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January 22, 2012

How the Amhara breathe differently

I have blogged about the genetics of altitude adaptation before. There seem to be three populations in the world which have been subject to very strong natural selection, resulting in physiological differences, in response to the human tendency toward hypoxia. Two of them are relatively well known, the Tibetans and the indigenous people of the Andes. But the highlanders of Ethiopia have been less well studied, nor have they received as much attention. But the capital of Ethiopia, Addis Ababa, is nearly 8,000 feet above sea level!

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

October 20, 2010

Genetic watersheds on the Great Himalayas

Indian_subcontinent

One of the great geological landmarks on earth are the Himalayas. Not only are the Himalayas of importance in the domain of physical geography, but they are important in human geography as well. Just as South Asians and non-South Asians agree that the valley of the Indus and its tributaries bound the west of the Indian cultural world, so the Himalayas bound it on the north. Unlike many pre-modern constructions, such as the eastern boundary of Europe, the northern limit of South Asia is relatively clear and distinct. It is stark on a relief map; the flat Gangetic plain gives way to mountains. And it is stark a cultural map, the languages of northern India give way to those of the world of Tibet. The religion of northern India gives way to the Buddhism of Tibet. In terms of human geography I believe that one can argue that the Himalayan fringe around South Asia exhibits the greatest change of ancestrally informative gene frequencies over the smallest distance when you exclude those regions separated by water barriers. Unlike the Sahara the transect from the northern India to Chinese Tibet at any given point along the border is permanently inhabited, albeit sparsely at the heights.

ResearchBlogging.orgAnd yet despite the geographical barriers people and ideas did move across the Himalaya. The cultural influences upon Tibet from India are obvious. The script of Tibet is derived from India, while its form of Buddhism is the direct descendant of the last efflorescence of that religion in northern India. But while culture moved north, I do not see much evidence genetically that South Asians have been significant as an influence. This is somewhat shocking when you realize these two facts: the population of the Tibetan Autonomous Region is on the order of 5-6 million, while that of northern South Asia around ~1 billion (including Pakistan and Bangladesh). A 200-fold difference. And yet there is evidence of admixture between the two groups exactly where you’d expect: in Nepal. Below is a figure from a recent paper which shows how South and East Asian populations relate to each other. I’ve highlighted the Nepali groups, which span the two larger classes:


tibetsou1

tibetsouth2From the above figure it’s clear that there is considerable admixture among the Indo-European populations of Nepal with a Tibetan element. The Magar are a tribe which is representative of Tibet, with little South Asian genetic input presumably. The Newar are the Nepalese hybrids par excellence. To a great extent they can be viewed as the indigenous peoples of the Kathmandu region at the heart of modern Nepal. Their language is of Tibetan affinity, and yet it is heavily overlain with an Indo-Aryan aspect, and seems to have within it an ancient Austro-Asiatic substrate. Though predominantly Hindu today, the Newar have a substantial Buddhist minority whose roots may go back to the original Mahayana traditions which were once prominent in northern India. The Brahmin and Chetri groups are upper caste communities who claim provenance from the north Indian plain. Some of these upper caste groups in Nepal are of recent vintage, having fled the Islamic conquests of the Gangetic plain within the last 1,000 years. And yet even they have obvious Tibetan admixture. This should make one cautious about the excessive claims to genetic purity which South Asian caste groups make.

But admixture of a Tibetan or East Asian component in South Asia is not limited to Nepal. I have reedited a figure from a 2006 paper on Indian Americans which shows the inferred components of ancestry of various language-groups. It is clear that the northeastern groups, Bengalis, Assamese, and Oriya, have an affinity to East Asians. This is not just ancient east Eurasian ancestry, the “Ancestral South Indians” hypothesized in Reich et al.. The South Indian groups (which I have excised from the figure) do not exhibit the same level of elevation of the ancestral quantum dominant among the Han Chinese in the bar plot. In fact the Reich et al. paper also reported evidence of an eastern ancestral element in some of the Munda speaking groups of northeast India. This stands to reason as the Munda are a South Asian branch of the Austro-Asiatic family of Southeast Asia. But much of it may also be more recent, as groups such as the Ahom of Assam and the Chakma of Bangladesh seem to have arrived from Burma of late.

