population dynamics

A paper by Silvana Condemi and colleagues examines the anatomy of a partial mandible from Riparo Mezzena, Italy [1]. The mandible is a relatively late Neandertal specimen by its archaeological association and mtDNA sequence. As the introduction to the paper notes, the identities of skeletal specimens in the timespan from 45,000 to 30,000 years ago across Europe have been shifting along with radiocarbon ages and further analyses of fragmentary specimens. In this case, like other late Neandertals, the specimen bears a chin:

This study of the Mezzena mandible shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, Saint Césaire). In our view, this change in morphology among late Neanderthals reopens the debate on the "more modern like" morphology of late Neanderthals and can lend support to the hypothesis of a certain degree of continuity with AMHs or a possible interbreeding with them.

The paper concludes that the Mezzena mandible lies morphologically amid the sample of modern humans from Upper Paleolithic and Levantine Middle Paleolithic contexts, even when compared to Neandertals like Saint Césaire or La Ferrassie 1 that have relatively vertical mandibular symphyses.

I prefer not to play the game, "is it a Neandertal?", "is it a modern human?" If we had a sample of well-dated relatively complete specimens across the period from 45,000 to 30,000 years ago, we could test the hypothesis that two populations (earlier Neandertals and later "modern" humans) were genetically well-differentiated from each other. We don't have that sample.

In my view, we shouldn't assume more than we know, which is that both the frequencies and combination of traits of earlier Neandertals are much more strongly present in Mousterian-associated specimens than in other, mostly later, industries. I don't yet see a reason to exclude the hypothesis that this pattern reflects both evolution and migration into Europe. And as I wrote last year, the late Neandertals may represent both evolution and migration into Europe from a central Asian or West Asian source population [2].

One effect of genetic sequences has been to demonstrate that anthropologists' morphological distinctions among Neandertals don't match the groupings we would make along purely genetic lines. I considered this problem in my paper last year, "Dynamics of genetic and morphological variability within Neandertals" (open access, PDF) [2]. Jim Ahern and colleagues (including me) have showed that the Vindija G3 Neandertals have morphological features that are not typical of classic Neandertals, and that are significantly different in the modern human direction [3], [4]. Here's what I wrote last year:

The discussion of genetic diversity among these Neandertals has not yet attempted to reconcile their genealogical arrangement with morphological classification schemes. The later Western European Neandertals that share a close mtDNA genealogical connection (Vindija-Feldhofer-El Sidrón) are not synonymous with "classic Neandertals". The well-known classic Neandertals include specimens such as La Chapelle-aux-Saints (France), La Ferrassie 1, Monte Circeo 1 (Guattari) as well as Feldhofer 1. This classic Neandertal sample includes specimens earlier than 70,000 years old and some as recent as 45,000 years ago. The classic Neandertals flank both the earlier and later sides of the 50,000-year-ago dispersal of Neandertals proposed by Dalen and colleagues (Dalen et al., 2012).

Meanwhile, the clade that connects late European Neandertal mtDNA into a tight cluster includes great morphological diversity. The two Vindija mtDNA sequences included by Dalén and colleagues (Dalen et al., 2012) are both from layer G3 of the site, perhaps 40,000 years old. Both are derived from postcranial fragments without diagnostic morphological traits. The other material from G3 includes cranial, mandibular and dental remains that are not synonymous with classic Neandertal morphology (Ahern, 2004). These late Neandertals from Vindija display less pronounced morphology than classic Neandertals and lack traits that are common in the earlier classic Neandertals (Smith, 1992). These specimens are connected to Feldhofer and El Sidrón not only by mtDNA relationships but also their very low nuclear DNA diversification. If the Vindija specimens can be lumped together in mtDNA and nuclear DNA diversity with the remains from El Sidrón and Feldhofer, it seems possible that traditional morphological groupings will fail to capture real biological differences among Neandertal populations.

Riparo Mezzena adds further to this pattern. I would note that this looks at the moment like the specimen most likely to give rise to an Italian Neandertal whole genome. As we begin to examine the data from the Denisova Neandertal specimen ("A new high-coverage Neandertal genome"), the population genetics of later Neandertals will come more and more into focus.

Steven Churchill and Fred Smith wrote a review of the initial Upper Paleolithic skeletal record several years ago [5] that still remains the best single summary of the remains from this time period. What strikes you in this review is the overall fragmentary nature of the record. That review is already out of date in some respects, as a number of specimens have been moved into or out of this period by radiocarbon revisions, and the archaeological conception of "early Aurignacian" has substantially changed.

There really ought to be an equivalent review for the latest Neandertals. I think that the sample has become more complex and confusing as we have developed a better idea of the genetics.

References

Alon Keinan and Andrew Clark have a short report in the current Science examining the effects of recent human population growth on the expected spectrum of human genetic variation [1]. Population growth skews the variation in a population so that there are many more rare alleles than would be expected in a constant-sized population.

Why is this? In a constant-sized population, individuals have an average of two offspring who survive to have offspring of their own. Many people have no children at all, or only one, while only a small proportion of people have more than four children. In the constant-sized population, a person born with a new mutation would have a 50% chance of passing it on to each child. In such a population, more than a third (36%) of mutations aren't passed on even once. The same fraction are inherited by only one child, and these face the same odds of extinction in the next generation. This isn't natural selection, it is random genetic drift -- and its net result is that most new mutations are lost.

In a growing population, individuals average more than two offspring. Every additional offspring increases the chance that a new mutation will be passed on to the next generation. In other words, more people means less genetic drift. As a population grows, new mutations begin to stack up at low frequencies in the population.

This is a very basic point in population genetic theory, and it interacts in a troubling way with the current generation of sequencing technology. Short-read shotgun sequencing yields a high number of false positive mutations, which must be aggressively filtered out of whole genome data. If we don't filter these out, we will arrive at incorrect conclusions about many aspects of human biology. The simplest means of filtering require some understanding of how many rare mutations you expect to find, in particular how many should be found in only one person in a sample of people. That expectation is different in a growing population, resulting in a potentially large bias.

Despite an improvement in the accuracy of sequencing technologies, some errors remain unavoidable. For example, with a sequencing error rate of 1 in 10,000 bases, in a sample of 10,000 individuals, each base pair will exhibit two errors on average across the sample and the majority of monomorphic sites will appear polymorphic (most often as a singleton or a doubleton; i.e., with the rare allele present in one or two copies in the sample). On the other hand, strict filtering of the data will lead to missing many rare variants because they are not observed as reliably. Hence, any analysis of large sample sizes must account for the uncertainty inherent in sequencing by considering the variant calls probabilistically, and secondary validation of rare variants by an alternate sequencing procedure is essential.

Keinan and Clark present some models that show how much it matters to consider a growing population compared to the usual null model of constant population size.

It's so interesting to me to see human geneticists catching up to where anthropologists have been for a long time. Of course, we wrote about the effects of recent population expansions in 2007, noting the apparent acceleration of positive selection in post-agricultural populations ("Why human evolution accelerated") [2].

Large-scale sequencing projects have moved beyond simply categorizing common genetic variation. They are now at a stage where thousands of individuals need to be examined, to find increasingly rare genetic variations and determine their collective effects on phenotypes. That means that the next version of the 1000 Genomes Project really needs to be involve many of us who are directly concerned with human population history. The growth and dynamics of actual historic human populations are going to matter to how we understand their genetic variation and its effects on phenotypes. Fortunately, archaeology and written history can help -- if anthropologists are involved in this work from the start!

References

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:

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