Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats

In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.

Do the four clades of the mtDNA haplogroup L2 evolve at different rates?

Forty-seven mtDNAs collected in the Dominican Republic and belonging to the African-specific haplogroup L2 were studied by high-resolution RFLP and control-region sequence analyses. Four sets of diagnostic markers that subdivide L2 into four clades (L2a-L2d) were identified, and a survey of published African data sets appears to indicate that these clades encompass all L2 mtDNAs and harbor very different geographic/ethnic distributions. One mtDNA from each of the four clades was completely sequenced by means of a new sequencing protocol that minimizes time and expense. The phylogeny of the L2 complete sequences showed that the two mtDNAs from L2b and L2d seem disproportionately derived, compared with those from L2a and L2c. This result is not consistent with a simple model of neutral evolution with a uniform molecular clock. The pattern of nonsynonymous versus synonymous substitutions hints at a role for selection in the evolution of human mtDNA. Regardless of whether selection is shaping the evolution of modern human mtDNAs, the population screening of L2 mtDNAs for the mutations identified by our complete sequence study should allow the identification of marker motifs of younger age with more restricted geographic distributions, thus providing new clues about African prehistory and the origin and relationships of African ethnic groups.

Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade

The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro-Eurasian superhaplogroup L3 (-3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS-I motifs, as the ancestral HVS-I type of L3e cannot be distinguished from the putative HVS-I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS-I, with additional support coming from HVS-II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid-Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS-I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (+/-14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.

Human Y-chromosome variation in the western Mediterranean area: implications for the peopling of the region

Y-chromosome variation was analyzed in a sample of 1127 males from the Western Mediterranean area by surveying 16 biallelic and 4 multiallelic sites. Some populations from Northeastern Europe and the Middle East were also studied for comparison. All Y-chromosome haplotypes were included in a parsimonious genealogic tree consisting of 17 haplogroups, several of which displayed distinct geographic specificities. One of the haplogroups, HG9.2, has some features that are compatible with a spread into Europe from the Near East during the Neolithic period. However, the current distribution of this haplogroup would suggest that the Neolithic gene pool had a major impact in the eastern and central part of the Mediterranean basin, but very limited consequences in Iberia and Northwestern Europe. Two other haplogroups, HG25.2 and HG2.2, were found to have much more restricted geographic distributions. The first most likely originated in the Berbers within the last few thousand years, and allows the detection of gene flow to Iberia and Southern Europe. The latter haplogroup is common only in Sardinia, which confirms the genetic peculiarity and isolation of the Sardinians. Overall, this study demonstrates that the dissection of Y-chromosome variation into haplogroups with a more restricted geographic distribution can reveal important differences even between populations that live at short distances, and provides new clues to their past interactions.

Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade

A sample of mitochondrial DNA (mtDNA) from the southeastern African population of Mozambique has been shown to have affinities with populations both to its north and south. From the north came sequences that may have been involved in the Bantu expansion (from western, through eastern, to southern Africa), such as members of haplogroups L3b, L3e1a and a subset of L1a. The dating of the major component of Mozambican mtDNAs, the subset L2a of haplogroup L2, displayed an age range compatible with the Bantu expansion. The southern influence was traced by the presence of sequence types from haplogroup L1d, a probable relict of Khoisan-speaking populations that inhabited the region prior to their displacement by the Bantu-speaking incomers. Within historical times, the forced displacement of Mozambicans as part of the slave trade, mainly documented as being to the Americas, generated a differential input of eastern African sequences into the mtDNA pools of the Americas and of Europe, as testified to by the greater number of sequence matches between Mozambique and the Americas, compared to those between Mozambique and Europe.

Patterns of male-specific inter-population divergence in Europe, West Asia and North Africa

We typed 1801 males from 55 locations for the Y-specific binary markers YAP, DYZ3, SRY10831 and the (CA)n microsatellites YCAII and DYS413. Phylogenetic relationships of chromosomes with the same binary haplotype were condensed in seven large one-step networks, which accounted for 95% of all chromosomes. Their coalescence ages were estimated based on microsatellite diversity. The three largest and oldest networks undergo sharp frequency changes in three areas. The more recent network 3.1A clearly discriminates between Western and Eastern European populations. Pairwise Fst showed an overall increment with increasing geographic distance but with a slope greatly reduced when compared to previous reports. By sectioning the entire data set according to geographic and linguistic criteria, we found higher Fst-on-distance slopes within Europe than in West Asia or across the two continents.

