The African mtDNA landscape

In the comments of a previous post, I mentioned that the present-day populations of East Africa are only partially descended from the prehistoric East Africans which gave rise to all non-African groups. Apart from the physical anthropological evidence for a lack of craniometric continuity in the region, we also have the findings of population genetics.

Most non-African mtDNA belongs to two macro-groups, called N (frequent in West Eurasians) and M (frequent in East and South Asians and Americans). Both M and N are derived from a particular African group called L3. Thus, it appears that non-Africans are descended from a prehistoric African population which had L3-type mtDNA.

A comprehensive study [1] has studied the distribution of mtDNA haplogroups in present-day African populations:



As we can see, modern East Africans have less than 50% of L3-group mtDNA, with the remainder being either M1 (whose origin is disputed, with some considering it Asian and others African in origin), a little bit of U6 (which is of North African origin), and the remainder (~50%) belongs to L-groups other than L3.

It is clear that this latter component was not present in the East African source of non-African populations in the past. If it were, then it would be present outside Africa. But, even in the Near East, African-specific mtDNA are a minority, mostly confined to Arab populations and attributed to the slave trade [2].

Thus, it appears that a large fraction of present-day East African mitochondrial ancestry is derived from different populations than the ones that spawned non-Africans. This element is probably responsible for the introduction of the Negroid type in the region, which now forms a major element in the population, together with the pre-Negroid East Africans and more recent Caucasoid arrivals from across the Red Sea.


[1] Am. J. Hum. Genet., 71:1082-1111, 2002
[2] Am. J. Hum. Genet., 72:1058-1064, 2003

Anthropological complexes of European Russia, Baltic States, Belarus and Ukraine

An interesting excerpt translated into English together with a descriptive map. Some terminology of N. N. Cheboksarov regarding the Europeoid race is used in this article which might not be familiar to most people, so I list it here as a reference, text copied from an online source.

II. Europeoid (Eurasian) Great Race:

1. South European (Indo-Mediterranean) Race:

(i) South Indian (Dravidian). ------- "C"
(ii) Anterior Asian
(iii) Mediterranean-Balkan
(iv) Atlanto-Black Sea. ------- "C"
(v) East European --------"C"

2. North European (Atlanto-Baltic) Race:

(i) Atlanto-Baltic
(ii) White Sea-Baltic

"C" -------- contact or transitional group

North Europeans take more sickies

Workers in northern Europe are more likely than their southern counterparts to take sick leave, a study has found.

Rates of absenteeism vary hugely around Europe

Staff in Germany, the Netherlands and Finland take the most time off in Europe, a report in the Occupational and Environmental Medicine journal said

Workers in Ireland, Greece and Portugal take the least time off for illness, the study found.

On average, 14.5% of European workers took at least one day off in 2000, the year covered by the study.

Greece had the lowest rate of absenteeism at 6.7% and Finland the highest at 24%.

"This study provides the first scientifically valid description of sickness absence across EU countries," said Dr David Gimeno of the University of Texas School of Public Health in Houston.

The survey looked at absenteeism and ill health in 2000 in the then 15 members of the European Union (EU).

The EU has expanded to 25 members since the survey was carried out.

High cost of 'duvet days'

Sick leave - real and feigned - currently costs UK businesses an estimated £11bn a year.

It is widely perceived to be higher in the public sector than in the private sector, though there is evidence to suggest that absenteeism in large private sector companies matches that in the public sector.

Research carried out by the Confederation of British Industry (CBI) indicates that small firms, where an employee calling in sick often has to talk to the owner, suffer far less absence than large firms.

Link (BBC)

Inferring Human History: Clues from Y-chromosome haplotypes

It's easy to get lost in the technical jargon of many genetics papers, but this excellent review (pdf) by P.A. Underhill is a great primer on human Y chromosome phylogeny.

Move + New Article

After a few years hosted at geocities, I have finally moved, re-named and reorganized the "Greek Anthropology and Racial Identity" site. The new Anthropological Research Page is now available, and to coincide with its launch, I have put online a new short article on Model-Based Clustering of World Craniometric Variation. I've been playing with Howells' data for several months now, but I've finally decided to scrap the plans for a joint analysis of both his "recent" and "prehistoric" populations for some time in the future. For the time being, readers can read how a large collection of unlabelled crania from recent human populations assort themselves to racial clusters, and hopefully the analysis of the "prehistoric" material will also be added soon.

