Proc. Natl. Acad. Sci. (Published online)
Anterior tooth growth periods in Neandertals were comparable to those of modern humans
Debbie Guatelli-Steinberg et al.
Abstract
A longstanding controversy in paleoanthropology surrounds the question of whether Neandertals shared the prolonged growth periods of modern humans. To address this question, this investigation compares the duration of enamel formation in Neandertals with that of three comparative modern human groups. Because dental and somatic growth are correlated with each other, dental growth periods are indicative of overall periods of growth. Growth increments on the anterior teeth of Neandertals, modern Inuit, and modern people from Newcastle and southern Africa were counted and their means compared. In addition, potential variation in the time spans represented by growth increments was considered and incorporated into the analysis of enamel formation times. These analyses show that Neandertal imbricational enamel formation times, although likely to have been faster than those of the Inuit, are not likely to have been faster than those of the Newcastle sample and for some teeth are clearly slower than those of the southern African sample. Thus, Neandertal tooth growth and, by extension, somatic growth, appears to be encompassed within the modern human range of interpopulation variation.
Link
John Hawks has more on this topic.
September 25, 2005
September 24, 2005
Out of Africa vs. Multiregionalism, the debate that will not end
I was recently glancing through the excellent Human Evolutionary Genetics, and one of the opinion boxes in the book was titled "Modern Human origins - why it's time to move on". In it, Robert Foley and Marta Mirazon Lahr pronounce the victory of the out of Africa model and the death of multiregionalism:
For example Michael Hammer and colleagues have recently published a paper which explicitly rejects the African-ness of a particular haplotype on the X chromosome. A paper on the non-admixture between moderns and Neanderthals, but also a paper on a 3-million year old polymorphism in Europeans which may have been introduced into the European gene pool by Neanderthals. Not to mention of lice speaking of modern human-erectus hybridization in Asia, a 2 million year old non-African polymorphism in Asians, 1.1 million year polymorphism in North Africa and the Middle East, and research which suggests that the fact that Africans have more ancestral alleles than non-Africans should not be interpreted as evidence of an African origin of humanity (all of them here).
Henry Harpending and Vinayak Eswaran have written a letter in the latest issue of Science, in which he takes issue with another article on ancient Out-of-Africa migrations and their Orang Asli descendants:
What do you think?
Read also, the Multiregional Stipulation Society by John Hawks.
The 'out of Africa' model of human evolution has basically proved to be empirically sound, and the field is now (at last!) moving on.On the other hand, Erik Trinkaus, on a recent article on modern human emergence seems to reject the pure Out of Africa model as well as the regional continuity model:
Versions of the assimilation model have remained contenders for the interpretation of modern human phylogenetic emergence, if frequently overshadowed by the more polarized regional continuity (with gene flow) and (out of Africa with) replacement scenarios. The last two interpretations are finally intellectually dead. Both are contradicted by available evidence, and it is time for the discussion to move on. Yet, despite the general acceptance of some form of the assimilation model, issues remain.So, perhaps we should move on, but where? Most anthropologists and geneticists today may reject the multiregional model, and accept that most recent human ancestry is derived from Africa, yet the existence and extent of non-African ancestry in modern humans is a matter of great controversy.
For example Michael Hammer and colleagues have recently published a paper which explicitly rejects the African-ness of a particular haplotype on the X chromosome. A paper on the non-admixture between moderns and Neanderthals, but also a paper on a 3-million year old polymorphism in Europeans which may have been introduced into the European gene pool by Neanderthals. Not to mention of lice speaking of modern human-erectus hybridization in Asia, a 2 million year old non-African polymorphism in Asians, 1.1 million year polymorphism in North Africa and the Middle East, and research which suggests that the fact that Africans have more ancestral alleles than non-Africans should not be interpreted as evidence of an African origin of humanity (all of them here).
Henry Harpending and Vinayak Eswaran have written a letter in the latest issue of Science, in which he takes issue with another article on ancient Out-of-Africa migrations and their Orang Asli descendants:
For example, nuclear loci rarely, if ever, show the low coalescence times (~200,000 years) seen in mtDNA, nor do they show strictly African roots. Indeed, there is now growing evidence of strictly non-African polymorphisms that date to before the birth of modern humans (1-5).Vincent Macaulay and the other authors of the paper reply:
In cases where autosomal loci do have the necessary resolution, they suggest the replacement model (6-8). The discordant population-size estimates referred to by Harpending and Eswaran are likely more apparent than real, since these long-term values are usually obtained with the multiregional stipulation of random mating and constant population size. The analysis of overly simplistic models with methods that throw away what little information there is in most of these loci throws up straw men, such as the apparent lack of "strong signals of expansion" in some autosomal loci (9).It is becoming awfully hard to keep up with the debate, especially since the experts themselves interpret the evidence in completely different ways. Should we despair of the ability of genetics to throw any light on our species' origin, and go back on discovering and measuring skulls? The African mitochondrial Eve discovery seemed to tilt the balance towards the Out of Africa hypothesis (first proposed forcefully by W.W. Howells), but our optimism that genetics would succeed where palaeoanthropology had failed may have been premature. Almost twenty years later, the discussion seems to have barely just begun!
What do you think?
Read also, the Multiregional Stipulation Society by John Hawks.
Phylogenetic methods and Melanesian languages
Traditional linguistic methods compare languages by noting the similarities in vocabulary between them. However, vocabulary changes at a relatively high rate, so beyond a few thousand years in the past, the shared vocabulary of two related languages will be about the same as that between two randomly chosen languages.
Language, however, is not limited to vocabulary, but extends to grammatical rules, syntax, phonology, etc. So, two related languages will be similar to each other in these respects as well. Perhaps by using the knowledge which they provide we might be able to reconstruct the relationships between languages beyond the time barrier posed by vocabulary, and into a Paleolithic time frame.
