Instantaneous vs. continuous admixture dynamics (Jin et al. 2012)

A new paper in AJHG discusses the distribution of chromosomal segments of distinct ancestry (CSDAs) under three different models of admixture dynamics (left). In the hybrid isolation (HI) model, admixture is instantaneous and results in a hybrid population that evolves with drift and recombination only. In the gradual admixture (GA) model, the hybrid population continues to receive admixture from the unadmixed parental populations. Finally, in the continuous gene flow model (CGF), one of the populations becomes admixed while the other continues to exist unadmixed and to contribute to the admixed one.

In practical terms, the HI model results in the diminution of CSDA length due to recombination over time, and at "present" there is a paucity of long CSDAs. In the GA model there are more long CSDAs for both populations, while in the CGF model there is an asymmetry in the CSDAs donated by Pop1 and Pop2, with those from the "donor" population being longer (because fresh "long" segments are added in every generation).

The conclusions of the paper regarding some particular admixture cases are also interesting. For African Americans:

Although the actual population admixture of African Americans might be more complex than what our simulation suggested, the CGF1 model setting at 14 generations was found to be reasonably  epresentative, capturing the main pattern of the population admixture dynamics.

The CGF1 model has Africans as recipients and Europeans as donors. This makes sense, since African Americans are descended from slaves who were transported to the New World, with the slave trade ending centuries ago, hence there was mostly no replenishment of the AA population with fresh African-origin individuals. On the other hand, European Americans, both due to social dynamics and their numerical majority continued to exist as a distinct population that contributed to the AA population.

I should mention that according to HAPMIX, the admixture time was 7 generations, with is close to the 6 +/- 1 generations inferred by rolloff analysis by Moorjani et al. So, in this case this admixture time appears to be an "average" of a continuing process of admixture that began 14 generations ago.

Onto Mexicans:

In short, the GA model at 24 generations fit the empirical data best among all these simulated scenarios, as indicated by the distribution of EMDs.

Again, this makes sense, because in Mexico there continued to exist unadmixed populations of Europeans and Amerindians that contributed to the Mestizo population of the country.

On the African admixture in Mozabites:

Comparing the empirical distribution of CSDAs with that simulated, we found that the Mozabite admixture process essentially fit the HI model with 100 generations since admixture. There was an almost complete absence of recent gene flow from European populations to the Mozabite gene pool (Figure 6A). For the Sub-Saharan African ancestral component, there were more long CSDAs at the tail of empirical distribution than those in the HI model, which confirmed that recent gene flow from African populations had contributed to the Mozabite gene pool (Figure 6B). 

Again, this makes sense: Berber groups were not replenished from other Caucasoid sources, so their original admixture with native Africans resulted in a blend that persisted largely unaffected by "Europeans", but did find occasion of admixture with Sub-Saharans. Hence, the asymmetry in the presence of long "European" vs. "Sub-Saharan" segments.

A similar pattern was evident for Bedouin, Palestinians, and Druze:

Analyses of European ancestral component in Bedouin and Palestinian populations also showed that the empirical distributions essentially fit the HI model for both populations (Figures 6C and 6E). Although the empirical CSDA distribution of Sub-Saharan African ancestral component also fit the HI model  best, both distributions showed a long tail at the right compared with those under the HI model, indicating that recent gene flow from Sub-Saharan Africans also contributed to the two admixed populations (Figures 6D and 6F). ... For Druze, their European component of ancestry fit the HI model very well. However, their African ancestral component contained much shorter CSDAs than those of simulated (Figure S14), which might indicate that previous studies had underestimated the admixture time of Druze. In addition, populations receiving recent gene flow from their parental populations showed higher variation of individual ancestral proportions than those who did not (Figure S13).

The Druze have well-known Egyptian connections, and they may have largely avoided Sub-Saharan African admixture during the Islamic period, principally because of its avoidance of proselytism. Hence, their African admixture may stem from Egyptian adherents who were themselves a product of much earlier Caucasoid/Sub-Saharan admixture during the course of pre-Islamic Egypt.


The American Journal of Human Genetics, 25 October 2012 doi:10.1016/j.ajhg.2012.09.008

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-Wide Distribution of Ancestral Chromosomal Segments

Wenfei Jin et al

Abstract

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations.

Link

Back to (North) Africa (Henn et al. 2012)

A great new paper has just appeared, presenting new data, new conclusions about African prehistory, and new methodologies. I'll have to read it before I comment on it, but since it's open access you can read it for yourselves.