Latitude-correlated genetic polymorphisms: selection or gene flow?

Latitude-correlated polymorphisms can be due to either selection-driven evolution or gene flow. To discriminate between them, we propose an approach that studies subpopulations springing from a single population that have lived for generations at different latitudes and have had a low genetic admixture. These requirements are fulfilled to a large extent by Ashkenazi and Sephardi Jews. The original population lived at a latitude of 35 degrees N, where the Sephardis still live. The Ashkenazis, however, moved to a latitude of 50 degrees N, starting about 10 centuries ago. The present study examines 3 latitude-correlated polymorphisms: PGP, PGM1, and AHSG. We found that PGP*2 and AHSG*2 alleles most likely underwent selection-driven evolution, but that PGM1*ts allele was not similarly affected. Since temperature might have been considered a reasonable selective factor, we also studied a population living at >800 m above sea level from Aosta Valley (Italy).

The A1555G mutation in the 12S rRNA gene of human mtDNA: recurrent origins and founder events in families affected by sensorineural deafness

The mtDNA variation of 50 Spanish and 4 Cuban families affected by nonsyndromic sensorineural deafness due to the A1555G mutation in the 12S rRNA gene was studied by high-resolution RFLP analysis and sequencing of the control region. Phylogenetic analyses of haplotypes and detailed survey of population controls revealed that the A1555G mutation can be attributed to >/=30 independent mutational events among the 50 Spanish families and that it occurs on mtDNA haplogroups that are common in all European populations. This indicates that the relatively high detection rate of this mutation in Spain is not due to sampling biases or to a single major founder event. Moreover, the distribution of these mutational events on different haplogroups is compatible with a random occurrence of the A1555G mutation and tends to support the conclusion that mtDNA backgrounds do not play a significant role in the expression of the mutation. Overall, these findings appear to indicate that the rare detection of this mutation in other populations is most likely due to inadequacy in patient ascertainment and molecular screening. This probable lack of identification of the A1555G mutation in subjects affected by sensorineural hearing loss implies that their maternally related relatives are not benefiting from presymptomatic detection and information concerning their increased risk of ototoxicity due to aminoglycoside treatments.

Combined use of biallelic and microsatellite Y-chromosome polymorphisms to infer affinities among African populations

To define Y-chromosome haplotypes, we studied seven biallelic polymorphic sites. We combined data with those from four dinucleotide-repeat polymorphisms, to establish Y-chromosome compound superhaplotypes. Eight biallelic haplotypes that matched the dendrogram proposed by other investigators were identified in 762 Y chromosomes from 25 African populations. For each biallelic site, coalescence time of lineages carrying the derived allele was estimated and compared with previous estimates. The "ancestral" haplotype (haplotype 1A) was observed among Ethiopians, "Khoisan" (!Kung and Khwe), and populations from northern Cameroon. Microsatellite distributions within this haplotype showed that the Khoisan haplotypes 1A are widely divergent from those of the other two groups. Populations from northern Africa and northern Cameroon share a haplotype (i.e., 1C), which is not observed in other African populations but represents a major Eurasian cluster. Haplotypes 1C of northern Cameroon are clearly distinct from those of Europe, whereas haplotypes 1C of northern African are well intermingled with those of the other two groups. Apportionment of diversity for the Y-chromosomal biallelic haplotypes was calculated after populations were clustered into different configurations. Despite some correspondence between language affiliation and genetic similarity, geographic proximity seems to be a better predictor of genetic affinity.

Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy

With 10 segregating sites (simple nucleotide polymorphisms) in the last intron (1089 bp) of the ZFX gene we have observed 11 haplotypes in 336 chromosomes representing a worldwide array of 15 human populations. Two haplotypes representing 77% of all chromosomes were distributed almost evenly among four continents. Five of the remaining haplotypes were detected in Africa and 4 others were restricted to Eurasia and the Americas. Using the information about the ancestral state of the segregating positions (inferred from human-great ape comparisons), we applied coalescent analysis to estimate the age of the polymorphisms and the resulting haplotypes. The oldest haplotype, with the ancestral alleles at all the sites, was observed at low frequency only in two groups of African origin. Its estimated age of 740 to 1100 kyr corresponded to the time to the most recent common ancestor. The two most frequent worldwide distributed haplotypes were estimated at 550 to 840 and 260 to 400 kyr, respectively, while the age of the continentally restricted polymorphisms was 120 to 180 kyr and smaller. Comparison of spatial and temporal distribution of the ZFX haplotypes suggests that modern humans diverged from the common ancestral stock in the Middle Paleolithic era. Subsequent range expansion prevented substantial gene flow among continents, separating African groups from populations that colonized Eurasia and the New World.

