john hawks weblog

paleoanthropology, genetics and evolution

phylogeography

  • Taking the mtDNA pulse of Neandertal populations

    Tue, 2012-02-28 11:01 -- John Hawks

    Neandertals have strikingly limited genetic variation. They once lived across a range from Spain to Siberia. Yet when we compare sequences across their whole genomes, we find them to be much less different across this geographic range than people living in the same regions today.

    I think this is one of the most fascinating findings of ancient genomics. It may tell us something about Neandertal populations that we did not begin to suspect without their DNA.

    But there is one explanation for this fact that I and others pointed out long before DNA evidence: The Neandertal population was surely much, much smaller than Holocene population of Europe. Small population size over a long time can restrict genetic diversity. So maybe the Neandertals preserved little genetic variation simply because there were so few of them.

    Neandertal mtDNA dynamism

    Love Dalén and colleagues [1] add some perspective to this question. The paper adds one novel mtDNA sequence, of the Neandertal from Valdegoba, Spain, to the record of Neandertals. This builds on earlier work by Ludovic Orlando and colleagues, who performed some analysis of Neandertal variation over time when they reported the sequence of the 100,000-year-old Scladina mtDNA sequence [2]. The main contribution of the current paper is its separation of Neandertals into earlier and later subsamples, showing that the Neandertals after 48,000 years ago in Western Europe have greatly restricted mtDNA diversity compared to the earlier sample of Neandertals.

    That's a tricky comparison. The paper illustrates it with this figure:

    Neandertal mtDNA phylogeny from Dalen et al. 2012

    Figure 1 from Dalén et al. 2012. Original caption: "Figure 1. Phylogenetic relationships and geographic distribution of Neandertals. Recent (<48 kyr) western Neandertals are placed within a well defined monophyletic group (blue box), whereas specimens older than 48 kyr constitute a paraphyletic group together with eastern Neandertals (red box). The sampling locations for the specimens are shown with corresponding colour coding."

    The blue clade includes all Neandertals after 48,000 years ago from Western Europe; the red clade includes earlier Neandertals from the west as well as both earlier and later Neandertals from the east.

    The meat in this phylogram is not only that the later western Neandertals are close relatives, but that they share an ancestor only around 60,000 years ago. That's a mere 20,000 to 25,000 years before the later western Neandertals lived. The variation within these Neandertals is roughly the same as that within a single mtDNA clade within Europe today, such as clade H1.

    Comparing the later Neandertal diversity to the variation of present-day Europeans helps to clarify the meaning of low diversity. Low mtDNA diversity doesn't necessarily imply that the later Neandertals in western Europe were few in number. Certainly there are millions of Europeans today who carry clade H1, for example. Low mtDNA diversity tells us something more limited about the ancestors of these Neandertals. Sometime after 60,000 years ago, a pulse of mitochondria came from the east and were remarkably successful in the west.

    Looking at the red clade in the figure is also illustrative. Eastern Neandertals and earlier western Neandertals had a lot more diversity than the later western Neandertals. We have to remember that the Scladina individual lived 40,000 years before the common ancestor of the blue clade, so that the greater ages of these specimens matters. Still, when we look at the diversity in that red clade, it is greater than the mtDNA diversity today in the most widespread basal clade outside Africa, the M clade. Taking the mtDNA phylogeny alone, we would say that the 13 Neandertals had a greater sequence difference than all the people who with ancestry outside Africa today. Only when we look at the predominantly African clades today (the L clades) do we start to see sequence differences as great as among these Neandertals.

    I began the post by pointing out that small population size alone might explain the low mtDNA diversity of Neandertals. Dalén and colleagues provide a key comparison that helps to reject that hypothesis. Small population size alone cannot explain the discrepancy of mtDNA diversity of these Neandertals across space and time.

    The whole-genome perspective

    Now, the question is whether this pattern holds true only for mtDNA, or whether the rest of the genome also shows some dynamic within Neandertal populations.

    We have quite a lot of information on this point, because the initial sequencing of the Vindija Neandertals was accompanied by a smattering of sequencing of the nuclear genomes of one individual from El Sidrón, the original Feldhofer specimen and the Mezmaiskaya Neandertal specimen. The inclusion of Mezmaiskaya is important, because it alone is not included in the "low mtDNA diversity" red clade pictured above. If the pattern observed for mtDNA is reflected by the rest of the genome, the comparison between Mezmaiskaya and western Neandertal genomes should show substantially more diversity.

    When they published the draft Denisova genome, Reich and colleagues [3] used it as an outgroup to investigate variation among the Neandertals, and they focused initially on Mezmaiskaya:

    Using the 56 Mb of autosomal DNA sequences determined from [the Mezmaiskaya specimen], we estimate that the DNA sequence divergence between the Vindija and Mezmaiskaya Neanderthals corresponds to a date of 140,000 +/- 33,000 years ago (Supplementary Information section 6) (Fig. 1). This remarkably low divergence—which is about one-third of the closest pair of present-day humans that we analysed—is in agreement with the observation that diversity among Neanderthal mtDNAs is low relative to present-day humans and indicates that the Vindija and Mezmaiskaya Neanderthals descend from a common ancestral population that experienced a drastic bottleneck since separating from the ancestors of the Denisova individual.

    That adds substantially to the mtDNA picture. The mtDNA variation of western Neandertals may reflect population turnover after 50,000 years ago. But the nuclear genome comparison cannot be explained by this single event. The variation of nuclear genomes between Mezmaiskaya and El Sidrón spans across more than half the Neandertal geographic range and requires mechanisms that restricted genetic variation across at least the period after 140,000 years ago.