Michael Dunn and colleagues have applied phylogenetic methods inspired by biology to this problem. Biological populations are quite similar to languages, because they also change over time, becoming dissimilar when they are separated, while retaining some of the structure of their common ancestors. So, by applying biological thinking we might be able to reconstruct a linguistic phylogeny.
Dunn et al. first applied this approach to Oceanic Austronesian languages, confirming that their method is able to reproduce the branching pattern of a well-understood language family. Next, they applied their method to Papuan languages of Melanesia, which are considered isolates without any clear relationships to each other. The resulting phylogeny shows a remarkable correspondence with geography. Thus, phylogenetic methods applied to non-vocabulary elements of language were able to trace the differentiation of Melanesian languages during the Paleolithic settlement of that region of the world.
Science, Vol 309, Issue 5743, 2072-2075
Structural Phylogenetics and the Reconstruction of Ancient Language History
Michael Dunn et al.
The contribution of language history to the study of the early dispersals of modern humans throughout the Old World has been limited by the shallow time depth (about 8000 ± 2000 years) of current linguistic methods. Here it is shown that the application of biological cladistic methods, not to vocabulary (as has been previously tried) but to language structure (sound systems and grammar), may extend the time depths at which language data can be used. The method was tested against well-understood families of Oceanic Austronesian languages, then applied to the Papuan languages of Island Melanesia, a group of hitherto unrelatable isolates. Papuan languages show an archipelago-based phylogenetic signal that is consistent with the current geographical distribution of languages. The most plausible hypothesis to explain this result is the divergence of the Papuan languages from a common ancestral stock, as part of late Pleistocene dispersals.
Link
Language, however, is not limited to vocabulary, but extends to grammatical rules, syntax, phonology, etc. So, two related languages will be similar to each other in these respects as well. Perhaps by using the knowledge which they provide we might be able to reconstruct the relationships between languages beyond the time barrier posed by vocabulary, and into a Paleolithic time frame.
Michael Dunn and colleagues have applied phylogenetic methods inspired by biology to this problem. Biological populations are quite similar to languages, because they also change over time, becoming dissimilar when they are separated, while retaining some of the structure of their common ancestors. So, by applying biological thinking we might be able to reconstruct a linguistic phylogeny.
Dunn et al. first applied this approach to Oceanic Austronesian languages, confirming that their method is able to reproduce the branching pattern of a well-understood language family. Next, they applied their method to Papuan languages of Melanesia, which are considered isolates without any clear relationships to each other. The resulting phylogeny shows a remarkable correspondence with geography. Thus, phylogenetic methods applied to non-vocabulary elements of language were able to trace the differentiation of Melanesian languages during the Paleolithic settlement of that region of the world.
Science, Vol 309, Issue 5743, 2072-2075
Structural Phylogenetics and the Reconstruction of Ancient Language History
Michael Dunn et al.
The contribution of language history to the study of the early dispersals of modern humans throughout the Old World has been limited by the shallow time depth (about 8000 ± 2000 years) of current linguistic methods. Here it is shown that the application of biological cladistic methods, not to vocabulary (as has been previously tried) but to language structure (sound systems and grammar), may extend the time depths at which language data can be used. The method was tested against well-understood families of Oceanic Austronesian languages, then applied to the Papuan languages of Island Melanesia, a group of hitherto unrelatable isolates. Papuan languages show an archipelago-based phylogenetic signal that is consistent with the current geographical distribution of languages. The most plausible hypothesis to explain this result is the divergence of the Papuan languages from a common ancestral stock, as part of late Pleistocene dispersals.
Link
September 22, 2005
Affinities of Early Upper Paleolithic Europeans (II)
W.W. Howells, 1997, Getting Here: the story of Human Evolution, p. 188.
If Upper Paleolithic people were "European" from about 35,000 B.P., then such population distinctions are at least that old. And the Cro-Magnons were already racially European, i.e., Caucasoid. This has always been accepted because of the general appearance of the skulls: straight faces, narrow noses, and so forth. It is also possible to test this arithmetically ... Except for Predmosti 4, which is distant from every present and past population population, all of these skulls show themselves to be closer to "Europeans" than to other peoples - Mladec and Abri Pataud comfortably so, the other two much more remotely.See also Affinities of Early Upper Paleolithic Europeans.
Selection in human mtDNA
The issue of selection on human mtDNA is quite controversial, because mtDNA has been used to infer patterns of human history and prehistory. In particular, the identification of the coalescence of human mitochondria types to a recent "African Eve" ancestor has been one of the arguments in favor of the recent Out of Africa replacement hypothesis.
A new study in Genetics examines the role that selection has played in the evolution of human mtDNA.
Getting back to the paper:
One has to wonder whether the basic branches may also have been the remnant of selection from a wider pool of mtDNA variants. That is, they may be the variants that have survived in competition with their cousins when they too were young, tens of thousands of years ago.
Genetics (online early)
The role of selection in the evolution of human mitochondrial genomes
Toomas Kivisild et al.
Abstract
High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (p<0.01) excess of rRNA and non-synonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, together with thymine to cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of non-synonymous changes from and to threonine and valine differed significantly (P=0.003) between populations with neutral (22/58) and those with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of non-silent mutations is characteristic to Arctic populations implying their role in cold adaptation, we demonstrate that the surplus of non-synonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.
Link
A new study in Genetics examines the role that selection has played in the evolution of human mtDNA.
The coalescent date of the human mitochondrial DNA tree using this rate is 160,000 (S.D. 22,000) years. This coalescent date is broadly consistent with the dates of the Homo sapiens fossils recognized so far from Ethiopia (CLARK et al. 2003; MCDOUGALL et al. 2005; WHITE et al. 2003). The most recent common ancestor of all the Eurasian, American, Australian, Papua New Guinean and African lineages in clade L3 dates to 65,000 ± 8,000 years while the average coalescent time of the three basic non-African founding haplogroups M, N, and R is 45,000 years.This confirms my previous observation that mtDNA variation in humans points to increased diversity among African populations who are descended partially from ancient "Paleoafrican" populations, while Africans and non-Africans are descended from "Afrasians", a group probably living in Africa in the last few tens of thousands of years and containing a subset of the diversity of the widely dispersed anatomically modern population of Africa. The date of the "Afrasian" group L3 is roughly compatible with the ~40kBP date for the wide appearance of modern humans in Eurasia and the emergence of modern behavior. The coalescence times of Eurasian mtDNA are also comparable with that of the Microcephalin variants, which (like M, N, and R) also show a primary non-African distribution.