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 approximately 50,000 years ago.

mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America?

On the basis of comprehensive RFLP analysis, it has been inferred that approximately 97% of Native American mtDNAs belong to one of four major founding mtDNA lineages, designated haplogroups "A"-"D." It has been proposed that a fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage in Native Americans. Unlike haplogroups A-D, haplogroup X is also found at low frequencies in modern European populations. To investigate the origins, diversity, and continental relationships of this haplogroup, we performed mtDNA high-resolution RFLP and complete control region (CR) sequence analysis on 22 putative Native American haplogroup X and 14 putative European haplogroup X mtDNAs. The results identified a consensus haplogroup X motif that characterizes our European and Native American samples. Among Native Americans, haplogroup X appears to be essentially restricted to northern Amerindian groups, including the Ojibwa, the Nuu-Chah-Nulth, the Sioux, and the Yakima, although we also observed this haplogroup in the Na-Dene-speaking Navajo. Median network analysis indicated that European and Native American haplogroup X mtDNAs, although distinct, nevertheless are distantly related to each other. Time estimates for the arrival of X in North America are 12,000-36,000 years ago, depending on the number of assumed founders, thus supporting the conclusion that the peoples harboring haplogroup X were among the original founders of Native American populations. To date, haplogroup X has not been unambiguously identified in Asia, raising the possibility that some Native American founders were of Caucasian ancestry.

Network analyses of Y-chromosomal types in Europe, northern Africa, and western Asia reveal specific patterns of geographic distribution

In a study of 908 males from Europe, northern Africa, and western Asia, the variation of four Y-linked dinucleotide microsatellites was analyzed within three "frames" that are defined by mutations that are nonrecurrent, or nearly so. The rapid generation and extinction of new dinucleotide length variants causes the haplotypes within each lineage to diverge from one another. We constructed networks of "adjacent" haplotypes within each frame, by assuming changes of a single dinucleotide unit. Two small and six large networks were obtained, the latter including 94.9% of the sampled Y chromosomes. We show that the phenetic relationships among haplotypes, represented as a network, result largely from common descent and subsequent molecular radiation. The grouping of haplotypes of the same network thus fits an evolutionarily relevant criterion. Notably, this method allows the total diversity within a sample to be partitioned. Networks can be considered optimal markers for population studies, because reliable frequency estimates can be obtained in small samples. We present synthetic maps describing the incidence of different Y-chromosomal lineages in the extant human populations of the surveyed areas. Dinucleotide diversity also was used to infer time intervals for the coalescence of each network.

Genetic structure of the ancestral population of modern humans

Neutral DNA polymorphisms from an 8-kb segment of the dystrophin gene, previously ascertained in a worldwide sample (n = 250 chromosomes), were used to characterize the population ancestral to the present-day human groups. The ancestral state of each polymorphic site was determined by comparing human variants with their orthologous sites in the great apes. The "age before fixation" of the underlying mutations was estimated from the frequencies of the new alleles and analyzed in the context of these polymorphisms' distribution among 13 populations from Africa, Europe, Asia, New Guinea, and the Americas (n = 860 chromosomes in total). Seventeen polymorphisms older tan 100,000-200,000 years, which contributed approximately 90% to the overall nucleotide diversity, were common to all human groups. Polymorphisms endemic to human groups or continentally restricted were younger than 100,000-200,000 years. Africans (six populations) with 13 such sites stood out from the rest of the world (seven populations), where only 2 population-specific variants were observed. The similarity of the frequencies of the old polymorphisms in Africans and non-Africans suggested a similar profile of genetic variability in the population before the modern human's divergence. This ancestral population was characterized by an effective size of about 10,000 as estimated from the nucleotide diversity; this size may describe the number of breeding individuals over a long time during the Middle Pleistocene or reflect a speciation bottleneck from an initially larger population at the end of this period.