    I think we can do quite a bit better using the nuclear genetic information already available, keeping an explicit phylogeographic model in mind. My view is that Neandertal populations were dynamic throughout their existence, with repeated waves of population turnover across broad geographic scales. The mtDNA of later western Neandertals may reflect a large, recent event. But there must also have been earlier ones to limit variation of the nuclear genome. The implication is that early Neandertals like Krapina may have had relatively little genetic connection to later Neandertals in the same region, like Vindija.

    That picture matches what we are beginning to understand about the population history of Europe during the last 30,000 years. I think that's how human populations have always behaved.

    Revisiting Neandertal races

    I wrote extensively about Neandertal mtDNA in 2009, noting the work of Virginie Fabre and colleagues [4], which showed the geographic structure of Neandertal mtDNA variation ("Neandertal races?"). Fabre and colleagues showed that Neandertal mtDNA variation is apportioned unequally across space, and made sense of the variation using a phylogeographic model with three broad geographic groups. I pointed out then that an alternative explanation might be that the specimens represent different times:

    Many have pointed out, going back to McCown and Keith (1939), that time is another possible cause of morphological differentiation of Neandertals. The mtDNA sequences cover a wide range of times -- the Scladina sequence comes from roughly 100,000 years ago, the others cover the span from 50,000 down to 29,000 years ago. Why not test temporal groups instead of geographic groups? Temporal clusters might reflect interglacial colonizations, differential gene flow, or natural selection. There is a good precedent -- last year a report of complete mtDNA sequences from woolly mammoths found evidence for geographic structure among mtDNA lineages, one of which apparently replaced the other (Gilbert et al. 2008).

    Time is just one example of an alternative model for variation. But I think it helps to clarify the basic problem of the a priori models -- you have to draw boundaries between the specimens somewhere.

    The problem still remains even in the current paper. Why should we divide time arbitrarily at 48,000 years ago? Why divide time in western Europe but not across the eastern part of the Neandertals' range?

    Combining space and time into a single phylogeographic picture is complicated. We end up using a null model to generate millions of pseudosamples to represent the exact time and place we found specimens, hoping to show the null model wrong. Refuting a null model doesn't necessarily tell us much about the behavior of ancient populations that flowed across space and interacted at different times. I think that life was more complicated rather than less, and look to models from more recent populations to understand it.

    How not to publicize your work

    The paper by Dalén and colleagues is such a neat piece of work, I think it's a shame that Uppsala University had to go and spoil it with this silly press release: "European Neanderthals Were On the Verge of Extinction Even Before the Arrival of Modern Humans".

    The paper pointedly does not show that Neandertals were on the "verge of extinction". Neandertals in the eastern part of their range show no sign of any demographic collapse, and the western part of the range arguably only shows signs of recovery and expansion.

    What the paper actually tells us is about the dynamism of Neandertal populations, which is very comparable to that of the Europeans of the last 10,000 years. Keeping this comparison in mind helps remind us that very large groups of people may still have low mtDNA diversity, reflecting the history of population movements and interactions in the past. Comparing the mtDNA with nuclear genetic evidence is also essential to this picture. Neither of these tell us that Neandertals were near extinction.

    Please, if you're putting together a press package about Neandertals, stop framing it around the concept of Neandertal extinction. You aren't going to say anything novel about this, and it just encourages lazy science writing. And it's a false concept. The Neandertals didn't become extinct.

    UPDATE (2012-03-06): A reader points out that several of the dates for specimens in the paper are different than reported in the literature. I noticed that too, and don't know quite what to make of it. I don't think that the differences in dates affect the general result, that later specimens in Western and Central Europe are relatively invariant compared to the Eastern European and Asian sample. But it is a reminder that the results do depend on a certain ordering and geographic sampling of specimens and may change if we fill in the gaps.

    References

    1. Dalén L, Orlando L, Shapiro B, Durling MB, Quam R, Gilbert TMP, Díez Fernández-Lomana CJ, Willerslev E, Arsuaga JL, Götherström A. Partial genetic turnover in Neandertals: continuity in the east and population replacement in the west. Molecular biology and evolution. 2012;29(8):1893-1897.
    2. Orlando L, Darlu P, Toussaint M, Bonjean D, Otte M, Hänna C. Revisiting Neandertal Diversity with a 100,000 Year Old mtDNA Sequence. Current Biology [Internet]. 2006;16:R400–R402. Available from: http://dx.doi.org/10.1016/j.cub.2006.05.019
    3. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature [Internet]. 2010;468:1053–1060. Available from: http://dx.doi.org/10.1038/nature09710
    4. Fabre V, Condemi S, Degioanni A. Genetic evidence of geographical groups among Neanderthals. PloS one. 2009;4(4):e5151.
    Tags: 
    Neandertal DNA
    mtDNA
    Neandertals
    population dynamics
    migration
    phylogeography
    Synopsis: 
    Neandertals in western Europe have a recent mtDNA ancestor, pointing to the dynamics within their population.

  • Diversity doesn't point reliably to source populations

    Mon, 2011-11-07 23:08 -- John Hawks

    Worth amplifying from Dienekes' Anthropology Blog, "Y chromosomes of the Bahamas":

    I like the line about there being substantially more Y-STR variation in E1b1a7a-U174 and E1b1ba8-U175 in the Bahamas than any African collection. I have argued for years that the central assumption of phylogeography, that the location of highest Y-STR diversity is not necessarily the point of origin of a haplogroup, since Y-STR diversity can be affected both by antiquity and by admixture. Nonetheless, I keep reading papers where tiny differences in Y-STR variation, even if we forget about the noisiness of Y-STRs themselves, are taken as evidence of ancient migrations. Thankfully, the time when Y-STRs were used to infer ancient migrations is over, and the huge collection of Y-STR haplotypes amassed by population geneticists, forensic specialists, and genealogists alike can be put to uses for which it is more amenable.