Getting back to the paper:
The direction of threonine and valine substitution with other amino acids was significantly different between populations with neutral and significantly negative Tajima’s D values, respectively (Table 3), and between haplogroups: in H1 sequences sampled broadly from Europe and Near East, 7 of 11 non-synonymous mutations resulted in the replacement of threonine and valine with alanine and isoleucine, while only three mutations resulted in a change towards threonine or valine (Figure 1). In contrast to this pattern, in haplogroup V sequences from Finland (FINNILÄ et al. 2001), where populations continued to rely largely on hunting and fishing for subsistence even after the first contacts with farmers, 6 of 7 replacement polymorphisms resulted in a change to threonine and valine, and none in the replacement of the latter two amino acids (p<0.01). style="font-weight: bold;">The potential role of selection in affecting fixation probabilities at different non-silent positions undermines the appropriateness of using the average mitochondrial clock over all sites in dating events in human population history. Despite the evidence of departures from neutrality and high levels of homoplasy at the interspecies level, the phylogenetic approach for analyzing mtDNA sequence data at the intraspecies level remains viable because the reconstruction of the basic branches is robust and the excess of non-synonymous substitutions affects mainly the terminal branches of the tree.What the authors are basically saying is that the basic branches of the tree don't show a substantial evidence of selection. This is not surprising, since these are old lineages that have withstood the test of time. It is the younger "unproven" terminal branches, i.e., the more recent lineages within the major branches that show evidence of selection.
One has to wonder whether the basic branches may also have been the remnant of selection from a wider pool of mtDNA variants. That is, they may be the variants that have survived in competition with their cousins when they too were young, tens of thousands of years ago.
Genetics (online early)
The role of selection in the evolution of human mitochondrial genomes
Toomas Kivisild et al.
Abstract
High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (p<0.01) excess of rRNA and non-synonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, together with thymine to cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of non-synonymous changes from and to threonine and valine differed significantly (P=0.003) between populations with neutral (22/58) and those with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of non-silent mutations is characteristic to Arctic populations implying their role in cold adaptation, we demonstrate that the surplus of non-synonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.
Link
September 21, 2005
Human population genetic structure
I was re-reading a classic paper [1] by Wilson et al. which first used the model-based software STRUCTURE program to cluster human populations. This approach was later used by Rosenberg et al. [2] with many more populations and markers. The following two tables from the paper are quite useful. The first table shows (right column) the probability of the number of clusters K given the data.
As you can see, this probability is ~1 for K=4. Contrary to often repeated claims, the number of subdivisions ("races") of a group of individuals is not arbitrary, but for a set of individuals some numbers (in this case 4) are much better than others. Of course with more markers or larger samples, some of these clusters may be further refined, but the basic structure would not change. An alternative clustering with say 2 or 3 clusters would not emerge.
The second table shows that human populations usually fall within the clusters that correspond to the classical anthropological racial categories.
It is also interesting that the Ethiopians belong in the Caucasoid cluster A and also in the Negroid cluster C. The Ethiopians don't "fit well" in the 4-race scheme, but this is a fact that was also appreciated by traditional anthropology. In all likelihood, both ancient links between Proto-Eurasians and East Africans and recent migrations of Caucasoids into East Africa are responsible for Ethiopian intermediacy.
Admixture analysis using K clusters summarizes the genetic structure of populations and individuals with K numbers adding up to 1, i.e., with K-1 degrees of freedom. But, they cannot distinguish between similarity deriving from common descent, or from recent admixture.
For example, Kazakhs and South Asians both score highly for European and Asian ancestry in Ancestry By DNA type tests. But, in the case of the former, this is due to admixture between Caucasoids and Mongoloids in Central Asia, whereas in the latter it is due to admixture between Caucasoids and Proto-Asians, i.e., non-Mongoloid people sharing common descent with East Asians.
This is why autosomal markers are useful for determining overall (genomic) similarity, but we have to turn to haploid markers such as mtDNA and the Y chromosome to interpret this similarity. Such markers can be tied to regions and times of origin and can thus be used to determine the actual processes of expansion and admixture that have led to the observable genetic variation.
[1] J.F. Wilson et al. Nature Genetics 29, 265 - 269 (2001)
[2] N.A. Rosenberg et al. Science, Vol 298, Issue 5602, 2381-2385
As you can see, this probability is ~1 for K=4. Contrary to often repeated claims, the number of subdivisions ("races") of a group of individuals is not arbitrary, but for a set of individuals some numbers (in this case 4) are much better than others. Of course with more markers or larger samples, some of these clusters may be further refined, but the basic structure would not change. An alternative clustering with say 2 or 3 clusters would not emerge.
The second table shows that human populations usually fall within the clusters that correspond to the classical anthropological racial categories.
It is also interesting that the Ethiopians belong in the Caucasoid cluster A and also in the Negroid cluster C. The Ethiopians don't "fit well" in the 4-race scheme, but this is a fact that was also appreciated by traditional anthropology. In all likelihood, both ancient links between Proto-Eurasians and East Africans and recent migrations of Caucasoids into East Africa are responsible for Ethiopian intermediacy.
Admixture analysis using K clusters summarizes the genetic structure of populations and individuals with K numbers adding up to 1, i.e., with K-1 degrees of freedom. But, they cannot distinguish between similarity deriving from common descent, or from recent admixture.
