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SHUpdate Ignore stuff on mutation rate. Confused mutation rate per year with per generation. Moral of story: read more closely! End update

The genetic data from the Sima de los Huesos (SH) hominins has finally been published in Nature. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins:

A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago…While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals…Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.

I don’t want to denigrate mtDNA, but the whole field of phylogeography and inference of evolutionary relationships in non-human organisms has been confused by the fact that many scientists drew a straight-line between the genealogy of a single locus, mtDNA, and the genealogy of a whole species. In light of results from molecular ecology, which long relied on mtDNA, but is finally moving toward genome-wide marker sets because of new technologies, I’m absolutely not shocked that mtDNA is not particularly predictive of whole genome relatedness. Recall that the Denisovan hominin had an mtDNA lineage which was more distant from Neanderthals than the whole genome turned out to be.

More importantly for this paper is that they find that whole genome inferences suggest that the SH hominins are genetically closer to Neanderthals than they were to Denisovans. I’ll skip over their quality control of the ancient samples…the group that published this paper is the best in the business, and it’s broadly persuasive to me…though I don’t know much about this topic, so you shouldn’t put much weight on my opinion. Because of the small amount of data retrieved they used a rather simple method to establish relatedness: shared derived mutations. Basically these are unique mutations which distinguish particular hominin lineages from each other and the outgroup population (other primates).

The above figure shows that the the SH hominin samples share much more with Neanderthals than with Denisovans, and more with Denisovans than with modern humans. From that one might reasonably infer then that:

1) The ancestry of modern humans diverged before the SH-Neanderthal-Denisovan clade.

2) But Denisovans diverged rather quickly from the SH-Neanderthal clade.

3) Since the SH hominin site seems to date to ~400,000 years before the present, and is found in part of the traditional range of Neanderthals, and these individuals share morphological characteristics with this group, the SH hominins may be the ancestral population, or related to the ancestral population, of Neanderthals.

How robust is this date? I don’t know enough geology or paleontology to judge, so I won’t follow the citations. But a lot of the discussion and novelty of these results seems to hinge on this date. From the paper:

This age is compatible with the population split time of 381,000–473,000 years ago estimated for Neanderthals and Denisovans on the basis of their nuclear genome sequences and using the human mutation rate of 0.5 × 10−9 per base pair per year…This mutation rate also suggests that the population split between archaic and modern humans occurred between 550,000 and 765,000 years ago.

A more conventional mutation rate I’ve seen is closer to 1 to 2 × 10−8, or two to four times faster than the one above. But the mutation rate literature is rather confusing for me, and does not totally align well together, possibly due to variation in rate over time.

The picture above is often derived from a model where we fit the diversification of the human lineage to a tree. But within the paper they suggest Neanderthal mtDNA might have been African, and that there may have been an earlier migration out of Africa before the one that occurred ~50-100,000 years ago. I don’t see a priori why this couldn’t be so, but I’m also not clear how we’re going to get a good grasp of the details of the dynamics at play.

Perhaps the dominance of the African “Out of Africa” lineage over the last 100,000 years is an aberration. It may be that much of human history was characterized by the sorts of meta-population dynamics described by classical multi-regionalists. The possibility that Neanderthal-Denisovan divergence might be as old as ~450,000 years before the present suggests to me that the massive replacement and assimilation we saw ~50-100,000 years ago was somehow atypical in terms of how it disrupted deep regional population structure….

 
• Category: Science • Tags: Human Evolution 
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  1. I don’t want to denigrate mtDNA, but the whole field of phylogeography and inference of evolutionary relationships in non-human organisms has been confused by the fact that many scientists drew a straight-line between the genealogy of a single locus, mtDNA, and the genealogy of a whole species. In light of results from molecular ecology, which long relied on mtDNA, but is finally moving toward genome-wide marker sets because of new technologies, I’m absolutely not shocked that mtDNA is not particularly predictive of whole genome relatedness. Recall that the Denisovan hominin had an mtDNA lineage which was more distant from Neanderthals than the whole genome turned out to be.

