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DYF387S1 is a major Y-chromosome short tandem repeat (Y-STR) used in forensic genetics that is included in the Y-chromosomal haplotype reference database (YHRD, https://yhrd.org) and it is known as a rapidly mutating Y-STR. DYF387S1 is a multi-locus marker and the two paralogs are within a palindromic sequence which is a region prone to structural chromosome mutation. In this study, we investigated DYF387S1 copy number distribution and separately typed the two DYF387S1 paralogs in a Japanese population. We found different DYF387S1 copy numbers among haplogroups indicating that the differences had been caused by haplogroup-specific ancestral Y-chromosomal mutations, such as deletion, duplication and non-allelic gene conversion. In haplogroup C, it is likely that gene conversion between two DYF387S1 paralogs had occurred in the common ancestral Y-chromosome for paragroup C-M130* and duplication of DYF387S1 had occurred in the common ancestral Y-chromosome for haplogroup C-M131. Meanwhile, in haplogroup D, deletion of the upstream DYF387S1 paralog is likely to have occurred in the common ancestral Y-chromosome for paragroup D-M57* and duplication of the remaining DYF387S1 paralog is indicated in the common ancestral Y-chromosome for haplogroup D-M125. In haplogroup O, structural mutations changing the DYF387S1 copy number had probably not occurred in the common ancestral Y-chromosome. We also suggest that deletion of one DYF387S1 paralog occurred in haplogroup N and that deletion of one DYF387S1 paralog or DYF387S1 gene conversion occurred in haplogroup Q. This is the first study that has separately typed the two DYF387S1 paralogs in a large population dataset. As haplogroups C, D, N, O and Q are also observed in other populations, the ancestral mutation events indicated by this study may have affected DYF387S1 polymorphism in other areas of the world.

Objective Understanding the origins of Aboriginal Australians is crucial in reconstructing the evolution and spread of Homo sapiens as evidence suggests they represent the descendants of the earliest group to leave Africa. This study analyzed a large sample of Y-chromosomes to answer questions relating to the migration routes of their ancestors, the age of Y-haplogroups, date of colonization, as well as the extent of male-specific variation. Methods Knowledge of Y-chromosome variation among Aboriginal Australians is extremely limited. This study examined Y-SNP and Y-STR variation among 657 self-declared Aboriginal males from locations across the continent. 17 Y-STR loci and 47 Y-SNPs spanning the Y-chromosome phylogeny were typed in total. Results The proportion of non-indigenous Y-chromosomes of assumed Eurasian origin was high, at 56%. Y lineages of indigenous Sahul origin belonged to haplogroups C-M130*(xM8,M38,M217,M347) (1%), C-M347 (19%), K-M526*(xM147,P308,P79,P261,P256,M231,M175,M45,P202) (12%), S-P308 (12%), and M-M186 (0.9%). Haplogroups C-M347, K-M526*, and S-P308 are Aboriginal Australian-specific. Dating of C-M347, K-M526*, and S-P308 indicates that all are at least 40,000 years old, confirming their long-term presence in Australia. Haplogroup C-M347 comprised at least three sub-haplogroups: C-DYS390.1del, C-M210, and the unresolved paragroup C-M347*(xDYS390.1del,M210). Conclusions There was some geographic structure to the Y-haplogroup variation, but most haplogroups were present throughout Australia. The age of the Australian-specific Y-haplogroups suggests New Guineans and Aboriginal Australians have been isolated for over 30,000 years, supporting findings based on mitochondrial DNA data. Our data support the hypothesis of more than one route (via New Guinea) for males entering Sahul some 50,000 years ago and give no support for colonization events during the Holocene, from either India or elsewhere. Am J Phys Anthropol 159:367–381, 2016. © 2015 Wiley Periodicals, Inc.

The association between a geographical region and an mtDNA haplogroup(s) has provided the basis for using mtDNA haplogroups to infer an individual's place of origin and genetic ancestry. Although it is well known that ancestry inferences using mtDNA haplogroups and those using genome-wide markers are frequently discrepant, little empirical information exists on the magnitude and scope of such discrepancies between multiple mtDNA haplogroups and worldwide populations. We compared genetic-ancestry inferences made by mtDNA-haplogroup membership to those made by autosomal SNPs in ∼940 samples of the Human Genome Diversity Panel and recently admixed populations from the 1000 Genomes Project. Continental-ancestry proportions often varied widely among individuals sharing the same mtDNA haplogroup. For only half of mtDNA haplogroups did the highest average continental-ancestry proportion match the highest continental-ancestry proportion of a majority of individuals with that haplogroup. Prediction of an individual's mtDNA haplogroup from his or her continental-ancestry proportions was often incorrect. Collectively, these results indicate that for most individuals in the worldwide populations sampled, mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin.

The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic but also in archeological and forensic studies. The genotype of 35 JSNP markers were determined, of which 14 were assigned to appropriate positions on the Y-chromosomal haplogroup tree, together with 5 additional new non-JSNP markers. These markers defined 14 new branches (C3/64562+13, C3/2613-27, D2a1b/006841*, D2a1b/119166-11A, D2a/022456*, D2a/119166-11A, D2a/119167rec/119167-40rec*, D2a/75888-GC, O3a3c/075888-9T/10T*, O3a3c/075888-9T/9T, O3a3/8425+6, O3a3/119166-13A*, O3a3/008002 and O3a4/037852) and 21 new internal markers on the 2008 Y-chromosome haplogroup tree. These results will provide useful information for Y-chromosomal polymorphic studies of East Asian populations, particularly those in and around Japan, in the fields of anthropology, genetics and forensics.

An A-to-G transition at position 16247 in the human mtDNA genome denotes haplogroup B4a1a1a and its sublineages. Informally known as the “Polynesian motif,” this haplogroup has been widely used as a marker in Oceania of genetic affiliation with the Austronesian expansion. The 16247G allele has arisen only once in the human mtDNA phylogeny, about 7,000 thousand years ago, and is nearly fixed in Remote Oceania. We analyzed 536 complete mtDNA genome sequences from the Solomon Islands from haplogroup B4a1a1 and associated subhaplogroups and found multiple independent back mutations from 16247G to 16247A. We also find elevated levels of heteroplasmy at this position in samples with the 16247G allele, suggesting the ongoing occurrence of somatic back-mutations and/or transmission of heteroplasmy. Moreover, the G allele is predicted to introduce a novel stem-loop structure in the DNA sequence that may be structurally unfavorable, thereby accounting for the remarkable number of back-mutations observed at the 16247G allele in this short evolutionary time span. More generally, haplogroup-calling scripts result in inaccurate haplogroup calls involving the back-mutation and need to be supplemented with other types of analyses; this may be true for other mtDNA lineages because no other lineage has been investigated to the same extent (over 500 complete mtDNA sequences).

