The Unz Review: An Alternative Media Selection
A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
Email This Page to Someone

 Remember My Information

Authors Filter?
 TeasersGene Expression Blog

Bookmark Toggle AllToCAdd to LibraryRemove from Library • BShow CommentNext New CommentNext New ReplyRead More
ReplyAgree/Disagree/Etc. More... This Commenter This Thread Hide Thread Display All Comments
These buttons register your public Agreement, Disagreement, Thanks, LOL, or Troll with the selected comment. They are ONLY available to recent, frequent commenters who have saved their Name+Email using the 'Remember My Information' checkbox, and may also ONLY be used three times during any eight hour period.
Ignore Commenter Follow Commenter
🔊 Listen RSS

The above figure is from a paper which leaves me somewhat befuddled, Genome-wide data substantiate Holocene gene flow from India to Australia. The authors ran several hundred thousand SNPs through treemix, and generated the above graph which leads one to the conclusion that there has been significant gene flow from Indian populations to Australia. More precisely, from Dravidian populations to the Aboriginal peoples of Northern Australia. In plain English the authors found the tree which was the best fit to the data, and then they improved it by by adding migration across branches which were the poorest fits.

Obviously the whole paper is not going to rest on the above graph. They performed some clustering analysis on the data, which you’ll recognize. PCA and Admixture:

Additionally they ran f4 statistics to infer admixture by testing various trees of populations. They confirmed that there seemed to be some evidence of gene flow from India to these Australian Aboriginal populations which was not found in Papuans.

Finally, they estimated that the admixture between these Indians and Northern Australians dates to ~4,320 years ago. I haven’t ever used this method so I can’t really say much about this, but I did not see any confidence interval in the paper or the supporting information. That’s important to me because I want to know the window of this date of admixture, as that matters (I don’t know the method well enough to know whether you can’t really compute a confidence).

The authors’ general line of reasoning seems to be that there’s a lot of modest evidence using separate methods pointing to this admixture, so we shouldn’t dismiss it. Additionally, the date of admixture aligns with the change in archaeology and the introduction of the dingo, a wild dog which happens to resemble the feral populations of India. This seems a prudent way to go. But I have some reservations.

First, it would be nice if we could see these Australian data. In the HGDP data set Papuans are used as proxies for Australasians. One wouldn’t discern peculiarity in Australian admixture, because those data sets aren’t floating around. As alluded to in many press treatments this is a political issue. Second, several years ago some of the best minds in human phylogenomics already tackled the issue of Australian affinities with other populations. One of the groups even had Indian samples and used some of the same Northern Australians. How is it that they didn’t see this with clarity?

I am not convinced that this interpretation of the population genetic data is correct. There is something about the affinities of Australasians going by the Papuan samples which intrigues me. But I can’t speak with any intuition about the Australians, because I have never touched Australian data. Of course I have become concerned with the abstruse and nearly opaque nature of statistical genetics. One solution is for a wide array of individuals to develop intuition by taking data and methods for a “spin.” That’s not likely in this case because of the sensitivity of this line of research

And yet let’s consider this paper as yielding a genuine result which will stand the test of time. What the hell does this mean? ~4,000 years ago there flourished in South Asia what we term the Indus Valley civilization. In the Near East this society was known as Meluhha. Because we can not read the script of the Indus Valley civilization they are silent to us, evident in literary documentation only as an aside in Mesopotamian chronicles. But we do know that the Meluhhans were active traders in the ancient Persian Gulf, and Mesopotamian accounting records note descendants of Meluhhan merchants resident in particular villages.

Language families of Australia

We know that these people went west. But did they go east, even as far as Australia? It seems to me and others that if such an admixture occurred, and some elements of cultural changed were catalyzed by South Asians, it was an accident. A ship blown off course which somehow arrived on the shores of ancient Australia. This is where the genetics ends. We need to look at archaeology and folklore. Lingistics and anthropology.

In a few years other workers will look at whole genome data from Australians and other populations. The question of their affinities will be definitively answered. Until then I suspect we’ll muddle on….

🔊 Listen RSS

Just realized. The Science paper has some interesting dates which allows us to make the above inference.

– Separation between Europeans and East Asians 25-38 thousand years before present.

– Gene flow between proto-East Asians and proto-Australians before the Native Americans diverged from the former 15 thousand years before the present.

