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Monday, 19 March 2012

Neanderthal Family Tree Reflects Geography

Neanderthal + Denisovan Family Tree.
Denisovans are in with the Asiatic Neanderthals, about as far removed from them as the Asiatics are from the European Neanderthals. They are NOT sufficiently different to warrant a new species

There’s a new paper out, Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. The primary results are above. Basically, using 13 mtDNA samples the authors conclude that it looks as if there was a founder effect for Neanderthals in Western Europe ~50 K years ago, generating a very homogenized genetic background for this particular population before the arrival of modern humans. Perhaps it’s just me, but press releases with headlines such as “European Neanderthals Were On the Verge of Extinction Even Before the Arrival of Modern Humans” strike me as hyperbolic. I’m also confused by quotes like the one below:

“The fact that Neanderthals in Europe were nearly extinct, but then recovered, and that all this took place long before they came into contact with modern humans came as a complete surprise to us. This indicates that the Neanderthals may have been more sensitive to the dramatic climate changes that took place in the last Ice Age than was previously thought”, says Love Dalén, associate professor at the Swedish Museum of Natural History in Stockholm.
There are several points that come to mind, from the specific to the general. First, from what I gather Neandertals were actually less expansive in pushing the northern limits of the hominin range than the modern humans who succeeded them. From this many suppose that despite the biological cold-adapted nature of the Neandertal physique they lacked the cultural plasticity to push the range envelope (e.g., modern humans pushed into Siberia, allowing them to traverse Beringia). One might infer from this that Neandertals were more, not less, sensitive to climate changes than later human populations. Second, there is the fact that as the northern hominin lineage one would expect that Neandertals would be subject to more population size variations than their cousins to the south during the Pleistocene due to cyclical climate change. This is not just an issue just for Neandertals, but for slow breeding or moving organisms generally. The modern human bottleneck is in some ways more surprising, because modern humans derive from a warmer climate. Finally, there is the “big picture” issue that though we throw these northern adapted hominins into the pot as “Neandertals,” one shouldn’t be surprised if they exhibit structure and variation. Non-African humans have diversified over less than 100,000 years, at a minimum the lineages which we label Neandertals were resident from Western Europe to Central Asia for ~200,000 years. Wouldn’t one expect a lot of natural history over this time?
Presumably the authors focused on mtDNA because this is copious relative to autosomal DNA, making ancient DNA extraction easier. I’m a bit curious how it aligns with the inference from the Denisovan paper that Vindija and Mezmaiskaya Neandertals both went through a population bottleneck using autosomal markers. The dates from the paper’s supplements are not clear to me, though it seems possible that they may have sampled individuals where the Vindija population may have been post-resettlement. At some point presumably we may be able to get a better sense of the source population of the Neandertal admixture into our own genomes if the genomic history of this population is well characterized.

February 26th, 2012 Tags:
by in Human Evolution, Paleontology | 7 comments | RSS feed | Trackback >