For example, Kazakhs and South Asians both score highly for European and Asian ancestry in Ancestry By DNA type tests. But, in the case of the former, this is due to admixture between Caucasoids and Mongoloids in Central Asia, whereas in the latter it is due to admixture between Caucasoids and Proto-Asians, i.e., non-Mongoloid people sharing common descent with East Asians.
This is why autosomal markers are useful for determining overall (genomic) similarity, but we have to turn to haploid markers such as mtDNA and the Y chromosome to interpret this similarity. Such markers can be tied to regions and times of origin and can thus be used to determine the actual processes of expansion and admixture that have led to the observable genetic variation.
[1] J.F. Wilson et al. Nature Genetics 29, 265 - 269 (2001)
[2] N.A. Rosenberg et al. Science, Vol 298, Issue 5602, 2381-2385
September 20, 2005
BARCODE and the dating of sub-haplogroups
A new paper introduces BARCODE, a new software program that can be used to infer the age of different sub-haplogroups. The age is presented as a fraction of the time for the entire haplogroup, thus allowing for the comparative dating of the antiquity of lineages. Below is the dating of several sub-haplogroups within Y-haplogroups E, J, and I.
Human Genetics (Online first)
Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father–son transmissions
Francesca Luca et al.
Abstract Five datasets consisting of samples jointly typed for Y-chromosomal Unique Event Polymorphism (UEP) and simple tandem repeat (STR) markers were re-examined with independent methods for dating the different UEP-defined lineages. We report on the results obtained with an original program which performs comparative dating (BARCODE) in comparison with coalescent analyses performed with BATWING under various prior conditions. For the first time these are equalized across datasets. We also report on the results concerning STR mutability as obtained with both methods. The dating results for the entire series of sub-haplogroups are highly correlated. Within coalescent analyses, dating-estimates under a wide range of priors tend to converge. As to STR mutation rates the main findings are: (1) large variations among loci within the same dataset with both methods, also when the same prior was used for all loci; (2) figures in most cases above 1×10−3 and often above 2×10−3; (3) a few loci that mutate differently across studies. These results closely match those obtained from direct observation of father–son transmissions. Overall, this work supports the use of genetic dating procedures that take into account the complexity of the phenomenon, with a repertoire of priors tailored on the particular dataset.
Link
Human Genetics (Online first)
Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father–son transmissions
Francesca Luca et al.
Abstract Five datasets consisting of samples jointly typed for Y-chromosomal Unique Event Polymorphism (UEP) and simple tandem repeat (STR) markers were re-examined with independent methods for dating the different UEP-defined lineages. We report on the results obtained with an original program which performs comparative dating (BARCODE) in comparison with coalescent analyses performed with BATWING under various prior conditions. For the first time these are equalized across datasets. We also report on the results concerning STR mutability as obtained with both methods. The dating results for the entire series of sub-haplogroups are highly correlated. Within coalescent analyses, dating-estimates under a wide range of priors tend to converge. As to STR mutation rates the main findings are: (1) large variations among loci within the same dataset with both methods, also when the same prior was used for all loci; (2) figures in most cases above 1×10−3 and often above 2×10−3; (3) a few loci that mutate differently across studies. These results closely match those obtained from direct observation of father–son transmissions. Overall, this work supports the use of genetic dating procedures that take into account the complexity of the phenomenon, with a repertoire of priors tailored on the particular dataset.
Link
Blind test of DNA BioScience
DNA Bioscience is a British firm which offers (among other things) the Ancestry By DNA test. Recently, the company was featured in a Guardian story, in which four journalists from the paper submitted their DNA samples and the company predicted their skin color and ethnic origin. Person A was an Eastern European Jew who was predicted as being European with East Asian admixture, a reasonable finding, since both Ashkenazi Jews and eastern Slavs have some degree of Asian admixture. Person B was a Sub-Saharan African who was classified as such, again a reasonable result. Person C was a native Briton who was however given minor Native American ancestry, again underscoring the tendency of the test to wrongly predict such ancestry in persons without any possible Native American connection. Person D was a native Indian. The company shrewdly inferred his origin, even though a European-East Asian-Sub-Saharan-Native American mix does not reflect the origin of Indians. The suggestions that the individual had East Asian grandparents or his ancestors reached Britain through Africa (to explain the Sub-Saharan component) are of course rationalizations, and a good example of a case where this type of test is not useful.
All in all, this small test establishes once again the strength of admixture testing in predicting majority ancestry, its overreporting of minority ancestry that does not exist, and its difficulty in dealing with populations that fall outside the group of a priori chosen populations.
All in all, this small test establishes once again the strength of admixture testing in predicting majority ancestry, its overreporting of minority ancestry that does not exist, and its difficulty in dealing with populations that fall outside the group of a priori chosen populations.
Stability of British height in England since the Neolithic
Medieval ancestors measured up to our height standards
OUR ANCESTORS were as tall as we are, contrary to popular belief. Over the past five millennia the average height of men in Britain has remained stable at about 170cm (5ft 7in), and that of women at 160cm (5ft 3in).
Link
OUR ANCESTORS were as tall as we are, contrary to popular belief. Over the past five millennia the average height of men in Britain has remained stable at about 170cm (5ft 7in), and that of women at 160cm (5ft 3in).
Link
Botai and horse domestication
See also the updated entry on the redating of the Dereivka stallion, including some comments from Dr. David Anthony. Now that Dereivka has been redated as belonging to the Scythian Iron Age, the Botai (east of the Urals) represents the earliest evidence of possible horse riding. Levine writes:
The redating of the Dereivka stallion casts doubt on the idea that horse domestication spread from west to east. Certainly it might have, but there is no direct evidence for the prior existence of domesticated horses in Ukraine than in Kazakhstan (Botai). But is the pattern of tooth wear interpreted as bit wear unambiguous evidence of horse riding? Levine writes:
From the conclusions:
Journal of Anthropological Archaeology
Volume 18, Issue 1 , March 1999, Pages 29-78
Botai and the Origins of Horse Domestication
Marsha A. Levine
Abstract
This paper explores some issues related to the origins of horse domestication. First, it focuses on methodological problems relevant to existing work. Then, ethnoarchaeological and archaeozoological methods are used to provide an alternative approach to the subject. Ethnological, ethological, and archaeological data are used to construct a series of population structure models illustrating a range of human–horse relationships. Analysis of assemblages from the Eneolithic sites of Botai (northern Kazakhstan) and Dereivka (Ukraine) suggests that horses at these sites were obtained largely by hunting.