    Once we have population mixture, hypotheses about phylogeography become much harder to test. A population model with mixture has many ways of generating the same pattern of relative diversity among populations.

    Tags: 
    Y chromosome
    phylogeography
    population structure
    migration

  • Leprosy evolution in humans

    Fri, 2009-11-27 02:59 -- John Hawks

    Where did leprosy come from as a human pathogen, and how did it spread through the world? Two years ago, this new research would have merited a whole book. Now it's all packed into a single Nature Genetics paper by Marc Monot and coworkers.

    I mean, there's a lot in here:

    1. They used next-gen sequencing platforms to get three additional whole-genome sequences for the pathogen that causes leprosy, Mycotuberculum leprae.

    2. By comparing the different strains together with an already-available one, representing patients in four countries, they measured the genome diversity and found SNPs between strains.

    3. They then genotyped the resulting SNPs in 400 isolates, building a phylogeny of worldwide strains of M. leprae today.

    4. They did a phylogeographic analysis of the strains, testing hypotheses about past transfers of the bacterium among regions.

    5. And then, on top of all that, they recovered skeletal remains from "leprosy graveyards" in six countries, diagnosed the skeletal correlates of leprosy in 13 cases and genotyped the resulting extracts for M. leprae, placing them on the global phylogenetic tree.

    Whew!

    Well, I assume that the skeletal work was done separately, with samples being sent to the lab folks to do their DNA extraction.

    This would be a really good topic for a documentary. There's all the historical information about leprosy to draw upon, including of course its prominent appearance in the Bible and Father Damien. There's the triumph of effective treatments in developed parts of the world -- an aspect that this paper emphasizes, as it attempted to find out whether regions of the world that now lack M. leprae once had the strains expected from their geographic placement. And there's the continuing tragedy of the disease in many less developed parts of the world, with the need to deliver treatment more effectively. Meanwhile, the phylogeographic aspects of this paper provide another historical angle, about the spread of leprosy around the world on human trade routes.

    Plus there's the whole mystery of how it got into humans in the first place:

    Finally, it is worth discussing the enormous discrepancy between the period at which pseudogene formation is thought to have arisen and the origin of early humans. It has been estimated recently that the bulk of the pseudogenes in M. leprae arose no earlier than 9 million years ago. Pseudogene formation is an indicator of radical change in the lifestyle of the host bacterium, such as from the free-living to pathogenic state or of adaptation to life within a particular tissue or cell type. In the case of M. leprae, obligate parasitism of humans or another primate species would represent such a change. Although modern humans represented by H. sapiens have existed only since approximately 250,000 years ago and left Africa within the last 100,000 years to settle other regions, earlier hominids are thought to have diverged from chimpanzees over 5 million years ago. Reconciliation of the estimated time of pseudogene formation with human evolution could be achieved if an ancestor of M. leprae infected an early primate and then underwent genome decay and was subsequently transmitted vertically—although this seems unlikely, given that more genetic diversity among M. leprae isolates would be expected if this were true. Alternatively, the genome decay could well be ancient, but M. leprae may only recently have become a human pathogen. For instance, it is conceivable that an ancestral form of M. leprae infected an invertebrate host such as an insect, which later acted as a vector for transmitting the bacillus to humans. Support for the latter scenario is provided by studies of the related pathogen Mycobacterium ulcerans, which is at an early stage of reductive evolution and appears to be transmitted to humans by water bugs and/or mosquitoes. Further insight into the timing of pseudogene formation in M. leprae will be provided by microbiology and paleomicrobiology and by deeper genome sequence analysis.

    In rough outline, you "date" a pseudogene by counting the number of nonsynonymous substitutions in comparison to some other species where the gene is functional. When the gene was functional, most substitutions of nonsynonymous mutations would have been prevented by purifying selection. You generally apply more detailed assumptions, but that's the basic process. I raise the point because dating a 9-million-year-old event in a bacterial species on the basis of nonsynonymous mutations is probably not going to give a very tight confidence interval, to put it charitably. Maybe 9 million is 4 million?

    In any event, leprosy is one more addition to a growing story about the coevolution of pathogens with Homo. It may have a long history with us, like its congener, tuberculosis. It apparently doesn't have a long history of coevolution within different regionally variable human populations -- tuberculosis does. Possibly it is a relatively recent invasion from another species, which would make it maybe more like the evolutionary dynamics of vivax malaria.

    We don't lack for examples, and tabulating the histories of all of these pathogens may give us a better picture of the population ecology of Homo in Pleistocene times.

    References:

    Monot M and many others. 2009. Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 41:1282-1289. doi:10.1038/ng.477

    Tags: 
    genomics
    disease
    paleogenomics
    health
    pathogens
    phylogeography

  • When history gets complicated

    Tue, 2009-09-22 20:30 -- John Hawks

    Razib posts some thoughts on how the study of human migration history has gotten more and more complex during the last fifteen years.

    Sometimes I wonder if the period between the publication of The History and Geography of Human Genes and The Journey of Man, roughly from the mid-90s to the early 2000s, will be seen as a golden age for historical population genetics in hindsight. A few weeks ago I pointed to new data based on DNA extraction which really confuses the picture of how Europe was populated over the past 25,000 years. It seems the more data we get, the more interesting things get. In the late 1990s the emergence of powerful technologies to extract and amplify genetic material and sequence it shed light on several questions which had long tantalized researchers ever since Alan Wilson's group began to push the frontiers of molecular evolution in the 1970s. Where in the 1980s there was only the mitchondrial Eve story, by the year 2000 there was enough to go around for several books. The Journey of Man, Mapping Human History and The Seven Daughters of Eve all came out very close together chronologically. These scientists and writers knew that striking fast was imperative.