Y chromosome single nucleotide polymorphisms (Y-SNPs) are indispensable markers for haplogroup determination. Since Y chromosome haplogroups show a high specific geographical distribution, they play a major role in population genetics but can also benefit forensic investigations. Although haplogroup prediction methods based on Y chromosome short tandem repeats (Y-STRs) exist and are frequently used, precaution is required in this regard. In this study we determine the Y chromosome haplogroups of a Nicaraguan population using several Y-SNP multiplex reactions. Y chromosome haplogroups have been predicted before, but our results show that a confirmation with Y-SNP typings is necessary. These results have revealed a 4.8% of error in haplogroup prediction based on Y-STR haplotypes using Athey's Haplogroup Predictor. The Nicaraguan Mestizo population displays a majority of Eurasian lineages, mainly represented by haplogroup R-M207 (46.7%). Other Eurasian lineages have been observed, especially J-P209 (13.3%), followed by I-M170 (3.6%) and G-M201 (1.8%). Haplogroup E-P170 was also observed in 15.2% of the sample, particularly subhaplogroup E1b1b1-M35. Finally, the Native American haplogroup Q-M242 was found in 15.2% of the sample, with Q1a3a-M3 being the most frequent.

We performed a molecular characterization of Korean Y-chromosomal haplogroups using a combination of Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and Y-chromosomal short tandem repeats (Y-STRs). In a test using DNA samples from 706 Korean males, a total of 19 different haplogroups were identified by 26 Y-SNPs including the newly redefined markers (PK4, KL2, and P164) in haplogroup O. When genotyping the SNPs, phylogenetic nonequivalence was found between SNPs M117 and M133, which define haplogroup O3a3c1 (O3a2c1a according to the updated tree of haplogroup O by Yan et al. (European Journal of Human Genetics 19:1013-1015, 2011)), suggesting that the position of the M133 marker should be corrected. We have shown that the haplotypes consisted of DYS392, DYS393, DYS437, DYS438, DYS448, and DYS388 loci, which exhibit a relatively lower mutation rate, can preserve phylogenetic information and hence can be used to roughly distinguish Y-chromosome haplogroups, whereas more rapidly mutating Y-STRs such as DYS449 and DYS458 are useful for differentiating male lineages. However, at the relatively rapidly mutating DYS447, DYS449, DYS458, and DYS464 loci, unusually short alleles and intermediate alleles with common sequence structures are informative for elucidating the substructure within the context of a particular haplogroup. In addition, some deletion mutations in the DYS385 flanking region and the null allele at DYS448 were associated with a single haplogroup background. These high-resolution haplogroup and haplotype data will improve our understanding of regional Y-chromosome variation or recent migration routes and will also help to infer haplogroup background or common ancestry.

Summary To reconstruct the phylogenetic structure of Y-chromosome haplogroup (hg) C in populations of northern Eurasia, we have analyzed the diversity of microsatellite (STR) loci in a total sample of 413 males from 18 ethnic groups of Siberia, Eastern Asia and Eastern Europe. Analysis of SNP markers revealed that all Y-chromosomes studied belong to hg C3 and its subhaplogroups C3c and C3d, although some populations (such as Mongols and Koryaks) demonstrate a relatively high input (more than 30%) of yet unidentified C3 ∗ haplotypes. Median joining network analysis of STR haplotypes demonstrates that Y-chromosome gene pools of populations studied are characterized by the presence of DNA clusters originating from a limited number of frequent founder haplotypes. These are subhaplogroup C3d characteristic for Mongolic-speaking populations, “star cluster” in C3 ∗ paragroup, and a set of DYS19 duplicated C3c Y-chromosomes. All these DNA clusters show relatively recent coalescent times (less than 3000 years), so it is probable that founder effects, including social selection resulting in high male fertility associated with a limited number of paternal lineages, may explain the observed distribution of hg C3 lineages.

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Y-chromosomal haplogroups composition and frequencies were analyzed in Northern and Southern Altaians. In the gene pool of Altaians a total of 18 Y-chromosomal haplogroups were identified, including C3xM77, C3c, DxM15, E, F*, J2, I1a, I1b, K*, N*, N2, N3a, O3, P*, Q*, R1*, R1a1, and R1b3. The structuring nature of the Altaic gene pool is determined by the presence of the Caucasoid and Mongoloid components, along with the ancient genetic substratum, marked by the corresponding Western and Eastern Eurasian haplogroups. Haplogroup R1a1 prevailed in both ethnic groups, accounting for about 53 and 38% of paternal lineages in Southern and Northern Altaians, respectively. This haplogroup is thought to be associated with the eastward expansion of early Indo-Europeans, and marks Caucasoid element in the gene pools of South Siberian populations. Similarly to haplogroup K*, the second frequent haplogroup Q* represents paleo-Asiatic marker, probably associated with the Ket and Samoyedic contributions to the Altaic gene pool. The presence of lineages N2 and N3a can be explained as the contribution of Finno-Ugric tribes, assimilated by ancient Turks. The presence of haplogroups C3xM77, C3c, N*, and O3 reflects the contribution of Central Asian Mongoloid groups. These haplogroups, probably, mark the latest movements of Mongolian migrants from the territory of contemporary Tuva and Mongolia. The data of factor analysis, variance analysis, cluster analysis, and phylogenetic analysis point to substantial genetic differentiation of Northern and Southern Altaians. The differences between Northern and Southern Altaians in the haplogroup composition, as well as in the internal haplotype structure were demonstrated.