– A conservative first landing in Australia 40-45 thousand years before the present.

The Native American result, where they share some derived variants unique to East Eurasians (mutations which emerged after the separation from West Eurasians) with Aborigines, pegs a minimum date of admixture ~15,000 years ago. But, obviously the admixture had to occur after the divergence of West and East Eurasians. Let’s say ~30,000 years ago. Even assuming that the gene flow between East Eurasians and proto-Australians occurred immediately after the separation 38,000 ago, there were anatomically modern humans in Australia for thousands of years already! The implication is that the first Australians by necessity can not have contributed in totality the ancestry of modern Aborigines. The AJHG paper gives a 50:50 estimate for the ratio of proto-Australian and the Andaman Islander/Malaysian-Negrito related population. We don’t need to be certain of the exact value to assume that numbers like this imply considerable admixture above trace levels.

Of all the dates I’m probably most confident about the archaeological ones about the settlement of Australia by anatomically modern humans. 46,000 years ago the megafauna started going extinct. That’s an immediate tell that humans have been let into the garden.

🔊 Listen RSS

The most interesting chart below is infant mortality rate over time.

🔊 Listen RSS

ozlang2Richard Broome’s Aboriginal Australians is one of those books which I own which I finally managed to finish recently. It was a quick overview of Australian Aboriginals and their relationship with the settler society, and later in modern Australia. From what I could tell it was a serviceable introduction, though it took a persistent preachy tone whereby one was repeatedly reminded that the Aboriginals were an ever-peaceful people in harmony with nature, notwithstanding their regular burnings of the landscape and inter-tribal brawls. They were in timeless equilibrium with the land that they loved before the white man arrived to destroy their idyll with the shock of modern civilization. The narrative is presented as if the Aboriginals were almost totally static, and perfectly optimized to the environment that was Australia. I personally think this sort of model makes indigenous people less than human, even if it turns them into angels instead of beasts. Of course it’s probably impossible to not have a strong perspective in this sort of material, and I suppose this type of treatment evens out the ledgers of the past. But one can discern the major themes from the subtle and not-so-subtle polemic easy enough.

One aspect of Aboriginal culture which I have wondered about is its perceived uniformity. The Dreamtime is discussed as if it’s a cultural universal among Australian Aboriginals. Is it? A little poking around indicates that Aboriginals seem to share the idea, though with variations. How’d that come to be? Broome’s model seems to assume that the Dreamtime has deep roots in Aboriginal culture, but we know that the roots likely don’t preexist their arrival in Australia, the people of New Guinea and Melanesia don’t have the concept. It may be that they lost the concept, but I doubt that all of them would. Rather the Dreamtime’s ubiquity in Australia may reflect demographic and cultural change within Australia since the arrival of modern humans ~50,000 years ago.

A paper I reviewed last summer used a thick survey of SNPs to place Australian Aboriginals in their proper global genetic context. One of the major shortcomings of that paper was that it had a small sample size from one specific Aboriginal population, and, that population was heavily admixed with Europeans. With intermarriage rates on the order of 70-80%, and a large load of European ancestry already in the Aboriginal community, the number of “pure” Aboriginals will decline rapidly in the the coming century. So I was curious enough to look for a paper which surveyed a wider range of Australian Aboriginal people. I found one, from 2007, A comprehensive analysis of microsatellite diversity in Aboriginal Australians:

Indigenous Australians have a unique evolutionary history that has resulted in a complex system of inter and intra-tribal relationships. While a number of studies have examined the population genetics of indigenous Australians, most have used a single sample to illuminate details of the global dispersal of modern humans and few studies have focussed on the population genetic features of the widely dispersed communities of the indigenous population. In this study we examine the largest Aboriginal Australian sample yet analysed (N = 8,868) at fifteen hypervariable autosomal microsatellite loci. A comprehensive analysis of differentiation indicates different levels of heterogeneity among indigenous peoples from traditional regions of Aboriginal Australia. The most genetically differentiated populations inhabit the North of the country, in particular the Tiwi of Melville and Bathurst islands, Arnhem Land (itself divided into West and East Arnhem), and Fitzmaurice regions. These tribal groups are most differentiated from other Aboriginal Australian tribes, especially those of the Central Desert regions, and also show marked heterogeneity from one another. These genetic findings are supportive of observations of body measurements, skin colour, and dermatoglyphic features which also vary substantially between tribes of the North (e.g. Arnhem Land) and Central Australian regions and, more specifically, between the Tiwi and West and East Arnhem tribes. This study provides the most comprehensive survey of the population genetics of Aboriginal Australia.