Link
UPDATE
Dr. Anthony writes in the comments section. I have placed his comments in the blog entry because haloscan comments get deleted after a few months.
Another example of this commitment to an earliest date is Anthony’s argument that the domesticated horse was present in the Ukraine earlier than in Kazakhstan. His evidence for this comes from bitwear studies of two samples of lower second premolars from two Eneolithic sites, Botai in northern Kazakhstan (5 from a total of 19 teeth) and Dereivka in the Ukraine (2 from a total of 6 teeth). He implies from this that horse domestication spread from west to east (Anthony 1995).
The redating of the Dereivka stallion casts doubt on the idea that horse domestication spread from west to east. Certainly it might have, but there is no direct evidence for the prior existence of domesticated horses in Ukraine than in Kazakhstan (Botai). But is the pattern of tooth wear interpreted as bit wear unambiguous evidence of horse riding? Levine writes:
The question of whether the wear pattern described by Anthony and Brown could have had other causes has not been adequately addressed. Their unbitted sample of feral horses consisted of 20 individuals from two North American populations (mustangs from the mountains of Nevada and barrier island ponies from the Atlantic Coast). They have generalized from this small sample that unbitted horses could not manifest the wear pattern they describe as unique to bitwear. On the other hand, Angela von den Driesch (personal communication) has observed
that similar, if not identical, wear on the lower second premolar can result from abnormal occlusion with the upper second premolar.
As far as we know, then, beveling on the anterior part of the lower P2 masticatory surface could be caused by bitwear or abnormal occlusion. Either a domesticated horse or a wild one that had been tamed could be bitted. The absence of bitwear could indicate that a horse had not been ridden recently or regularly before its death, that it was ridden unbitted, or that it never was ridden. We must conclude from this that bitwear should not be used without corroboration as proof of domestication. This is not to say that bitwear studies should not be carried out. On the contrary, their use should be much more widespread, but in conjunction with other methods of analysis.
From the conclusions:
The results of the analyses carried out on the data from Dereivka and Botai suggest that the vast majority of the horses from those sites were killed in the hunt. Different hunting techniques were employed at each of them: stalking or chasing at Dereivka and driving or surrounding at Botai. The possibility that some of the horses might have been tamed or domesticated, as suggested by Anthony and Brown’s bitwear studies, is certainly not excluded. However, the possibility that the wear pattern they define as bitwear could have other causes has not been disproved.See also Domestication, Breed Diversification and Early History of the Horse.
Journal of Anthropological Archaeology
Volume 18, Issue 1 , March 1999, Pages 29-78
Botai and the Origins of Horse Domestication
Marsha A. Levine
Abstract
This paper explores some issues related to the origins of horse domestication. First, it focuses on methodological problems relevant to existing work. Then, ethnoarchaeological and archaeozoological methods are used to provide an alternative approach to the subject. Ethnological, ethological, and archaeological data are used to construct a series of population structure models illustrating a range of human–horse relationships. Analysis of assemblages from the Eneolithic sites of Botai (northern Kazakhstan) and Dereivka (Ukraine) suggests that horses at these sites were obtained largely by hunting.
Link
UPDATE
Dr. Anthony writes in the comments section. I have placed his comments in the blog entry because haloscan comments get deleted after a few months.
1. I have argued that horse domestication spread from west to east because the cultures of Ukraine and the the Volga-Ural region certainly had domesticated animals (cattle and sheep) before 5000 calBC, while the cultures of northern Kazakhstan remained foragers until at least 3500 calBC (when they probably adopted horse-herding), and perhaps until 2500 calBC (when they finally began to adopt domesticated cattle and sheep, 2500 years after the cultures of the western steppes). Horses were included with cattle and sheep in funeral sacrifices in the western steppes between 5000-4500 calBC and were portrayed there in mobile art, while in the eastern (Kazakh) steppes horses played no special role in ritual or in art until the Botai culture appeared, about 3500 BCE. Botai was a radically new kind of culture in the Kazakh steppes, with large settlements and dense deposits of animal bone consisting of 70-90% horse bones. This specialized horse hunting economy appeared with bit wear and stabling soils full of horse dung in the settlement of Botai. Bit wear also appeared at the related settlement of Kozhai 1. The Botai people were foragers who rode domesticated horses to hunt wild horses, a peculiar adaptation that existed only in Kazakhstan and only between 3500-3000 calBC.
2. Levine is incorrect in stating that what we have defined as bit wear can appear on the teeth of wild horses; her description of our sample size is incorrect; and her statement that bit wear could have other causes is an unsupported speculation. In a forthcoming paper in a BAR volume edited by Sandra Olsen we describe a new sample of 74 never-bitted Pleistocene equid teeth, studied with our methods. None of them shows a bevel measurement of 3mm, our threshold for bit wear. No one, including von den Dreisch and Levine, has described a population of wild horses that exhibits this kind of wear facet as the result of natural wear. Bit wear clearly distinguishes bitted from never-bitted populations at better than the .001 level of confidence. Levine's criticism of our bit wear statistics in the Journal of Anthropological Anthropology confused the issue by comparing our median measurement for bitted horses to our maximum measurement for never-bitted horses, implying that only .5mm separated them. This was a basic error. Comparing median to median and maximum to maximum, the statistical separation is very good.