We present a simple sufficient condition for triviality of obstruction in the orbifold construction. As an application, we can show the existence of subfactors with principal graph $D_{2n}$ without full use of Ocneanu's paragroup theory., 8pages

Y chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, and are thereby widely used in the fields such as human evolution, anthropology and forensic genetics. The Y haplogroup tree was recently revised with newly suggested Y-SNP markers for designation of several subgroups of haplogroups C2, O2b and O3a, which are predominant in Koreans. Therefore, herein we analyzed these newly suggested Y-SNPs in 545 unrelated Korean males who belong to the haplogroups C2, O2b or O3a, and investigated the reconstructed topology of the Y haplogroup tree. We were able to confirm that markers L1373, Z1338/JST002613-27, Z1300, CTS2657, Z8440 and F845 define the C2 subhaplogroups, C2b, C2e, C2e1, C2e1a, C2e1b and C2e2, respectively, and that markers F3356, L682, F11, F238/F449 and F444 define the O subhaplogroups O2b1, O2b1b, O3a1c1, O3a1c2 and O3a2c1c, respectively. Among six C2 subhaplogroups (C2b, C2e, C2e1*, C2e1a, C2e1b and C2e2), the C2e haplogroup and its subhaplogroups were found to be predominant, and among the four O2b subhaplogroups (O2b*, O2b1*, O2b1a and O2b1b), O2b1b was most frequently observed. Among the O3a subhaplogroups, O3a2c1 was predominant and it was further divided into the subhaplogroups O3a2c1a and O3a2c1c with a newly suggested marker. However, the JST002613-27 marker, which had been known to define the haplogroup C2f, was found to be an ancestral marker of the C2e haplogroup, as is the Z1338 marker. Also, the M312 marker for the O2b1 haplogroup designation was replaced by F3356, because all of the O2b1 haplotypes showed a nucleotide change at F3356, but not at M312. In addition, the F238 marker was always observed to be phylogenetically equivalent to F449, while both of the markers were assigned to the O3a1c2 haplogroup. The confirmed phylogenetic tree of this study with the newly suggested Y-SNPs could be valuable for anthropological and forensic investigations of East Asians including Koreans.

The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across Eurasia. Here we genotype 13 new highly informative single-nucleotide polymorphisms in a worldwide sample of 4413 males that carry the derived allele at M526, and reconstruct an NRY haplogroup tree with significantly higher resolution for the major clade within haplogroup K, K-M526. Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a–d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R. Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.

This paper addresses the problem of how to directly read off the 'fusion coefficients' (for the tensor-products of bimodules arising in the 'tower of the basic construction) for a subfactor, from the data of the associated paragroup. The solution to this problem is closely related to a reformulation, which is obtained here, of the flatness condition to be satisfied by the connection on a paragroup; our reformulation is best described by the phrase '1 ∗ flatness', in contrast with Ocneanu's initial formulation as '4 ∗ flatness' and Kawahigashi's subsequent reformulation as '2 ∗ flatness'.

An association between mitochondrial DNA (mtDNA) mutations 11778G>A and 14484T>C and mtDNA haplogroup J suggests that this haplogroup harbors substitutions capable of modifying the phenotype of Leber's disease. Our knowledge of the compilation of substitutions in haplogroup J is based on only a small number of complete mtDNA sequences, however. We constructed phylogenetic networks for mtDNA haplogroup TJ that were based on the sequence of the complete coding region and the hypervariable segment I, respectively, in 28 Finnish samples. The networks revealed a subdivision of the haplogroup into subclusters T1, T2, J1, and J2, while comparison of the two networks suggested nine fast evolving nucleotide sites in the hypervariable segment I. Genotypes of patients harboring 11778G>A or 14484T>C were obtained from the literature and were then placed in the network. Only four substitutions were found to be common to the patients, but none of these was unique to haplogroup J. If increased penetrance of the 11778G>A and 14484T>C mutations in patients belonging to haplogroup J is assumed, combinations of ancient substitutions must be implicated.

As a first step we define an extremality condition for paragroups, then we prove that any given extremal paragroup is equivalent to a Popa system constructed with the string algebras associated with the starting paragroup. As a corollary, we get that any extremal paragroup can be thought of as the paragroup coming from a (generally non-hyperfinite) extremal inclusion of II1 factors. Then we define a free composition for paragroups, using as a model the definition by V. Jones and D. Bisch of free composition of subfactors; and we prove that for any two given paragroups P1 and P2 there always exists a third paragroup P which realizes the free composition of P1 and P2 .

summary The mitochondrial haplogroup T, characterized by the nucleotide motif 16126C‐16294T in the hypervariable segment I (HVS I), is one of the most frequent among Europeans. It has been shown that this haplogroup includes the only well-resolved subgroup, T1, but that other HVS I sequences cannot be dierentiated into subgroups due to possible homoplasies at nucleotide positions 16292, 16296 and 16304, leading to the reticulations in the topology of phylogenetic networks. To study the problem of molecular instability at these positions, we have performed an analysis of 159 previously published West Eurasian HVS I sequences belonging to haplogroup T, together with 12 new HVS I sequences of Eastern Slavs. These 12 sequences represent 16‐9% of a total of 71 samples analysed and identified as haplogroup T mtDNAs by RFLP analysis in this study. A search for rare point mutations associated with dierent combinations of nucleotides 16292T, 16296T and 16304C within the haplogroup T sequences, and specific to certain populations or a group of closely related-bydescent populations, was performed. This analysis revealed 11 marker mutations, each of which was characteristic for a certain group of linguistically or geographically close individuals ‐ the Adygei, Germans, Kazakhs and linguistic isolates of the Eastern Italian Alps. The occurrence of these rare population-specific polymorphisms in association with various combinations of mutations at positions 16292 and 16296 on the haplogroup T background provides evidence of molecular instability at these nucleotide positions. Molecular instability in the haplogroup T HVS I sequences is also suggested by multiple independent losses of the haplogroup T diagnostic nucleotide variants in dierent populations. The results of the present study suggest that identical haplogroup T HVS I sequence types might have arisen independently in dierent human populations.

Ocneanu has obtained a certain type of quantized Galois correspondence for the Jones subfactors of type An and his arguments are quite general. By making use of them in a more general context, we define a notion of a subequivalent paragroup and establish a bijective correspondence between generalized intermediate subfactors in the sense of Ocneanu and subequivalent paragroups for a given strongly amenable subfactors of type II1 in the sense of Popa, by encoding the subequivalence in terms of a commuting square. For this encoding, we generalize Sato's construction of equivalent subfactors of finite depth from a single commuting square, to strongly amenable subfactors. We also explain a relation between our notion of subequivalent paragroups and sublattices of a Popa system, using open string bimodules.

The ≈400 m-thick Carajas Formation, of northern Brazil, is one of the most extensive Precambrian banded iron-formations (BIFs) of the Gondwanaland continents. The formation lies within the Grao ParaGroup, a gently folded and weakly metamorphosed volcanosedimentary sequence which unconformably overlies older gneissose and granitoid rocks of the Xingu Complex. Zircons extracted from five samples selected to provide age constraints for the Carajas Formation have yielded good U–Pb data following ion-microprobe analysis. Our results, combined with those available from earlier U–Pb zircon work, constrain deposition of the Carajas Formation between ≈2750 and ≈2740 Ma. A 2681±5 Ma age from an overlying sandstone with abundant zircons, apparently derived from syndepositional volcanism, suggests that deposition in the Grao Para“Basin” may have lasted less than 100 Ma. Our data hint at late metamorphic and/or metasomatic events, as young as 569±11 Ma, whose significance remains unresolved. Our results are in accord with previously published U–Pb zircon data constraining the maximum age of the Carajas Formation, but also provide close constraint on its minimum age that is not reliant on regional stratigraphic correlation.