mtDNA analysis reveals a major late Paleolithic population expansion from southwestern to northeastern Europe

mtDNA sequence variation was studied in 419 individuals from nine Eurasian populations, by high-resolution RFLP analysis, and it was followed by sequencing of the control region of a subset of these mtDNAs and a detailed survey of previously published data from numerous other European populations. This analysis revealed that a major Paleolithic population expansion from the "Atlantic zone" (southwestern Europe) occurred 10,000-15,000 years ago, after the Last Glacial Maximum. As an mtDNA marker for this expansion we identified haplogroup V, an autochthonous European haplogroup, which most likely originated in the northern Iberian peninsula or southwestern France at about the time of the Younger Dryas. Its sister haplogroup, H, which is distributed throughout the entire range of Caucasoid populations and which originated in the Near East approximately 25,000-30,000 years ago, also took part in this expansion, thus rendering it by far the most frequent (40%-60%) haplogroup in western Europe. Subsequent migrations after the Younger Dryas eventually carried those "Atlantic" mtDNAs into central and northern Europe. This scenario, already implied by archaeological records, is given overwhelming support from both the distribution of the autochthonous European Y chromosome type 15, as detected by the probes 49a/f, and the synthetic maps of nuclear data.

Nuclear DNA diversity in worldwide distributed human populations

Nucleotide variation was examined in an 8 kb intronic DNA bordering exon 44 of the human dystrophin gene on Xp21. Thirty-six polymorphisms (substitutions, small insertions/deletions and one (T)n microsatellite) were found using SSCP/heteroduplex analysis of DNA samples from mixed Europeans, Papua New Guineans as well as from six African, three Asian and two Amerindian populations. In this way the European bias in the nuclear polymorphism ascertainment has been avoided. In a maximum likelihood tree constructed from the frequency data, Africans clustered separately from the non-African populations. Fifteen polymorphisms were shared among most of the populations compared, whereas 13 sites were found to be endemic to Africans and four to non-Africans. The common sites contributed most to the average heterozygosity (Hn=0.101%+/-0.023), whereas the endemic ones, being rare, had little effect on this estimate. The F(ST) values were lower for Africans (0.072) than for non-Africans (0.158), suggesting a higher level of gene exchange within Africa, corroborating the observation of a greater number of segregating sites on this continent than elsewhere. The data suggest a recent common origin of the African and non-African populations, where a greater geographical isolation of the latter resulted in a smaller number of newly acquired polymorphisms.

Differential structuring of human populations for homologous X and Y microsatellite loci

The global pattern of variation at the homologous microsatellite loci DYS413 (Yq11) and DXS8174 and DXS8175 (Xp22) was analyzed by examination of 30 world populations from four continents, accounting for more than 1,100 chromosomes per locus. The data showed discordant patterns of among- and within-population gene diversity for the Y-linked and the X-linked microsatellites. For the Y-linked polymorphism, all groups of populations displayed high FST values (the correlation between random haplotypes within subpopulations, relative to haplotypes of the total population) and showed a general trend for the haplotypes to cluster in a population-specific way. This was especially true for sub-Saharan African populations. The data also indicated that a large fraction of the variation among populations was due to the accumulation of new variants associated with the radiation process. Europeans exhibited the highest level of within-population haplotype diversity, whereas sub-Saharan Africans showed the lowest. In contrast, data for the two X-linked polymorphisms were concordant in showing lower FST values, as compared with those for DYS413, but higher within-population variances, for African versus non-African populations. Whereas the results for the X-linked loci agreed with a model of greater antiquity for the African populations, those for DYS413 showed a confounding pattern that is apparently at odds with such a model. Possible factors involved in this differential structuring for homologous X and Y microsatellite polymorphisms are discussed.

Characterization of a small family (CAIII) of microsatellite-containing sequences with X-Y homology

Four X-linked loci showing homology with a previously described Y-linked polymorphic locus (DYS413) were identified and characterized. By fluorescent in situ hybridization (FISH), somatic cell hybrids, and YAC screening, the X-linked members of this small family of sequences (CAIII) all map in Xp22, while the Y members map in Yq11. These loci contribute to the overall similarity of the two genomic regions. All of the CAIII loci contain an internal microsatellite of the (CA)n type. The microsatellites display extensive length polymorphism in two of the X-linked members as well as in the Y members. In addition, common sequence variants are found in the portions flanking the microsatellites in two of the X-linked members. Our results indicate that, during the evolution of this family, length variation on the Y chromosome was accumulated at a rate not slower than that on the X chromosome. Finally, these sequences represent a model system with which to analyze human populations for similar X- and Y-linked polymorphisms.

