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Monthly Archives: April 2013

Brotherton 2013: cherry-picking the evidence for mtDNA H

Unlike the conceptually akin paper by Fu 2013 (PPV – discussed here), this one is very neatly explained and allows no doubts on how they reached their conclusions. Another thing is to agree with the method being good enough to provide for any conclusions at all. It is still an interesting study on the evolution of mtDNA lineage H in the specific context of the Elba-Saale region of Germany.
Paul Brotherton et al., Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nature Communications 2013. Pay per viewLINK. [doi:10.1038/ncomms2656]

Abstract

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
Let’s deal with the interesting part first and then with their impossible molecular clock speculations. 
All the samples used in this study belong to haplogroup H as you can see in table 1. This does not allow to consider the overall apportion of H in each population, for which we would need to go to the original studies. For example in the region’s LBK samples, H was just some 20% of the total, what alone talks of a population that was not at all like the modern one, never mind N1a. On the opposite side of the spectrum are the Bell Beaker (BBC) samples, where H made up 88% of the total (Adler 2012, discussed here), again non-modern but a possible source of H increase in frequency. 
We must keep in mind all the time that in this study only H is considered, with all the derived pros and cons. 
Maybe the most interesting result is therefore the comparison with modern populations done in fig. 2a:

Figure 2 | Population affinities of select Neolithic cultures. (a) PCA biplot based on the frequencies of 15 hg H sub-haplogroups (component loadings) from 37 present-dayWestern Eurasian and three ancient populations (light blue:Western Europe; dark blue: Central and Eastern Europe; orange; Near East,Caucasus and Anatolia; and pink: ancient samples). Populations are abbreviated as follows: GAL, Galicia; CNT, Cantabria; CAT, Catalonia; GAS, Galicia/Asturia; CAN, Cantabria2; POT, Potes; PAS, Pasiegos; VIZ, Vizcaya; GUI, Guipuzcoa; BMI, Basques; IPNE, Iberian Peninsula Northeast; TUR, Turkey; ARM, Armenia; GEO, Georgia; NWC, Northwest Caucasus; DAG, Dagestan; OSS, Ossetia; SYR, Syria; LBN, Lebanon; JOR, Jordan; ARB, Arabian Peninsula;ARE, Arabian Peninsula2; KBK, Karachay-Balkaria; MKD, Macedonia; VUR, Volga-Ural region; FIN, Finland; EST, Estonia; ESV, Eastern Slavs; SVK, Slovakia; FRA, France; BLK, Balkans; DEU, Germany; AUT, Austria, ROU, Romania; FRM, France Normandy; WIS, Western Isles; CZE, Czech Republic; LBK, Linear pottery culture; BBC, Bell Beaker culture; MNE, Middle Neolithic.

BBC (Bell Beaker) and LBK (Linear Pottery Culture) are clear-cut cultures in this graph. However MNE (Middle Neolithic) is a pooled agglomeration of several not too related cultures from the Late Neolithic and Early and Middle Chalcolithic. So, using the haplogroup vectors (grey), I remapped its unlikely components:

Fig. 2a annotated by Maju: green “MNE” cultures, grey: other cultures. Dotted circles just for reference.

Suddenly the mirage of modernity and homogeneity in MNE’s H collapses, very specially for Salzmünde (2/2 H3) but really also for the other components of the MNE pool: Rössen (directly derived from LBK) appears here as Balcano-Estonian and similar to Bronze Age Sardinia, Schöningen (derived from Rössen) appears Norman French and close to the original LBK pool, the first Kurgan culture in Central Europe, Baalberge, is the only one really close to the MNE dot but its closest modern relatives are NE Iberians (IPNE), while its successor Salzmünde is “hyper-Iberian” much as Bell Beaker after them – however the intermediate Corded Ware, C.W., leans back to the right and appears Catalan.
No conclusions can be inferred from this, for that we’d need to compare whole genetic pools and not just H, which is minority in most ancient samples but for whatever is worth… I made yet another annotated version of this graph:

Fig. 2a annotated by Maju: changes in Central European mtDNA H composition along time (arrows).