In 1020 males out of 13 population samples from Argentina, Brazil, Costa Rica, Macao, Mozambique, Portugal and Spain, GATA allele 17 was found exclusively in Mozambique [Forensic Sci. Int. 135 (2003) 158]. In the present work, allele 17 was further observed in samples from Angola (9.33%), Mozambique (10.79%) and S. Tome e Principe (3.53%). This allele differs by at least two repeat units from all reported alleles: no instance of allele 18 was ever found. Allele 17 frequency and distribution, together with the absence of one-step-derived alleles, is compatible with a very low mutation rate and so potentially a good marker for African ancestry and haplogroup identification. We verified this hypothesis in two ways: (a) the sequencing of nine alleles 17 showed that the small number of uninterrupted repeats can explain the low mutation rate and (b) the simultaneous GATA C4 and SNP typing in 75 individuals from Angola, 85 from S. Tome e Principe and 417 from Mozambique proved that, out of 56 samples carrying allele 17, 55 belong to B* paragroup and one to A*, both said to be ancient African lineages. Therefore, GATA C4 allele 17 most probably was originated as a unique event and its extreme association with AB* is compatible with its use as a marker for the assignment to this paragroup.

International audience; Haplogroup G, together with J2 clades, has been associated with the spread of agriculture, especially in the European context. However, interpretations based on simple haplogroup frequency clines do not recognize underlying patterns of genetic diversification. Although progress has been recently made in resolving the haplogroup G phylogeny, a comprehensive survey of the geographic distribution patterns of the significant sub-clades of this haplogroup has not been conducted yet. Here we present the haplogroup frequency distribution and STR variation of 16 informative G sub-clades by evaluating 1472 haplogroup G chromosomes belonging to 98 populations ranging from Europe to Pakistan. Although no basal G-M201* chromosomes were detected in our data set, the homeland of this haplogroup has been estimated to be somewhere nearby eastern Anatolia, Armenia or western Iran, the only areas characterized by the co-presence of deep basal branches as well as the occurrence of high sub-haplogroup diversity. The P303 SNP defines the most frequent and widespread G sub-haplogroup. However, its sub-clades have more localized distribution with the U1-defined branch largely restricted to Near/Middle Eastern and the Caucasus, whereas L497 lineages essentially occur in Europe where they likely originated. In contrast, the only U1 representative in Europe is the G-M527 lineage whose distribution pattern is consistent with regions of Greek colonization. No clinal patterns were detected suggesting that the distributions are rather indicative of isolation by distance and demographic complexities.

Background: Among the founding mitochondrial haplogroups involved in the peopling of the Americas, haplogroup C1d has been viewed as problematic because of its phylogeny and because of the estimates of its antiquity, apparently being much younger than other founding haplogroups. Several recent analyses, based on data from the entire mitochondrial genome, have contributed to an advance in the resolution of these problems. The aim of our analysis is to compare the conclusions drawn from the available HVR-I and HVR-II data for haplogroup C1d with the ones based on whole mitochondrial genomes. Methodology/Principal Findings: HVR-I and HVR-II sequences defined as belonging to haplogroup C1d by standard criteria were gathered from the literature as well as from population studies carried out in Uruguay. Sequence phylogeny was reconstructed using median-joining networks, geographic distribution of lineages was analyzed and the age of the most recent common ancestor estimated using the r-statistic and two different mutation rates. The putative ancestral forms of the haplogroup were found to be more widespread than the derived lineages, and the lineages defined by np 194 were found to be widely distributed and of equivalent age. Conclusions/Significance: The analysis of control region sequences is found to still harbor great potential in tracing microevolutionary phenomena, especially those found to have occurred in more recent times. Based on the geographic distributions of the alleles of np 7697 and np 194, both discussed as possible basal mutations of the C1d phylogeny, we suggest that both alleles were part of the variability of the haplogroup at the time of its entrance. Moreover, based on the mutation rates of the different sites stated to be diagnostic, it is possible that the anomalies found when analyzing the haplogroup are due to paraphyly.

Y-chromosome Haplogroup O is the dominant lineage of East Asians, comprising more than a quarter of all males on the world; however, its internal phylogeny remains insufficiently investigated. In this study, we determined the phylogenetic position of recently defined markers (L127, KL1, KL2, P164, and PK4) in the background of Haplogroup O. In the revised tree, subgroup O3a-M324 is divided into two main subclades, O3a1-L127 and O3a2-P201, covering about 20 and 35% of Han Chinese people, respectively. The marker P164 is corrected from a downstream site of M7 to upstream of M134 and parallel to M7 and M159. The marker PK4 is also relocated from downstream of M88 to upstream of M95, separating the former O2(*) into two parts. This revision evidently improved the resolving power of Y-chromosome phylogeny in East Asia.

Haplogroup E1b1, defined by the marker P2, is the most represented human Y chromosome haplogroup in Africa. A phylogenetic tree showing the internal structure of this haplogroup was published in 2008. A high degree of internal diversity characterizes this haplogroup, as well as the presence of a set of chromosomes undefined on the basis of a derived character. Here we make an effort to update the phylogeny of this highly diverse haplogroup by including seven mutations which have been newly discovered by direct resequencing. We also try to incorporate five previously-described markers which were not, however, reported in the 2008 tree. Additionally, during the process of mapping, we found that two previously reported SNPs required a new position on the tree. There are three key changes compared to the 2008 phylogeny. Firstly, haplogroup E-M2 (former E1b1a) and haplogroup E-M329 (former E1b1c) are now united by the mutations V38 and V100, reducing the number of E1b1 basal branches to two. The new topology of the tree has important implications concerning the origin of haplogroup E1b1. Secondly, within E1b1b1 (E-M35), two haplogroups (E-V68 and E-V257) show similar phylogenetic and geographic structure, pointing to a genetic bridge between southern European and northern African Y chromosomes. Thirdly, most of the E1b1b1* (E-M35*) paragroup chromosomes are now marked by defining mutations, thus increasing the discriminative power of the haplogroup for use in human evolution and forensics.

