The Emerging Tree of West Eurasian mtDNAs: A Synthesis of Control-Region Sequences and RFLPs
Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged ~50,000 years ago.
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The origins of southern and western Eurasian populations: an mtDNA study
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THE TRANS-CAUCASUS AND THE EXPANSION OF THE CAUCASOID-SPECIFIC HUMAN MITOCHONDRIAL DNA
The topology of the network of western Eurasian mitochondrial DNA (mtDNA) lineage clusters in the context of their expansion and spread in this geographic area is analysed. Special attention is devoted to the inner nods of the reconstructed median network tree, ancestral to mtDNA lineage clusters H and V, to the Caucasus and Trans-Caucasus area populations and to the problem of timing of the expansion of the Caucasoid-specific mtDNA lineage clusters in western Europe versus in the Trans-Caucasus. It appears on several examples that typical for Western Europe mtDNA lineage clusters exhibit significantly earlier expansion in the Trans-Caucasus area. Furthermore, the lineage cluster, radiating from the pre-HV node, is significantly more frequent and divergent in the Trans-Caucasus populations than it is in Europe. Meanwhile, a comparison of the Central Asian and the Trans-Caucasus area populations shows that the former have a significant share of eastern Asian-specific mtDNA lineages, which are almost absent in the latter. Finally, a picture starts to emerge, revealing an ancient Indian—Trans-Caucasian—European continuum of a significant proportion of human maternal lineage clusters, dating back to the period between the Upper and Lower Pleniglacials.
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A comprehensive analysis of Arabs and Berbers maternal lineages in Morocco
Morocco is situated on the Northwestern Africa. As far as the genetics of the present-day Moroccan populations is concerned, one may say that both its geography and history point to a possible influence from the Iberian Peninsula, northwestern Africa, the near East and sub-Saharan Africa. The two major ethnics populations of Morocco are the Arabs and the Berbers. Fossil evidences suggests that anatomically modern humans inhabited this area as early as 40,000 years ago. Around 22 000 years ago, the Iberomaurusians, Cro-Magnon hunters type, started to succeed the previous populations. The Berbers have been regarded as aboriginal North Africans (Brett and Fentress, 1996) descendents of the Iberomaurusians people. On the other hand, during the historical time, North Africa had been under several waves of east-west invasions. Several empires spread their kingdom as far as Morocco. However, it is not at all obvious how significant was their contributions to the local gene pool, especially as far as maternally inherited mtDNA is concerned. It is often speculated that one of the major events that might have had a significant impact on the Moroccan population could be the Islamic expansion some 1300 years ago, bringing, inter alia, Araics language to the area and introducing the current division of people to Berbers and Arabs. Yet again, there has been no serious study addressing genetics of this scenario. Here, we report the results of our analysis of the mtDNA pool in the Moroccan population: in Arabs and in Berbers. Although maternal lineages do not tell the full story, they can speak about important part of it- and in a rather clear way.
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Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages
Background:
Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.
Results:
The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub- lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports.
Conclusions:
This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non-existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.
PDF file
Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged ~50,000 years ago.
PDF file
The origins of southern and western Eurasian populations: an mtDNA study
PDF file
THE TRANS-CAUCASUS AND THE EXPANSION OF THE CAUCASOID-SPECIFIC HUMAN MITOCHONDRIAL DNA
The topology of the network of western Eurasian mitochondrial DNA (mtDNA) lineage clusters in the context of their expansion and spread in this geographic area is analysed. Special attention is devoted to the inner nods of the reconstructed median network tree, ancestral to mtDNA lineage clusters H and V, to the Caucasus and Trans-Caucasus area populations and to the problem of timing of the expansion of the Caucasoid-specific mtDNA lineage clusters in western Europe versus in the Trans-Caucasus. It appears on several examples that typical for Western Europe mtDNA lineage clusters exhibit significantly earlier expansion in the Trans-Caucasus area. Furthermore, the lineage cluster, radiating from the pre-HV node, is significantly more frequent and divergent in the Trans-Caucasus populations than it is in Europe. Meanwhile, a comparison of the Central Asian and the Trans-Caucasus area populations shows that the former have a significant share of eastern Asian-specific mtDNA lineages, which are almost absent in the latter. Finally, a picture starts to emerge, revealing an ancient Indian—Trans-Caucasian—European continuum of a significant proportion of human maternal lineage clusters, dating back to the period between the Upper and Lower Pleniglacials.
PDF file
A comprehensive analysis of Arabs and Berbers maternal lineages in Morocco
Morocco is situated on the Northwestern Africa. As far as the genetics of the present-day Moroccan populations is concerned, one may say that both its geography and history point to a possible influence from the Iberian Peninsula, northwestern Africa, the near East and sub-Saharan Africa. The two major ethnics populations of Morocco are the Arabs and the Berbers. Fossil evidences suggests that anatomically modern humans inhabited this area as early as 40,000 years ago. Around 22 000 years ago, the Iberomaurusians, Cro-Magnon hunters type, started to succeed the previous populations. The Berbers have been regarded as aboriginal North Africans (Brett and Fentress, 1996) descendents of the Iberomaurusians people. On the other hand, during the historical time, North Africa had been under several waves of east-west invasions. Several empires spread their kingdom as far as Morocco. However, it is not at all obvious how significant was their contributions to the local gene pool, especially as far as maternally inherited mtDNA is concerned. It is often speculated that one of the major events that might have had a significant impact on the Moroccan population could be the Islamic expansion some 1300 years ago, bringing, inter alia, Araics language to the area and introducing the current division of people to Berbers and Arabs. Yet again, there has been no serious study addressing genetics of this scenario. Here, we report the results of our analysis of the mtDNA pool in the Moroccan population: in Arabs and in Berbers. Although maternal lineages do not tell the full story, they can speak about important part of it- and in a rather clear way.
PDF file
Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages
Background:
Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.
Results:
The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub- lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports.
Conclusions:
This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non-existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.
PDF file