Though not totally representative of the geographic expanse of Aboriginal peoples, the sample size here was still huge. But, they looked only at fifteen microsatellite. Microsatellites mutate fast and so have a lot of variation to draw upon, but fifteen is a rather low number compared to the 160,000 core SNPs used in the paper from last summer. So here you have a trade off between population converge and depth of the genomic survey.

Below are the primary results. First are the Fst values comparing regions, and sub-regions. Second a PCA which shows the relationship between populations. Finally, a fine-grained neighbor-joining tree which shows the geographical clusters.

[nggallery id=17]

My Australian readers can make more informed inferences, so I won’t say too much, aside from the impression that genetic distinction seems to correlate well with linguistic distinction. Here’s their conclusion:

The principal findings of this study are that the most differentiated tribal groups are located in three regions, West Arnhem Land, East Arnhem Land and Tiwi, all of which share borders with one another in the Central North of the continent. These tribal groups are most differentiated from other Aboriginal Australian tribes, especially those of the Central Desert regions, and also show marked heterogeneity from one another. These genetic findings are supportive of observations on body measurements….

Citation: Journal of Human Genetics 52, 712-728 (September 2007) | doi:10.1007/s10038-007-0172-z

Image Credit: Wikipedia Commons

• Category: Science • Tags: Anthropology, Australia, Genetics 
🔊 Listen RSS


“…the occupation of Australia/New Guinea is momentous in that it demanded watercraft and provides by far the earliest evidence of their use in history. Not until about 30,000 years later (13,000 years ago) is there strong evidence of watercraft anyway else in the world, from the Mediterranean.

Initially, archaeologists considered the possibility that the colonization of Australia/New Guinea was achieved accidentally by just a few people swept to sea while fishing on a raft near an Indonesian island. In an extreme scenario the first settlers are picture as having consisted of a single pregnant young woman carrying a male fetus. But believers in the fluke-colonization theory have been surprised by recent discovers that still other islands, lying to the east of New Guinea, were colonized soon after New Guinea itself, by around 35,000 years ago….”

– page 42 of Guns, Germs and Steel

The settlement of Australia is a breakthrough in the “human story.” Very soon after anatomically modern humans began to replace (and to some extent assimilate) other lineages of our genus in Eurasia we pushed beyond the previous outer limits of the domains of humankind. The ancestors of Australian Aboriginals swept past the Wallace Line, and quickly settled the Ice Age continent of Sahul, consisting of Australia and Papua New Guinea. The biogeography of Australia is well known. Aside from bats and some endemic rodents the continent was free of placental mammals before modern humans arrived.

As for when these humans made landfall, there is some debate as to that particular issue. The oldest remains from Australia, Mungo Man, has been dated to anywhere between 70,000, and 30,000, years before the present. If we took the older date then Australia would have been settled almost immediately after the expansion of non-African modern humanity. If we accepted the younger date, then the settlement of Australia would have been concurrent with the final replacement of Neandertals by modern humans in Europe. The current consensus seems to be that Mungo Man dates to approximately 46,000 years before the present. As the first dating of a particular individual from a species in a region is liable to miss earlier individuals who were not fossilized it seems likely that Australia was settled by anatomically modern humans on the order of 46,000 years before the present, but somewhat earlier than that date. That would imply that Australia was populated by anatomically modern humans at least 10,000 years before Europe. One should probably not be too surprised by this. Out-of-Africa humans were probably initially tropically adapted so lateral migration would have been easier, but also, there were no hominin competitors in Australia.

