasian populations. Therefore, we can potentially make some inferences about the power of migration in spreading distinctive alleles. Often we partition selection from genealogical information, because selection so often serves to distort the signal. But the genealogical patterns may lay at the heart of the distribution of different natural selective events at the LCT locus.

Overall, I would say that the results from ancient DNA are disordering and clouding simple elegant models. One hopes and presumes that as sample sizes increase in this domain we’ll start to see more clarity as new paradigms crystallize.

Citation: European Journal of Human Genetics, 10.1038/ejhg.2011.254

For me the simplest option is to look at relatives. Each of my grandparents happens to have had siblings, so there are many sets of relatives related to just each of those individuals of interest. I also have many cousins, so pooling all the genotypes together and using the information of a pedigree one could ascertain which chromosomal segments are likely to derive from a particular grandparent. To give a concrete example, my mother has a maternal cousin to whom she is quite close. By typing my mother and her cousin one could infer that the segments shared across the two individuals derive from the common maternal grandparents. Of course there’s a problem that cousins have a coefficient of relatedness of only 1/8th, so there is going to be a lot of information missing. But, if you had lots of cousins you could presumably reconstruct the genotypes far better.

But what if you didn’t have any of this? I came up with a crazy idea, and I want to throw it out there to see how crazy it is. The issue from the perspective of you, the indivdual without grandparental information, is that for either your mother or your father you don’t know which homologous chromosomes come from which parent (your grandparents, their parents). As it happens, everyone has a male parent and a female parent. So if you can assign a a chromosomal region as having come from the male, and another as having come from the female, then you can reconstruct some of your grandparents’ genotypes because you know their sexes. How can you make this determination?

Genomic imprinting. This is a phenomenon where genes from a given parent, often of a particular sex, are expressed, while those of the other sex are repressed (often it manifests in terms of methylation or lack of methylation). Therefore, if you have a gene, A, which is usually expressed if inherited from a male parent and repressed if it is inherited from a female parent then the state of that gene within a chromosomal region can be a “tag” for the sex of the parent of origin. With enough of these imprinted genes you can create a mosaic of the genome of the individual in terms of sex of origin. Obviously genomic regions from different sexes are from different parents. If you have enough children of these two parents you should be able to infer the whole genomes of these individuals.

The big reason this probably won’t work is that there just aren’t enough imprinted genes in the human genome. But what do readers think?

There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with just one group. The first author on this new paper is Brenna Henn, who was also first author on another paper with a diverse African data set. Importantly the data was posted online. Unfortunately though most of the populations didn’t have too many markers. This isn’t an issue in an of itself, but it becomes a big deal when trying to combine it with other data sets. If you limit the markers to those which intersect across two data sets you start to thin them down a lot, to the point where they’re not useful. Though the the results of the paper are worth talking about, the authors claim that they’ll be putting the data online. This is important because they used a large number of markers, so the intersections will be nice (I can, for example, envisage exploring the relationship between the North Africans and the IBS Iberian sample in the near future).

As for the paper itself, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations:

Proposed migrations between North Africa and neighboring regions have included Paleolithic gene flow from the Near East, an Arabic migration across the whole of North Africa 1,400 years ago (ya), and trans-Saharan transport of slaves from sub-Saharan Africa. Historical records, archaeology, and mitochondrial and Y-chromosome DNA have been marshaled in support of one theory or another, but there is little consensus regarding the overall genetic background of North African populations or their origin and expansion. We characterize the patterns of genetic variation in North Africa using ~730,000 single nucleotide polymorphisms from across the genome for seven populations. We observe two distinct, opposite gradients of ancestry: an east-to-west increase in likely autochthonous North African ancestry and an east-to-west decrease in likely Near Eastern Arabic ancestry. The indigenous North African ancestry may have been more common in Berber populations and appears most closely related to populations outside of Africa, but divergence between Maghrebi peoples and Near Eastern/Europeans likely precedes the Holocene (>12,000 ya). We also find significant signatures of sub-Saharan African ancestry that vary substantially among populations. These sub-Saharan ancestries appear to be a recent introduction into North African populations, dating to about 1,200 years ago in southern Morocco and about 750 years ago into Egypt, possibly reflecting the patterns of the trans-Saharan slave trade that occurred during this period.