Racial Affinities of Prehistoric East Africans

Afrocentrists and Nordicists alike tend to assert that early East Africans were "Negroid". Since East Africa was the source of multiple migrations of early humans out of Africa, this allows the former to assert a "Negroid" stage in the evolution of Eurasians, or to postulate a later (mythological) stage of "Negroid" East African culture-bearers. Nordicists of the other hand, dissatisfied with the paucity to non-existence of genuine Sub-Saharan African genetic markers in Southeastern Europe have insinuated that Y-haplogroup E3b which originated in East Africa 26ky ago is "Negroid" or that mtDNA haplogroup M1 which according to some also originated in East Africa in Paleolithic times is also "Negroid".

W.W. Howells' study of world craniometric variation is especially relevant to the racial affinity of East Africans before the expansion of Negroids into the region. Howells studied some 2,500+ skulls from 28 populations of recent Homo sapiens based on 57 metric variables [1], including skulls from the Teita tribe of East Africa. These recent Teita tribesmen (and women) clustered with other Sub-Saharan Africans, indicating that (as is obvious) recent Kenyans belong primarily to the Negroid race.

Howells then studied prehistoric East Africans and other humans from around the world to determine whether or not they show any affinities with living races [2]. He did this to examine whether the morphological complexes of modern races can be discerned in remote times. Using the same multivariate approach he studied the Elmenteita, Nakuru and Willey's Kopje skulls from Kenya. His conclusion was that there is no racial continuity between recent Negroid East African skulls and these prehistoric remains, as the following passage illustrates ([2, p. 41]:

(...) The DISPOP [Dienekes: DISPOP is Howells' program] results here are not indicative of anything, except a general non-African nature for all these skulls. Display of POPKIN distances (infra) reinforces this and seems to find nearer neighbors among such more generalized populations as Peru, Guam, or Ainu, but also Europeans or even Easter Island.

Remembering that the Teita series (Bantu speakers of southeastern Kenya), and the recent East African skulls in table 4 above, do clearly exhibit African affiliations, it is fair to say, contra Rightmire, that there seems to be no clear continuity here in late prehistory. On the broad scale, looking at an "Out-of-Africa" scenario, one would expect that, in some region between southern and northeastern Africa, some differentiation would have been taking place within a Homo sapiens stock, evolving into something beginning to approximate later Sub-Saharan peoples on the one hand, and evolving in another direction on the other hand. East Africa would be a likely locale for appearance of the latter. So anyone is welcome to argue that this is what Elmenteita et al. are manifesting. The ensuing picture for East Africa, that is to say, would later have beeen changed through replacement by the expansion of Bantu or other "Negroid" tribes.

[1] Howells WW (1989) Skull shapes and the map: craniometric analyses in the dispersion of modern Homo. Peabody Museum Papers 79:1-189.
[2] Howells WW (1995) Who's Who in skulls: ethnic identification of crania from measurements. Peabody Museum Papers 82:1-108.

Positive Selection on MMP3 in Europe

Current Biology 14(7), 7 September 2004, Pages 1531-1539

Positive Selection on MMP3 Regulation Has Shaped Heart Disease Risk

Matthew V. Rockman et al.

Abstract

Background: The evolutionary forces of mutation, natural selection, and genetic drift shape the pattern of phenotypic variation in nature, but the roles of these forces in defining the distributions of particular traits have been hard to disentangle. To better understand the mechanisms contributing to common variation in humans, we investigated the evolutionary history of a functional polymorphism in the upstream regulatory region of the MMP3 gene. This single base pair insertion/deletion variant, which results in a run of either 5 or 6 thymidines 1608 bp from the transcription start site, alters transcription factor binding and influences levels of MMP3 mRNA and protein. The polymorphism contributes to variation in arterial traits and to the risk of coronary heart disease and its progression.

Results: Phylogenetic and population genetic analysis of primate sequences indicate that the binding site region is rapidly evolving and has been a hot spot for mutation for tens of millions of years. We also find evidence for the action of positive selection, beginning approximately 24,000 years ago, increasing the frequency of the high-expression allele in Europe but not elsewhere. Positive selection is evident in statistical tests of differentiation among populations and haplotype diversity within populations. Europeans have greater arterial elasticity and suffer dramatically fewer coronary heart disease events than they would have had this selection not occurred.

Conclusions: Locally elevated mutation rates and strong positive selection on a cis-regulatory variant have shaped contemporary phenotypic variation and public health.