7 Responses to “Neandertal population structure”

  1. 1. Onur Says:
    None of the dates of the bottlenecked Western European Neanderthal specimens are prior to the modern human migration to Western Europe. The date of the Neanderthal bottleneck in Western Europe (<50,000 years before present) clearly coincides with the date of the appearance of modern humans in Western Europe (again <50,000 years before present) . It seems modern humans pushed Neanderthals to certain corners of Western Europe when they colonized Western Europe and this triggered a population bottleneck in Western European Neanderthals. Because that it would take longer for modern humans to colonize Eastern Europe with its harsh climate, Eastern [Western?-DD] European Neanderthals would preserve their earlier genetic structure longer.[ Does this mean"The Advent of Modern Humans in EASTERN Europe?" Basic wisdom has it they appeared in the East and went West. In  articles, the Western European examples-out of NW Africa no doubt-are younger than their Eastern European counterparts by several thousand years-DD]
  2. 2. Maju Says:
    Nice map, it helps a lot to see the big picture.
    The only thing that this says is that the late West Neanderthals of Feldhofer, Vindija and El Sidrón were, matrilineally, descendants from a single population, which was distinct from their geographic predecessors of Valdegoba and Scladina but closely related to the “old school” Neanderthals from Italy. It can therefore be imagined that West and Central Europe were re-colonized from Italy (or maybe the nearby West Balcans).
    Instead Caucasian and Altaian Neanderthals retained their distinct lineages. We lack info from the late Southern Iberian Neandetrhals, which I would imagine more archaic than their continental neighbors (but just a guess).
    Feldhofer is characterized by a Micoquian culture (big almond shaped axes, often, but not in this case, intersped with Mousterian). Vindija and El Sidrón are both Mousterian. I say because I was kind of expecting this bottleneck to be related to Chatelperronian or other early UP techno-cultural expansion but there’s lack of data on that, I realize now.
    Whatever the case the appearance is of a population replacement by Neanderthals on other Neanderthals with an Italian or Balcanic source. As Onur says, it is at least curious that those dates are already within the probable time-frame of H. sapiens penetration in Europe: Istallosko, the earliest Aurignacian site, is 47.7 calBP, 44.3 BP uncal., with even older “aurignacoid” dates existing in Swabia and a number of other loosely “aurignacian” sites at the Pyrenees, South Germany, etc. before 45 Ka calBP.
    There is a modern (H. sapiens) individual dated to c. 55 Ka BP (OSL, stratigraphy) in Palestine (Emirian culture, considered precursor of other “Aurignacoid” groups). So we must realize that Neanderthals were already interacting with “us” since very early, even in Europe itself.
  3. 3. Eurologist Says:
    Not sure what is going on with this blog’s software, but my posts are no showing up. Another try:
    I have a hard time with the authors’ interpretation. It all hinges on a very small number of early western specimen, and their dating.
    If one believes the timing, there was an expansion of the tight group (blue in the figure) ~60,000ya. The other branches may very well have expanded, too – we have simply insufficient data prior to ~42,000ya.
    Now, all or nearly all of the finds of the tight group are dated to when AMHs were already present in the region. Since the expansion occurred well beforehand, I don’t see a bottleneck, but rather a very strong selection event. Could this group have had physiological features that spared them? Were they resistant to newly brought-in diseases?
    I also miss a discussion of the archeological context. Surely, instead of relying on the very few specimen we have, one should compare to known sites and occupation timings. IIRC, there indeed were expansions at some sites ~60,000ya and shortly before AMHs arrived.
    Interesting also that none of the tight group survived the Phlegraean Fields eruption…
  4. 4. Jacob Roberson Says:
    I go into pop-sci articles expecting speculative scifi.
  5. 5. Randall Parker Says:
    ~50 years ago???
  6. 6. Razib Khan Says:
    Since the expansion occurred well beforehand, I don’t see a bottleneck, but rather a very strong selection event. Could this group have had physiological features that spared them? Were they resistant to newly brought-in diseases?
    i don’t understand what you’re trying to say. you don’t consider a selection event a bottleneck?
  7. 7. Eurologist Says:
    “you don’t consider a selection event a bottleneck?”
    Perhaps I am misunderstanding something here, but my reading of the authors indicates that they place a bottleneck just before the expansion @ ~60kya — ~15-20ky before what I see as a selection event. My argument is that while there may have very well been a contraction (expected ~70ka-60ka ago due to climate), there are noteworthy logical fallacies, here.
    Firstly, there is a strong ascertainment bias: the vast majority of specimen from which mtDNA has been extracted is of course the most recent material (<42kya).
    If, on the one hand, the analysis indicates a population expansion 60-50kya, but on the other hand we have almost no data from that time period nor from the time until 42kya, then we cannot say much about the makeup of the population during that time.
    Lacking that, a reasonable *conjecture* would be that *all* then-existing branches expanded – because the one that we *have* data from shows this pattern. Then, the only conclusion one is left with is that – although somewhat plentiful – all but the "blue" branch vanished with the arrival of AMHs. That's selection – not a bottleneck, at *that* time. And note – I am usually extremely cautious about selection.
    In other words, envision figure one with another pink and green and yellow tree (think "little boxes" song), similar to the "blue" lineage – except the other ones didn't make it past 42kya. It's like our Sun or planets or Saturn's ring syndrome: we are hardwired to initially think – based on a single data point – they are exceptions – until we realize they are not.