UPDATE I:


The new data are publicly available here, with information about samples here.
The new PCADMIX software is also available.

PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397 

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations 

Brenna Henn et al.

 North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

Link

Activity patterns of Garamantes

A different paper on cranial nonmetric traits from the same team and on the same population (Garamantes).

From the current paper:

The study of the activity patterns of the Garamantes, a population that flourished at Central Sahara approximately 3,000 years ago, offers some interesting insights on the levels of stress imposed by a sedentary life in a hyper-arid environment. The population showed low bilateral asymmetry, possibly due to limited task specialization. Moreover, the Garamantes exhibited low sexual dimorphism in the upper limbs, which is consistent to the pattern found in agricultural populations and implies that the engagement of males in warfare  and construction works was not particularly intense. In the lower limbs, males were stronger in TA possibly as a result of their involvement in herding and mobility on the uneven terrain of Fezzan. Finally, the Garamantes did not appear systematically more robust than other North African populations occupying less harsh environments, indicating that life in the Sahara did not require particularly strenuous daily activities.

AJPA DOI: 10.1002/ajpa.21597

Activity patterns in the Sahara Desert: An interpretation based on cross-sectional geometric properties

Efthymia Nikita et al.

The Garamantian civilization flourished in modern Fezzan, Libya, between 900 BC and 500 AD, during which the aridification of the Sahara was well established. Study of the archaeological remains suggests a population successful at coping with a harsh environment of high and fluctuating temperatures and reduced water and food resources. This study explores the activity patterns of the Garamantes by means of cross-sectional geometric properties. Long bone diaphyseal shape and rigidity are compared between the Garamantes and populations from Egypt and Sudan, namely from the sites of Kerma, el-Badari, and Jebel Moya, to determine whether the Garamantian daily activities were more strenuous than those of other North African populations. Moreover, sexual dimorphism and bilateral asymmetry are assessed at an intra- and inter-population level. The inter-population comparisons showed the Garamantes not to be more robust than the comparative populations, suggesting that the daily Garamantian activities necessary for survival in the Sahara Desert did not generally impose greater loads than those of other North African populations. Sexual dimorphism and bilateral asymmetry in almost all geometric properties of the long limbs were comparatively low among the Garamantes. Only the lower limbs were significantly stronger among males than females, possibly due to higher levels of mobility associated with herding. The lack of systematic bilateral asymmetry in cross-sectional geometric properties may relate to the involvement of the population in bilaterally intensive activities or the lack of regular repetition of unilateral activities.

Link

Cranial nonmetric traits of Garamantes

Am J Phys Anthropol DOI: 10.1002/ajpa.21645


Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

Efthymia Nikita et al.

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ∼3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D2 distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D2 distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.

Link

Y chromosomes of Andalusians from Huelva

Annals of Human Biology

The Andalusian population from Huelva reveals a high diversification of Y-DNA paternal lineages from haplogroup E: Identifying human male movements within the Mediterranean space.

B. Ambrosio et al.

Abstract

Gene flow among human populations is generally interpreted in terms of complex patterns, with the observed gene frequencies being the consequence of the entire genetic and demographic histories of the population. Aims: This study performs a high-resolution analysis of the Y-chromosome haplogroup E in Western Andalusians (Huelva province). The genetic information presented here provides new insights into migration processes that took place throughout the Mediterranean space and tries to evaluate its impact on the current genetic composition of the most southwestern population of Spain. Subjects and methods: 167 unrelated males were previously typed for the presence/absence of the Y-chromosome Alu polymorphism (YAP). The group of YAP (+) Andalusians was genotyped for 16 Y-SNPs and also characterized for 16 Y-STR loci. Results: The distribution of E-M81 haplogroup, a Berber marker, was found at a frequency of 3% in our sample. The distribution of M81 frequencies in Iberia seems to be not concordant with the regions where Islamic rule was most intense and long-lasting. The study also showed that most of M78 derived allele (6.6%) led to the V13* subhaplogroup. We also found the most basal and rare paragroup M78* and others with V12 and V65 mutations. The lineage defined by M34 mutation, which is quite frequent in Jews, was detected as well. Conclusions: The haplogroup E among Western Andalusians revealed a complex admixture of genetic markers from the Mediterranean space, with interesting signatures of populations from the Middle East and the Balkan Peninsula and a surprisingly low influence by Berber populations compared to other areas of the Iberian Peninsula.

Link

mtDNA of Libyan Tuaregs

The sample consisted of haplogroups H1, V, M1, and an assortment of African L subclades.