3. Levine distinguishes between horses that are merely 'tamed' and those that are 'domesticated'. Tamed horses might have been ridden regularly in the hunt and in war, but this is unimportant in her scheme if they do not show the measurements she expects for a 'domesticated' horse. Culturally, this turns anthropological zoology upside down. When people began to ride horses regularly the world was changed. Whether leg bone measurements changed at the same time is an interesting question, but not nearly as interesting as identifying ridden horses.
September 17, 2005
Y chromosome haplogroups in Byelorussians
Genetika. 2005 Aug;41(8):1132-6.
[Frequencies of Y chromosome binary haplogroups in Belarussians]
[Article in Russian]
[No authors listed]
The compositions and frequencies of Y-chromosome haplogroups identified by genotyping 23 biallelic loci of its nonrecombining region (YAP, 92R7, DYF155S2, 12f2, Tat, M9, M17, M25, M89, M124, M130, M170, M172, M174, M173, M178, M201, M207, M242, M269, P21, P25, and P37) have been determined in a sample of 68 Belarussians. Eleven haplogroups have been found in the Belarussian gene pool (E, F*, G, I, I1b, J2, N3a*, Q*, R1*, R1a1, and R1b3). Haplogroup R1a1 is the most frequent; it includes 46% of all Y chromosomes in this sample. The frequencies of haplogroups I1b and I are 17.6 and 7.3%, respectively. Haplogroup N3a* is the next in frequency. The frequencies of haplogroups E, J2, and R1b3 are 4.4% each; that of R1* is 3%; and those of F*, G, and Q* are 1.5% each.
Link
[Frequencies of Y chromosome binary haplogroups in Belarussians]
[Article in Russian]
[No authors listed]
The compositions and frequencies of Y-chromosome haplogroups identified by genotyping 23 biallelic loci of its nonrecombining region (YAP, 92R7, DYF155S2, 12f2, Tat, M9, M17, M25, M89, M124, M130, M170, M172, M174, M173, M178, M201, M207, M242, M269, P21, P25, and P37) have been determined in a sample of 68 Belarussians. Eleven haplogroups have been found in the Belarussian gene pool (E, F*, G, I, I1b, J2, N3a*, Q*, R1*, R1a1, and R1b3). Haplogroup R1a1 is the most frequent; it includes 46% of all Y chromosomes in this sample. The frequencies of haplogroups I1b and I are 17.6 and 7.3%, respectively. Haplogroup N3a* is the next in frequency. The frequencies of haplogroups E, J2, and R1b3 are 4.4% each; that of R1* is 3%; and those of F*, G, and Q* are 1.5% each.
Link
September 16, 2005
Haplogroup frequency correlations in Southeastern Europe (part II)
I've added five new populations to my previous dataset (SIT: Southern Italians, ESC: East Sicilians, SWS: Southwest Sicilians, NWS: Northwest Sicilians, CYP: Cyprus), taken from this recent paper. The resulting principal components plot again shows the J2/R1b/E3b "coastal" vs. I/R1a1 "continental" groupings along the first principal component (right vs. left respectively).
Viruses, mitochondria, cells, etc.
Carl Zimmer posts a fascinating description on new research about the ever-more-fascinating stuff that is found in our cells. It was first thought that cells are nice containers, designed to keep our DNA safely shielded in their nuclei, but it turns out that our cells contain DNA fragments of quite diverse origins, which have managed to strike up an alliance for their joint proliferation:
Here’s the history as they now see it: the free-living, oxygen-breathing ancestors of mitochondria were infected with some nasty T3/T7 viruses. Most of the time the viruses were fatal. But some mutant tried to replicate itself inside a proto-mitochondrion and failed. Its genes were trapped in the genome of its host. Its host was able to reproduce, and one of its descendants took up residence inside the cell of a eukaryote. At some point after this merger, a mutation caused the virus’s DNA and RNA copying genes to come back online. They took over the job of making these molecules, and the mitochondria’s own genes for this job were later stripped out of its genome.It’s a plausible hypothesis for a number of reasons. Filee and Forterre didn’t just pull the notion that viral genes can become active again out of a hat; this sort of viral resurrection has been documented in other species. Not only is the hypothesis plausible, but it’s a tantalizing as well. It suggests that we are chimeras built from the DNA of eukaryotes, bacteria, and viruses, all mixed together through a natural version of genetic engineering. Forterre even argues that these sorts of results are going to turn out to be the tip of the iceberg. Like many scientists, he believes that before life was based on DNA, the Earth was inhabited by RNA-based life. He argues that DNA was an invention of viruses of these RNA-based organisms, which the RNA-based organisms then seized for their own use. All this may not make you any fonder of the chickenpox you may have had as a kid, but it may at least give you a feeling of kinship.
September 15, 2005
Y chromosome perspective on Mediterranean populations
Capelli et al. have written an important new article on Y-chromosomal variation in the Mediterranean basin. This is the most comprehensive study yet on the region, using a combination of biallelic polymorphisms defining haplogroups and microsatellites over several Mediterranean populations, including many population samples taken from the literature. Moreover, mtDNA and autosomal data are also included, and these tend to support the authors' broad findings.
The key finding is that Mediterranean populations can be grouped into four main clusters: North Africa, Arab, Central-East, and West Mediterranean. The North African cluster exhibits high frequencies of North African specific haplotypes within haplogroup E3b. The Arab cluster exhibits high frequencies of J*(xJ2), which is rarer elsewhere.
According to the authors, there has been very little gene flow from North Africa into Europe. Moreover, Near Eastern populations should not be considered a unity, but are differentiated depending on the extent of Arab admixture exemplified by J*(xJ2) chromosomes. Modern Near Easterners are thus not representative of the early Neolithic people who migrated into Europe. J*(xJ2) chromosomes associated with Arabs are also present in North Africans, but North Africans have maintained their own Y-chromosomal peculiarities, typified by haplogroup E3b haplotypes.