Seccio ´n Antropologia Biologica, Instituto de Ciencias Antropologicas, Facultad de Filosofia y Letras,Universidad de Buenos Aires, Buenos Aires, ArgentinaKEY WORDS Y chromosome; SNP; microsatellites; south AmericaABSTRACT We analyzed 21 paragroup Q* Y chro-mosomes from South American aboriginal and urbanpopulations. Our aims were to evaluate the phyloge-netic status, geographic distribution, and genetic diver-sity in these groups of chromosomes and compare thedegree of genetic variation in relation to Q1a3a haplo-types. All Q* chromosomes from our series and fivesamples from North American Q* presented the deri-vate state for M346, that is present upstream to M3,and determined Q1a3* paragroup. We found a restric-tive geographic distribution and low frequency ofQ1a3* in South America. We assumed that this lowfrequency could be reflecting extreme drift effects.However, several estimates of gene diversity do notsupport the existence of a severe bottleneck. The meanhaplotype diversity expected was similar to that forSouth American Q1a3* and Q1a3a (0.478 and 0.501,respectively). The analysis of previous reports fromother research groups and this study shows the high-est frequencies of Q* for the West Corner and theGrand Chaco regions of South America. At present,there is no information on whether the phylogeneticstatus of Q* paragoup described in previous reports issimilar to that of Q1a3* paragroup though our resultssupport this possibility. Am J Phys Anthropol 140:578–582, 2009.

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR YFiler Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in 250 samples from Portugal. A total of 231 different haplotypes were found, where 17 haplotypes were shared by two individuals and one haplotype by three. The overall haplotype diversity (HD) was 0.9994. DYS458 non-consensus alleles found in 5 samples (out of 85) are all associated with paragroup J*(xJ1,2). Population comparisons with available Yfiler loci data in European samples were undertaken, namely with Northern Portuguese data (N=174) where no significant differences were observed with our sample (Rst=0.0000; P=0.8649+/-0.0310). Since both Portuguese databases can be joined (N=424; HD=0.9997; 394 distinct haplotypes), a study on the best loci for HD increment in this sample was also undertaken: by fixing the haplotypes generated from the minimal haplotype and SWGDAM core set (www.yhrd.org) and adding the other Yfiler loci one by one, the order in which the loci contribute more is DYS458, DYS456, GATA H4.1, DYS437 or DYS635, and finally DYS448. Therefore, at least in this population sample, all Yfiler loci are contributing for haplotype discrimination.

Population data on the hypervariable regions of the mitochondrial DNA (mtDNA) genome are used to convey the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, mtDNA profiles of Spanish individuals (n = 312) were analyzed to describe haplogroup distributions and to determine relevant single nucleotide polymorphisms (SNPs) of those haplogroups. All nine common European haplogroups were observed in the sample, and these were divided into subgroups when possible. Haplogroup H was the most common haplogroup. The haplogroups U, J, T, and V were the next most frequent groups, each occurring at a frequency of 6.4% or greater. In addition, African and Asian sequences were present though rare in the samples. The data were compared with and found to be similar to other published data sets. There were 109 SNPs observed in the data set, including 10 positions not previously reported. The most variable sites are consistent with other studies.

The human Y chromosome haplogroup E-M78 (E3b1a) occurs commonly and is distributed in northern and eastern Africa, western Asia, and all of Europe. Previously, only two rarely observed internal biallelic markers (UEPs) were known within the E-M78 clade. Here we report the identification of six novel UEPs that significantly refine the phylogeny of this haplogroup. Then, we evaluate the correspondence between the newly defined sub-haplogroups and the E-M78 haplotype clusters previously identified by an 11-microsatellite loci-based network encompassing 232 chromosomes (Cruciani et al., 2004). We observed considerable correspondence between the trees generated by the two types of markers, but also noted important discrepancies between microsatellite and UEP findings. Overall, this analysis reveals that the currently visible terminal branches of the Y tree still contain a large amount of information, in terms of undiscovered biallelic markers, and that caution is needed when using the microsatellite alleles as surrogates of unique event polymorphisms.

The history of human migratory events can be inferred from observed variations in DNA sequences. Such studies on non-recombinant mtDNA and Y-chromosome show that present day humans outside Africa originated from one or more migrations of small groups of individuals between 30K-70K YBP. Coalescence theory reveals that, any collection of non-recombinant DNA sequences can be traced back to a common ancestor. Mutations fixed by genetic drift act as markers on the timeline from the common ancestor to the present and can be used to infer migration and founder events that occurred in ancestral populations. However, most mutations seen in the data today are relatively recent and do not carry useful information about deep ancestry. The only ones that can be used reliably are those that can be shown to robustly distinguish large clusters of individuals and thus qualify as true representatives of population events in the past. In this talk, we present results from the analysis of 1737 complete mtDNA sequences from public databases to infer such a robust set of mutations that reveal the haplogroup phylogeny. Using principal component analysis we identify the samples in L, M and N clades and with unsupervised consensus ensemble clustering we infer the substructure in these clades. Traditional methods are inadequate to handle data of this size and complexity. The substructure is inferred using a new algorithm that mitigates the usual problems of sample size bias within haplogroups as well as the sampling bias across haplogroups. First, we cluster the data in each of the M, N, L clades separately into k=2,3,4,... kmax groups using an agreement matrix derived from multiple clustering techniques and bootstrap sampling. Repeated training/test splits of the samples identify robust clusters and patterns of SNPs which can assign haplogroup labels with a reliability greater than 90%. Even though the clustering at each k is done independently, the clusters split in a way that suggests that the data is revealing population events; a cluster at level k has k–2 clusters which are identical with those at level k–1 plus two more that obtain from a split of one of the clusters at level k–1. The clustering is repeated with equal number of samples from the first level clusters. The sequence in which the clusters now split defines a binary network which reveals population events unbiased by sample size. We root the network using an out-group and, assuming a molecular clock, identify an internal node in the bifurcation process which is equidistant from the leaves. This rooting removes the bias across haplogroups which would otherwise influence the order in which the clusters emerge. Our analysis shows that the African clades L0/L1, L2 and L3 have the greatest heterogeneity of SNPs, in agreement with their ancient ancestry. It also suggests that the M, N clades originated from a common ancestor of L3 in two separate migrations. The first migration gave rise to the M haplogroup, whose descendents currently populate South-East Asia and Australia. The second migration resulted in the N haplogroup, accounting for the current populations in China, Japan, Europe, Central Asia and North and South America. We reveal and robustly label many branches of the mtDNA tree, improving current results significantly. We find that for our choice of robust SNPs, the genetic distances between the NA and NRB haplogroups is smaller compared to that between B and J/T/H/V/U. The detailed N migratory sub-tree is rooted so that the T, J and U haplogroups are on one side of the root and the F, V/H, I, X, R5, B, N9, A and W are on the other. We also find a detailed structure for the M tree consistent with prior literature and we infer additional branches for the MD haplogroup. Finally we provide detailed SNP patterns for each haplogroup identified by our clustering. Our patterns can be used to infer a haplogroup assignment with reliability greater than 90%.