From the paper:

Of note is that the other Tuareg sample described in the literature (Watson et al., 1996) (Western Tuaregs) did not show a close genetic relationship with the Libyan Tuaregs, implying a genetic heterogeneity of the Tuaregs. This difference appears to be primarily caused by the low frequency (8%) of the European component in the Western Tuaregs, characteristic of northern African populations. After the removal of the H and V haplotypes, the Libyan Tuaregs showed a strong affiliation with the Eastern populations, while theWestern Tuaregs associated more with the Central and Western African populations (Fig. 2).

In other words, the Libyan Tuaregs are primarily "European"+"Eastern African" (or Saharan) in affiliation, while the Western Tuaregs from Nigeria, Niger, and Mali have a predominantly West African maternal heritage.

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00526.x

First Genetic Insight into Libyan Tuaregs: A Maternal Perspective

Claudio Ottoni et al.

Abstract

The Tuaregs are a semi-nomadic pastoralist people of northwest Africa. Their origins are still a matter of debate due to the scarcity of genetic and historical data. Here we report the first data on the mitochondrial DNA (mtDNA) genetic characterization of a Tuareg sample from Fezzan (Libyan Sahara). A total of 129 individuals from two villages in the Acacus region were genetically analysed. Both the hypervariable regions and the coding region of mtDNA were investigated. Phylogeographic investigation was carried out in order to reconstruct human migratory shifts in central Sahara, and to shed light on the origin of the Libyan Tuaregs. Our results clearly show low genetic diversity in the sample, possibly due to genetic drift and founder effect associated with the separation of Libyan Tuaregs from an ancestral population. Furthermore, the maternal genetic pool of the Libyan Tuaregs is characterized by a major "European" component shared with the Berbers that could be traced to the Iberian Peninsula, as well as a minor 'south Saharan' contribution possibly linked to both Eastern African and Near Eastern populations.

Link

mtDNA of Berbers from Morocco and Egypt

Annals of Human Genetics doi: 10.1111/j.1469-1809.2008.00493.x

The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

C. Coudray et al.

Abstract

The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.

Link

Reproductive isolates in Jerba Island

Am J Hum Biol. 2005 Dec 25;18(1):149-153 [Epub ahead of print]

Islands Inside an Island: Reproductive Isolates on Jerba Island.

Loueslati BY, Cherni L, Khodjet-Elkhil H, Ennafaa H, Pereira L, Amorim A, Ben Ayed F, Ben Ammar Elgaaied A.

Jerba Island, located in South Eastern Tunisia, is inhabited by four ethnic groups: Berbers, Arabs, sub-Saharans, and Jews. All live in distinct areas, although the Arabs are also distributed all over the island. The first Arab settlement was founded in the 7th century A.D., so co-existence with Berbers has lasted for more than a millennium. Religious and cultural differences have represented an obstacle to the intermixing of these groups, and among both Arabs and Berbers marriages usually occur between members from the same extended family. Using new mtDNA data and previously described Y-chromosome STR-defined haplotypes, we tested whether this reported inbreeding would be reflected in the differentiation between Berber and Arab communities. Concerning mtDNA, the Berber group presented a greater Eurasian contribution (87%), and, surprisingly, no U6 haplotypes were found; in contrast, the Arabs showed a larger contribution of sub-Saharan lineages (24%) and the U6 haplogroup amounted to 10%. Another source of evidence for the reproductive isolation of the two groups was revealed through the analysis of haplotype matching (both mtDNA and Y-chromosome), showing that matching probabilities between them is of the same order of magnitude of that observed when contrasting samples from different European countries.

Link

Lactase persistence in Africans and non-Africans

I had also posted before about lactose tolerance in Berbers. Interestingly:

While the current distribution of lactase persistence in Eurasia and the African Fulbe seems to be due to the dispersion of a single mutation, it is still unclear what is the significance of the recent finding that –13910*T allele is absent from most African populations in which high frequencies of lactase persistence have been previously found with physiological tests (Mulcare et al. 2004).

Human Genetics (online first)

Microsatellite variation and evolution of human lactase persistence

Margarida Coelho et al.

