January 31, 2013

Statistical analysis of HVS-I (mtDNA) in Niger-Congo populations

Not sure that the paper has much interest but it affects a region with not too many studies and is open access so a brief mention may be appropriate.

Valeria Montano et al. The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation. BMC Evolutionary Biology 2013. Open accessLINK [doi:10.1186/1471-2148-13-24]

Abstract (provisional)

Background

When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study.

Results

By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas.

Conclusions

Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling. 


One of the problems I find to their approach is the use of only the deprecated HVS-I (control region) of the mtDNA, along with absolutely no list of inferred haplogroups (not even in the supplemental materials apparently). Based on just HVS-I data, then they proceed to make statistical analysis of all sorts, which may have some interest but is not my cup of tea, really. Maybe someone else may find use for this stuff however.

14 comments:

  1. "Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling".

    I hope that by now you know exactly how to explain that. Humans do not move across the landscape link ink through blotting paper. They move through their prefered habitat. The authors seem to be making the assumption that the pre-agricultural people had in fact occupied the landscape like ink on blotting paper. To me that is a most unlikely position to assume.

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    1. I don't have much time for this kind of speculation but I can only imagine that, as the authors also suggest, recent (Neolithic and later) demic flows were faster and easier through the Sahel than through the forests, flattening out early diversity more easily in favor of the lineages of the expansive peoples.

      I don't see as very interesting your metaphor of "blotting paper". I can tentatively agree that people would initially favor habitats they are most familiar with but, said that, habitats are not as clear cut as you seem to imagine, being many transition zones and also our species is characterized by its opportunistic nature and also great intelligence and flexibility, allowing us to exploit very different habitats in very different forms. Therefore habitats are not per se any absolute barrier but at most an initial handicap.

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    2. "I can tentatively agree that people would initially favor habitats they are most familiar with but, said that, habitats are not as clear cut as you seem to imagine..."

      Nitpicking, at best. It makes no difference how you, personally, define this or that habitat.

      The broader point is that a people's behavior is both driven, at least to a degree, and certainly constrained by the technologies and skill sets that they actually possess. Adaptations well-suited to one environment may fail in another and failure meant hunger, disease, and death, for you and your offspring.

      I think you grossly underestimate just how conservative such prehistoric peoples were. Even today, modern psychology informs us that humans are strongly risk-averse. Innovation occurred at glacial speeds in the Stone Age. This is a fact. If flexibility were of such vital importance, surely there would be more evidence of flexibility in the material record.

      So, this is our "null hypothesis". People are not so terribly flexible and the earlier in history we look the less flexible their behavior appears to be. If you wish to assert otherwise, fine, I welcome the opportunity to learn, but it should take more than a mere plausible story to satisfy an informed audience. You must point to substantive evidence that such prehistoric populations so readily and quickly changed subsistence strategies as you suggest. And if you cannot do that, your objection to terry's "blotting paper" comment seems most unreasonable.

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    3. IMO you have a 'romanticized' concept of 'primitive' peoples and their conjecured conservatism.

      Did not Native American tribes migrated to remote, often very different, places? Did not they adopt the horse quickly and skilledly? Haven't you ever watched Pygmies hunting with crossbow, whose design was borrowed from the Portuguese? Etc.

      'Primitive' peoples are primarily pragmatic. And certainly very flexible.

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  2. "IMO you have a 'romanticized' concept of 'primitive' peoples and their conjecured conservatism".

    No Maju. It is you who have a romanticised view of the 'opportunistic nature and also great intelligence and flexibility' of our ancestors. I agree with Va_Highlander, 'I think you grossly underestimate just how conservative such prehistoric peoples were'.

    "People are not so terribly flexible and the earlier in history we look the less flexible their behavior appears to be".

    Yes.

    "Did not Native American tribes migrated to remote, often very different, places?"

    But only after several thousand years.