So we see that genes do flow around the margins of South Asia, and into it. And yet Tibet seems oddly insulated. Why? Because of adaptation. Like water, it seems in this case genes tend to flow downhill, not up, and the reason is likely the fitness differentials between lowland and highland populations along the slope of the Great Himalayas. A new paper in PNAS explores the issue by examining genetic variation among Indians, Tibetans, and worldwide populations, in relation to hypoxia implicated loci. EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda:

It is being realized that identification of subgroups within normal controls corresponding to contrasting disease susceptibility is likely to lead to more effective predictive marker discovery. We have previously used the Ayurvedic concept of Prakriti, which relates to phenotypic differences in normal individuals, including response to external environment as well as susceptibility to diseases, to explore molecular differences between three contrasting Prakriti types: Vata, Pitta, and Kapha. EGLN1 was one among 251 differentially expressed genes between the Prakriti types. In the present study, we report a link between high-altitude adaptation and common variations rs479200 (C/T) and rs480902 (T/C) in the EGLN1 gene. Furthermore, the TT genotype of rs479200, which was more frequent in Kapha types and correlated with higher expression of EGLN1, was associated with patients suffering from high-altitude pulmonary edema, whereas it was present at a significantly lower frequency in Pitta and nearly absent in natives of high altitude. Analysis of Human Genome Diversity Panel-Centre d’Etude du Polymorphisme Humain (HGDP-CEPH) and Indian Genome Variation Consortium panels showed that disparate genetic lineages at high altitudes share the same ancestral allele (T) of rs480902 that is overrepresented in Pitta and positively correlated with altitude globally (P< 0.001), including in India. Thus, EGLN1 polymorphisms are associated with high-altitude adaptation, and a genotype rare in highlanders but overrepresented in a subgroup of normal lowlanders discernable by Ayurveda may confer increased risk for high-altitude pulmonary edema.

The paper itself is a follow up to a previous work attempting to see if there was a sense to the classification of constitutions found within Ayurvedic medicine. Like Chinese medicine this is a non-Western tradition which has different philosophical roots and axioms (Galenic medicine might be analogous). But in theory all medical traditions emerged to battle illness, so their target was unitary, the ailments which plague the human body. Therefore one might suppose that in fact there would be some sense in any long-standing medical tradition which has any empirical grounding, because human biology is relatively invariant. It is the relative clause which is of interest for the purposes of this paper, because the authors show how the classifications of Ayurvedic medicine seem to comport with the recent genetic evidence of high altitude adaptation! Specifically they found that particular Ayurvedic classes of individuals who seem to have negative reactions to high altitude exposure in the form of hypoxia tend to be carriers of particular EGLN1 genotypes.

I will at this point observe that since I don’t know much about Ayurveda I won’t address or cover that issue in detail. The paper is Open Access so you can read it yourself. So let’s move to the genetics. EGLN1 should be familiar to you by now. It’s cropped up repeatedly over the past year in studies of high altitude adaptation. It is a locus which seems to be a target of selection in both the peoples of the Andes and Tibet. Additionally, it has a peculiar aspect where the ancestral variant, the one found most frequently within Africa, seems to be the target of selection for altitude adaptation outside of Africa.

The slideshow below is an overview of the primary figures within this paper.



What do we take away from this? Well, one aspect which I think is important to emphasize is that genetic background matters, and there’s much we don’t know. In the conclusion the authors note that the altitude adaptation papers which I alluded to above were not published when the manuscript was being written, so they were not privy to the rather repeated robust evidence that EGLN1 has been the target of natural selection, and that variation on the locus is correlated with variation in adaptation to higher altitudes. The widespread coverage of populations in this paper seems to almost obscure as much as highlight. What has African variation to do with this after all? Additionally one must always remember that one given marker on a gene which shows a correlation does not entail functional causation. We saw this with the markers which seemed to predict the odds of an individual of European ancestry having blue eyes; it turned out that the markers themselves were simply strongly associated with another SNP which was probably the real functional root behind the difference in phenotype.