It is unfortunate that a mainland Greek sample was not included, but to make up for it, there is a Cypriot sample, in addition to three Sicilian samples. These populations which are largely of Greek origin are very similar to Greeks in general, and belong to the Central-East cluster. Their inclusion also allow us to test my previously expressed hypothesis that haplogroup R1a1 was rare in ancient Greek populations. Indeed, this haplogroup is found at a frequency of 1.8-3.1% in Sicilians, Cypriots and Southern Italians, thus essentially confirming my idea. On the other hand, haplogroup I*(xI1b2) is found at frequencies from 3.4-15.7%, and is thus (as I have said before), much more likely to have been present in the ancient Greek population.
The study also examines briefly the origins of the Jews. Sephardic Jews are shown to resemble Mediterraneans more, while Ashkenazi resemble Arabs more.
The table of frequencies also allows us to ascertain the prevalence of Negroid admixture in Sicily, a popular subject in certain circles, and one which is shown to be without any basis in fact. In 212 Sicilians in total, no haplogroup A, E3a, or E*(xE3a,E3b) chromosomes were detected. Two haplogroup A chromosomes were detected in Cyprus, one in Sardinia, and two E3a, E*(xE3b, E3a) chromosomes in Malta. This is about the extent of male Sub-Saharan African introgression in the Mediterranean: 5 out of 656.
From the conclusions:
Annals of Human Genetics (online early)
Population Structure in the Mediterranean Basin: A Y Chromosome Perspective
C. Capelli et al.
Abstract
The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.
Link
The key finding is that Mediterranean populations can be grouped into four main clusters: North Africa, Arab, Central-East, and West Mediterranean. The North African cluster exhibits high frequencies of North African specific haplotypes within haplogroup E3b. The Arab cluster exhibits high frequencies of J*(xJ2), which is rarer elsewhere.
According to the authors, there has been very little gene flow from North Africa into Europe. Moreover, Near Eastern populations should not be considered a unity, but are differentiated depending on the extent of Arab admixture exemplified by J*(xJ2) chromosomes. Modern Near Easterners are thus not representative of the early Neolithic people who migrated into Europe. J*(xJ2) chromosomes associated with Arabs are also present in North Africans, but North Africans have maintained their own Y-chromosomal peculiarities, typified by haplogroup E3b haplotypes.
It is unfortunate that a mainland Greek sample was not included, but to make up for it, there is a Cypriot sample, in addition to three Sicilian samples. These populations which are largely of Greek origin are very similar to Greeks in general, and belong to the Central-East cluster. Their inclusion also allow us to test my previously expressed hypothesis that haplogroup R1a1 was rare in ancient Greek populations. Indeed, this haplogroup is found at a frequency of 1.8-3.1% in Sicilians, Cypriots and Southern Italians, thus essentially confirming my idea. On the other hand, haplogroup I*(xI1b2) is found at frequencies from 3.4-15.7%, and is thus (as I have said before), much more likely to have been present in the ancient Greek population.
The study also examines briefly the origins of the Jews. Sephardic Jews are shown to resemble Mediterraneans more, while Ashkenazi resemble Arabs more.
The table of frequencies also allows us to ascertain the prevalence of Negroid admixture in Sicily, a popular subject in certain circles, and one which is shown to be without any basis in fact. In 212 Sicilians in total, no haplogroup A, E3a, or E*(xE3a,E3b) chromosomes were detected. Two haplogroup A chromosomes were detected in Cyprus, one in Sardinia, and two E3a, E*(xE3b, E3a) chromosomes in Malta. This is about the extent of male Sub-Saharan African introgression in the Mediterranean: 5 out of 656.
From the conclusions:
The significant genetic structuring of populations facing the Mediterranean basin into three groupings, Near Eastern Arab, Mediterranean and North African, is related to the demographic processes that have occurred since first populating the area. The distribution of Neolithic technologies was probably paralleled by demographic expansion in the Mediterranean basin, and subsequent westward migration by Phoenicians and Greeks contributed to the distribution of Y chromosome types of most likely Near East origin. The Arab conquest in particular appears to have had a dramatic influence on the East and South Mediterranean coasts, with differential sex-related gene flow playing a major role in the distribution of genetic variation. The presence of Arab Y chromosome lineages in the Middle East suggests that most have experienced substantial gene flow from the Arabian peninsula. This result raises the issue of the correctness of identifying all Near Eastern populations as reliable representations of the original Neolithic groups that expanded from the Middle East towards the European peninsula.
Annals of Human Genetics (online early)
Population Structure in the Mediterranean Basin: A Y Chromosome Perspective
C. Capelli et al.
Abstract
The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.
Link
Allele for light pigmentation has been positively selected in Europeans
A new paper shows that a polymorphism on the AIM1 locus which is associated with human pigmentation has been under strong positive selection in Europeans, reaching almost fixation in tested European populations (0.89 in South Africans and 0.96 in Germans), while being rare elsewhere. The derived allele is associated with lighter overall pigmentation. This contrasts to the situation with the MC1R locus in which the ancestral variant is maintained by selection in Negroids, but multiple unrelated mutations outside Africa have resulted in lighter-skinned phenotypes. Unlike the MC1R where relaxation of selection constraints were observed in non-Africans, the new AIM1 polymorphism has been positively selected.
The time of the common ancestor of alleles bearing the haplotype is estimated to be 10,965 years, although the 95% confidence interval is wide from 1,328 to 39,609 years. We should probably not speculate on what triggered the selection based on this very uncertain dating, but the repopulation of Europe after the last glaciation may be a candidate. As humans spread to higher latitudes, they may have been subjected to higher selective pressures for light pigmentation. It would be interesting to determine the frequency of the polymorphism in different Caucasoid populations and determine the most likely ancestral populations.
Molecular Biology and Evolution (published online)
Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population
Mikiko Soejima et al.