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    1. [crowd of imps singing menacingly at the rhythm of percussion]
      Data, data!
      What the fuck is that for?!
      Data, data!
      We don't need any data!
      Data, data!
      Data, data!
      We're just right and you are wrong
      because I just said so!
      Data, data...
      [/vision]

      "But only after several thousand years".

      LOL

      Firstly several thousand years (like 2-3, less than five at most for whole continent expansion) are like your blotting paper and not like your ecological barriers claim: from Arctic to Antarctic going through prairie, jungle, deserts and mountains, never mind the coast! Maybe there are veins (coastal migration?) that are more conductive than others but in the end all the "paper" is "blotted".

      Secondly I was actually thinking of much more recent and brief migrations of North American natives, usually resulting in the branching of their ethnicities. For example the Na-Dené occupy Cold Arctic, Temperate Coast and Semi-Desert niches; Uto-Aztecan extends from Montana to central Mexico; etc. There is some niche-peference but they still show ability to occupy varied niches without further problem (it needs some generations to consolidate the adaption, of course, but nothing too dramatic). Even the Inuit had to learn nearly all survival techniques for their homeland in what is now Canada from the older inhabitants of the Dorset culture: they expanded in a few centuries anyhow.

      Irregular quality blotting paper but blotting paper in any case.

      Delete
  3. "Data, data!
    What the fuck is that for?!
    Data, data!
    We don't need any data!"

    Don't be an idiot once more. we have data in the form of haplogroup distribution, archeology and common sense.

    "Firstly several thousand years (like 2-3, less than five at most for whole continent expansion) are like your blotting paper and not like your ecological barriers claim"

    Rubbish, again. The population can spread right through both continents without occupying every square centimetre.

    "Secondly I was actually thinking of much more recent and brief migrations of North American natives, usually resulting in the branching of their ethnicities".

    Once they'd adopted the horse and iron implements no doubt. Not to mention the pre-European adoption of farming which allowed greater numbers to survive in appropriate regions.

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  4. You almost invariably begin your sentences with subjective statements, in the form of "I think", "I believe" or adverbs that try to convey the impression of certainty (while not being sustained by anything at all, being in fact just variants of "I think"), these are "certainly", "surely", "necessarily" and the like (almost never "probably", "maybe", "possibly", "apparently" or any of the adverbs I tend to prefer - not because I'm less correct than you, just because Science demands humility, doubt and caution).

    And then there are the disqualification one liners of the kind of "rubbish!", followed by something that makes sense only in your mind, for example today:

    "The population can spread right through both continents without occupying every square centimetre".

    Of course... because they would die of starvation long before that. But the tendency is to occupy every zone according to the technological and ecological capabilities available. Maybe the population A first expanded through the savanna-like corridors but soon those corridors would be more and more packed (for the standards of the time) and heading to non-savanna niches like jungle or whatever becomes more and more desirable (and soon the jungle would be "packed" as well with peoples increasingly specialized in that ecosystem).

    In an initially virgin geography, all this process would take place in few generations, centuries at most. Only really hostile environments like deserts or very cold regions would remain out of reach: jungles, swamps, hills, coasts... all that is perfectly exploitable and would be inhabited soon.

    "Once they'd adopted the horse and iron implements no doubt".

    It was before! Learn first, speak later.

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  5. "You almost invariably begin your sentences with subjective statements, in the form of "I think", "I believe""

    I see not a single example here. Look again. At least in using such expressions I am being honest. You state with complete confidence that 'Y-DNA F is South Asian in origin', 'mt-DNA R is South Asian in origin', mtDNA N is East Asian in origin', MNOPS is Bengali in origin'. The actual evidence fails to suport any of those statements.

    "'probably', 'maybe', 'possibly', 'apparently' or any of the adverbs I tend to prefer"

    I see no examples of such usage here, and I don't recall any such usage on your part anywhere else. I will check though.

    "the tendency is to occupy every zone according to the technological and ecological capabilities available".