I considered here Rössen as different from Schöningen, as Rössen or Epi-Rössen persisted in much of Germany and nearby Alpine areas for long, but feel free to draw or imagine it differently.
Whatever the case the appearance is of gradual “modernization” or “Germanization” of haplogroup H culminating in Baalberge, followed by an “Iberization” of the haplogroup pool in the Middle and Late Chalcolithic, coincident roughly with the expansion of Megalithism and Bell Beaker and just mildly countered by Indoeuropean expansion from the East (Corded Ware, Unetice). Here they mention six Unetice H sequences but, judging on Adler 2012, H was very very rare in this culture at least in the Elbe-Saale area (1/31).
Beyond this I doubt that the paper can provide us with any more enlightenment.
Molecular-clock-o-logy
It does provide for some false leads however.
The authors use this Elbe-Saale limited ancient mtDNA evidence to construct a “molecular clock”:

Another major advantage of the temporal calibration points provided by ancient hg H mt genomes is that the data allow a relatively precise estimate of the evolutionary substitution rate for human mtDNA. The temporal dependency of evolutionary rates predicts that rate estimates measured over short timespans will be considerably higher than those using deep fossil calibrations, such as the human/chimpanzee split at ~6 million years.

6 million years?! Where have you been in the last five years, Paul? Ahem…
It doesn’t really matter but it illustrates the reactionary scholastic inertia that plagues the Academia, very especially in the field of population genetics.

What matters is that they continue as follows:

(…) The rate calibrated by the Neolithic and Bronze Age sequences is 2.4 x10⁻⁸ substitutions per site per year (1.7–3.2×10⁻⁸; 95% high posterior density) for the entire mt genome, which is 1.45 (44.5%) higher than current estimates based on the traditional human/chimp split (for example, 1.66 x10 ⁻⁸ for the entire mt genome and 1.26x 10⁻⁸ for the coding region). Consequently, the calibrated ‘Neolithic’ rate infers a considerably younger coalescence date for hg H (10.9–19.1 kya) than those previously reported (19.2–21.4 kya for HVSI, 15.7–22.5 kya for the mt coding region or 14.7–22.6 kya when corrected for purifying selection).

What matters is that by cherry-picking only some sequences of ancient mtDNA H, they are denying themselves (and the rest of us by extension) a realistic calibration of the haplogroup. What happened with the Cantabrian Magdalenian and Epipaleolithic Basque H? What happened with Epipaleolithic Karelian H? Never mind Sunghir’s Gravettian H17’27 or Taforalt’s massive pool of R*-CRS, most likely H1 (Kéfi 2005), which may be more questionable but never rejected without direct negative evidence.
In other words: they are cherry-picking the evidence. They could argue that the Elbe-Saale data was the only one readily available for them to sequence in full or whatever and that therefore the evidence was cherry-picked by Destiny… but that would not justify in any case the arrogance of their conclusions: they should have been much more humble and admit that this evidence is only part of all the ancient mtDNA H (known or suspected), some of which is clearly much older and therefore much more relevant.
I illustrated this problem using their fig. 1a:

Fig. 1a, annotated by Maju.
(Note: one of the “Magdalenian” H* sequences from North Iberia is actually Epipaleolithic, my error)

In orange color I have marked an alternative minimal “molecular clock” extrapolation using the La Chora H6 sequence (Hervella 2006 open access). This is minimal because I’m assuming this sequence to be underived H6, if it’d be derived (what I don’t know), the estimate would be even larger.
I have annotated all the sequences I am aware of ancient confirmed (unquestionable) mtDNA H. There are many more that are very likely, and in many cases older (see maps), but not yet confirmed.
So well, molecular-clock-o-logical pseudoscience again. It’s a pity that otherwise respectable scientists pay tribute to this academic fetish.
The molecular clock hypothesis has never been proven, being a mere statistical construct, and it has many problems particularly in mitochondrial DNA, where branches are dramatically unequal, obeying to either: (a) randomness, (b) differential adaptive fitness or (c) ancient population dynamics (variable drift results depending on population size). I discussed some of that here and also here.

I beg here to population geneticists to be more serious and careful and not try to push their ideas against the available evidence. That is not proper of scientists but belongs to the field of ideological propaganda.

Update: La Chora Magdalenian H6 is probably H6a1, with implications for the age estimate of H.

All known H6 of Iberia and all or most of Western Europe is H6a1, while the “famous” Central Asian H6 (very minor overall) is all H6(xH6a), which is also relatively important in Eastern Europe. See Álvarez Iglesias 2009 (open access), especially Supp. Table 3. H6a(xH6a1) has only been detected so far in Austria (oversampled – I miss data from France again).

Brotherton’s H6 only sample (Corded Ware) is H6a1a. Álvarez Iglesias did not test for this phylogenetic level, hence would show in his data as H6a1 but he did test for H6a1a1, only found precisely in Cantabria.