The model outline here is straightforward:

- A population of West Eurasian provenance migrated across the fringe of the southern Mediterranean >10,000 years B.P. (Maghrebi)

- This was later overlain by a later West Asian migration (Near Eastern)

- A third major element here seems to be Sub-Saharan African admixture, which these authors claim is rather new (post-Roman)

Two of the methods used will be familiar to readers of this weblog. They used ADMIXTURE to generate barplots which fractionate putative ancestral components given K number of components. Second, they also use PCA to visualize the largest components genetic variation within the samples on a plane.

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As you “move up” the K’s you note that Maghrebi populations “split” from the Near Eastern reference, the Qataris. This is supported by the PCA, which shows that there is a dimension of variation which separates Near Easterners & Europeans from Maghrebis. The authors note that this dimension is orthogonal to the Sub-Saharan African vs. Eurasian component. That suggests that the putative Maghrebi component is likely to be part of the set of “Out of Africa” populations, rather than an African population which simply experienced continuous gene flow with West Eurasians.

They also estimate a Fst, a statistic which partitions genetic variation within and between groups. The value between Sub-Saharan Africans and Europeans is ~0.15 using HGDP SNP data, and between Europeans and East Asians ~0.10.  Using the Tuscans and Qataris as European and West Asian references against the North African populations along their east-west cline they estimate Fsts from ~0.03 to ~0.06. The higher end values are from populations which are less admixed with Near Eastern elements, and the colored polygons illustrate the domain generated by ADMIXTURE Fsts across inferred ancestral components. You also see in the chart estimated time of divergence. I won’t get into the assumptions in the model, but the authors do note that ~12,000 years B.P. seems to be the low bound estimate for when the Maghbrebis diverged from other West Eurasians. This is important, because it predates agriculture.

The final set of methods outlined in this paper looked at ancestry on a more fine-grained genomic scale. To the left you see a plot where each horizontal bar represents an individual’s chromosome 1 (among a set of North Africans). Each color in that bar indicates a component of ancestry (except the black, which are centromeres). This sort of information is important, because saying someone is 50% X and 50% Y summarizes information to the point of eliding it. An individual who is a first generation product of a Chinese-European marriage is going to have the same ancestral proportions as someone who is a Uyghur for those respective populations. But a fine-scale mapping of the genomic ancestry would look very different, because the history of the admixture is very different.

There are many inferences in the paper which I won’t address. Rather, let me focus on this one assertion:

After accounting for putative recent admixture (Figure 1), the indigenous Maghrebi component (k-based) is estimated to have diverged from Near Eastern/Europeans between 18–38 Kya (Figure 3), under a range of Ne and k values. We hence suggest that the ancestral Maghrebi population separated from Near Eastern/Europeans prior to the Holocene, and that the Maghrebi populations do not represent a large-scale demic diffusion of agropastoralists from the Near East.

This is not implausible on the face of it. The component of ancestry modal in the Mozabite HGDP sample tends to have a relatively high Fst in relation to other West Eurasian groups. I had wondered if this was due to ancient Sub-Saharan African admixture which had produced a particular stabilized hybrid, but these results indicate that the component is no closer than other West Eurasians. What I’m confused and skeptical about are the range of divergence times which different papers are producing which seem somewhat implausible taken together.

There are papers which posit that East Asians separated from Europeans ~25,000 years B.P. This is in the same range as the divergence between Maghrebis and West Eurasians, but the Maghrebi genetic distance (Fst) is about 1/2 as great. Also, these sets of results which generate a “bunching” together of the separation of many extant non-African lineages in the 20-40,000 year range imply very rapid differentiation after the “Out of Africa” event, if that event did occur ~50,000 years ago (at least for most Eurasians, even assuming a revised model whereby Australian Aboriginals derive from an earlier wave). One at a time any given divergence estimate may be broadly plausible, but the literature is just not particularly coherent on this matter, and it often seems archaeologically implausible.