Haplotype and phylogenetic analyses suggest that one European-specific mtDNA background plays a role in the expression of Leber hereditary optic neuropathy by increasing the penetrance of the primary mutations 11778 and 14484

mtDNAs from 37 Italian subjects affected by Leber hereditary optic neuropathy (LHON) (28 were 11778 positive, 7 were 3460 positive, and 2 were 14484 positive) and from 99 Italian controls were screened for most of the mutations that currently are associated with LHON. High-resolution restriction-endonuclease analysis also was performed on all subjects, in order to define the phylogenetic relationships between the mtDNA haplotypes and the LHON mutations observed in patients and in controls. This analysis shows that the putative secondary/intermediate LHON mutations 4216, 4917, 13708, 15257, and 15812 are ancient polymorphisms, are associated in specific combinations, and define two common Caucasoid-specific haplotype groupings (haplogroups J and T). On the contrary, the same analysis shows that the primary mutations 11778, 3460, and 14484 are recent and are due to multiple mutational events. However, phylogenetic analysis also reveals a different evolutionary pattern for the three primary mutations. The 3460 mutations are distributed randomly along the phylogenetic trees, without any preferential association with the nine haplogroups (H, I, J, K, T, U, V, W, and X) that characterize European populations, whereas the 11778 and 14484 mutations show a strong preferential association with haplogroup J. This finding suggests that one ancient combination of haplogroup J-specific mutations increases both the penetrance of the two primary mutations 11778 and 14484 and the risk of disease expression.

Mitochondrial DNA and Y chromosome-specific polymorphisms in the Seminole Tribe of Florida

Mitochondrial DNA (mtDNA) sequence variation was examined in 37 Seminoles from Florida by polymerase chain reaction amplification and high resolution restriction endonuclease analysis. The Y chromosome TaqI restriction fragment length polymorphisms detected by the probes 49a, 49f, and 12f2 were examined in the 26 males of this group. Analysis of the mtDNA revealed that all four Native American haplogroups (A, B, C and D) were present in the Seminoles encompassing about 95% of the Seminole mtDNAs. No European mtDNAs were found among the Seminoles, but two mtDNAs (about 5%) were members of the African-specific haplogroup L1, thus indicating that a limited number of African women were incorporated in the Seminole tribe. Analysis of Y chromosome haplotypes supports the hypothesis that haplotypes 18 and 63 are the most likely founding Native American Y chromosome haplotypes from Asia. However, 11% of the Seminole Y chromosomes represented haplotypes generally attributed to Europeans, though none harbored standard African haplotypes. These findings support historical evidence that the Seminole tribe has integrated individuals of European and African ancestry, but suggests that the sex ratio of nonnatives from different continents may have varied.

Classification of European mtDNAs from an analysis of three European populations

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. 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. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. 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. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations.

Novel tetranucleotide repeat polymorphism in the human adenosine deaminase gene: interethnic comparison of three major human groups

A new tetranucleotide repeat polymorphism was revealed at the human adenosine deaminase (ADA) locus by using the polymerase chain reaction and denaturing polyacrylamide gel electrophoresis. Allele frequencies were estimated in seven populations from three major ethnic groups. Heterozygosity values were calculated and found to differ significantly between Africans and non-Africans.

Geographical structuring in the mtDNA of Italians

Geographical patterns of mtDNA variation were studied in 12 Italian samples (1072 individuals) by two different spatial autocorrelation methods. Separate analyses of the frequencies of 12 restriction morphs show North-South clines, differences between Sardinia and the mainland populations, and the effects of isolation by distance. A recently developed autocorrelation statistic summarizing molecular similarity at all sites (AIDA; autocorrelation index for DNA analysis) confirms the presence of a clinical pattern; differences between random pairs of haplotypes tend to increase with their geographical distance. The partition of gene diversity, however, reveals that most variability occurs within populations, whereas differences between populations are minor (GST = 0.057). When the data from the 12 samples are pooled, two descriptors of genetic variability (number of polymorphic sites and average sequence difference between pairs of individuals) do not behave as expected under neutrality. The presence of clinal patterns, Tajima's tests, and a simulation experiment agree in suggesting that population sizes increased rapidly in Italy and Sicily but not necessarily so in Sardinia. The distribution of pairwise sequence differences in the Italian peninsula (excluding Sardinia) permits a tentative location of the demographic increase between 8000 and 20,500 years ago. These dates are consistent with archaeological estimates of two distinct expansion processes, occurring, respectively, in the Neolithic and after the last glacial maximum in the Paleolithic. Conversely, there is no genetic evidence that such processes have had a major impact on the Sardinian population.