Abstract
Two missense polymorphisms (E272K and L374F) of the AIM1 locus, encoding a melanocyte differentiation antigen, were shown to have a clear association with human ethnicities. These two nonpathogenic SNPs may be associated with human pigmentation variation. In this study, we investigated sequence variation in the coding region and exon-flanking sequence and found low genetic variation only in subjects of European descent. All four statistical tests applied to the 7.55-kb region surrounding the L374F polymorphism detected statistically significant deviations from selective neutrality in Europeans. In addition, haplotype analysis revealed that one haplotype carrying 374F was overrepresented in this population, and the low rate of variation, with some features of selective sweeps, was shown to be statistically significant. These results suggest that positive selection recently has been acting or has acted on at least this region of the melanogenic gene and that an advantageous haplotype spread rapidly in Europe.
Link
The time of the common ancestor of alleles bearing the haplotype is estimated to be 10,965 years, although the 95% confidence interval is wide from 1,328 to 39,609 years. We should probably not speculate on what triggered the selection based on this very uncertain dating, but the repopulation of Europe after the last glaciation may be a candidate. As humans spread to higher latitudes, they may have been subjected to higher selective pressures for light pigmentation. It would be interesting to determine the frequency of the polymorphism in different Caucasoid populations and determine the most likely ancestral populations.
Molecular Biology and Evolution (published online)
Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population
Mikiko Soejima et al.
Abstract
Two missense polymorphisms (E272K and L374F) of the AIM1 locus, encoding a melanocyte differentiation antigen, were shown to have a clear association with human ethnicities. These two nonpathogenic SNPs may be associated with human pigmentation variation. In this study, we investigated sequence variation in the coding region and exon-flanking sequence and found low genetic variation only in subjects of European descent. All four statistical tests applied to the 7.55-kb region surrounding the L374F polymorphism detected statistically significant deviations from selective neutrality in Europeans. In addition, haplotype analysis revealed that one haplotype carrying 374F was overrepresented in this population, and the low rate of variation, with some features of selective sweeps, was shown to be statistically significant. These results suggest that positive selection recently has been acting or has acted on at least this region of the melanogenic gene and that an advantageous haplotype spread rapidly in Europe.
Link
Horses were not ridden in the fifth millennium BC
The first domesticated horses were used for meat and for drawing wheeled vehicles. The idea that horses were ridden before the 1st millennium BC is one of the arguments of the adherents of the Pontic steppe thesis of Indo-European origins, because ridden horses would give a significant military advantage, and thus allow the steppe people to overwhelm the settled agricultural populations of Old Europe.
There are however no depictions of horse riding in art before the 1st millennium BC, or in the earliest texts of Indo-European speakers. So, some archaeologists have sought alternative ways of establishing that horses were ridden. To ride a horse, one needs a bit which is put in the horse's mouth and reins by which the horse is controlled. The teeth of a horse that have a hard bit will show evidence of wear in a distinctive pattern, and this will allow us to infer that it was ridden.
The following excerpt from a recent review of Robert Drews' Early riders: the beginning of mounted warfare in Asia and Europe by Karlene Jones-Bley in Journal of Indo-European Studies vol 33, no. 1/2 shows how this ingenuous hypothesis has not survived radiocarbon dating.
UPDATE
Dr. David Anthony, who proposed the bit wear hypothesis has sent me an e-mail in which he gives some additional information.
There are however no depictions of horse riding in art before the 1st millennium BC, or in the earliest texts of Indo-European speakers. So, some archaeologists have sought alternative ways of establishing that horses were ridden. To ride a horse, one needs a bit which is put in the horse's mouth and reins by which the horse is controlled. The teeth of a horse that have a hard bit will show evidence of wear in a distinctive pattern, and this will allow us to infer that it was ridden.
The following excerpt from a recent review of Robert Drews' Early riders: the beginning of mounted warfare in Asia and Europe by Karlene Jones-Bley in Journal of Indo-European Studies vol 33, no. 1/2 shows how this ingenuous hypothesis has not survived radiocarbon dating.
Nevertheless, the entire bit wear thesis collapsed once the skull of the "cult stallion" was subjected to radiocarbon dating and was found to have died before 700 and 200BC. Thus, even if the evidence for bit wear were valid (and there are those who still question even this), it didn't happen at Dereivka until the Iron Age when no one doubts the existence of horse riding and hard bits.
UPDATE
Dr. David Anthony, who proposed the bit wear hypothesis has sent me an e-mail in which he gives some additional information.
The date of the domestication of the horse is still poorly understood, but horses certainly were domesticated and used for riding in the northern Eurasian steppes by the middle of the fourth millennium BCE, and they were grouped with cattle, sheep, and humans in funeral rituals that excluded obviously wild animals during the fifth millennium BCE. The 3500BCE date for riding is supported at Khvalynsk in northern Kazakhstan, dated 3500-3000 BCE, where in addition to bit wear on horse premolars, stabling soils full of horse dung were found, and whole horse carcasses were regularly brought into the settlement for butchering as a regular practice over the course of hundreds of years. The occupants had no cattle or sheep, no draft animals other than horses, so if the horses at Botai were wild it is difficult to understand how they were brought into the settlement. The inclusion of horses in human graves dated 4500 BCE is documented at Khvalynsk on the middle Volga, a cemetery where the sacrificed animals included parts of 52 sheep/goat, 23 cattle, and 11 horses, and no obviously wild animals. Khvalynsk sites also have yielded stone maceheads shaped like horseheads and bone plaques carved in the shape of horses. The bit-worn horse teeth at Dereivka were re-dated to 700-200 BCE by me, the same person who identified the bit wear, but the article in which I announced the re-dating of the Dereivka teeth also described the evidence from Botai and Khvalynsk. Dereivka was not the only site with early bit wear in the steppes. No credible or accurate criticisms of bit wear analysis have yet been published, so the detection of bit wear remains a valid way to identify bitted horses in the archaeological record. Please see Anthony, David W. and Dorcas Brown, 2000, "Eneolithic horse exploitation in the Eurasian steppes: diet, ritual and riding," Antiquity 74: 75-86.
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