Citation: Henn BM , Botigué LR , Gravel S , Wang W , Brisbin A , et al. 2012 Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397

Image Credit: Raphaël Labbé

Less than a month after Kraus’s announcement, Eric Rittmeyer and Christopher Austin from Louisiana University have found an even smaller frog, just 7 to 8 millimetres long. It’s dwarfed by a dime. It’s not just the world’s smallest frog, but the world’s smallest back-boned animal.

The new species, Paedophryne amauensis, is a close relative of the tiny pair from December – Paedophryne dekot and Paedophryne verrucosa). Extremely tiny frogs have evolved at least 11 times, but the Paedophryne group is unique in that all of its members are miniscule. They were first discovered in 2002, and six species have been discovered so far. All of them live in Papua New Guinea. Clearly, this corner of the world is a haven for the tinier side of life.

The Paedophryne frogs are, for obvious reasons, almost impossible to spot. But they can be easily heard. Their high-pitched calls make them sound like crickets, and perhaps explorers have long mistaken them for insects. “It doesn’t sound like a frog at all,” says Austin, who had no idea what was making the call when he first heard it. “After several failed attempts to find it, we ended up just scooping up a big handful of leaf litter where the call was coming from and putting it all in a clear plastic bag. We went through that bag leaf by leaf until we discovered the incredibly small frog making the call.”

The frogs all have a number of space-saving features to help them cope with such small bodies. Their feet and skulls have simplified and now contain fewer bones. Some of their toes have shrunk to useless nubs. They have lost some of their vertebrae. They never go through a tadpole stage either. They begin life looking like adults, albeit even smaller.

Many other normal-sized frogs have done away with their tadpole forms, probably because tadpoles are very vulnerable to underwater predators from fish to insects. Austin thinks that extremely small tadpoles would be so susceptible to such predators that they couldn’t survive. This means that the tiniest of frogs could only have evolved from lineages that have no tadpole stage.

The Paedophryne frogs also have a much higher surface area for their size than their bigger relatives, so they’re very vulnerable to drying out. For amphibians, which are usually so reliant on their ties to water, that would be fatal. This might explain why all the Paedophryne frogs live in the damp leaf litter of tropical rainforests, or among moist moss. They spend their lives in a perpetually moist world. It’s probably no coincidence that in drier forests, further from the equator, there are no extremely tiny frogs.

The frogs probably evolved to be tiny by stunting their growth early. There’s evidence for this in their skeleton. In normal-sized frogs, some parts of the skeleton only harden into solid bone later on in adult life. In the tiny Paedophryne frogs, these pieces stay relatively soft. They live an adult life in a youngster’s body.

This phenomenon is called paedomorphosis, and it’s a common trend in evolution. For example, it accounts for the tiny size of Paedocypris progenetica, the fish that held the record of world’s smallest vertebrate, until P.amauensis snatched the title by a millimetre.

These frogs aren’t rare oddities. Based on these calls, Rittmeyer and Austin thinks that they are are everywhere. If you found one, there would probably be another within 50 centimetres. They are important parts of their communities. “The insect like mating call and incredibly small size of these frogs, combined with relatively limited research effort in New Guinea, is why they have gone undetected for over 200 years,” says Austin. Discoveries like these tell us how much we still don’t know about amphibians, just as the group is struggling to survive.

Reference: Rittmeyer, Allison, Grundler, Thompson & Austin. 2011. Ecological Guild Evolution and the Discovery of the World’s Smallest Vertebrate. PLoS ONE http://dx.doi.org/10.1371/journal.pone.0029797

More on really tiny things:

• How tiny wasps cope with being smaller than amoebas
• Coin-sized frog becomes mite-y thanks to poisonous diet
• Newly discovered fish crosses Peter Pan with Dracula