But how do these archaeological insights relate to the current Aboriginal population of Australia? Such questions are fraught with politics, but let’s put that to the side. We know that Australia was not totally isolated from the rest of the world. The dingo arrived from Southeast Asia within the last 4,000 years. The Aboriginals of northern Australia were certainly familiar with the idea of agriculture, because they traded with the Torres Straits Islanders, who were farmers and seafarers, and who had contacts with New Guinea (see After the Ice). Some anthropologists, such as Joseph Birdsell, proposed that modern Aboriginals were a compound of multiple migration events, and had undergone a great deal of evolution in situ. Additionally, classically trained physical anthropologists in the early 20th century noted morphological parallels between Australian Aboriginals and the peoples of India, giving rise to the construct of the Australoid race (a term still used by Indian anthropologists). As I noted earlier the connection between South Asia and Australia genetically seems likely to be distant and tenuous at best, inferring from what we know of uniparental markers (genetic variants passed only through the mother or father, the mtDNA and Y). The genetic data tentatively seem to reject Birdsell’s model, and favor a more parsimonious one of a single original settlement on Sahul, and subsequent diversification and isolation (Australia, Tasmania and Papua New Guinea were separated only ~10,000 years ago with rising sea levels).

But there’s only so much that uniparental lineages can tell us. There are limits to the information one can glean from relatively short sequences of mtDNA and Y, and, these gene lineages are subject to their own particular dynamics. Not only do human mating patterns exhibit sex-specific biases, but the neutrality of these lineages from an evolutionary perspective has been questioned. And, the haploid nature of these loci also mean that the effective population size is small (i.e., only copy of each per person, instead of two as in the case of most genes) and stochastic fluctuations may be more extreme than in the rest of the genome. On the one hand more random variation could allow for the emergence of greater between population differences which might be informative, but on the other hand it can also swamp out the past history too quickly and result in convergences which tell us nothing about phylogenetic connections. All this is why a new paper looking at the broader genomic patterns of variation in Australian Aboriginals is important for clarifying and adding more precision to our evolutionary historical assumptions, which would frame more specific inferences about this population. There are, and were, difficulties in obtaining the data for historical and political reasons. But now that the barrier has been breached, I assume that we’ll be seeing more in the near future. Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry:

Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region . The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent’s unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.

The sample consisted of 38 individuals, 30 females and 8 males, from the Riverina region of New South Wales. The sample size may be small, but for the broad-brush and relatively coarse questions being asked in this paper they’re sufficient. Consider that genomic sequencing of one Native American and one Bushman could tell you that the latter is likely to come from a far more genetically diverse population than the former. If you constructed a phylogenetic tree with half a dozen individuals of each of the populations you’d see that the Native Americans are a subset of the Bushman genetically, so to speak. If you’re trying to distinguish between questions such as, “did the last common ancestor of Australian Aboriginals and Javanese live 5,000, or 50,000, years before the present”, then this is a sufficient sample. A bigger issue is that the sample has substantial European admixture through the paternal lineages. From what I have heard attempts were made to get a more “pure” Aboriginal group, but the logistics were too difficult in the end. Science is the art of the possible.

They used an Affymetrix chip with nearly 1 million SNPs (out of 3 billion base pairs), but filtered it down even further for this analysis. Most of the work used a data set of ~160,000 SNPs, arrived via quality controls, as well as the intersection with HapMap3 and HGDP SNP sets. Again, in light of the coarse questions asked 160,000, let along 16,000, should probably suffice. Remember they’re trying to move beyond what we can infer from classical autosomal markers and uniparental lineages. This is a big step in that direction.

abofig1The figure to the left shows two phylogenetic trees (note: I may reedit these figures for ease of display or clarity). The utility of the trees is obvious: they’re showing you how populations relate to each other. So you throw all the individuals in each given population into a pot, average out their genetic character, and perform pairwise calculations on them. The other groups are from the HGDP data set. The statistic they’re using is F st; basically a measure of between population genetic variation. Alleles, genetic variants, vary in frequency from population to population, as well as the fact that different individuals within populations have different genotypes, and this is just capturing the component which is varying across populations. So as an example, if the allele x in two populations is at frequency 0.5 for both, then the F st is 0. There’s no difference. If x is at 1 in one population and 0 in the other, then F st = 1. All the variation is between the populations, since there is none within the populations.

The trees illustrate visually the relationships in an F st matrix of pairwise population comparisons. Populations which are genetically close are not very distant from each other along the length of the tree, while those which are genetically very different are farther from each other terminus-to-terminus. But remember that these visualizations don’t tell us anything necessarily in a concrete manner before we interpret them through the filter of what we already know. For example, the Mozabites, “MOZ”, are outside of the main clusters. Why? Without knowing anything about their history we might assume that they were isolated from the original African population at an early point in time (though observe the minimal distance from the trunk, peculiar). But we know their history, and the topology in that region of the network is an outcome of admixture. The Mozabites have a substantial amount of recent Sub-Saharan African ancestry. Similarly, two of the groups near the root of the East Eurasian cluster are actually relatively recent admixtures between West and East Eurasian populations, the Uyghurs and Hazaras.