Abstract The levels of haplotype diversity within the lineages defined by two single-nucleotide polymorphisms (SNPs) (–13910 C/T and –22018 G/A) associated with human lactase persistence were assessed with four fast-evolving microsatellite loci in 794 chromosomes from Portugal, Italy, Fulbe from Cameroon, São Tomé and Mozambique. Age estimates based on the intraallelic microsatellite variation indicate that the –13910*T allele, which is more tightly associated with lactase persistence, originated in Eurasia before the Neolithic and after the emergence of modern humans outside Africa. We detected significant departures from neutrality for the –13910*T variant in geographically and evolutionary distant populations from southern Europe (Portuguese and Italians) and Africa (Fulbe) by using a neutrality test based on the congruence between the frequency of the allele and the levels of intraallelic variability measured by the number of mutations in adjacent microsatellites. This result supports the role of selection in the evolution of lactase persistence, ruling out possible confounding effects from recombination suppression and population history. Reevaluation of the available evidence on variation of the –13910 and –22018 loci indicates that lactase persistence probably originated from different mutations in Europe and most of Africa, even if 13910*T is not the causal allele, suggesting that selective pressure could have promoted the convergent evolution of the trait. Our study shows that a limited number of microsatellite loci may provide sufficient resolution to reconstruct key aspects of the evolutionary history of lactase persistence, providing an alternative to approaches based on large numbers of SNPs.

Link

Y-chromosome Lineages from Portugal, Madeira and Açores

A very interesting new paper on Portuguese Y-chromosomes. Three important conclusions are derived from the study of Sub-Saharan African, E3b, and J1 lineages in Portugal. The Sub-Saharan component seems to be small (0.7%) unlike the corresponding mtDNA component. The E3b lineages are highly heterogeneous, and include various sub-types, including the Aegean E-M78 cluster α as well as North African E3b2 and Middle Eastern E3b3. Interestingly, the North African component seems to be primarily of earlier Berber rather than historical Moorish origin:

North African component at least for mtDNA, is mainly concentrated in the North of Portugal. The mtDNA and Y data indicate that the Berber presence in that region dates prior to the Moorish expansion in 711 AD. Our Y chromosome results are also consistent with a continuous and regular assimilation of Berbers in North of Portugal. This argues against previous interpretations of Moorish mediated contributions, based on Y chromosome data (Bosch et al. 2001; Pereira et al. 2000b; Cruciani et al. 2004) and provides an alternative view of an earlier Berber presence in the North of Portugal.

Finally, the J lineages in Portugal are mainly in the J2 clade, but there is a substantial presence of the J1 clade as well, which is found in Arabs and Jews and not as often in European populations. The Portuguese J1 chromosomes cluster around the Cohen Modal Haplotype, rather than the known modal haplotypes of the Arabs. Therefore, it seems probable that these were introduced by Sephardic Jews, rather than Arabs.



Annals of Human Genetics (OnlineEarly)

Y-chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

Rita Gonçalves et al.

Summary

A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78-83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub-populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.

Link

Lactose tolerance gene supports a Eurasian origin of Berber populations

A new study lends further support in the Eurasian origin of the Berbers. This further explains their Caucasoid racial character and argues against some theories of Afrocentrist scholars that Berbers are simply adapted supra-Saharan Africans. An excerpt:

The data presented here are consistent with a scenario in which proto-Berber-speaking ovicaprid pastoralists introduced the –13910T allele, and thereby lactose tolerance, into North Africa. This scenario implies a genetic input from migrating pastoralists from the Middle East and suggests that contemporary Berber populations share a Middle Eastern dairying origin with other Eurasian populations.

See also A Predominantly Neolithic Origin for Y-Chromosomal DNA Variation in North Africa and Lactase Persistence in Africans and Back-Migration from Eurasia.

Human Genetics (Online Early)

Genetic evidence in support of a shared Eurasian-North African dairying origin

Sean Myles

Abstract The process by which pastoralism and agriculture spread from the Fertile Crescent over the past 10,000 years has been the subject of intense investigation by geneticists, linguists and archaeologists. However, no consensus has been reached as to whether this Neolithic transition is best characterized by a demic diffusion (with a significant genetic input from migrating farmers) or a cultural diffusion (without substantial migration of farmers). Milk consumption and thus lactose tolerance are assumed to have spread with pastoralism and we propose that by looking at the relevant mutations in and around the lactase gene in human populations, we can gain insight into the origin(s) and spread of dairying. We genotyped the putatively causal allele for lactose tolerance (–13910T) and constructed haplotypes from several polymorphisms in and around the lactase gene (LCT) in three North African Berber populations and compared our results with previously published data. We found that the frequency of the –13910T allele predicts the frequency of lactose tolerance in several Eurasian and North African Berber populations but not in most sub-Saharan African populations. Our analyses suggest that contemporary Berber populations possess the genetic signature of a past migration of pastoralists from the Middle East and that they share a dairying origin with Europeans and Asians, but not with sub-Saharan Africans.