    That's also when Colin Renfrew's "archaeogenetics" really got going, with a number of symposia and a couple of books. So what happened? As Razib points out, things got complicated -- we started adding more autosomal markers, and larger samples of mtDNA and Y chromosomes, and the trees didn't line up so cleanly. In retrospect this was predictable, as one-locus genealogies have so much variance that it's easy to confuse noise for signal.

    Heck, it's not just hindsight, the problem was predicted at the time, by me and others!

    Still, I've learned to appreciate science's self-correcting nature. Phylogeography grew into a serious science, not flawless, but driven increasingly by testing hypotheses instead of promoting "consistency" with them. This happened partly by extending the same genetic techniques to other species, where the basic modeling questions didn't have the same headline-grabbing emotional appeal as in humans.

    Many shark-jumping moments of human genetics are still out there, waiting to be re-evaluated with new evidence.

    Tags: 
    mtDNA
    phylogeography
    mtDNA migrations

  • "The worm in the fruit of the mitochondrial DNA tree"

    Thu, 2009-09-17 09:39 -- John Hawks

    François Balloux (2009) has a polemic in the online access area of Heredity presenting references about mtDNA selection, and arguing that the use of this single genetic marker is no longer warranted without support from other loci.

    Yay! I've been saying that both here, and in peer-reviewed articles, for several years. I think serious workers know that one gene is not enough; two genes (mtDNA and Y chromosome, for example) aren't enough -- we have to integrate information across every possible source, genetic, skeletal, and anthropological, to really test hypotheses about the past.

    Still, an industry of mtDNA sequencing has grown up, reviewing each others' grants and papers, and shutting down any discussion of adaptive changes. Balloux's commentary addresses this problem -- I'm going to quote the same paragraph as Dienekes:

    Let us assume I gave a seminar. I would tell the audience about my latest results on the population history of the pigmy shrew. My findings would be based on a stretch of DNA comprising several metabolic genes, showing no signs of genetic recombination. Armed with sequences from a large number of individuals sampled over a broad geographical area, I would make some inference on the colonization routes and times. To make life easier, I would restrict my analysis to the mutations I liked best, with nice names having been given to related sequences, rather than relying on dull mathematical quantities. As I reach one of the key conclusions of the lecture, which would go as follows: 'It is obvious from the distribution of haplotypes Amanda, Eugenie* and Hector_2 that the Outer Hebrides were colonised about 50,000 years ago, this was followed by considerable population fluctuations, a bottleneck during the last Ice Age, a swift recovery and a dramatic recent expansion over the last 200 years and...'. Imagine that, at that climactic stage I was interrupted by someone in the audience. The impertinent would say, 'Sir, can I just ask you whether this confidence in your conclusions may not be misplaced; your analysis is based on a single genetic marker, which comprises genes with a central role in metabolism and is thus likely to have been affected by natural selection'. An awkward silence may ensue, as I would find it difficult to dismiss this criticism easily.

    Well, let me tell you, I've been in dozens of audiences, and have raised that exact point. Here is a sample of the bogus responses I've gotten to this question:

    Bogus answer 1: There are no functional differences between humans and chimpanzees in the mtDNA, so it can't have been selected during human evolution. False, false false!

    Bogus answer 2: Metabolic processes are highly conserved, and humans couldn't have changed much. Hello? Have you noticed that your breakfast didn't exist in the Paleolithic?

    Bogus answer 3: But the pattern of variation can be equally explained by a bottleneck. Some aspects can, others can't so easily.

    Bogus answer 4: We examined only noncoding parts of the mtDNA, so there could be no selection. Yes, believe it or not, this is the most common response. I guess they don't teach people about linkage anymore.

    Bogus answer 5: There's little or no evidence of selection on any gene in recent human evolution. Human evolution may have stopped entirely. Oh, lord. Yes, I've gotten this one many times.

    There have been others over the years. Yet mtDNA is a big business -- people seem to be worried that the slightest criticism will bring down the whole thing like a house of cards. That's not true, even if mtDNA has sometimes been selected during human prehistory or history, that doesn't mean it isn't a useful marker for many purposes. But many seem more comfortable avoiding the issue entirely.

    I think that taking the hypothesis of selection seriously would improve most of the work in this field. The possibility of selection doesn't eliminate demographic interpretation -- for example, the high ancient African mtDNA variation allows us to test hypotheses about African demography before 50,000 years ago, and there the data appear to reject the hypothesis of selection, at least after around 150,000 years ago. Gene genealogies don't allow us to see the whole past, just the time and forces that they experienced. If we ignore one of the major forces, we are reducing our knowledge.

    There is an obvious problem testing the hypothesis of selection with mtDNA. When we consider any one single locus, it's always possible to find some demographic scenario that yields exactly the same predictions as selection. It's just a mathematical necessity -- selection is fundamentally a demographic phenomenon, and the increase in frequency of selected alleles looks similar to exponential growth of a small population.

    So what can we do? Fortunately we have lots of options. We can test the proposed demographic hypotheses against the historical record. When we make observations that show that people 1000 years ago had very different frequencies of common haplotypes, well, we know it was selection. There hasn't been any genetically significant bottleneck in the last 1000 years! When we see small Neolithic population samples dominated by haplotypes that are very rare today, again, no historically possible bottleneck could have caused that.

    Balloux with his colleagues (2009) has shown that one aspect of mtDNA patterning -- the association of haplogroup diversity with geography -- is very unlikely to have arisen by genetic drift. Here's part of their abstract:

    We show that populations living in colder environments have lower mitochondrial diversity and that the genetic differentiation between pairs of populations correlates with difference in temperature. These associations were unique to mtDNA; we could not find a similar pattern in any other genetic marker. We were able to identify two correlated non-synonymous point mutations in the ND3 and ATP6 genes characterized by a clear association with temperature, which appear to be plausible targets of natural selection producing the association with climate. The same mutations have been previously shown to be associated with variation in mitochondrial pH and calcium dynamics. Our results indicate that natural selection mediated by climate has contributed to shape the current distribution of mtDNA sequences in humans.