The Australian Aboriginals are similar to the Mozabites, Uyghurs and Hazaras. Their position in the first panel is near the root of the Oceanian cluster. This is due to their substantial European admixture, which we know is present through their oral history, recorded history, and, the physically composite nature of many modern Australian Aboriginals. To generate the second tree the authors reconstructed the allele frequencies of the Australian Aboriginals by subtracting the European component of admixture. They did this by noting that they had Western European populations in HapMap3, and the offspring population between these groups which they knew, and the unknown Aboriginal parent population. Using the Structure program they simply performed the algebra, whereby Aboriginal = Admixed Aboriginal – European (OK, not “simply”). And as you can see, by using the reconstructed Aboriginal allele frequencies the tree now places this group, AuR*, firmly within the Oceanian cluster.

abofig2The clustering of the Oceanian groups itself alone gives us strong evidence that the settlement of Sahul was by one population which later diversified, rather than separate independent groups. But let’s back up a bit, and look at the admixture aspect again. To the left you see the PCA plots of the HGDP data set which you should be familiar with. Each axis represents and independent dimension of genetic variation. For the first panel the x-axis, PC1, is the separation between Africans and non-Africans. This is the biggest dimension of variation, and points to the Out-of-Africa event. The second dimension seems to map well onto the east-west axis, more or less. Remember that each PC is rank ordered in terms of the proportion of the total genetic variation which it can explain independently. Interestingly PC3 and PC4 allow for the separation of Oceanians and Amerindians from other groups. In isolation-by-distance and serial bottleneck models it shouldn’t be too surprising that these two groups on the geographic margins of the traditional human range would exhibit some genetic peculiarities due to their history after separation from Eurasian groups. This is why the Kalash of Pakistan are also outliers, this non-Muslim tribe remained isolated in their mountain valley and so accumulated their own genetic distinctiveness.

And yet note the position of Amerindians and Oceanians in the first panel, they’re somewhat closer to West Eurasians than East Asians. In the case of Amerindians there has long been the model whereby the ancient Beringian population which expanded into the New World had a component of ancestry which was closer to West Eurasia. This is true today among Siberian groups such as Yakuts, but differentiating the more recent introgression of Russian ancestry with an ancient West Eurasian substratum is difficult.

But admixture is surely part of the puzzle too. Compare the linear topology of Aboriginals and Amerindians with African Americans. The PCA plot is putting the focus on between population differences, so these sorts of distributions, so cleanly linear, are indicative of possible recent admixture between two distinct populations. The populations of the New World and Australia were relatively small and thin in terms of distribution, so it should not be too surprising that a substantial uptake of European ancestry has occurred in both cases. Isolated cases of individuals “going native” probably illustrate a bigger trend. The 2002 film Rabbit-Proof Fench was a dramatization of the reality that quite often children of mixed heritage will identify with one culture and parent. This is not an atypical disjunction between genes and culture in terms of their mode of inheritance. Both parents contribute equally genetics to the autosome, but cultural contribution is more of a contingent matter.

abofig3To further explore the admixture within Aboriginals the authors performed a frappe and Structure analysis. These two methods differ in the details but perform basically the same operation; they take individuals and assign components of their genome to K putative ancestral groups. So K = 2 would indicate 2 ancestral groups, while K = 10 would indicate 10. Here’s we’re looking at K = 5. Again, proper caution is warranted with these methods because without context we may not be able to interpret the results. But in this case the ends are clear and distinct: what is the extent and range of European ancestry in this Australian Aboriginal sample? Both the frappe and Structure programs paralleled each other in outcome; the Aboriginal sample varied quite a bit in ancestral quanta. The Papuans and Melanesians serve as appropriate Oceanian references. The Melanesians have a residual component (shaded orange and yellow top to bottom) which is similar to East Asians. This is a marker of the Austronesian expansion into the Pacific. The Papuans and Aboriginals generally lack this, which stands to reason considering their greater cultural isolation from the Austronesians.