So the La Chora H6 Magdalenian sequence can be:

  • H6(xH6a): extremely rare in Western Europe modernly
  • H6a: reported in Austria only (modern sample)
  • H6a1: most common in Western Europe and especially North Iberia
  • H6a1a: like Brotherton’s Corded Ware sequence
  • H6a1a1: found only in Cantabria modernly, it seems
  • etc. (PhyloTree allows for some other options)

I already discussed the possible age (using molecular clock theory, calibrated) of H if La Chora H6 would be H6-root. But, considering that H6b and H6c seem to be Eastern European or Central Asian, it seems more reasonable to think it is H6a or downstream of it. What would be the age range of H for the other possible assignations of La Chora’s H6, would it be tested for coding region mutations? Let’s see:

  • If H6a-root: 47,500 to 24,500 years ago (median: 36,000 BP)
  • If H6a1: 73,200 to 34,800 years ago (median: 54,000 BP)

Of course I do not really think that the molecular clock can be easily applied, if at all, to mtDNA, because the rarity of accumulating mutations poses way too many challenges. But if it had to be applied, as Brotherton, Fu, their teams and some amateurs seem to think, then we’d have to test the La Chora and La Pasiega (and Sunghir and others) for coding region mutations in order to have the most valid calibration points.

Otherwise is like the blind man who touched the trunk of an elephant and imagined it was like a snake.

 

Synthesis of the Spanish-language series on the expansion of H. sapiens (2)

One of the reasons I have been a bit too saturated and maybe not writing as much as usual is that I am collaborating in a series in Spanish language for the blog Noticias de Prehistoria – Prehistoria al Día.
I already mentioned last month the initial article[es] of the series by David Sánchez, which dealt with the African Middle Paleolithic (MSA, Lupembian, Aterian, etc.) We have not been idle in the meantime but actually wrote a number of other articles that may well be of your interest:
There is still a lot to do for the series to be complete but the time for a synthetic review in this blog is quite overdue. I will skip the brief intro to population genetics on the belief that most readers here have a decent idea, but the other three articles ask for due mention.

Expansion of H. sapiens in Africa (genetic viewpoint)

This is something that complements David’s analysis of the African MP and that to a great extent I dealt with already at my former blog Leherensuge. I like graphs and maps because they often tell more than just words:

Basic mtDNA tree of Humankind
Branch length is proportional to coding region mutations from root per PhyloTree v.15 (L0k excepted)

We can see in this graph two main “moments” of diversification or expansion:
  1. The L0 and L2-6 nodes, followed soon by the L1 and L0a’b’f’k nodes
  2. The L0a’b’f, L0d and L2’3’4’6 nodes
The latter may well be calibrated with the archaeological evidence for the arrival of H. sapiens (MSA) to Southern Africa (L0d), which may be as old as 165 Ka but shows a clear increase in density since c. 130 Ka. I’d rather lean for the later date, that is roughly coincidental with the beginning of the Abbassia Pluvial, which must have provided good opportunities for expansion also in more northernly latitudes (the other nodes).
The first expansion is harder to estimate but c. 160 Ka. is a time in which we can see some of the first signs of expansion of our species within Africa (Jebel Irhoud and the already mentioned first Southern African MSA) so it is a tentative date. 
The geography of both expansions should be as follows (based on the raw data of Behar 2008):

Approx. geography of the first expansion of H. sapiens
(Purple dotted area indicates the max. likelihood for ‘mtDNA Eve’ location)
Approx. geography of the second expansion of H. sapiens

I also mentioned the expansion of L3, which preludes the migration Out of Africa, but this was already discussed in this entry.

Arrival to Arabia and Palestine

While most of the entries I am doing for this series deal with the genetic aspects, in this case I worked mostly with the archaeology, recycling many materials that are readily available in this blog and achieving the following synthetic map (recycling one by Armitage 2011) as central element of the article:

In addition to reviewing the archaeological discoveries of the last few years (and few older ones) I also discussed the issue of Neanderthal admixture, which most likely happened in this phase, and the possibility of some L(xM,N) lineages found in Arabia being from this period (see here).

Synthesis of Asian Prehistory

The last article so far in the series, authored by David Sánchez, has been published just today and is a very good visual review of the complex archaeological record of most of Asia in the period that interests us (most Middle Paleolithic with marginal mention of the earliest UP of West Asia, Siberia and neighboring areas, which will be reviewed more in depth in later articles). Probably the maps say it all, although we must understand that they only consider the best known sites:

Prior to Toba event (120-74 Ka BP)
(open circles: human remains, dots: other archaeological sites)
(notice that the date of Narmada hominin is most unclear, what is not reflected in the map)
Blue: 74-45 Ka BP
(stars: Neanderthal sites, open circles: other human remains, dots: archaeological sites, black: previous map)
Red: 45-35 Ka BP
(stars: neanderthal sites, open circles: other human remains, dots: archaeological sites, black & blue: previous maps)
Green: later expansion of H. sapiens in Northern Asia
(stars: Neanderthals, open circles: other human remains, dots: other archaeological sites, black, blue & red: previous maps)

I must say that the design of the maps is not quite the way I would have done myself but is still interesting. Very especially I miss lots of info on post-Toba South Asia. Also the Altai transition is not really well explained in my understanding. On the other hand East Asia is full of details and the overall picture of the archaeology of the Eurasian expansion is well described nonetheless.