Genetic studies on the Senegal population. II. Polymorphisms of the plasma proteins F13A, F13B, ORM1, AHSG, C6, C7, and APOC2

Using isoelectric focusing and immunoblotting techniques, we tested 270 plasma samples from 3 populations of Senegal (Wolof, Peul, Tukulor) to determine genetic variation at 7 protein loci (F13A, F13B, ORM1, AHSG, C6, C7, APOC2). Four of the seven systems (F13A, ORM1, AHSG, C6) have not been studied previously in sub-Saharan Africa, and one system (C7) has never been examined in any population of African ancestry. The assumption that F13B*6, F13B*23, and APOC2*2 represent African marker alleles is supported by this study. At the AHSG locus we observed a four-allele polymorphism rather than the two-allele polymorphism commonly seen in other ethnic groups. At the C6 locus, in addition to the two common alleles C6*A and C6*B, we observed three other alleles, one of which (C6*A3), found at polymorphic frequencies, seems to be another example of a unique African allele. The C7 locus was found to be monomorphic in the Peul but polymorphic in the Wolof and the Tukulor. At the F13A and ORM1 loci, Senegalese have allele frequencies similar to those reported for American blacks. All three Senegalese samples display typical African features, such as a high frequency of the F13B*2 allele and the presence of the APOC2*2 allele at a polymorphic level. However, some differences in allele frequencies have been found between the three groups, and this could have implications for reconstructing their remote history.(ABSTRACT TRUNCATED AT 250 WORDS)

An MspI polymorphism in the X-specific region proximal to the pseudoautosomal boundary. A new example of a unique "African" marker?

A polymorphic MspI site was located in the X-specific region proximal to the pseudoautosomal boundary. Two alleles defined by the absence or the presence of the MspI site were detected by the polymerase chain reaction (PCR) in a sample of Bantu-speaking individuals from Cameroon. No variation for this site was observed in a population sample from Italy.

Genetic studies in Cameroon: mitochondrial DNA polymorphisms in Bamileke

In two population samples of 77 Bamileke (Bantu sensu lato) and 18 Bakaka (Bantu sensu stricto) from southwestern Cameroon, the mtDNA RFLPs for the HpaI, HaeII, MspI, AvaII, and HincII enzymes were studied. Two of the MspI morphs had not been reported before. Six new types were found, four of which represent new combinations of previously described morphs. The AvaII morph 3 was found in association with the "African" HpaI morph 3. This finding is in line with previous observations in Negroids and demonstrates the usefulness of this combination as an indicator of black African ancestry. Two differences were noted between the groups: a lower frequency of HpaI morph 3 and a higher frequency of HaeII morph 4 in the Bakaka with respect to the Bamileke (0.44 versus 0.62 and 0.17 versus 0.03, respectively). The importance of these differences could not be evaluated because the Bakaka sample was too small. Nevertheless, because the Bamileke show a relatively low frequency of mtDNA type 1 (2.1.1.1.-) and high frequencies of mtDNA types 2 (3.1.1.1.3.-) and 7 (3.1.1.1.1.-), they can be placed with the other Negroids so far examined, but they are closer to the Senegalese than to the Bantu from South Africa. In comparing the Bamileke and the Bantu, mtDNA type 3 (3.1.1.2.2.-) appears particularly discriminative because it is present in all the Bantu subgroups examined but not in the Bamileke. mtDNA type 39 (2.1.4.1.1.-), which was observed only in the Bamileke, might be considered likewise discriminative, although to a lesser degree.