    A similar thing is going on with dogs and wolves, though the time scale is shorter.

    MtDNA of dogs and wolves could in theory be interpreted to represent something as drastic as multiple full-on domestication events since separation between all wolves and all dogs doesn’t exist in phylogeny.

    http://journals.plos.org/plosone/article/asset?unique&id=info:doi/10.1371/journal.pone.0057754.s004

    But working with autosomal data in TreeMix we see a structure analoguous to Homo Sapiens and extinct humans. All wolves are basal to all dogs, and in a way reminiscent of Africans in a human tree Southeast Asian dogs occupy a basal position to other dogs, while certain breeds of dogs have admixture from wolves just like certain Sapiens groups have admixture from archaic humans.

    http://www.nature.com/cr/journal/v26/n1/extref/cr2015147x20.pdf

  2. The paper relies on a lot of arcane technical inferences to make its claims, and it isn’t well written (the graphs are horrible), and will take more than a few hours to digest, but we’ll just take it at face value for now:

    If the split between the lineage that contributed the bulk of human ancestry and the lineages that contributed much of the remainder occurred 600,000 years ago, is it even plausible that they remained confined to Africa for 500,000 years whilst the other, more primitive, hominids strolled all over the planet? All of this while they allegedly accumulate the mutations that lead to behavioral and anatomical modernity which would make migration along a relatively benign and homogeneous coastal biome trivial?

    Consider that Australoids, in contrast to this 500,000 year stasis, are thought to have raced from Africa to the tip of South America in a few thousand years according to Out of Africa

    So instead of Out of Africa being an “abberation” perhaps it is better thought of as a misinterpretation. It relies on one fossil specimen to assert African antiquity over more plausible locales such as the Levant: Omo 1. Isn’t it time we revisit that too convenient finding? After all, if you put your thumb over Omo 1, then the story becomes crystal clear: a Levantine genesis for modernity with radiations into Africa, Europe, East Asia wherein the main lineage picks up some DNA from local hominids rather than the other way around once the numerical flow of migrants overwhelms the more smaller recipient populations due to some economic / genetic advantage (probably language / general intelligence).

    The only reason that this is still in question is the political importance of “Africa” to the post-War narrative: not white, not Biblical therefore Good rather than Evil.

    • Replies: @Razib Khan
    So instead of Out of Africa being an “abberation” perhaps it is better thought of as a misinterpretation.

    it's still an aberration because the extant ancient DNA (e.g., here with SH) indicates deep local structure. the lack of such deep local structure is the aberration.

    then the story becomes crystal clear: a Levantine genesis for modernity with radiations into Africa, Europe, East Asia wherein the main lineage picks up some DNA from local hominids rather than the other way around once the numerical flow of migrants overwhelms the more smaller recipient populations due to some economic / genetic advantage (probably language / general intelligence).

    it's not crystal clear at all. SS african populations have a lot more diversity and deep structure than the non-african groups, who all exploded out ~50,000 years. this can be consistent with a levantine expansion, but it's not a slam-dunk, or even the most parsimonious model.

    i suspect ancient DNA will resolve this issue within 10 years.
    , @Megalophias
    Could you explain your Levantine origin in more detail - as in, at what time, and carrying what kind of ancestry? "Crystal clear" is not how I'd describe your hypothesis as expressed in the above post.
  3. Perhaps the dominance of the African “Out of Africa” lineage over the last 100,000 years is an aberration. It may be that much of human history was characterized by the sorts of meta-population dynamics described by classical multi-regionalists. The possibility that Neanderthal-Denisovan divergence might be as old as ~450,000 years before the present suggests to me that the massive replacement and assimilation we saw ~50-100,000 years ago was somehow atypical in terms of how it disrupted deep regional population structure….