In order to attain a finer reconstruction of the peopling of southern and central-eastern Europe from the Levant, we determined the frequencies of eight lineages internal to the Y chromosomal haplogroup J, defined by biallelic markers, in 22 population samples obtained with a fine-grained sampling scheme. Our results partially resolve a major multifurcation of lineages within the haplogroup. Analyses of molecular variance show that the area covered by haplogroup J dispersal is characterized by a significant degree of molecular radiation for unique event polymorphisms within the haplogroup, with a higher incidence of the most derived sub-haplogroups on the northern Mediterranean coast, from Turkey westward; here, J diversity is not simply a subset of that present in the area in which this haplogroup first originated. Dating estimates, based on simple tandem repeat loci (STR) diversity within each lineage, confirmed the presence of a major population structuring at the time of spread of haplogroup J in Europe and a punctuation in the peopling of this continent in the post-Neolithic, compatible with the expansion of the Greek world. We also present here, for the first time, a novel method for comparative dating of lineages, free of assumptions of STR mutation rates.

The characterization of Y chromosome haplogroups is currently done by genotyping SNPs and a few InDels. However, InDels are increasingly gaining importance, so the aim of this work was to create an InDel PCR multiplex allowing a fast, simple and straightforward characterization of the main Y-haplogroups. For this, we have selected the InDels already accepted by the Y Chromosome Consortium. However, due to their position in the Y chromosome phylogenetic tree, they only allow classifying chromosomes from 6 of the 20 main Y haplogroups. Thus, we have extended the search to already described and validated InDels in dbSNP and MGS. All 154 InDels retrieved from that search were subjected to multiple screenings and just 10 were found to be new, potentially polymorphic and Y specific. Their typing in samples for 13 distinct haplogroups confirmed only 2 polymorphisms (named M2 and M14). M2 is polymorphic in R haplogroup but it also shows a reversion within the R1b1b2 sub-haplogroup. Therefore, it is not recommended for the characterization and distinction between R and the other haplogroups. M14 shows variation in R and Q and so it can be used to identify samples belonging to the paragroup P, which was not possible before using the InDels in the phylogenetic tree of the Y Chromosome Consortium. The detailed analysis of all the available information allowed us to conclude that the creation of the aimed multiplex will only be possible with the detection and phylogenetic characterization of new InDels.

mtDNA sequence variation was studied in 121 dental samples from four Basque prehistoric sites, by high-resolution RFLP analysis. The results of this study are corroborated by (1) parallel analysis of 92 bone samples, (2) the use of controls during extraction and amplification, and (3) typing by both positive and negative restriction of the linked sites that characterize each haplogroup. The absence of haplogroup V in the prehistoric samples analyzed conflicts with the hypothesis proposed by Torroni et al., in which haplogroup V is considered as an mtDNA marker for a major Paleolithic population expansion from southwestern Europe, occurring approximately 10,000-15,000 years before the present (YBP). Our samples from the Basque Country provide a valuable tool for checking the previous hypothesis, which is based on genetic data from present-day populations. In light of the available data, the most realistic scenario to explain the origin and distribution of haplogroup V suggests that the mutation defining that haplogroup (4577 NlaIII) appeared at a time when the effective population size was small enough to allow genetic drift to act-and that such drift is responsible for the heterogeneity observed in Basques, with regard to the frequency of haplogroup V (0%-20%). This is compatible with the attributed date for the origin of that mutation (10,000-15, 000 YBP), because during the postglacial period (the Mesolithic, approximately 11,000 YBP) there was a major demographic change in the Basque Country, which minimized the effect of genetic drift. This interpretation does not rely on migratory movements to explain the distribution of haplogroup V in present-day Indo-European populations.

The most common European lineage (haplogroup H) represents more than 50% of a South Portuguese population sample, which can be poorly discriminative in forensic casework. To detect haplogroup H sub-lineages, seven mitochondrial DNA coding-region SNPs have been studied—3010, 3915, 3992, 4336, 4769, 4793 and 6776, using minisequencing methodology. In our population, seven haplogroup H sub-lineages were obtained, although the paraphyletic cluster H* still predominates. The most frequent sub-lineages were H1 (3010A) and H3 (6776C), in agreement with other Portuguese and Spanish population studies. H7 (4793G) haplogroup was also detected in our study, being rare in some populations. SNaPshot ® methodology provides a simple, rapid and informative method to sub-type haplogroup H for forensic casework.

In patrilineal societies, surnames and Y-specific haplotypes and haplogroups are expected to be correlated. This characteristic could help defining an initial pool of suspects in forensic genetics analysis. Here we evaluated this correlation in a sample of Central-Brazilian men. Surnames and Y-SNP haplogroup and Y-STR haplotype were analyzed in 55 pairs of Central-Brazilian men sharing surnames ( n =110). Seven haplogroups and thirty-two haplotypes have been observed, none correlated solely to any of the twenty-eight surnames represented here. In this sample, two men with the same surname showed a chance of 0.41 of sharing a Y-specific haplogroup. This chance is higher for surnames of intermediate frequencies, whereas rare surnames show distinct chances as zero and one. Observed results may be over-estimated due to a predominance of a specific haplogroup (P92R7=49%) in the sample, what makes it possible for two men with no coancestry to share this haplogroup. Considering STR, only three pairs of men shared haplotypes. The average difference between the haplotypes in each pair was 2.45 mutational steps. This relatively low correlation is due to some historical and cultural peculiarities of the country, what makes it improper for forensic purposes in Brazil.

A commentary on assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

In this paper, we introduce a notion calledM 2-graded hypergroup, which extends the notion of hypergroup and is motivated by the example of a ‘paragroup’ in the context of the inclusion of a pair ofII 1factors. After discussing the example of the ‘paragroup’ we derive certain consequences of the definition and then prove that every finite irreducibleM 2-graded hypergroup possesses a unique dimension function, in analogy with a result for hypergroups.