    Which would be the regions most easily exploited. Va_Highlander's comment is correct, 'I think you grossly underestimate just how conservative such prehistoric peoples were. '.

    "It was before! Learn first, speak later".

    As I understand things the western praire, for example, was very sparsely inhabited until the horse arrived. That is presumably why there were so many bison on it. Wikipedia:

    http://en.wikipedia.org/wiki/Plains_Indians

    Quote:

    "The horse enabled the Plains Indians to gain their subsistence with relative ease from the seemingly limitless buffalo herds. They were able to travel faster and further in search of bison herds and to transport more goods, thus making it possible to enjoy a richer material environment than their pedestrian ancestors".

    "Plains Indians are usually divided into two broad classifications which overlap to some degree. The first group became fully nomadic and dependent upon the horse during the 18th and 19th centuries, following the vast herds of buffalo, although some tribes occasionally engaged in agriculture; growing tobacco and corn primarily".

    "The second group of plains Indians includes the aboriginal peoples of the Great Plains, as well as the Prairie Indians who come from as far east as the Mississippi River. These tribes were semi-sedentary, and in addition to hunting buffalo, they lived in villages, raised crops, and actively traded with other tribes".

    Agriculture would not have been possible on the open praire, only near rivers. I'm sure we can find other examples of regions very sparsely settled until the arrival of horses and iron.

    ReplyDelete
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    1. So the plains, according to yourself, the favorite territory of hunter-gatherers, were sparsely inhabited before the horse arrived... and you don't even raise an eyebrow.

      "Agriculture would not have been possible on the open praire, only near rivers".

      Why? Actually European FARMER colonists actively sought those lands and FARMER Natives from the East were successfully transferred to some of them as well.

      But well, who cares?

      Delete
  6. "So the plains, according to yourself, the favorite territory of hunter-gatherers, were sparsely inhabited before the horse arrived... and you don't even raise an eyebrow".

    Tell me. Why do you think it strange that humans were unable to exploit the open plains effectively before they obtained the horse?

    "Why? Actually European FARMER colonists actively sought those lands"

    You certainly do provide entertainment. Surely you realise those plains were ideal for providing domestic animals with grazing. What domestic grazing animals did the Indigenous Americans have available to them?

    "FARMER Natives from the East were successfully transferred to some of them as well".

    And again those 'Natives from the East' used introduced plants and animals. The locals also adopted such of course. The Navajo are noted sheep herders and the Utes became noted horse breeders. Neither of these professions were open until the arrival of Europeans and their livestock.

    "But well, who cares?"

    Try considering reality occassionally instead of staying in that imaginary land where you spend your time.

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    1. I thought it was you the one obsessed with prairie-philia and savanna-philia of PALEOLITHIC peoples. Never mind.

      Anyhow, while cattle is no doubt a European introduction, plants like maize are not and that is precisely what they grow in the prairies today... massively.

      So there are many contradictions in your discourse which cannot be excused with an appeal to the introduction of European cattle or sheep, which, as happens with horses, pre-date the Far West epoch (all are Spanish introductions, just that Natives were not forced to adopt them yet because the bisons still roamed the prairies in huge numbers).

      Delete
  7. "I thought it was you the one obsessed with prairie-philia and savanna-philia of PALEOLITHIC peoples. Never mind".

    'Savanana' and 'prairie' are different things, althoughn some use the terms interchangeably. Savanna has trees scattered through it, the North American praire usually does not.

    http://en.wikipedia.org/wiki/Savanna

    "A savanna, or savannah, is a grassland ecosystem characterized by the trees being sufficiently small or widely spaced so that the canopy does not close. The open canopy allows sufficient light to reach the ground to support an unbroken herbaceous layer consisting primarily of grasses.[1][2][3] Some classification systems[which?] also recognize a grassland savanna from which trees are absent.[4] This article deals only with savanna under the common definition of a grassy woodland with a significant woody plant component".

    http://en.wikipedia.org/wiki/Prairie

    "a composition of grasses, herbs, and shrubs, rather than trees, as the dominant vegetation type".