    Is there any evidence of hybridization from back-to-Africa migrations? Or any evidence against them for that matter? I’m curious as to how much the apparently small effective population size (at least for the samples we have) too much of a hindrance?

    Also, how does this mutation rate line up with the inferred population history of currently sampled Neanderthal and Denisovan populations like this:

    Is that sharp drop in effective population size more or less the out-of-Africa event for Neanderthals?

    BTW, in terms of disrupting deep regional structure, I’d put that even later. We don’t seem to have had such a completely devastating impact on other human subspecies until the Upper Paleolithic.

    • Replies: @Razib Khan
    Is there any evidence of hybridization from back-to-Africa migrations?

    yes.

    http://genome.cshlp.org/content/early/2016/02/08/gr.196634.115.abstract

    i blogged it.
  4. @Afterthought
    The paper relies on a lot of arcane technical inferences to make its claims, and it isn't well written (the graphs are horrible), and will take more than a few hours to digest, but we'll just take it at face value for now:

    If the split between the lineage that contributed the bulk of human ancestry and the lineages that contributed much of the remainder occurred 600,000 years ago, is it even plausible that they remained confined to Africa for 500,000 years whilst the other, more primitive, hominids strolled all over the planet? All of this while they allegedly accumulate the mutations that lead to behavioral and anatomical modernity which would make migration along a relatively benign and homogeneous coastal biome trivial?

    Consider that Australoids, in contrast to this 500,000 year stasis, are thought to have raced from Africa to the tip of South America in a few thousand years according to Out of Africa

    So instead of Out of Africa being an "abberation" perhaps it is better thought of as a misinterpretation. It relies on one fossil specimen to assert African antiquity over more plausible locales such as the Levant: Omo 1. Isn't it time we revisit that too convenient finding? After all, if you put your thumb over Omo 1, then the story becomes crystal clear: a Levantine genesis for modernity with radiations into Africa, Europe, East Asia wherein the main lineage picks up some DNA from local hominids rather than the other way around once the numerical flow of migrants overwhelms the more smaller recipient populations due to some economic / genetic advantage (probably language / general intelligence).

    The only reason that this is still in question is the political importance of "Africa" to the post-War narrative: not white, not Biblical therefore Good rather than Evil.

    So instead of Out of Africa being an “abberation” perhaps it is better thought of as a misinterpretation.

    it’s still an aberration because the extant ancient DNA (e.g., here with SH) indicates deep local structure. the lack of such deep local structure is the aberration.

    then the story becomes crystal clear: a Levantine genesis for modernity with radiations into Africa, Europe, East Asia wherein the main lineage picks up some DNA from local hominids rather than the other way around once the numerical flow of migrants overwhelms the more smaller recipient populations due to some economic / genetic advantage (probably language / general intelligence).

    it’s not crystal clear at all. SS african populations have a lot more diversity and deep structure than the non-african groups, who all exploded out ~50,000 years. this can be consistent with a levantine expansion, but it’s not a slam-dunk, or even the most parsimonious model.

    i suspect ancient DNA will resolve this issue within 10 years.

    • Replies: @Anonymous
    Or, it could be symptomatic of a crossing between homo sapiens and the mysterious, postulated African 'hominid X'.
  5. @CupOfCanada

    Perhaps the dominance of the African “Out of Africa” lineage over the last 100,000 years is an aberration. It may be that much of human history was characterized by the sorts of meta-population dynamics described by classical multi-regionalists. The possibility that Neanderthal-Denisovan divergence might be as old as ~450,000 years before the present suggests to me that the massive replacement and assimilation we saw ~50-100,000 years ago was somehow atypical in terms of how it disrupted deep regional population structure….
     
    Is there any evidence of hybridization from back-to-Africa migrations? Or any evidence against them for that matter? I'm curious as to how much the apparently small effective population size (at least for the samples we have) too much of a hindrance?