Due to the replication of EGLN1 in both Andeans and Tibetans I am moderately confident that variation on this gene does have something to due with high altitude adaptation. What I am curious about is the fact that the ancestral alleles in many cases seem to be driven up on frequency. Is there an interaction between the genetic background of non-Africans and the SNPs in question which make it beneficial toward altitude adaptation? Was there an initial relaxation of function as human populations moved out of Africa, which was slammed back on at high altitudes? There does seem a correlation within South Asian populations between hypoxia and high altitudes and particular variants on EGLN1. Focusing just on this region we can draw some reasonable inferences, but taking a bigger picture view and encompassing the whole world we’re confronted with a rather more confused, and perhaps more interesting, picture.

Back to the specific issue of the lack of South Asian imprint on the genes of Tibetan peoples, I think one can chalk this up to the fact that humans are animals, and so we’re constrained by geography and biology. Tibetans can operate efficiently at lower altitudes, and so have mixed with South Asians in these regions. In contrast, South Asians can not operate at higher altitudes, and so the impact on Tibetans was purely cultural, and not genetic. More broadly this may also point to long term geopolitical implications: the Han Chinese demographic domination of Tibet is always going to be a matter of water flowing uphill. Unless of course we flesh out the genetic architecture of these traits well enough that the Chinese government knows exactly which individuals among the 1.2 billion Han population would be most biologically prepared to reside in the Tibetan Autonomous Region, and so can proactively recruit them to settle in Lhasa and other strategic locations.

Citation: Shilpi Aggarwal, Sapna Negi, Pankaj Jha, Prashant K. Singh, Tsering Stobdan, M. A. Qadar Pasha, Saurabh Ghosh, Anurag Agrawal, Indian Genome Variation Consortium, Bhavana Prasher, & Mitali Mukerji (2010). EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda PNAS : 10.1073/pnas.1006108107

Image Credit: Wikimedia Commons

May 14, 2010

Breathing like Buddha: altitude & Tibet

443px-PaldenLhamoYou probably are aware that different populations have different tolerances for high altitudes. Himalayan sherpas aren’t useful just because they have skills derived from their culture, they’re actually rather well adapted to high altitudes because of their biology. Additionally, different groups seem to have adapted to higher altitudes independently, exhibiting convergent evolution. But in terms of physiological function they aren’t all created equal, at least in relation to the solutions which they’ve come to to make functioning at high altitudes bearable. In particular, it seems that the adaptations of the peoples of Tibet are superior than those of the peoples of the Andes. Superior in that the Andean solution is more brute force than the Tibetan one, producing greater side effects, such as lower birth weight in infants (and so higher mortality and lower fitness).

The Andean region today is dominated by indigenous people, and Spanish is not the lingua franca of the highlands as it is everyone in in the former colonial domains of Spain in the New World. This is largely a function of biology; as in the lowlands of South America the Andean peoples were decimated by disease upon first contact (plague was spreading across the Inca Empire when Pizzaro arrived with his soldiers). But unlike the lowland societies the Andeans had nature on their side: people of mixed or European ancestry are less well adapted to high altitudes and women without tolerance of the environment still have higher miscarriage rates.

