1. Tracing European Founder Lineages in the Near Eastern mtDNA Pool
Using mtDNA, we examine the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2,804, and 208 samples, respectively. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.
[The American Journal of Human Genetics, Volume 67, Issue 5, 1251-1276, 1 November 2000
doi:10.1016/S0002-9297(07)62954-1]

2.Classification of European mtDNAs From an Analysis of Three European Populations - PDF document
A study of mtDNA sequence variations as examined in Finns, Swedes and Tuscany. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations.
[Genetics. 1996 Dec;144(4):1835-50.
A. Torroni, K. Huoponen, P. Francalacci, M. Petrozzi, L. Morelli, R. Scozzari, D. Obinu, M. L. Savontaus, and D. C. Wallace]

3. Phylogeography of mitochondrial DNA in western Europe
Recently, phylogenetic analyses of DNA sequences that incorporate geographical information have provided a high-resolution tool for the investigation of prehistoric demographic events, such as founder effects and population expansions. These events can be dated using a molecular clock when the mutation rate and founder haplotypes are known. We have previously applied such methods to sequence data from the mitochondrial DNA control region, to suggest that most extant mitochondrial sequences in western Europe have a local ancestry in the Early Upper Palaeolithic, with a smaller proportion arriving from the Near East in the Neolithic. Here, we describe a cladistic notation for mitochondrial variation and expand upon our earlier analysis to present a more detailed portrait of the European mitochondrial record.
[Blackwell Synergy, Annals of Human Genetics, Volume 62 Issue 3 Page 241-260, May 1998]

4. Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia (PDF)
To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen for complete sequencing from a collection of 1800 control-region sequences sampled across India. We identified five new autochthonous haplogroups (R7, R8, R30, R31, and N5) and fully characterized the autochthonous haplogroups (R5, R6, N1d, U2a, U2b, and U2c) that were previously described only by first hypervariable segment (HVS-I) sequencing and coding-region restriction-fragment–length polymorphism analysis. Our findings demonstrate that the Indian mtDNA pool, even when restricted to macrohaplogroup N, harbors at least as many deepest-branching lineages as the western Eurasian mtDNA pool. Moreover, the distribution of the earliest branches within haplogroups M, N, and R across Eurasia and Oceania provides additional evidence for a three-founder-mtDNA scenario and a single migration route out of Africa.
[The American Society of Human Genetics; Am J Hum Genet. 2004 December; 75(6): 966–978.
Published online 2004 October 1.]

5. mtDNA and the Islands of the North Atlantic: Estimating the Proportions of Norse and Gaelic Ancestry
A total of 1,664 new mtDNA control-region sequences were analyzed in order to estimate Gaelic and Scandinavian matrilineal ancestry in the populations of Iceland, Orkney, the Western Isles, and the Isle of Skye and to investigate other aspects of their genetic history. A relative excess of private lineages in the Icelanders is indicative of isolation, whereas the scarcity of private lineages in Scottish island populations may be explained by recent gene flow and population decline. Differences in the frequencies of lineage clusters are observed between the Scandinavian and the Gaelic source mtDNA pools, and, on a continent-wide basis, such differences between populations seem to be associated with geography.
[The American Society of Human Genetics; Am J Hum Genet. 2001 March; 68(3): 723–737. Published online 2001 February 1.]

6. mtDNA and the Origin of the Icelanders: Deciphering Signals of Recent Population History
Previous attempts to investigate the origin of the Icelanders have provided estimates of ancestry ranging from a 98% British Isles contribution to an 86% Scandinavian contribution. We generated mitochondrial sequence data for 401 Icelandic individuals and compared these data with 12,500 other European sequences from published sources, to determine the probable origins of women who contributed to Iceland’s settlement. Although the mean number of base-pair differences is high in the Icelandic sequences and they are widely distributed in the overall European mtDNA phylogeny, we find a smaller number of distinct mitochondrial lineages, compared with most other European populations. The frequencies of a number of mtDNA lineages in the Icelanders deviate noticeably from those in neighboring populations, suggesting that founder effects and genetic drift may have had a considerable influence on the Icelandic gene pool. This is in accordance with available demographic evidence about Icelandic population history. A comparison with published mtDNA lineages from European populations indicates that, whereas most founding females probably originated from Scandinavia and the British Isles, lesser contributions from other populations may also have taken place.
[PubMed.gov; The American Society of Human Genetics; Am J Hum Genet. 2000 Mar;66(3):999-1016.]

7. Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area
The phylogeography of Y-chromosome haplogroups E (Hg E) and J (Hg J) was investigated in >2,400 subjects from 29 populations, mainly from Europe and the Mediterranean area but also from Africa and Asia. The observed 501 Hg E and 445 Hg J samples were subtyped using 36 binary markers and eight microsatellite loci. Spatial patterns reveal that (1) the two sister clades, J-M267 and J-M172, are distributed differentially within the Near East, North Africa, and Europe; (2) J-M267 was spread by two temporally distinct migratory episodes, the most recent one probably associated with the diffusion of Arab people; (3) E-M81 is typical of Berbers, and its presence in Iberia and Sicily is due to recent gene flow from North Africa; (4) J-M172(xM12) distribution is consistent with a Levantine/Anatolian dispersal route to southeastern Europe and may reflect the spread of Anatolian farmers; and (5) E-M78 (for which microsatellite data suggest an eastern African origin) and, to a lesser extent, J-M12(M102) lineages would trace the subsequent diffusion of people from the southern Balkans to the west. A 7%–22% contribution of Y chromosomes from Greece to southern Italy was estimated by admixture analysis.
[The American Society of Human Genetics; Am J Hum Genet. 2004 May; 74(5): 1023–1034.
Published online 2004 April 6.]

8. Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups
The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small umber of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups.
[Pubmed.gov; The American Society of Human Genetics; Am J Hum Genet. 2002 May;70(5):1152-71. Epub 2002 Apr 5.]

9. 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 or 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.
[The American Society of Human Genetics; Am J Hum Genet. 1999 January; 64(1): 232–249.]

10. Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears
Approximately 10 miles separate the Horn of Africa from the Arabian Peninsula at Bab-el-Mandeb (the Gate of Tears). Both historic and archaeological evidence indicate tight cultural connections, over millennia, between these two regions. High-resolution phylogenetic analysis of 270 Ethiopian and 115 Yemeni mitochondrial DNAs was performed in a worldwide context, to explore gene flow across the Red and Arabian Seas. Nine distinct subclades, including three newly defined ones, were found to characterize entirely the variation of Ethiopian and Yemeni L3 lineages. Phylogeographic identification of potential founder haplotypes revealed that approximately one-half of haplogroup L0–L5 lineages in Yemenis have close or matching counterparts in southeastern Africans, compared with a minor share in Ethiopians. Newly defined clade L6, the most frequent haplogroup in Yemenis, showed no close matches among 3,000 African samples.
[PubMed.gov; The American Society of Human Genetics; Am J Hum Genet. 2004 November; 75(5): 752–770. Published online 2004 September 27.]

11. Multiple Origins of Ashkenazi Levites: Y Chromosome Evidence for Both Near Eastern and European Ancestries
Previous Y chromosome studies have shown that the Cohanim, a paternally inherited Jewish priestly caste, predominantly share a recent common ancestry irrespective of the geographically defined post-Diaspora community to which they belong, a finding consistent with common Jewish origins in the Near East. In contrast, the Levites, another paternally inherited Jewish caste, display evidence for multiple recent origins, with Ashkenazi Levites having a high frequency of a distinctive, non–Near Eastern haplogroup. Here, we show that the Ashkenazi Levite microsatellite haplotypes within this haplogroup are extremely tightly clustered, with an inferred common ancestor within the past 2,000 years. Comparisons with other Jewish and non-Jewish groups suggest that a founding event, probably involving one or very few European men occurring at a time close to the initial formation and settlement of the Ashkenazi community, is the most likely explanation for the presence of this distinctive haplogroup found today in >50% of Ashkenazi Levites.
[The American Society of Human Genetics; Am J Hum Genet. 2003 October; 73(4): 768–779. Published online 2003 September 17.]

12. Persistent Heteroplasmy of a Mutation in the Human mtDNA Control Region: Hypermutation as an Apparent Consequence of Simple-Repeat Expansion/Contraction
In the genealogical and phylogenetic analyses that are reported here, we obtained evidence for an unusual pattern of mutation/reversion in the human mitochondrial genome. The cumulative results indicate that, when there is a TrC polymorphism at nt 16189 and a CrT substitution at nt 16192, there is an extremely high rate of reversion (hypermutation) at the latter site. The 16189 TrC polymorphism lengthens a (C:G)n simple repeat, which then undergoes expansion and contraction, probably through replication slippage. This proclivity toward expansion/contraction is more pronounced when there is a C residue, rather than a T, at nt 16192. The high TrC reversion frequency at nt 16192 apparently is the result of polymerase misincorporation or slippage during replication, the same mechanism that also causes the expansion/contraction of this simple-repeat sequence. In addition to the first analysis of this mitochondrial hypermutation process, these results also yield mechanistic insights into the expansion/contraction of simple-repeat sequences in mtDNA.
[PubMed.gov; The American Society of Human Genetics; Am J Hum Genet. 2000 May; 66(5): 1589–1598. Published online 2000 April 10.]

13. Human mtDNA Haplogroups Associated with High or Reduced Spermatozoa Motility
Some mtDNA mutations responsible for human diseases have been associated with molecular defects in the OXPHOS system. It was suggested that if sperm dysfunction is the main phenotypic consequence, these mutations could be fixed as stable mtDNA variants, because mtDNA is maternally inherited. To test this possibility, we have performed an extensive analysis of the distribution of mtDNA haplogroups in white men having fertility problems. We have found that asthenozoospermia, but not oligozoospermia, is associated with mtDNA haplogroups in whites. Thus, haplogroups H and T are significantly more abundant in nonasthenozoospermic and asthenozoospermic populations, respectively, and show significant differences in their OXPHOS performance.
[PubMed.gov; The American Society of Human Genetics; Am J Hum Genet. 2000 Sep;67(3):682-96. Epub 2000 Aug 9.Click here to read]