    Also, how does this mutation rate line up with the inferred population history of currently sampled Neanderthal and Denisovan populations like this: http://www.nature.com/nature/journal/v505/n7481/images_article/nature12886-f4.jpg

    Is that sharp drop in effective population size more or less the out-of-Africa event for Neanderthals?

    BTW, in terms of disrupting deep regional structure, I'd put that even later. We don't seem to have had such a completely devastating impact on other human subspecies until the Upper Paleolithic.

    Is there any evidence of hybridization from back-to-Africa migrations?

    yes.

    http://genome.cshlp.org/content/early/2016/02/08/gr.196634.115.abstract

    i blogged it.

    • Replies: @CupOfCanada
    I thought that was from African archaics, not Eurasian archaics returning to Africa?
  6. @Razib Khan
    So instead of Out of Africa being an “abberation” perhaps it is better thought of as a misinterpretation.

    it's still an aberration because the extant ancient DNA (e.g., here with SH) indicates deep local structure. the lack of such deep local structure is the aberration.

    then the story becomes crystal clear: a Levantine genesis for modernity with radiations into Africa, Europe, East Asia wherein the main lineage picks up some DNA from local hominids rather than the other way around once the numerical flow of migrants overwhelms the more smaller recipient populations due to some economic / genetic advantage (probably language / general intelligence).

    it's not crystal clear at all. SS african populations have a lot more diversity and deep structure than the non-african groups, who all exploded out ~50,000 years. this can be consistent with a levantine expansion, but it's not a slam-dunk, or even the most parsimonious model.

    i suspect ancient DNA will resolve this issue within 10 years.

    Or, it could be symptomatic of a crossing between homo sapiens and the mysterious, postulated African ‘hominid X’.

  7. @Razib Khan
    Is there any evidence of hybridization from back-to-Africa migrations?

    yes.

    http://genome.cshlp.org/content/early/2016/02/08/gr.196634.115.abstract

    i blogged it.

    I thought that was from African archaics, not Eurasian archaics returning to Africa?

    • Replies: @Razib Khan
    some trace neanderthal in a few groups you might not expect (yoruba). but yeah, the eurasian archaics we have don't seem to have contributed much to SS africa. that being said, we only have the neanderthal-denisovan lineage. there were others according to some of the work coming out of the reich lab...
  8. The low effective population size of the ancestral Neanderthal/Denisovan population is not consistent with back-migration of the ancestral AMH population, which underwent a population boom right after diverging from their Homo cousins.

    This is more consistent with the mtDNA of (recent) Neanderthals being from more recent migrations out of Africa, alternatively the mtDNA may just not be representative of their overall population history.

  9. @CupOfCanada
    I thought that was from African archaics, not Eurasian archaics returning to Africa?

    some trace neanderthal in a few groups you might not expect (yoruba). but yeah, the eurasian archaics we have don’t seem to have contributed much to SS africa. that being said, we only have the neanderthal-denisovan lineage. there were others according to some of the work coming out of the reich lab…

    • Replies: @Anonymous
    When will this Reich work be published?
    , @CupOfCanada
    Oh, does Reich have some new ancient samples to look at? Or is he trying to infer admixture events like that team from Shanghai (http://arxiv.org/ftp/arxiv/papers/1404/1404.7766.pdf).

    Yah, I'm aware of the Neanderthal admixture in Yoruba and other SSA populations. It correlates to Eurasian modern human admixture in pretty much all cased doesn't it? I definitely think that's an interesting subject, but I meant more back-to-Africa migrations before "our" Out-of-Africa event ~100 kya, whether before or after our split from Neanderthals. Though I guess we don't know for certain if our common ancestor was in Africa or somewhere else.

    Still, I look at the effective population sizes of Neanderthals and Denisovans, I have to wonder if they were doomed from the start due to simple demographics? Were there successive waves of Out-of-Africa events simply because Eurasia couldn't support very large human populations until the Upper Paleothic, or is this just an artifact of having ancient samples from the margins of Neanderthal and Denisovan ranges?
  10. @Razib Khan
    some trace neanderthal in a few groups you might not expect (yoruba). but yeah, the eurasian archaics we have don't seem to have contributed much to SS africa. that being said, we only have the neanderthal-denisovan lineage. there were others according to some of the work coming out of the reich lab...