So despite the suboptimal nature of the Andean adaptations vis-a-vis the Tibetan ones, they are certainly better than nothing, and in a relative sense have been very conducive to higher reproductive fitness. And yet why might the Andeans have kludgier adaptations than Tibetans? One variable to consider is time. The probability is that the New World was populated by humans only for the past ~10,000-15,000 years or so, with an outside chance of ~20,000 years (if you trust a particular interpretation of the genetic data, which you probably shouldn’t). By contrast, modern humans have had a presence in the center of Eurasia for ~30,000 years. Generally when populations are exposed to new selective regime the initial adaptations are drastic and exhibit major functional downsides, but they’re much better than the status quo (remember, fitness is relative). Over time genetic modifications mask the deleterious byproducts of the genetic change which emerged initially to deal with the new environment. In other words, selection perfects design over time in a classic Fisherian sense as the genetic architecture converges upon the fitness optimum.*

Another parameter may be the variation available within the population, as the power of selection is proportional to the amount of genetic variation, all things equal. The peoples of the New World tend to be genetically somewhat homogeneous, probably due to the fact that they went through a bottleneck across Berengia, and that they’re already sampled from the terminus of the Old World. A physical anthropologist once told me that the tribes of the Amazon still resemble Siberians in their build. It may be that it takes a homogeneous population with little extant variation a long time indeed to shift trait value toward a local ecological optimum (tropical Amerindians are leaner and less stocky than closely related northern populations, just not particularly in relation to other tropical populations). In contrast, populations in the center of Eurasia have access to a great deal of genetic variation because they’re in proximity to many distinctive groups (the Uyghurs for example are a recent hybrid population with European, South Asian and East Asian ancestry).

So that’s the theoretical backdrop for the differences in adaptations. Shifting to the how the adaptations play out concretely, some aspects of the physiology of Tibetan tolerance of high altitudes are mysterious, but one curious trait is that they actually have lower levels of hemoglobin than one would expect. Andean groups have elevated hemoglobin levels, which is the expected “brute force” response. Interestingly it seems that evolution given less time or stabilizing at a physiologically less optimal equilibrium is more comprehensible to humans! Nature is often more creative than us. In contrast the Tibetan adaptations are more subtle, though interestingly their elevated nitric acid levels may facilitate better blood flow. Though the inheritance patterns of the trait had been observed, the genetic mechanism underpinning it has not been elucidated. Now a new paper in Science identifies some candidate genes for the various physiological quirks of Tibetans by comparing them with their neighbors, and looking at the phenotype in different genotypes with the Tibetan population. Genetic Evidence for High-Altitude Adaptation in Tibet:

Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in several regions that contain genes whose products are likely involved in high-altitude adaptation. Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia response pathways in humans.

Here’s what they did. First, Tibetans are adapted to higher altitudes, Chinese and Japanese are not. The three groups are relatively close genetically in terms of ancestry, so the key is to look for signatures of positive selection in regions of the genome which have been identified as possible candidates in terms of functional significance in relation to pathways which may modulate the traits of interest. After finding potential regions of the genome possibly under selection in Tibetans but not the lowland groups, they fixed upon variants which are at moderate frequencies in Tibetans and noted how the genes track changes in the trait.

This figure from the supplements shows how the populations are related genetically:

tib1

In a worldwide context the three groups are pretty close, but they also don’t overlap. The main issue I would have with this presentation is that the Chinese data is from the HapMap, and they’re from Beijing. This has then a northeast Chinese genetic skew (I know that people who live in Beijing may come from elsewhere, but recent work which examines Chinese phylogeography indicates that the Beijing sample is not geographically diversified), while ethnic Tibetans overlap a great deal with Han populations in the west of China proper. In other words, I wouldn’t be surprised if the separation between Han and Tibetan was far less if you took the Chinese samples from Sichuan or Gansu, where Han and Tibetans have lived near each other for thousands of years.

tib2But these issues of phylogenetic difference apart, we know for a fact that lowland groups do not have the adaptations which are distinctive to the Tibetans. To look for genetic differences they focused on 247 loci, some from the HIF pathway, which is important for oxygen homeostasis, as well genes from Gene Ontology categories which might be relevant to altitude adaptations. Table 1 has the breakdown by category.