Three Neanderthal Sub-Groups Confirmed

ScienceDaily (Apr. 15, 2009) — The Neanderthals inhabited a vast geographical area extending from Europe to western Asia and the Middle East 30,000 to 100,000 years ago. Now, a group of researchers are questioning whether or not the Neanderthals constituted a homogenous group or separate sub-groups (between which slight differences could be observed).
Paleoanthropological studies based on morphological skeletal evidence have offered some support for the existence of three different sub-groups: one in Western Europe, one in southern Europe and another in the Levant.
Researchers Virginie Fabre, Silvana Condemi and Anna Degioanni from the CNRS Laboratory of Anthropology (UMR 6578) at the University of Marseille, France, have given further consideration to the question of diversity of Neanderthals by studying the genetic structure of the mitochondrial DNA (mtDNA) and by analyzing the genetic variability, modeling different scenarios. The study was possible thanks to the publication, since 1997, of 15 mitochondrial DNA (mtDNA) sequences (the mtDNa is maternally transmitted) that originated from 12 Neanderthals.
The new study confirms the presence of three separate sub-groups and suggests the existence of a fourth group in western Asia. According to the authors, the size of the Neanderthal population was not constant over time and a certain amount of migration occurred among the sub-groups. The variability among the Neanderthal population is interpreted to be an indirect consequence of the particular climatic conditions on their territorial extension during the entire middle Pleistocene time period.
Degioanni and colleagues obtained this result by using a new methodology derived from different biocomputational models based on data from genetics, demography and paleoanthropology. The adequacy of each model was measured by comparing the simulated results obtained using BayesianSSC software with those predicted based on nucleotide sequences.
The researchers hope that one day this methodology might be applied to questions concerning Neanderthal cultural diversity (for example the lithic industry) and to the availability of natural resources in the territory. This could provide new insights into the history and extinction of the Neanderthals.
Journal Reference:
  1. Fabre et al. Genetic Evidence of Geographical Groups among Neanderthals. PLoS ONE, 2009; 4 (4): e5151 DOI: 10.1371/journal.pone.0005151

 A discriminant functions analysis for fossil Homo skulls. They basically fall into four natural groups (from the top)as  Homo erectus, H. sapiens heidelbergensis (archaic Homo sapiens), H sapiens neanderthalensis (Neanderthals) and modern Homo sapiens, more distinctive from all the rest. There are sound reasons for including ALL of them in one species as Homo sapiens
    In a conference about the neanderthal genome, Carles Lalueza told to us that neanderthals didn't seem to come only from one group of hominids, because looking at their genome(s) they found that they came at least from two different groups, one of them being more closely related to us (modern humans) and the other diverged from our line earlier.
    It seems that neanderthals' ancestors mixed with other archaic groups when they left Africa, although we don't know when and where.

    It is possible that they come mainly from a group who diverged from us about a million of years ago, but then, once in Europe/Asia, these archaic hominids mixed again with another group of hominids more akin to us?

    This may explain why neanderthals are anatomically quite different from us, but genetic information tell us another different history.

    'This is ongoing research anyhow and we'll know better for sure some years from now.'

    I hope so, it'd be very interesting to sequence more genomes from neanderthals and modern humans, but unfortunately the Neanderthal genome project already finished.

    Carles Lalueza is seeking for more neanderthal DNA in El Sidrón, but there's no enough money to start another project :(

    Antigen analysis suggests that modern Homo sapiens mixed with Neanderthals three separate times in different places, and with groups of Neanderthals that were more primitive or advanced relative to each other. Below is the initial DNA analysis chart showing how different Neanderthals were to the rest of us. The two curves do have a small degree of overlap in the zone marked between 15 and 20 genetic differances.
Neanderthals by Zdenek Burian. Below, Specific points of difference in the Neanderthal skeleton.

Neanderthal distributions: basically Neanderthals inhabited the warmer zones to the South, below the tree line during the Last Ice Age: they also inhabited the tundra areas here marked Western Palearctic and Central Palearctics they seem to have lived by following the herds of herd mammals, picking off scavengers and finding winter kills. Below, the tree line in the Mediterranean area.
Below, areas of late-persisting Neanderthals around the European Fringe, Western Neanderthals. Eastern Neanderthals also persisted to this larte date (approx 25000 BC or later) in the Caucasusl Siberia and in the Mountainous regions of Central Asia. These areas are of interest because they are also areas from which eminate more recent reports of Wildmen. The black sanctuary areas indicated below were not supposed to have persisted nearly so long.
The following charts are from Austin Whittal's Patagonian Monsters site anvokithat Neanderthals might very well have headed into the Americas at an early date, possibly in reaction to the movements of humans Out of Africa in the era of 65000 to 35000 BC. Thcates the expansion of Neanderthal territories Eastward and the solid yellow indicates the area they were "Classically" said to inhabit.

Another map from Patagonian Monsters indicates that the frequency of certain persisting genes out of the Neanderthal Genome are not only found in North and South America, the frequencies are actually higher there than in the Old World.orized a large proportion of Neanderthal admixture present during the peopling of the Americas. Below, Maurice Burton's Neanderthals

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