    They took a dual approach to testing the hypothesis of selection. First, they modeled the evolution of haplotype diversity under neutrality, and showed that the empirical distribution lies significantly outside that range of results. But even so, we might imagine some bottleneck scenario that would cause low diversity in high-latitude peoples, and this would be difficult to refute historically because many of those populations have poor historical documentation. But demography should have similar effects on other genes, and they were able to show that the rest of the genome doesn't share the mtDNA pattern.

    It's really not that hard to test demographic hypotheses, using comparative genomics and anthropological knowledge. That's what anthropological genetics should be doing more and more. There was a time when obtaining a reasonable sample of mtDNA was an accomplishment, and comparing that sample to other genes was not feasible. But that time is past, and hopefully the review process -- journals and grants -- will start demanding some integration of mtDNA phylogeography with results from the rest of the genome.

    Back to Balloux's conclusion:

    Exploiting these new resources of autosomal variation will present significant challenges, but it will not help overcoming them if a large fraction of the community of human population biologists persists in sticking to mtDNA as the marker of choice.

    Mitochondrial DNA isn't the tip of the iceberg -- it's an ice cube on top of the tip of the iceberg.

    Related:

    "Mitochondrial DNA selection review"

    "Mitochondrial DNA and sperm"

    "mtDNA selection in Iceland?"

    "Complete Neandertal mitochondrial sequence, and selection on human (not Neandertal) mtDNA"

    "Did Neandertals need better mitochondria?"

    "Has the dam broken on mtDNA selection?"

    Mitochondrial DNA adaptations in living human populations"

    OK, that's enough related posts. But you can find a whole lot more by searching the topic!

    References:

    Balloux F. 2009. Mitochondrial phylogeography: The worm in the fruit of the mitochondrial DNA tree. Heredity (advance online): doi:10.1038/hdy.2009.122

    Balloux F, Lawson Handley L-J, Jombart T, Liu H, Manica A. 2009. Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. Proc Roy Soc Lond B 276:3447-3455. doi:10.1098/rspb.2009.0752

    Tags: 
    genetic drift
    mtDNA migrations
    phylogeography
    recent selection
    mtDNA

  • Neandertals and bears

    Fri, 2009-04-17 00:14 -- John Hawks

    For most of their prehistory, humans were highly mobile hunter-gatherers. We can expect that Neandertals were also highly mobile, at least compared to sedentary post-agricultural human populations. Great apes are our closest living relatives, but they live in tropical forests -- a pretty different environment than the Neandertals. There are constraints on ape mobility, including difficulty of locomotion, habitat complexity, and extreme territoriality, that might not have constrained ancient humans, including Neandertals.

    We might then consider the population structure of other highly mobile large mammals. Brown bears have been sympatric with humans in Europe since the Middle Pleistocene. Bear ecology has similarities and differences from Neandertals -- bears were omnivores accentuating meat consumption to a similar extent, but did not live in groups. Like Neandertals they may have exploited edges between habitat types, although brown bears are effective in open country as well.

    For bears, like other European mammals, one of the most important questions is what happened to their population during the Last Glacial Maximum (LGM). The LGM was only around 18,000 years ago, so it's not an issue for Neandertals who were long gone by that time. But because the LGM is relatively recent, we have a relatively large representation of bear mitochondrial genetics spanning that time interval. So it gives us a chance to look at the relationship of population structure and genetic diversity in a large, mobile, European mammal. The bear comparison also lets us consider the effects of a smaller sample on our conclusions about ancient population structure and dynamics.

    Brown bears are very common in archaeological and subfossil paleontological faunal lists. During the LGM, brown bears are known from northern Spain and Moldova. Evidence from today's bears suggests the occupation of at least four refugia (Sommer and Benecke 2005) -- basically Iberia, Italy, the Balkans and the Carpathians. These four areas can be expected to have housed substantial diversity during the LGM. The subsequent recolonization of northern Europe may be the largest factor organizing the present pattern of genetic variability, with the differential expansion of lineages through space.

    Interspecific patterns of recolonization from refugia

    Taberlet and colleagues (1998) collated phylogeographic evidence from 10 European species, ranging from plants to large mammals and including brown bears, to trace the likely pathways of postglacial recolonization of Europe. They found evidence for the importance of three refugia -- basically Iberia, Italy, and the Balkans. But most interesting, they found that each of their 10 species showed different patterns of postglacial expansion dynamics.

    It seems that each taxon has responded independently to Quaternary cold periods, and therefore is largely a unique case with its own history. For example, if we compare lineages present in Italy and in the Iberic peninsula, they are closely related in Ursus (less than 1% of sequence divergence in the cytochrome b gene) but much more distantly related in Crocidura (6.4%), in Arvicola (7.6%) and in Triturus (8.5%), while the Sorex species considered here exhibit two lineages in each of these two refugia. Populations occurring in France come either from a refugium in the Iberic peninsula (e.g., Arvicola sapidus, Triturus marmoratus), or from a refugium in the Balkans (e.g., Chorthippus parallelus, Fagus sylvaticus).

    ...[T]he results obtained in Europe and North America (Zink 1996) suggest that congruence is the exception at the continental scale. The consequence of an independent history for each taxon is that assemblages of plants and animals comprising particular communities are not stable over time, an observation consistent with previous findings based mainly on fossil pollen data (Bennett 1990) (Taberlet et al. 1998:459).

    Before going on to cite their conclusion, I want to note one possibility that they don't consider -- namely, that the species have similar dynamics of range constriction and expansion but that the mtDNA evidence represents these dynamics with substantial variance.