The frappe and Structure results dovetail perfectly with the PCA plots. Both suggest that the Aboriginal population is admixed, with the parental populations being West Eurasian (European) and Oceanian, and, that that admixture varies from individual to individual. The F st also suggested this, though at a coarser population wide scale, and only with prior knowledge of the possibility of admixture. Not only that, but the mtDNA and Y chromosomal results on these individuals also comes out to the same inferred proportion. Recall that there were only 8 males, so the Y sample is small. But they calculate that ~40% of the Y lineages are not Aboriginal, while nearly ~100% of the female ones are. This sort of disjunction is common in the New World among Mestizo and African American populations, as well as the mixed Cape Coloured population of South Africa. The proportional of autosomal ancestry inferred from these uniparental markers is about what was calculated with their SNP-chip, suggesting the persistence of this sex-biased admixture pattern over the past two centuries. Remember that if something more complex demographically had occurred we may not have been able to infer admixture from uniparental lineages. Imagine if the Aboriginal tribes in New South Wales which were admixed were decimated by an unadmixed group, so that only the females from the admixed group survived. After that event both mtDNA and Y chromosomal lineages would have been Aboriginal, but the European ancestry would persist in the autosome.

abofig4To the left is an estimate of individual-to-individual ancestral quanta. The mode, the most frequent value, is near the total genome estimate of the whole population, around ~2/3 Aboriginal. There is clearly a wide range of variation in admixture. It looks like that within this Australian Aboriginal community 20% of this sample are 50% or more European in ancestry. Interestingly one man is ~100% Aboriginal. The authors do remark that their estimates are probably low balling the Aboriginal ancestral quantum; the SNP-chip was constructed with European genetic variation as a baseline, so it is missing Australian variation on loci where Europeans are monomorphic. But even with that taken into account the Aboriginal group here is substantially admixed. This prompts me to ask: is it possible that there is more distinctive indigenous genetic material in the ~20 million white citizens of Australia than within the indigenous groups themselves? I’ve already suggested that this dynamic is exactly what is operative in Brazil, but the analogy is only rough a best. Many Australian whites derive from recent waves of migration and may not have any ancestors with roots back to the 19th century (i.e., all their grandparents and/or parents may have been born in Europe or the British Isles). But that must be balanced against the fact that Australian Aboriginals are much more European in ancestry than Brazilian Amerindians likely are. The rapid growth of indigenous Australians can’t be a function purely of high fertility. Rather, many people of mixed heritage are identifying as indigenous. The outmarriage rates for urban Aboriginals in some of the literature is estimated to be in the 70-90% range.

So far we’ve covered aspects of Australian Aboriginal genetics relevant to paleoanthropology and historical population genetics. But as I have observed many a time, one of the primary reasons for this sort of population analysis is to clarify background parameters for medical genetics. The life expectancy gap between indigenous and non-indigenous Australians is on the order of 10 years. It also seems plausible that the same disease-driven population crash which occurred in the New World after contact with Europeans was also driving population changes in Australia around the time of European settlement. Since Aboriginals were generally hunter-gatherer groups many infectious diseases which required higher densities could only be incubated among Europeans. Aboriginals near European settlements, or those who settled within them, would naturally be exposed to these infections and suffer greater morbidity and mortality. One wonders if some of the diseases which Aboriginals suffer from are due to genetic differences between the populations in regards to immunity, as well as the “diseases of civilization” (e.g., type 2 diabetes).

As noted in the paper admixed populations present both pitfalls and opportunities when it comes to elucidating risk alleles:

Whereas the admixture present in the AuR [the Riverina Aboriginals -Razib] sample presents a potential challenge in conducting traditional association methods for disease gene discovery…it opens the possibility of using admixture mapping…Admixture mapping is most suitable for traits, like CKD, that differ in frequency between the two parental populations of an admixture group. The approach essentially looks for genomic regions with an excess of higher-risk population ancestry relative to other regions or controls..A set of markers, spread across the genome, that are highly informative as to ancestry (ancestry informative markers or AIMs) is an essential requirement for admixture mapping.

figabo6CKD above refers to chronic kidney disease, which Aboriginals suffer at ~10 times greater rates than non-Aboriginals. To the left is a figure which shows the distribution of SNP rs12458349, a derived allele which has the highest F st value between AuR* and HapMap3 populations. The genomic region which rs12458349 is embedded within has been implicated in diabetic nephropathy, a major cause of CKD. Derived here means that the SNP is evolutionarily novel in relation to the ancestral state, which all other human populations exhibit.