Mitochondrial DNA polymorphisms among Hindus: a comparison with the Tharus of Nepal

The polymorphisms of mitochondrial DNA for the restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HinecII were studied in a sample of 79 Hindus, 45 from New Delhi (India) and 34 from Terai (Nepal), both to characterize another Caucasian population and to investigate some possible Hindu component in the genetic structure of the Tharus, a Nepalese population, the anthropological position of which is still disputed. 1. A new BamHI polymorphism was detected: about 5% of the Hindu mtDNAs have lost the site at 14258 bp and lack any BamHI site. Once again a BamHI polymorphism was found in a Caucasian population. 2. New site mutations were found to yield morphs previously described (MspI-7, AvaII-18). 3. Variant morphs for two different enzymes were found due to a shared mutation (morphs BamHI-0/AvaII-30 and morphs MspI-7Hindu/AvaII-18Hindu). 4. Comparison between Hindu and Tharu data does not show any evidence of a specific Indian component in the Tharu genetic structure and allows us to conclude that Tharus are clearly differentiated from modern Hindus.

Y chromosome DNA polymorphisms in human populations: differences between Caucasoids and Africans detected by 49a and 49f probes

Several Y-specific TaqI fragments are recognized by 49a and 49f probes in human male DNA digests. The occurrence of polymorphic variations in six of these fragments (A, B, C, D, F and I) has recently been reported, providing a potentially powerful tool for the study of the population genetics of the Y chromosome. The 49a-49f/TaqI polymorphisms were studied in 121 Africans (Senegal and Cameroon) and 125 Caucasians (Italy). In addition to the variability described already, four new bands were observed. Moreover, three patterns were found in which bands constantly present so far (G, O and H-P-R) were missing. At variance with previously reported findings, the coexistence of two different fragments of the same 'allelic' series (A or D) was frequently observed in the Italian sample (10.4%). For some of these 'double-banded' patterns their holoandric transmission could be demonstrated by family studies. In the light of these new findings, the hypothesis of A or D fragments being allelic forms, as advanced by the authors who first described these polymorphisms, has to be reconsidered. A total of 34 haplotypes were encountered, 22 of which are new. The Africans tested all lack C and D fragments. Moreover, about 80% of them are characterized by a band, A1, not present in the Italian group. The combination of A1C0D0 could therefore be a powerful genetic marker of paternal African ancestry. This combination occurs in five haplotypes, one of which, haplotype IV, accounts for 68% of the African sample. In contrast with the results of the mtDNA analysis on the same population samples, the degree of variability displayed by the Y chromosome sequences appears to be much lower in Africans than in Caucasians.

Mitochondrial DNA polymorphisms in Italy. III. Population data from Sicily: a possible quantitation of maternal African ancestry

mtDNA polymorphisms were studied in a sample of 90 individuals of the Sicilian population using six restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII and HincII. (1) Three new patterns, for MspI, AvaII and HincII, have been detected. (2) At least two different mutations were found to account for both the AvaII morph 3 and the AvaII morph 9 as in many other Caucasian groups so far examined. (3) Seventeen types were found; of these six are new. The frequency (54.5%) of type 1-2 (2.1.1.1.1.2) is lower than in the rest of Italy whereas those of type 6-2 (2.1.2.1.1.2) (10.0%) and type 18-2 (2.3.1.4.9*.2) (12.2%) lie at the upper level of the Italian range. The 18-derivative, type 57-2 (2.3.1.4.13*.2), which is consistently found in all Italian samples, is present also among Sicilians with an incidence of 2.2%. (4) Of particular interest is that the HpaI-3/AvaII-3 complex, which is unique to groups of African ancestry, was found in Sicily at a frequency of 4.4%. For the first time an estimate of the amount of gene flow from Blacks to the Sicilian gene pool could be obtained.

Genetic studies on the Senegal population. I. Mitochondrial DNA polymorphisms

The mtDNA of 186 Senegalese, mainly Wolof and Peuls, were analyzed by means of six restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII, and HincII. Two of the HpaI, one of the HaeII, two of the MspI, and one of the AvaII morphs had not been described before. The only enzymes which enabled Wolof and Peuls to be differentiated were HincII and, to a lesser extent, HaeII. Important differences emerge in the comparison of Senegalese with Bantu of South Africa and with Bushmen, the only other Africans who, as far as we know, were studied for the same genetic markers. Though Senegalese mtDNAs display typical African features (presence and frequency of HpaI morph 3 and high incidence of AvaII morph 3), the distribution of MspI and AvaII patterns markedly differentiates Senegalese from the others. The phylogeny of mtDNA types in Africa well portrays how the three African groups are clearly distinguishable genetic entities. Bushmen lie at one end of the range of variability, Senegalese being at the other end but still fairly closely related to Bantu. The information provided by individual restriction enzymes to the distinction among the three major ethnic groups is reviewed and discussed.