    One aspects of that study stands out as interesting as applied to the Neandertals. Although the species did not share any single pattern of expansion from refugia, one aspect was shared: species did not expand from Italy. The authors speculated that the Alps are an effective barrier to rapid recolonization of northern Europe from Italian refugia, and indeed most northern species were recolonized either from Iberia or from the Balkans, or both. Thus Italy today contains many endemic lineages that were stuck in Italy during the LGM or other contractions, and never left. The possibility of an Italian-Croatian population of Neandertals was raised by Fabre and colleagues (2009). Was recolonization from this population possible during warmer phases of the Pleniglacial? If not, this population of Neandertals may have been exceptionally variable -- containing many long-standing endemic variants compared to other Neandertal populations. It may also have been substantially divergent from those other populations. Since Vindija is the most important source of the Neandertal genome, it's an important aspect of biogeography to try to understand.

    Recolonization by brown bears

    So much for the general pattern of recolonization. Now back to brown bears.

    Sommer and Benecke (2005:161) considered further the present population of European brown bears and likely refugia in southern Europe. They returned to the genetic data developed in earlier studies by Taberlet and colleagues to conclude:

    It is possible to detect three different glacial refugia from their data: (i) the Iberian Peninsula (Spain), (ii) the Italian Peninsula and (iii) the Balkans (Bulgaria/Greece). Furthermore, the investigation into the mitochondrial DNA of brown bears in Europe (Taberlet & Bouvet, 1994) shows four main points:

    1. The individuals of southern Scandinavia originated from the Iberian Peninsula are closely related to the individuals from the Balkans and the Italian Peninsula, and form a 'western lineage'.

    2. The bears of northern and eastern Scandinavia, from the Baltic States, from north-western Russia and the Carpathians differ with a sequence divergence of 7.13% from those individuals in the western lineage (Fig. 5).

    3. Based on their genetic similarity, the brown bears from northern and eastern Scandinavia, the Baltic States, and north-western Russia are designated as 'eastern lineage' and a glacial refuge in eastern Europe is assumed to be the origin of this genotype (Hewitt, 1999).

    4. Within the mitochondrial DNA of brown bears from the Carpathians, three different genotypes can be identified, whereas the genotype of bears from north of the Carpathians (Slovakia) is distributed throughout bears from Norway, Finland, the Baltic States and north-western Russia (Fig. 5).

    They used these observations to argue for a refuge in the Carpathians during the LGM, which seems eminently reasonable based on their observations.

    They did not point out (but I will add) that the expansion from an Iberian refugium toward Scandinavia mirrors the pattern of expansion of Magdalenian assemblages after the LGM. The recent literature has described this as a slow and tentative process of expansion (e.g., Jochim et al. 1999), but it was nonetheless as fast or faster than accomplished by small mammals, and may have mirrored the movements of the Magdalenians' large mammal prey animals. That human movement may also explain the distribution of mtDNA haplogroup H in Europe, which Pereira and colleagues (2005) attributed to a post-glacial recolonization from Iberia northeastward. This is not a new idea; Cavalli-Sforza wrote about this direction of postglacial migration some 30 years ago.

    Later, Sommer and Nadachowski (2006) extended the map of refugia to take in more species, using faunal records from LGM archaeological sites. The map below helps to put these observations into context:

    Map of Europe with LGM archaeological sties noted

    Figure 2 from Sommer and Nadachowski 2006. The position of Last Glacial Maximum archaeological sites is noted. The faunal lists from these sites provided the data underlying the inference of LGM refugia. I would point out that it seems not unlikely that a large mammal species like a bear might move in significant numbers across this entire range.

    The possible ranges of human occupation and mammal refugia seem very extensive across southern Europe but are not necessarily contiguous. For example, the Alps form a partial barrier around the northern part of Italy, and the Pannonian Basin might partially cut off from Italy/Dalmatia as well. But it's not hard to imagine a large mammal like a bear (or a human) traversing the distances between such refugia, or walking along corridors between them such as the coasts.

    More samples, more complexity

    We have to remember that the interpretation of semi-isolated refugia has been based on the pattern of genetic variation in living species in Europe. But geographic differentiation need not only have occurred because populations were once fragmented during glacials. Differentiation may also be a product of range expansion, selection, or later interaction with other species, including humans. Today's differentiation is not necessarily a trace of refugia in the past.

    So it becomes important to test the hypothesis of semi-isolated refugia, by looking at the variation of ancient DNA sequences. Last year, a study by Valdiosera and colleagues did exactly that -- looking at new sequence data from a larger set of brown bear subfossil remains from Iberia.

    Here's a paragraph from the discussion of that paper:

    Under traditional glacial refugia hypotheses (4, 17), the extant brown bear phylogeographic structure derives from ancestral glacial refugia: the western lineage originating from Iberia, Italy, and the Balkans, and the eastern lineage possibly derived from a Carpathian refugium (14, 16). In contrast to such a strict refugial model, but in concordance with a continuous European prehistoric population, we have identified a sequence from a Pleistocene Iberian brown bear from Arlanpe site (the Basque country) that belongs to the eastern clade. In our analyses, such a phylogenetic assignment is supported by maximal posterior probabilities (Fig. 1 A). This pattern is further supported by three Pleistocene brown bear sequences from Valdegoba (northern Spain), which cluster with a previously published sequence from Atapuerca (northern Spain) and with several sequences from modern Italian and Balkan bears. Furthermore, AMOVAs suggest little geographic substructure among Spanish and European Pleistocene populations. These new data confirm the lack of phylogeographic discontinuity in European brown bears before the LGM (23). Although Spanish and European Holocene populations appear geographically differentiated in our AMOVAs, a recent study has suggested that gene flow could have continued from the Pleistocene to the Holocene (20). An Iberian brown bear, dated to the time of the LGM from the site of Atapuerca in Burgos in the north of Spain, was more closely related to Italian/Balkan bears than to the Iberian ones. Moreover, during the Holocene in Mont Ventoux (southern France) three mitochondrial groups are found between 1,570 to 6,525 years B.P.: one belonging to the Iberian group, another one to the Italian/Balkan one, and yet a third one not associated with any of the three main glacial refugia (20). Note, however, that support for the Spanish and the Italian/Balkan clades are low in our tree. In this study, we have found three different individuals from Valdegoba, a Late Pleistocene site also in Burgos, that group together with the sample from Atapuerca (Valdiosera et al. 2008: emphasis added).