PS- from the commentaries by David at his blog, it seems clear that he gives for granted the occupation of South Asia after Toba and therefore he did not consider it important to mark any more recent sites in the subcontinent. 

     

    OSL dating: Brazilian site is 22,000 years ago

    Toca da Tira Peia is the new name of American prehistory, providing an OSL date for the layer of scattered stone tools of c. 22,000 years BP. Located near the also controversial Pedra Furada site, the date seems to give some support to those who dare to think outside the box on the early peopling of America.
    Christelle Lahaye et al., Human occupation in South America by 20,000 BC: the Toca da Tira Peia site, Piauí, Brazil. Science 2013. Pay per view LINK [doi:10.1016/j.jas.2013.02.019]

    Abstract


    When and how did the first human beings settle in the American continent? Numerous data, from archaeological researches as well as from palaeogenetics, anthropological and environmental studies, have led to partially contradictory interpretations in recent years, often because of the lack of a reliable chronological framework. The present study contributes to the establishment of such a framework using luminescence techniques to date a Brazilian archaeological site, the Toca da Tira Peia. It constitutes an exemplary case study: all our observations and measurements tend to prove the good integrity of the site and the anthropological nature of the artifacts and we are confident in the accuracy of the luminescence dating results. All these points underline the importance of the Toca da Tira Peia. The results bring new pieces of evidence of a human presence in the north-east of Brazil as early as 20,000 BC. The Toca da Tira Peia thus contributes to the rewriting of the history of the peopling of the American continent.

    There are slightly older sites in North America, however they are all surrounded into some degree of controversy: Topper in South Carolina is dated to c. 23,000 cal-BP (C14) while some sites in Alberta, located in the Mackenzie “ice-free corridor” have also dates under the LGM layer (i.e. > 21 Ka BP).
    There’s actually nothing impossible about such early dates in my understanding.

    See also:

     

    Australian Burrup Peninsula’s rock art is 30,000 years old

    The open air engravings have managed to survive thanks to the extremely low erosion rates produced by the hardness of the rock combined with the local climate. 

    The petroglyphs have been dated using the isotope beryllium-10. Based on current evidence, the archaeologists say, the occupation of the peninsula cannot be dated to before c. 42,000 years ago. 

    Source: Australian Geographic.

     
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    Posted by on April 22, 2013 in Australia, Oceania, rock art, Upper Paleolithic

     

    Spring near Stonehenge occupied since Epipaleolithic

    (CC by Jeffrey Pfau)
    The spiritual relevance of Amesbury may well stem from a much older time than Neolithic or Chalcolithic. Recent research at a spring not far from Stonehenge has got radiocarbon dates of c. 7500 years ago, some three millennia before the building of the world-famous monument, and up to 4,700 BP, when the megalith was already in use.
    The low budget research project led by David Jacques of Open University, who had spotted the site, known as Vespasian’s Camp, just a mile north of Stonehenge, in air photos a decade ago. The site had never been researched before.
    The findings imply some sort of continuity between the Epipaleolithic and Late Neolithic (i.e. Chalcolithic), although the details have yet to be systematized. 
    Source: BBC News (includes video).
     

    Ardipithecus ramidus’ skull is hominin

    Ardi’s skull reconstructed
    (CC by T. Michael Keesey)
    I recently mentioned that Sahelanthropus tchadiensis ‘Toumaï’ was quite clearly within the hominini biological tribe, i.e. in the line leading to us and not anymore in the one leading to chimpanzees and bonobos. Now I have to echo the claim that a more recent being, Ardipithecus ramidus ‘Ardi’ also seems to have skull characteristics that place it in the hominin group. 
    While the relevance of Toumaï’s grouping is much greater, because it help us to clarify the issue of Pan-Homo divergence dates, which seems to be of the order of c. 8-13 million years ago (Langergraber 2012), the case of Ardi is not without interest anyhow in the understanding of human evolution. 