    When will this Reich work be published?

  11. Am I missing something, or isn’t this just confirming what we already know? Neandertals lived in Europe (+ Middle East), and Denisovians somewhere in north-central Eurasia. Isn’t a sample from Spain clustering with the Neandertals exactly what we’d expect?

    • Replies: @Razib Khan
    older divergence from moderns. by 2 hundred thousand years according to some estimates

    https://en.wikipedia.org/wiki/Neanderthal#Origin
  12. @Anonymous
    Am I missing something, or isn't this just confirming what we already know? Neandertals lived in Europe (+ Middle East), and Denisovians somewhere in north-central Eurasia. Isn't a sample from Spain clustering with the Neandertals exactly what we'd expect?

    older divergence from moderns. by 2 hundred thousand years according to some estimates

    https://en.wikipedia.org/wiki/Neanderthal#Origin

  13. Does this mean they successfully got DNA from a 430,000 year old fossil?

    • Replies: @Razib Khan
    i glossed over the technical argument that they did (e.g., deamination), but it's persuasive. also, the results don't look to be the outcome of contamination obviously.... (why would SH hominin be closer to neanderthal-denisovan as opposed to modern human? though i suppose it could be something to do with DNA damage which effects the ancient and not modern)
  14. @Tobus
    Does this mean they successfully got DNA from a 430,000 year old fossil?

    i glossed over the technical argument that they did (e.g., deamination), but it’s persuasive. also, the results don’t look to be the outcome of contamination obviously…. (why would SH hominin be closer to neanderthal-denisovan as opposed to modern human? though i suppose it could be something to do with DNA damage which effects the ancient and not modern)

  15. @Afterthought
    The paper relies on a lot of arcane technical inferences to make its claims, and it isn't well written (the graphs are horrible), and will take more than a few hours to digest, but we'll just take it at face value for now:

    If the split between the lineage that contributed the bulk of human ancestry and the lineages that contributed much of the remainder occurred 600,000 years ago, is it even plausible that they remained confined to Africa for 500,000 years whilst the other, more primitive, hominids strolled all over the planet? All of this while they allegedly accumulate the mutations that lead to behavioral and anatomical modernity which would make migration along a relatively benign and homogeneous coastal biome trivial?

    Consider that Australoids, in contrast to this 500,000 year stasis, are thought to have raced from Africa to the tip of South America in a few thousand years according to Out of Africa

    So instead of Out of Africa being an "abberation" perhaps it is better thought of as a misinterpretation. It relies on one fossil specimen to assert African antiquity over more plausible locales such as the Levant: Omo 1. Isn't it time we revisit that too convenient finding? After all, if you put your thumb over Omo 1, then the story becomes crystal clear: a Levantine genesis for modernity with radiations into Africa, Europe, East Asia wherein the main lineage picks up some DNA from local hominids rather than the other way around once the numerical flow of migrants overwhelms the more smaller recipient populations due to some economic / genetic advantage (probably language / general intelligence).

    The only reason that this is still in question is the political importance of "Africa" to the post-War narrative: not white, not Biblical therefore Good rather than Evil.

    Could you explain your Levantine origin in more detail – as in, at what time, and carrying what kind of ancestry? “Crystal clear” is not how I’d describe your hypothesis as expressed in the above post.

    • Replies: @Razib Khan
    +1 & seconded. the adjective 'crystal clear' actually down-weighted my assessment of plausibility.
  16. @Megalophias
    Could you explain your Levantine origin in more detail - as in, at what time, and carrying what kind of ancestry? "Crystal clear" is not how I'd describe your hypothesis as expressed in the above post.

    +1 & seconded. the adjective ‘crystal clear’ actually down-weighted my assessment of plausibility.