So why is this derived variant at a high frequency in Aboriginals (and other Oceanians), but not other human populations? It could be random genetic drift. As populations migrated out of Africa they may have gone through bottlenecks and isolations in a step-wise fashion and each group down the spatial and temporal sequence would accumulate their own unique variants. Or, it may have been adaptation, which drive up frequencies through positive selection around that genomic region. But this is where limitations of sample size and representativeness crop up, as these are not quite the coarse questions which we were focusing on earlier. From the the text:

Genetic drift, or random changes in allele frequencies, is expected to be a major force in a population, like Aboriginal Australia, that has been relatively small and/or isolated for a long period of time. Differentiation could also be explained by natural selection. The presence of several highly differentiated SNPs in the region, spanning nearly 0.5 Mb in length, hints at the presence of a long common haplotype that might be indicative of genetic hitch-hiking and recent positive selection. However, it is difficult to distinguish between possible explanations because the sample is small, with extensive admixture hampering phasing and direct investigation of linkage-disequilibrium-based selection signals.

Note however the presence of the derived allele in Papuans and Aboriginals, but not Melanesians. In the phylogenetic network the Aboriginals are the outgroup, and yet on this character the Melanesians are. This is a locus which will no doubt be explored in the future, because the patterns here will be fascinating to tease apart, and, of possible medical relevance.

Overall this paper has confirmed much of what we know, or at least solidified our background assumptions. The contemporary peoples of Melanesia, New Guinea and Australia have a common ancestral heritage. Coalescence times back to the last common ancestor between these populations and non-Oceanian groups suggest that their residence in their current locations is antique, and possibly back to the first settlement. One should be duly cautious about extrapolating from contemporary patterns to variation to the past, but I think on this scale we’re on more solid ground. Parts of southern Australia and Tasmania may have an equitable climate where ancient DNA samples may have been preserved, so that could resolve the issues with more certainty in the future.

But aside from phylogeny, a closer study of Australian Aboriginal genetics may also give us insights into the impact which agriculture and higher population densities had upon our species’ genomes. The Australian Aboriginals were aware of agriculture because of contacts with the peoples of the Torres Straits, but they never seem to have adopted it. In contrast to Australia the highlands of New Guinea developed a relatively high population density with the spread of a gardening mode of production. So here you have two populations which were in contact ~10,000 years ago, and have diverged in mode of production subsequent to that period. A comparison in allele frequencies between these two populations would then be instructive as to the power of drift and selection to drive evolutionary change over 10,000 years.

Obviously there needs to be more work done, and extrapolating from one sample will not do. The north coast Aboriginals were certainly in contact with sailors from Southeast Asia before Europeans arrived, and they speak a different group of languages from those in the rest of the continent. The existence of tribes with non-trivial numbers of blonde individuals in the western deserts despite no other apparent European admixture also demands to be explored. From what Joseph Birdsell documented about the Mendelian inheritance patterns of blondism among these tribes it seems likely that the genetic architecture is very different from that in Europeans.

Over the past generation we’ve begun to really understand how the human tree of life branched out and flourished. Now it’s time to fill in the gaps, and with whole genome sequencing around the horizon many of the technical limitations will be removed. But what about the social and political ones? The consent given by this Aboriginal group has now opened a window into the evolutionary genetic history of all Australian Aboriginals, imperfect as that is. But what will happen when many more people in developed nations get sequenced, and so know their own genetic history with great detail? If a non-trivial proportion of Aboriginal ancestry is found across the old stock white population of Australia could a collaborative project just “reconstruct” the Aboriginal genome from these individuals, and so do an end-around the socio-political minefields? I suppose we’ll see soon enough.

Image credit: Aboriginal cricket team, 1868, Wikimedia Commons

Citation: McEvoy, Brian P., Lind, Joanne M., Wang, Eric T., Moyzis, Robert K., Visscher, Peter M., van Holst Pellekaan, Sheila M., & Wilton, Alan N. (2010). Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry The American Journal of Human Genetics : 10.1016/j.ajhg.2010.07.008

Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"