    I think this study is so interesting because of the way it shows the influence of sample size on the phylogeographic interpretation. Consider how the conclusions of the study would have been different if the sample had been smaller. The authors found one Iberian Pleistocene bear that belonged to a clade otherwise comprising bears from Austria, Germany and Russia. This one bear is their clearest indication of ancient movement between plausible refugia. Had they not found a sequence in this bear, the evidence favoring two distinct refugia would have been much stronger.

    Likewise, their sample includes three bears from Pleistocene France that belong to a clade of their own. This diversity no longer exists among today's bears -- at least, not the ones sampled up to now. If this region of France happened not to have produced bear remains, we would not have any evidence of this divergent clade at all. Again, the record would suggest that present bears derived from two largely isolated refugia. As it is, either another French refugium existed or the Pleistocene Iberian population harbored more diversity than present bears of Iberia.

    That last element, a reduction of diversity over time, is also suggested by the pattern of variation between Pleistocene and Holocene bear remains. It has a lesson for the interpretation of human variation -- some human mtDNA haplogroups have reduced in frequency in recent Europeans, others have apparently increased. In the case of humans, we may be looking at selection. Brown bears have had a smaller effective size than humans during the last 10,000 years, so we might be looking at an actual reduction in numbers or geographic range.

    In any event, with the bears every additional sample carries information about ancient population structure. We can expect that the addition of more Neandertal mtDNA samples will likewise add information about Neandertal population structure. The addition of samples is more likely to confuse a simple story than to confirm it, although either is possible.

    Valdiosera and colleagues conclude that brown bears were actually highly mobile during the LGM, moving easily across a range that, although limited compared to earlier and later time periods, extended from east to west across southern Europe. It's hard to believe that Neandertals weren't capable of similar movement. On the other hand, chimpanzees are likely capable of long-distance movement but still have substantial population differentiation. This may be because intervening groups prevent individuals from moving long distances. So the dispersal character of Neandertal populations may have depended upon their social dynamics, an aspect of behavior that we are poorly situated to test.

    References:

    Pereira L and 12 others. 2005. High-resolution mtDNA evidence for the resettlement of Europe from an Iberian refugium. Genome Res 15:19-24. doi:10.1101/gr.3182305

    Sommer RS, Benecke N. 2005. The recolonization of Europe by brown bears Ursus arctos Linnaeus, 1758 after the Last Glacial Maximum. Mammal Rev 35:156-164. doi:10.1111/j.1365-2907.2005.00063.x

    Sommer RS, Nadachowski A. 2006. Glacial refugia of mammals in Europe: evidence from fossil records. Mammal Rev 36:251-265. doi:10.1111/j.1365-2907.2006.00093.x

    Taberlet P, Fumagalli L, Wust-Saucy A-G, Cosson J-F. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453-464. doi:10.1046/j.1365-294x.1998.00289.x

    Valdiosera CE and 10 others. 2008. Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proc Nat Acad Sci USA 105:5123-5128. doi:10.1073/pnas.0712223105

    Tags: 
    bears
    mtDNA migrations
    Neandertals
    non-primate
    phylogeography
    Neandertal DNA

  • Neandertal races?

    Wed, 2009-04-15 23:41 -- John Hawks

    There's a new paper in PLoS ONE by Virginie Fabre, Silvana Condemi and Anna Degioanni, titled "Genetic evidence of geographical groups among Neanderthals." I think this is an ambitious paper -- it uses 12 mtDNA sequences recovered from Neandertal fossils to compare different phylogeographic scenarios for Neandertal populations.

    The authors applied several different models to the data, attempting to find a population history that matches the geographic distribution of mtDNA diversity in Neandertals. They found that a model in which Neandertals had been part of three long-standing geographic populations was a better fit than others. Here's the relevant part of the abstract:

    In this paper we used a new methodology derived from different bioinformatic models based on data from genetics, demography and paleoanthropology. The adequacy of each model was measured by comparisons between simulated results (obtained by BayesianSSC software) and those estimated from nucleotide sequences (obtained by DNAsp4 software). The conclusions of this study are consistent with existing paleoanthropological research and show that Neanderthals can be divided into at least three groups: one in western Europe, a second in the Southern area and a third in western Asia. Moreover, it seems from our results that the size of the Neanderthal population was not constant and that some migration occurred among the demes.

    I like the study, and I have no strong objections to the conclusion. It has always seemed sort of likely on morphological grounds that Neandertals may have had modest geographic differentiation. Amud 1 doesn't look like a French Neandertal; nor does Teshik Tash. So I'm inclined to think the results are not too surprising.

    Still, the data have some big weaknesses. Phylogeography is a tall order when we only have 12 sequences.

    Many have pointed out, going back to McCown and Keith (1939), that time is another possible cause of morphological differentiation of Neandertals. The mtDNA sequences cover a wide range of times -- the Scladina sequence comes from roughly 100,000 years ago, the others cover the span from 50,000 down to 29,000 years ago. Why not test temporal groups instead of geographic groups? Temporal clusters might reflect interglacial colonizations, differential gene flow, or natural selection. There is a good precedent -- last year a report of complete mtDNA sequences from woolly mammoths found evidence for geographic structure among mtDNA lineages, one of which apparently replaced the other (Gilbert et al. 2008).