Link

mtDNA in Iran and India

This article is a great survey of South and Southwest Asian mitochondrial diversity, showing a sharp difference between India and Iran, with the former having a high occurrence of "Proto-Asian" mtDNA types whose frequence falls drastically in Iran.

Indians have traditionally been characterized as being part of the periphery of the Caucasoid race. The subequatorial racial element which distinguishes Indians from Caucasoids-proper has been named Veddoid, Australoid or Palaeo-Indid by various researchers. These new genetic studies have shown Indians to be of mainly dual origins, with West Eurasian racial elements being added to a native South Asian base which persists more strongly in non-caste and southern populations of the subcontinent, and manifests itself primarily in Indian matrilineages.

BMC Genet. 2004 Aug 31;5(1):26.

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Metspalu et al.

BACKGROUND: Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia. RESULTS: Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades. CONCLUSIONS: Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.

Link

Importance of sexual selection in recent human evolution

See also the entry on Higher female effective population size in recent human evolution

Evolution Int J Org Evolution. 2004 Jul;58(7):1613-6.

Estimating the strength of sexual selection from Y-chromosome and mitochondrial DNA diversity.

Wade MJ et al.

We show that a sex difference in the opportunity for selection results in sex differences in the strength of random genetic drift and thus creates different patterns of genetic diversity for maternally and paternally inherited haploid genes. We derive the effective population size Ne for a male-limited or female-limited haploid gene in terms of I, the "opportunity for selection" or the variance in relative fitness. Because the variance in relative fitness of males can be an order of magnitude larger than that of females, the Ne is much smaller for males than it is for females. We derive both nonequilibrium and equilibrium expressions for F(ST) in terms of I and show how the portion of I owing to sexual selection, Imates, that is, the variation among males in mate numbers, is a simple function of the F's for cytoplasmic (female inherited) and Y-linked (male inherited) genes. Because multiple, transgenerational data are lacking to apply the nonequilibrium expression, we apply only the equilibrium model to published data on Y chromosome and mitochondrial sequence divergence in Homo sapiens to quantify the opportunity for sexual selection. The estimate suggests that sexual selection in humans represents a minimum of 54.8% of total selection, supporting Darwin's proposal that sexual selection has played a significant role in human evolution and the recent proposal regarding a shift from polygamy to monogamy in humans.

Link

Romany Gypsies came out of India

Monday, 6 September 2004

Anna Salleh
ABC Science Online

The research, by Professor Luba Kalaydjieva of the University of Western Australia and team, looked at the origins of eight to 10 million people in Europe commonly known as Gypsies.

Roma, Romani or Romany are other names for this community, which has featured in movies such as Latcho Drom.

"[The research] is the best evidence yet of the Indian origins of the Gypsies," the researchers write in an article published online ahead of print in the American Journal of Human Genetics.

Complete Story

Did the First Americans Come From, Er, Australia?

(Top Stories - Reuters)

EXETER, England (Reuters) - Anthropologists stepped into a hornets' nest on Monday, revealing research that suggests the original inhabitants of America may in fact have come from what is now known as Australia.

The claim will be extremely unwelcome to today's native Americans who came overland from Siberia and say they were there first.

But Silvia Gonzalez from John Moores University in Liverpool said skeletal evidence pointed strongly to this unpalatable truth and hinted that recovered DNA would corroborate it.

"This is very contentious," Gonzalez, a Mexican, said with a smile at the annual meeting of the British association for the Advancement of Science. "They (native Americans) cannot claim to have been the first people there."

She said there was very strong evidence that the first migration came from Australia via Japan and Polynesia and down the Pacific Coast of America.

Skulls of a people with distinctively long and narrow heads discovered in Mexico and California predated by several thousand years the more rounded features of the skulls of native Americans.

One particularly well preserved skull of a long-face woman had been carbon dated to 12,700 years ago, whereas the oldest accurately dated native American skull was only about 9,000 years old.

"We have extracted her DNA. It is going to be a bomb," she said, declining to give details but adding that the tests carried out so far were being replicated to make sure they were accurate.

She said there were tales from Spanish missionaries of an isolated coastal community of long-face people in Baja California of a completely different race and rituals from other communities in America at the time.

These last survivors were wiped out by diseases imported by the Spanish conquerors, Gonzalez said.

The research is one of 11 different projects in America, Africa, Asia and the Middle East being funded over a four-year period by Britain's Natural Environment Research Council.

The projects, focusing on diet, dating and dispersal of people down the millennia in the face of climate change, aim to rewrite anthropology.