  17. @Razib Khan
    some trace neanderthal in a few groups you might not expect (yoruba). but yeah, the eurasian archaics we have don't seem to have contributed much to SS africa. that being said, we only have the neanderthal-denisovan lineage. there were others according to some of the work coming out of the reich lab...

    Oh, does Reich have some new ancient samples to look at? Or is he trying to infer admixture events like that team from Shanghai (http://arxiv.org/ftp/arxiv/papers/1404/1404.7766.pdf).

    Yah, I’m aware of the Neanderthal admixture in Yoruba and other SSA populations. It correlates to Eurasian modern human admixture in pretty much all cased doesn’t it? I definitely think that’s an interesting subject, but I meant more back-to-Africa migrations before “our” Out-of-Africa event ~100 kya, whether before or after our split from Neanderthals. Though I guess we don’t know for certain if our common ancestor was in Africa or somewhere else.

    Still, I look at the effective population sizes of Neanderthals and Denisovans, I have to wonder if they were doomed from the start due to simple demographics? Were there successive waves of Out-of-Africa events simply because Eurasia couldn’t support very large human populations until the Upper Paleothic, or is this just an artifact of having ancient samples from the margins of Neanderthal and Denisovan ranges?

    • Replies: @Rick
    "Still, I look at the effective population sizes of Neanderthals and Denisovans, I have to wonder if they were doomed from the start due to simple demographics?"

    These peoples were able to live through ice ages and terrible conditions for hundreds of thousands of years. As is clear from modern humans, the ability for cultural transmission of information can make up for a lot of genetic problems. And actually that might have been their downfall; too smart for their population size.

  18. @CupOfCanada
    Oh, does Reich have some new ancient samples to look at? Or is he trying to infer admixture events like that team from Shanghai (http://arxiv.org/ftp/arxiv/papers/1404/1404.7766.pdf).

    Yah, I'm aware of the Neanderthal admixture in Yoruba and other SSA populations. It correlates to Eurasian modern human admixture in pretty much all cased doesn't it? I definitely think that's an interesting subject, but I meant more back-to-Africa migrations before "our" Out-of-Africa event ~100 kya, whether before or after our split from Neanderthals. Though I guess we don't know for certain if our common ancestor was in Africa or somewhere else.

    Still, I look at the effective population sizes of Neanderthals and Denisovans, I have to wonder if they were doomed from the start due to simple demographics? Were there successive waves of Out-of-Africa events simply because Eurasia couldn't support very large human populations until the Upper Paleothic, or is this just an artifact of having ancient samples from the margins of Neanderthal and Denisovan ranges?

    “Still, I look at the effective population sizes of Neanderthals and Denisovans, I have to wonder if they were doomed from the start due to simple demographics?”

    These peoples were able to live through ice ages and terrible conditions for hundreds of thousands of years. As is clear from modern humans, the ability for cultural transmission of information can make up for a lot of genetic problems. And actually that might have been their downfall; too smart for their population size.

  19. “A more conventional mutation rate I’ve seen is closer to 1 to 2 × 10−8,…”

    You are mixing up the per year mutation rate with the per generation mutation rate.
    Estimates of population divergence time have also relied on “reasonable effective population sizes” that do not always align well with PSMC-like estimates of ancestral effective size.

    • Replies: @Razib Khan
    yes. that's why i posted an update at the top of the post.
  20. @Gregorios

    "A more conventional mutation rate I’ve seen is closer to 1 to 2 × 10−8,..."

     

    You are mixing up the per year mutation rate with the per generation mutation rate.
    Estimates of population divergence time have also relied on "reasonable effective population sizes" that do not always align well with PSMC-like estimates of ancestral effective size.

    yes. that’s why i posted an update at the top of the post.

  21. […] Hominid geno-tangles. Non-shared environment. European admixture in the Americas. Pharmacogenomics. Marking on a curve. […]

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