    Time is just one example of an alternative model for variation. But I think it helps to clarify the basic problem of the a priori models -- you have to draw boundaries between the specimens somewhere. In the current paper, Fabre and colleagues divided the samples into one, two, or three groups. The one-group model amounts to a simulation of panmixia. The other models are a little like the setup of a Bayesian STRUCTURE analysis -- how well does the sample fit a model in which the the latter as the more likely null hypothesis.

    But unlike STRUCTURE, in this case, each specimen had to be assigned deliberately to one group or another. That's why the authors generated three different versions of their three-group model -- in each version, the boundaries between groups were drawn in slightly different places.

    That's not a criticism of the paper; it's just an inherent property of the method. There's no better way to come up with boundaries of the groups, and I've done similar things in earlier work. It's rational to have the groups contiguous with respect to geography, but without clear isolating barriers, no special reason why the groups should be bounded along any particular line.

    In this case, one of the three-group models provided a substantially better fit between simulated data and the observed mtDNA sequences. So the paper concludes that three groups are supported.

    Thinking about it, I would probably use the data to test a slightly different set of hypotheses.

    I would start with an analytical approach, explicitly testing the hypothesis of panmixia; then explicitly testing isolation-by-distance. Panmixia should be easy to refute -- if you don't then phylogeography is a non-starter. I see isolation-by-distance as the appropriate null hypothesis, and while the time-dispersion of the samples makes life a little more complicated, a simple test of IBD would be straightforward. I don't expect you need simulations for either of these tests, although you could use simulations to explicitly include the ages of the specimens in the test.

    One reason to start with IBD is that the specimens are heterogeneously distributed through space. Since there are some large gaps in the geographic distribution, the observed sequences may tend to clump into groups even if no real boundaries between groups existed. The best-supported model in the paper divides the sample with a clump of Italian and Croatian specimens, a large gap between Ukraine and Uzbekistan, and most of the specimens in one large group. That looks like a pattern that might be consistent with IBD, complicated by the actual ages of the specimens.

    Archaeology

    At any rate, the conclusion in the paper should make one set of people nervous: those who think that Paleolithic archaeological industries reflect populations. I can't see any obvious alignment between these three "groups" of Neandertals and well-known cultural units at any time interval. There are some localized and relatively long-lasting industries or variants within the boundaries of some groups, and there are others that span the boundaries.

    Now, if these groups really reflect long-standing population boundaries -- spanning some 100,000 years in the model -- then we might expect it would have been hard to exchange information across them.

    The same should have been true of Africa, which I've mentioned shows evidence for population differentiation going far back into the Late Pleistocene if not earlier. In Africa, the MSA shows both long-standing variations in different regions and relatively rapid temporal fluctuations within regions. The same general picture holds for the Mousterian, although one may argue whether the correspondence is exact. In any event, the African regional variants show no obvious correspondence to the genetic differentiation of African populations today. Maybe that's because of subsequent changes in the African population -- today's differences don't necessarily reflect those of MSA populations.

    But suppose we take the Neandertal model seriously. Information transfer in living people occurs on a much more rapid timescale than genetic exchange. That cannot always have been true in human evolution -- it isn't generally true of other primates, where long-distance information transfer basically depends on the transfer of individuals from their natal groups. What should an intermediate stage look like, in which the amount of information transfer may be less than in recent human groups (with writing, accounting and vastly more people), but the pace of transfer may have been comparable? I doubt they would correspond well to genetic populations over much longer timescales, although they may be limited by them to some extent.

    Are these Neandertal races?

    I raised the question in my class today. If these really are groups of Neandertals, occupying different geographic ranges for a hundred thousand years, what do we call them? I thought it was a good lead-in to talk about species concepts in paleoanthropology, and of course it is.

    If these aren't species, why aren't they? Presumably because we think that genetic exchanges across this range would have been likely. You can test the hypothesis by comparison with living humans and other primates. Mitochondrial phylogeography of human populations includes some long-standing population structure going back more than 60,000 years. Within great apes, there are long-standing subspecies that go back much further, hundreds of thousands of years. In humans, we tend to call the resulting groups races or populations. Among great apes, we tend to call them subspecies.

    So are these subspecies of Neandertals? Races? Geographic populations? I wouldn't interpret further without really determining the nature of the boundaries here. As I mentioned earlier, I think the null hypothesis is isolation-by-distance. It's conceivable that the Neandertal population was patterned in a similar way to recent humans -- although considering our rapid recent evolution, I wouldn't be quick to assume that human differentiation is a good model.

    One other thing. Let's assume that the Neandertals really were differentiated from each other, and that the groups proposed by Fabre and colleagues are generally right. In that case, the Neandertal Genome Project has been concentrating on an individual from the Southern subpopulation, a subpopulation otherwise very far the population interface between Neandertals and other humans before 45,000 years ago. Hence, that sequence may be a bad place to look for evidence of interactions between Neandertals and modern humans. Genetic exchanges are more likely to have happened across long-standing areas of contact -- which in Fabre and colleagues' best model, would likely involve the Western or Eastern subpopulations.

    That's entirely speculative on my part, but it does seem to be one implication of the model.

    References:

    Fabre V, Condemi S, Degioanni A. 2009. Genetic evidence of geographic groups among Neanderthals. PLoS ONE 4:e5151. doi:10.1371/journal.pone.0005151

    Gilbert MTP and 32 others. 2008. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial sequences. Proc Nat Acad Sci USA 105:8327-8332. doi:10.1073/pnas.0802315105

    Tags: 
    phylogeography
    models
    population structure
    Neandertal DNA
    Neandertals
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