Link

Saami and Berbers

An excellent new paper on mtDNA haplogroup phylogenetics:

An age of ~60 ky indicates that haplogroup U arose very soon after the "out of Africa" exit. As for U5, its sequence divergence was 8.1 ± 1.8 substitutions, corresponding to 41.4 ± 9.2 ky, a time estimate in full agreement with its proposed proto-European origin (Richards et al. 2000). It is striking that the sequence divergence of U5b1b, the subclade encompassing mtDNAs from the Saami, Yakut, Berbers, and Fulbe, was 1.7 ± 0.5 substitutions, thus corresponding to only 8.6 ± 2.4 ky.

Am. J. Hum. Genet. (Online Early)

Saami and BerbersAn Unexpected Mitochondrial DNA Link

Alessandro Achilli et al.

The sequencing of entire human mitochondrial DNAs belonging to haplogroup U reveals that this clade arose shortly after the "out of Africa" exit and rapidly radiated into numerous regionally distinct subclades. Intriguingly, the Saami of Scandinavia and the Berbers of North Africa were found to share an extremely young branch, aged merely 9,000 years. This unexpected finding not only confirms that the Franco-Cantabrian refuge area of southwestern Europe was the source of late-glacial expansions of hunter-gatherers that repopulated northern Europe after the Last Glacial Maximum but also reveals a direct maternal link between those European hunter-gatherer populations and the Berbers.

Link

Phylogenetic systematics and the existence of human "races"

In phylogenetic systematics one of the necessary preconditions for the recognition of a taxon is its monophyletic status. In other words, members of a taxon must share common descent, and not just relative similarity as in phenetics.

If three groups of organisms A, B, C are such that A and B are more similar to each other than they are to C, then phenetics would consider classifying A and B in one taxon and C in another. By contrast, phylogenetics would try to establish whether A and B share common characters derived from an ancestor that was not an ancestor of C. If it turns out e.g., that B and C have such an ancestor, then B and C should be grouped together, even though B is closer to A than to C.

It has long been established that human beings can be grouped into clusters corresponding to major "continental" populations. This has been achieved using cranial traits, classical polymorphisms, as well as more recently large numbers of microsatellites. Therefore, we are justified in thinking about the existence of human races in the phenetic sense.

However, recent advances in phylogeography, especially based on uniparentally transmitted markers on the Y chromosome and mtDNA have shown that human continental populations which correspond to phenetic races such as "Caucasoids", "Negroids", "Mongoloids", etc. do not correspond to monophyletic groups.

For example, almost 9 out of 10 Ainu trace their paternal lineage to an ancestor who has also fathered approximately 9 out of 10 Moroccans and South African Bantu. That man, who first carried the YAP mutation, lived either in Asia or Africa, and yet his descendants belong to three of the major human races.

Similarly, 9 out of 10 Basques are descended from a man who has also fathered 9 out of 10 Kets from Siberia and 9 out of 10 Maya Indians from America. That man, founder of haplogroup P thus has descendants who belong to two of the major human races (or three, if Amerindians are considered as separate from Asian Mongoloids).

Thus, despite the close proximity between, e.g., Spain and Morocco, and the genetic and phenotypic similarity of their inhabitants, who are considered to belong to the Caucasoid race, it is the case that phylogenetically, Spanish Basques and Mayan Indians share recent ancestry not shared by Moroccan Berbers, and conversely, Moroccan Berbers share recent ancestry with South African Bantu not shared by Basques.

Should we then acknowledge the existence of a "YAP race", or a "P race" on the basis of these observations? Not at all, since by examining other phylogenetically informative systems, e.g., mtDNA, it turns out that Basques and Moroccans are phylogenetically linked to the woman founder of mtDNA haplogroup N, while Ainu and Mayans are linked to a woman founder of mtDNA haplogroup M.

In conclusion, human continental populations form groups of genetic and phenotypic similarity, and these groups can be considered races in the phenetic sense. However, these groups are not monophyletic, hence in the cladistic sense they should not be considered as valid taxa. Since the principle of common descent is generally applied in modern systematics (or at least it should!), I think it's best not to recognize human subspecies.

We may still however speak of human races as clusters of biological similarity, or as ecotypes, if we keep in mind the understanding that the commonly recognized races are not phylogenetically justified.