    By examining 79 skull bases of chimps, gorillas, modern humans and ancient hominids, Kimbel’s group identified relationships among anatomical landmarks that distinguish apes from people and hominids. The researchers estimated the total length of A. ramidus’ skull bottom and found that it fell within a range characteristic of hominids, not apes.

    As in more recent members of the Australopithecus genus, such as the 3.2-million-year-old partial skeleton nicknamed Lucy, Ardipithecus ramidus displays a relatively short, humanlike skull base, Kimbel said.

    A new 3-D analysis of Ardi’s previously reconstructed pelvis, also presented April 11 at the anthropology meeting, finds a mix of monkey, ape and hominid characteristics. Although not confirming a consistently upright gait, this version of Ardi’s hips doesn’t undermine her proposed hominid status, said Nicole Webb of City University of New York, who led the research.

    As for Ardi’s disputed mode of travel, she probably had a two-legged gait “but didn’t use her hands much while upright,” said Caley Orr of Midwestern University in Downers Grove, Ill., who didn’t participate in the new research. 

    While Ardipithecus ramidus is dated to c. 4.4 Ma BP, there is another specimen of the same genus, Ardipithecus kadabba, dated to c. 5,7 Ma.

    Ref. AAPA 2013 meeting (abstracts):

    • W. Kimbel et al. Ardipithecus ramidus and the evolution of the human cranial base.
    • N. Webb et al. An analysis of the Ardipithecus ramidus pelvis reconstruction using 3D geometric morphometric techniques.
     
    6 Comments

    Posted by on April 22, 2013 in human evolution, paleoanthropology

     

    Fu 2013: new ancient mtDNA sequences and "molecular clock" madness

    It took me quite a while to get time to look at this study in some depth and when I finally did I must say I was rather disappointed. In any case the popular demand makes necessary to discuss it.
    Qiaomei Fu et al., A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes. Current Biology 2013. Pay per viewLINK [doi:10.1016/j.cub.2013.02.044]
    The study has two aspects: one, of great interest, which is the sequencing of a number of ancient remains, the other a complex and quite poorly explained and rendered speculation on how these sequences could be used to produce a refined molecular clock. 
    Ancient mtDNA sequences
    Most of the sequences used by Fu et al. in their molecular clock speculations are new and that part is very interesting:

    I have highlighted in lime green the new sequences, otherwise also noted by the marker b. It is of note that the “Crô-Magnon 1” sequence produced a C14 age of just a few centuries, being therefore removed from the collection. Other Crô-Magnon 1 remains produced no useful data. 
    The authors also decided to discard as possibly contaminated the UP sequence  from Pagicci Str. 4b. I have highlighted in red why they decided to do so: because the C→T misincorporation rate, characteristic of ancient remains, is too low, what makes contamination at least a serious probability. 
    So we have as new data for the Upper Paleolithic landscape in Europe that the people of Dolni Vestonice carried lineages U* (found also in Swabian Magdalenian) and U8, in the line of haplogroups K, U8a (Basque) and U8b (Eastern Mediterranean). Also some late UP and Epipaleolithic sequences from Oberkassel (Low Rhineland, Germany), Loschbour (Luxemburg) and Continenza (Abruzzo, Italy) are U5b variants, consistent with other findings from various parts of Europe. In Paglicci (Apulia, Italy), another sequence yielded U2’3’4’7’8’9, surely an extinct variant of the ancestor of U8 and U2 (among other lineages). No radiocarbon date is available for any of the Italian remains.
    In East Asia, Boschan, with B4c1a, provides one of the first Epipaleolithic sequences for the region. 

    Molecular clock madness

    The authors seem to intend, or so declare, to refine the molecular clock estimates by means of using these sequences as intermediate calibration references. Here I get the first big question: with all the literature on ancient DNA, why only these sequences? No idea.
    Then the contradictions arise. I believe that I have synthesized the most obvious ones in the following marginal annotations (in red) to their molecular clock estimates:

    Furthermore, the authors claim in the text that U5 is the oldest branch to diverge from U, however their TRMCA figure is of only 34.4 Ka BP (coding region), while Kostenki 14 has an age of 38 Ka BP and already carried U2, what really makes this claim extremely unlikely: U2 and its ancestor U2’3’4’7’8’9 should be considered the oldest U sublineage. 
    I do not understand either why they force age estimates for many lineages for which they have no working aDNA references and instead desist of estimating the age of lineages for which they have several calibration points, like U2’3’4’7’8’9 or B4’5 (aka B). 
    In brief: the claims of this paper on molecular-clock-o-logy are ill-explained, confusing, incoherent… a total mess. The raw data on ancient mtDNA is however good looking and of doubtless interest.