    And this comment is very interesting:

    "Tallgrass Prairie evolved over tens of thousands of years with the disturbances of grazing and fire. Native ungulates such as bison, elk, and white-tailed deer, roamed the expansive, diverse, plentiful grassland before European colonization of the Americas.[3] For 10,000-20,000 years native people used fire annually as a tool to assist in hunting, transportation and safety.[4] Evidence of ignition sources of fire in the tallgrass prairie are overwhelmingly human as opposed to lightning".

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  8. "while cattle is no doubt a European introduction, plants like maize are not and that is precisely what they grow in the prairies today... massively".

    And the corn belt coincides almost exactly with the region where various settled Siouan-speaking Native Americans grew corn historically. Basically along the Mississippi and Misouri river valeys. The corn belt does not include the open prairie. Some quotes from a book I have, 'The Native Americans':

    "It was not, however, until the aquisition of the horse from the south and the gun from the east that a full flowering of historic Plains culture emerges"

    "Who the archaic Plains Pedestrians were is conjectural. However, it is almost certain, ... that several tribes [from the 'Plateau and Basin region] such as the Kutenai, Flathead and particularly the Shoshoni commonly travelled on foot to the plains region to hunt buffalo. Some archeological evidence suggests that several bands may even have lived on the western fringes of the plains 'for several thousand years'"

    Note: 'the western fringes of the plains'.

    "The Kutenai, Flathead and some of the Northern Shoshoni, in particular, viewed the Blackfeet and Crow as intruders into the western Plains region which for centuries they had used as intertribal buffalo country."

    So what about the Shoshoni themselves:

    "These central and western Shoshonean groups ... were, particularly in the mid-nineteenth century, when first described by whites, referred to as 'Digger Indians', a derogatory term, drawing attention to their extensive use of a pointed stick which was used to pry roots and wild vegetables from the ground."

    But that may have been because of a later poverty:

    "In the east, the Northern Shoshoni and Bannock had the luxury of buffalo which, prior to c. 1840, were to be found west of the continental divide. After this date, bereft of this resource locally, it was necessary for these tribes to travel annually to the Plains region - a hazardous venture in territory of gun-armed tribes - or accept the harsher alternatives of the more Central and Western Great Basin environment"

    So what about these 'gun-armed tribes' of the prairie:

    "The Northern Plains were largely dominated by Algonquians, the Central Plains by Siouans. These particular linguistic groups were not well represented on the Southern Plains although some Cheyenne and Arapaho formed strong military allegiances with the Kiowa and Comanche who dominated this region. The population was relatively small."

    "and by 1730 the horse had reached the Northern Shoshoni, who, rapidly adapting to an equestrian lifestyle, expanded their territory deep into the buffalo country of the Northern Plains and at least as far as the belly River in southern Saskatchewan. One group split off from the Eastern Shoshoni probably to be nearer the southern source of horses ... history knows them as the Comanches."

    So the 'Plains Indian' Comanches are post-horse. What about the Cheyenne:

    When the Cheyenne, for example, first moved out onto the Plains in the late eighteenth century ..."

    Finally:

    "Whilst the time-scale and pressures varied, similar patterns were replicated across both the Central and Southern Plains. Thus, into this vast area moved Algonquian and Athapaskan-speaking tribes from the north and east - the Blackfeet Confederacy, Cree, Arapaho, Cheyenne, Sarcee and Kiowa-Apache. From the east and southeast came the Siouan tribes - the Nakota, Lakota and Dakota, Crow, Hidatsa and Mandan and from both west and southeast the Pawnee, Arikara, Comanche and Kiowa."

    To fit all those groups in the prairie must have been fairly empty until the arrival of the horse and firearms.

    ReplyDelete

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