Across these regions of the genome they performed two haplotype based tests which detect natural selection, EHH and iHS. Both of these tests basically find regions of the genome which have reduced variation because of a selective sweep, whereby selection at a specific region of the genome has the effect of dragging along large neutral segments adjacent to the original copy of the favored variant. EHH is geared toward detection of sweeps which have nearly reached fixation, in other words the derived variant has nearly replaced the ancestral after a bout of natural selection. iHS is better at picking up sweeps which have not resulted in the fixation of the derived variant. The paper A Map of Recent Positive Selection in the Human Genome outlines the differences between EHH and iHS in more detail. They looked at the three populations and wanted to find regions of the genome where Tibetans, but not the other two groups, were subject to natural selection as defined by positive signatures with EHH and iHS. They scanned over 200 kb windows of the genome, and found that 10 of their candidate genes were in regions where Tibetans came up positive for EHH and iHS, but the other groups did not. Since these tests do produce false positives they ran the same procedure on 240 random candidate genes (7 genes were in regions where Chinese and Japanese came up positive, so these were removed from the set of candidates), and came up with average EHH and iHS positive hits of ~2.7 and ~1.4 genes after one million resamplings (specifically, these are genes where Tibetans were positive, the other groups negative). Their candidate genes focused on altitude related physiological pathways yielded 6 for EHH and 5 for iHS (one gene came up positive for both tests, so 10 total). This indicates to them these are not false positives, something made more plausible by the fact that we know that Tibetans are biologically adapted to higher altitudes and we have an expectation that these genes are more likely than random expectation to have a relationship to altitude adaptations.

Finally, they decided to look at two genes with allelic variants which exist at moderate frequencies in Tibetans, EGLN1 and PPARA. The procedure is simple, you have three genotypes, and you see if there are differences across the 31 individuals by genotype in terms of phenotype. In this case you want to look at hemoglobin concentration, where those who are well adapted have lower concentrations. Figure 3 is rather striking:

tib3

Even with the small sample sizes the genotypic effect jumps out at you. This isn’t too surprising, previous work has shown that these traits are highly heritable, and that they vary within the Tibetan population. There’s apparently a sex difference in terms of hemoglobin levels, so they did a regression analysis, and it illustrates how strong the genetic effect from these alleles are:

tib4

My main question: why do Tibetans still have variation on these genes after all this time? Shouldn’t they be well adapted to high altitudes by now? A prosaic answer may be that the Tibetans have mixed with other populations recently, and so have added heterozygosity through admixture. But there are several loci here which are fixed in Tibetans, and not the HapMap Chinese and Japanese. For admixture to be a good explanation one presumes that the groups with which the Tibetans mixed would have been fixed for those genes as well, but not the ones at moderate frequencies. This may be true, but it seems more likely that admixture alone can not explain this pattern. As the Andean example suggests adaptation to high altitudes is not easy or simple. Until better options arrive on the scene, kludges will suffice. It may be that the Tibetans are still going through the sieve of selection, and will continue to do so for the near future. Or, there may be balancing dynamics on the genes which exhibit heterozygosity, so that fixation is prevented.

No matter what the truth turns out to be, this is surely just the beginning. A deeper investigation of the genetic architecture of Andeans and Ethiopians, both of which have their own independent adaptations, will no doubt tell us more. Finally, I wonder if these high altitude adaptations have fitness costs which we’re not cognizant of, but which Tibetans living in India may have some sense of.

Citation: Tatum S. Simonson, Yingzhong Yang, Chad D. Huff, Haixia Yun, Ga Qin, David J. Witherspoon, Zhenzhong Bai, Felipe R. Lorenzo, Jinchuan Xing, Lynn B. Jorde, Josef T. Prchal, & RiLi Ge (2010). Genetic Evidence for High-Altitude Adaptation in Tibet Science : 10.1126/science.1189406

* Additionally, it may be that archaic hominin groups were resident in the Himalaya for nearly one million years. Neandertal admixture evidence in Eurasians should change our priors when evaluating the possibility for adaptive introgression on locally beneficial alleles.

Image Credit: Wikimedia Commons

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