BackgroundY-SNP haplogroup G (hgG), defined by Y-SNP marker M201, is relatively uncommon in the United States general population, with only 8 additional sub-markers characterized. Many of the previously described eight sub-markers are either very rare (2-4%) or do not distinguish between major populations within this hg. In fact, prior to the current study, only 2% of our reference Caucasian population belonged to hgG and all of these individuals were in sub-haplogroup G2a, defined by P15. Additional Y-SNPs are needed in order to differentiate between individuals within this haplogroup.Principal findingsIn this work we have investigated whether we could differentiate between a population of 63 hgG individuals using previously uncharacterized Y-SNPs. We have designed assays to test these individuals using all known hgG SNPs (n = 9) and an additional 16 unreported/undefined Y-SNPS. Using a combination of DNA sequence and genetic genealogy databases, we have uncovered a total of 15 new hgG SNPs that had been previously reported but not phylogenetically characterized. Ten of the new Y-SNPs are phylogenetically equivalent to M201, one is equivalent to P15 and, interestingly, four create new, separate haplogroups. Three of the latter are more common than many of the previously defined Y-SNPs. Y-STR data from these individuals show that DYS385*12 is present in (70%) of G2a3b1-U13 individuals while only 4% of non-G2a3b1-U13 individuals posses the DYS385*12 allele.ConclusionsThis study uncovered several previously undefined Y-SNPs by using data from several database sources. The new Y-SNPs revealed in this paper will be of importance to those with research interests in population biology and human evolution.

We describe the structure of (finite-index) inclusion of type III factors based on analysis of involved flows of weights. Roughly speaking, a type HI index theory splits into a “purely type III” index theory and an (essentially) type II index theory. The factor flows constructed in [1] serve as the complete invariant for the former in the AFD case while the latter can be analyzed by paragroups or quantized groups (as announced in [7]). Therefore, classification of subfactors in an AFD type III factor reduces to classification of factor flows and an “equivariant” paragroup theory.

To the Editor: Recently, an article by Simoni et al. (2000), who used (i) SAAP analysis to analyze the population frequencies of mtDNA haplogroups and (ii) AIDA analysis to examine both the frequency and the sequence similarity of truncated mtDNA sequences, appeared in this Journal. The main outcome of their study was that “the overall patterns of mtDNA diversity appear to be poorly significant in Europe.” The raw data comprised 2,619 hypervariable segment I (HVS-I) sequences (denoted as “HVR-I” [hypervariable region I] sequences by Simoni et al. [2000]) that were obtained from 36 regions or populations of Europe, the Near East, and the Caucasus and that were collected from both the literature and unpublished sources. Simoni et al. ostensibly grouped the HVS-I sequences according to haplogroup motifs proposed elsewhere (Richards et al. 1998), and they reported the resulting frequencies for each region/population in table 3 in their study. We have checked the input data displayed in table 3 and have found serious technical errors affecting numerous entries. More critically, the mtDNA categories that they report correspond neither to their own criteria nor to the haplogroup definitions established in the literature (to which they refer). Furthermore, their decision to truncate HVS-I information (and to disregard RFLP information) renders these data inadequate to differentiate even African and East Asian sequences from European sequences in many cases. Inspection of table 3 in the study by Simoni et al. (2000) reveals that (i) the data in the “Galicia” and “Spain: Central” rows have been, in part, crossed-over, (ii) the data in the “Belgium,” “Alps,” and “Turkey” rows have been computed with the use of sample sizes smaller than those reported in table 1 in the same study, (iii) the haplogroup “J” column has been totally randomized, and (iv) the “Other” column is complementary to the last four “superhaplogroup” columns but not to the first 11 haplogroup columns. As for item (iii), almost all positive entries in the haplogroup “J” column have been either displaced or calculated with the use of sample sizes corresponding to nearby rows. Hence, most entries in this column diverge widely from the real haplogroup J frequencies (see the last column of table 1 in the present study). Table 1 Haplogroup J Frequencies According to Simoni et al. (2000), a Crude Default Criterion, and Inference in the Present Study As an example of their haplogroup assignment, Simoni et al. (2000) specifically referred to the motif 16069T–16126C for haplogroup J, but they overlooked the fact that this criterion cannot formally be applied to the sequences in the study by Richards et al. (1996), since these were reported only between 16090 and 16365. This might explain some of the many “0” entries in the haplogroup “J” column of table 3 in the Simoni et al. study (see table 1 in the present study). Simoni et al. should have either adopted the haplogroup J frequencies reported by Richards et al. (1996), excluded these population samples from their study, or trimmed all data to the shortest common segment. In the latter case, by employing the motif 16126C–16294C, one could take the default cluster JT-T (comprising all JT sequences that are not T) as a crude default criterion for haplogroup J (see table 1 in the present study). The discrepancies in haplogroup frequencies are by no means restricted to haplogroup J. Table 2 in the present study shows the marked contrast between published haplogroup frequencies and those assumed by Simoni et al. (2000) for the well-characterized Tuscan, Druze, and Adygei samples (which were typed for RFLPs as well as for HVS-I sequences by Torroni et al. [1996] and Macaulay et al. [1999]). The large differences in frequency for haplogroup H, the most-common European haplogroup, are due to the premise of Simoni et al. (2000) that haplogroup “H contains all sequences . . . that show none of the 22 substitutions considered in this study.” This extreme simplification results, on the one hand, in the dumping of large numbers of haplogroup H mtDNAs mainly into the default category “Other” and, on the other hand, in the inclusion of several non-H sequences within their haplogroup H category. For instance, by their criterion, 10/20 haplogroup H mtDNAs from the Tuscan sample (Torroni et al. 1996) would no longer be scored as “H,” whereas the U sequence 16051G–16309G–16318C would be scored as “H.” In consequence, the haplogroup H category described by Simoni et al. (2000) is bound to be highly polyphyletic in the mtDNA genealogy and does not reflect the spatial patterns of haplogroup H. Table 2 Haplogroup Frequencies, According to Simoni et al. (2000) vs. the Original Studies, in Tuscan, Druze, and Adygei Populations At this point, it is important to clarify what haplogroup classification entails. An mtDNA haplogroup, when properly defined, is a monophyletic clade of the mtDNA genealogy. Originally, high-resolution RFLP analysis (employing 14 enzymes) had been used for identification of clades by signature sites (Torroni et al. 1992, 1993, 1994a, 1994b, 1996; Chen et al. 1995), and current haplogroup nomenclature originated in that context. In retrospect, this approach is indeed quite reliable, although recurrent changes at a few sites, such as 10394 DdeI, may occasionally cause problems. Potential ambiguities can largely be resolved by incorporation of information from other segments of mtDNA sequences or specific positions of the coding regions (Torroni et al. 1997; Brown et al. 1998; Starikovskaya et al. 1998; Macaulay et al. 1999; Quintana-Murci et al. 1999; Schurr et al. 1999). For instance, haplogroup K is now understood to be a clade (as are U1–U6) within haplogroup U. HVS-I data in combination with partial RFLPs can sometimes serve as a satisfactory substitute for a full RFLP analysis (Rando et al 1998, 2000; Kivisild et al. 1999a, 1999b). Unfortunately, HVS-I data alone, which have been produced en masse, often do not contain sufficient information for confident assignment of haplogroup affiliation. The truncation of the HVS-I data to only 13–22 variant positions, as performed by Simoni et al. (2000), yields even poorer results. For example, the motif 16223T–16278T, which was used by Simoni et al. to identify haplogroup X, would transfer most African L1/L2 sequences (Watson et al. 1997; Rando et al. 1998) into the then artefactual category “X.” For Europe, this is relevant insofar as a few L1/L2 sequences are present in Iberia (Rocha et al. 1999), and there even resides an African L1c sequence with the motif 16223T–16278T in the British data (Piercy et al. 1993). In addition, as was previously pointed out (Torroni et al. 1996; Macaulay et al. 1999), one has to be prepared for recurrent mutations in the HVS-I motifs (compare also figs. 4, 5, 8, and 9 of the study by Richards et al. [1998]). For instance, the frequency discrepancy (17.8% vs. 26.7%) for haplogroup X in the Druze sample (see table 2 in the present study) is due to the fact that Simoni et al. did not include four haplogroup X mtDNAs that have mutated to 16223C. Another of the many possible examples of misclassification caused by the use of truncated motifs is illustrated by 16129A–16223T, the motif used by Simoni et al. for classification of haplogroup I mtDNAs. Use of this truncated motif has led them to classify both the Asian haplogroup C mtDNAs (16129A–16223T–16298C–16327T) of the Adygei (6.0%) and the East African haplogroup M1 mtDNA (16129A–16189C–16223T–16249C–16311C–16359C) of the Druze (2.2%) as members of haplogroup I (see table 2 in the present study). The issue of haplogroups only affects the SAAP analysis. However, there are also serious difficulties with the AIDA analysis. Ideally, AIDA should be applied to full DNA-sequence data, but Simoni et al. (2000) included only 22/241 variant positions. One cannot expect that such a truncated data set would show much evidence of geographic patterns within Europe. Most of the haplogroup diagnostic variants in western Eurasian mtDNA are very ancient, and they probably evolved in the Near East and subsequently spread to Europe (Torroni et al. 1998; Macaulay et al. 1999); at any event, they occur throughout western Eurasia. The more recent “rare substitutions,” which have evolved since the earlier dispersals and which Simoni et al. (2000) discarded as “statistical noise,” are precisely those that are most likely to show regional distributions. The exclusion of such mutations severely restricts the capacity to identify phylogeographic units and, thus, is bound to have seriously reduced the power of the approach to detect autocorrelation. Even when haplogroup assignment is done with care, failure to detect significant clines in haplogroup frequencies does not prove the absence of any spatial structure in the mtDNA pool. Such structure would rather be manifest at a phylogenetically finer scale (defined on the basis of more-recent mutations). In any case, one would not expect that meaningful patterns of mtDNA diversity could emerge from analyses based on categories with no demonstrable phylogenetic support.