"We want to make headlines from heads," said Professor Clive Gamble of Southampton university. "DNA will give us a completely new map of the world and how we peopled it."

Link

Γενετική των Ελλήνων

Μιας και η ενημέρωση για θέματα πληθυσμιακής γενετικής στο διαδίκτυο στην Ελληνική γλώσσα είναι σχεδόν ανύπαρκτη, αποφάσισα να ξεκινήσω ένα καινούριο αρχείο για την παρουσίαση τέτοιων θεμάτων στην Ελληνική γλώσσα. Η Γενετική των Ελλήνων ξεκίνησε με μια εκτενή δημοσίευση σχετικά με τα Χρωματοσώματα Υ των Ελλήνων. Όπως αναφέρω και στην Ταυτότητα του Ιστότοπου ελπίζω να προστεθούν και άλλοι συγγραφείς με γνώσεις γενετικής στην καινούρια αυτή προσπάθεια.

Non-Caucasoid Admixture in Austria and Germany

According to [1] the following non-Caucasoid Y-chromosomes were found in a sample from Muenster, Germany and Innsbruck, Austria.

Austria: 1/129 E*(xE3b) (Sub-Saharan African). Total admixture: 0.8%
Germany: 1/95 A* (Sub-Saharan African), 2 BCD (African or Asian). Total admixture: 3.2%

[1] María Brion et al., A collaborative study of the EDNAP group regarding Y-chromosome binary polymorphism analysis, Forensic Science International, In Press, Corrected Proof, Available online 21 August 2004

mtDNA and the western Bantu expansion

Human Genetics (Online First)
DOI: 10.1007/s00439-004-1164-0

Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola

Stéphanie Plaza et al.

Abstract

Africa is the homeland of humankind and it is known to harbour the highest levels of human genetic diversity. However, many continental regions, especially in the sub-Saharan side, still remain largely uncharacterized (i.e. southwest and central Africa). Here, we examine the mitochondrial DNA (mtDNA) variation in a sample from Angola. The two mtDNA hypervariable segments as well as the 9-bp tandem repeat on the COII/tRNAlys intergenic region have allowed us to allocate mtDNAs to common African haplogroups. Angola lies in the southern end of the putative western branch of the Bantu expansion, where it met the local Khoisan populations. Angolan mtDNA lineages show basically a Bantu substrate with no traces of Khoisan lineages. Roughly, more than half of the southwestern mtDNA pool can be assigned to west Africa, ~25% to central Africa and a significant 16% to east Africa, which points to the western gene pool having contributed most to the mtDNA lineages in Angola. We have also detected signals of extensive gene flow from southeast Africa. Our results suggest that eastern and western Bantu expansion routes were not independent from each other, and were connected south of the rainforest and along the southern African savannah. In agreement with historical documentation, the analysis also showed that the Angola mtDNA genetic pool shows affinities with the African lineages from Brazil, the main American destination of the slaves from Angola, although not all lineages in Brazil can be accounted for by the Angolan mtDNA pool.

Link

Lithuanian Y-chromosomes and mtDNA

Annals of Human Genetics (OnlineEarly)
doi:10.1046/j.1529-8817.2003.00119.x

Y Chromosome and Mitochondrial DNA Variation in Lithuanians

D. Kasperaviit et al.

Summary

The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo-European) and Finno-Ugric speaking populations of Northern and Eastern Europe. Y-chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo-European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.

Link

Origin of Canary Islanders

Annals of Human Genetics (OnlineEarly)
doi:10.1046/j.1529-8817.2003.00125.x

A Tale of Aborigines, Conquerors and Slaves: Alu Insertion Polymorphisms and the Peopling of Canary Islands

N. Maca-Meyer et al.

Summary

Classical, mitochondrial DNA (mtDNA) and Y chromosome markers have been used to examine the genetic admixture in present day inhabitants of the Canary Islands. In this study, we report the analysis of ten autosomal Alu insertion polymorphisms in 364 samples from the seven main islands of the Archipelago, and their comparison to continental samples. The detection of population-specific alleles from the Iberian Peninsula and Northwest Africa, as well as their affinities on the basis of genetic distances and principal component analysis, support a clear link between these populations. Coincident with previous results, the Canarian gene pool can be distinguished as being halfway between those of its putative parents, although with a major Iberian contribution (62-78%). Both the substantial Northwest African contribution (23-38%), and the minor sub-Saharan African input (3%), suggest that the genetic legacy from the aborigines and slaves still persists in the Canary Islanders.

Link