We will give a proof of Ocneanu′s announced classification of subfactors of the AFD type II1 factor with the principal graphs An, Dn, E7, the Dynkin diagrams, and give a single explicit of exp π √ -1/24 and exp π √-1/60 for each of E6 and E8 such that its validity is equivalent to the existence of two (and only two) subfactors for these principal graphs. Our main tool is the flatness of connections on finite graphs, which is the key notion of Ocneanu′s paragroup theory. We give the difference between the diagrams D2n and D2n+1 a meaning as a Z/2Z-obstruction for flatness arising in orbifold construction, which is an analogue of orbifold models in solvable lattice models.

Haplogroup E, defined by mutation M40, is the most common human Y chromosome clade within Africa. To increase the level of resolution of haplogroup E, we disclosed the phylogenetic relationships among 729 mutations found in 33 haplogroup DE Y-chromosomes sequenced at high coverage in previous studies. Additionally, we dissected the E-M35 subclade by genotyping 62 informative markers in 5,222 samples from 118 worldwide populations. The phylogeny of haplogroup E showed novel features compared with the previous topology, including a new basal dichotomy. Within haplogroup E-M35, we resolved all the previously known polytomies and assigned all the E-M35* chromosomes to five new different clades, all belonging to a newly identified subhaplogroup (E-V1515), which accounts for almost half of the E-M35 chromosomes from the Horn of Africa. Moreover, using a Bayesian phylogeographic analysis and a single nucleotide polymorphism-based approach we localized and dated the origin of this new lineage in the northern part of the Horn, about 12ka. Time frames, phylogenetic structuring, and sociogeographic distribution of E-V1515 and its subclades are consistent with a multistep demic spread of pastoralism within north-eastern Africa and its subsequent diffusion to subequatorial areas. In addition, our results increase the discriminative power of the E-M35 haplogroup for use in forensic genetics through the identification of new ancestry-informative markers., The authors are grateful to all the donors for providing DNA samples and to the people that contributed to the sample collection. In particular, they thank João Lavinha (for the Portuguese samples); Farha El Chennawi, Anne Cambon-Thomsen, M.S. Issad, Eric Crubézy, Abdellatif Baali, Mohammed Cherkaoui, and Mohammed Melhaoui for their help in the collection of the Moroccan, Algerian, and Egyptian Berbers samples; and the National Laboratory for the Genetics of Israeli Populations. This work was supported by the Italian Ministry of Education, Progetti PRIN (grant numbers 2012JA4BTY_004 to F.C. and 2012JA4BTY_003 to A.N.) and by Sapienza University of Rome (grant number C26A13S9AR to F.C.). The sampling of the Berbers was made within the framework of the Inserm "Réseau Nord/Sud" No. 490NS1 (Mozabite Berbers), "The Origin of Man, Language and Languages," EUROCORES Programme and benefited from funding by the Région Midi-Pyrénées (Toulouse, France), the CNRS, and the E.C. Sixth Framework Programme under Contract ERASCT-2003-980409.