Genetic heterogeneity in Sardinia: 15 polymorphisms examined in 11 isolates

Blood group systems ABO, RH, MNS, KEL, FY, LU and P, red cell enzymes ACP1, PGM1, PGM2, ADA, DIA and PHI, serum markers GC, HP, IGHG1, IGHG3 and IGK were examined in about 900 individuals sampled in 11 Sardinian isolates. The genetic differentiation turned out to be relatively high and the relevance of selected and neutral genes has been evaluated.

Chromosome and blood marker studies in families of patients affected by xeroderma pigmentosum and trichothiodystrophy

Chromosome and blood marker studies were performed in the families of 4 patients in which the association of 2 rare recessive Mendelian disorders, xeroderma pigmentosum (XP-D) and trichothiodystrophy (TTD), was present. Blood genotypes did not indicate any linkage with the pathologic condition, nor any segregation anomaly. Cytogenetic analysis using high-resolution banding techniques showed a normal karyotype both in the heterozygous and in the homozygous individuals. These findings lead us to exclude a cytologically detectable chromosome rearrangement, such as a microdeletion, as a possible cause of the association of XP-D and TTD in our patients.

Mitochondrial DNA polymorphisms in Italy. II. Molecular analysis of new and rare morphs from Sardinia and Rome

A molecular analysis of morphs found in a previous survey of mtDNA restriction enzyme polymorphisms in Italy revealed that different site changes can give similar patterns and that the same mutation can yield variant morphs for apparently unrelated enzymes. 1. Alternative site variations were found to yield restriction fragment patterns resembling HpaI morph 4, HaeII morph 5 and AvaII morph 2. 2. A strong association was observed between the BamHI morph 3 (gain of site a) and the AvaII morph 9 and its derivatives (loss of site d). This association appears to result from an A to G transition at base pair (bp) 13,368 which simultaneously creates a new BamHI site and abolishes an AvaII site. On the other hand, the loss of the AvaII site d, which in Italy was only found in the above-mentioned association, does not always produce a new BamHI site, as observed in other Caucasian groups. Similarly, the BamHI morph 2 (gain of site b) was always found to be associated with AvaII morphs lacking site f. An A to G transition at bp 16,391 was shown to account for both changes. As in the previous case, the converse is not true. Hence, these data show that AvaII sites d and f were lost in more than one way and one of these seems to be typical of Caucasians. 3. The variation producing BamHI-3/AvaII-9 and derivatives is preferentially associated with MspI morph 4 but this is not a product of a shared mutation. Hence, this association must be the result of the linkage disequilibrium due to the maternal inheritance of mtDNA and lack of recombination. 4. The high frequency of the combination BamHI-3/AvaII-9 and derivatives with MspI-4 found in Italy (29 subjects out of 229 analysed) can best be explained by diffusion of the relevant haplotype rather than by repeated mutational events. 5. The phylogeny trees of all mtDNA morphs so far described and of mtDNA types in Caucasians have been revised taking into account both the inter- and the intra-morph heterogeneity detected by this analysis.

The p12f2/TaqI Y-specific polymorphism in three groups of Italians and in a sample of Senegalese

The TaqI/p12f2 Y-specific RFLP was studied in 258 Italians (69 from North, 74 from Centre-South and 115 from Southern Sardinia) and in 65 Senegalese. The two allelic fragments of 10 and 8 kb characterizing this polymorphism were both found in the Italians but only the 10 kb band was found among the Senegalese. The observed frequency of the 8 kb allele was 32.4% in Central-Southern Italians, 17.4% in Northern Italians and 13.0% in Southern Sardinians. The last figure is significantly lower than that (34.3%) previously reported for a smaller sample of the same population.

Family and population studies of SAHH and ADA polymorphisms. A possible pitfall in the ascertainment of SAHH electrophoretic phenotypes

Typing of both SAHH and ADA red cell electrophoretic patterns was carried out among the members of about 80 families from Latium (Central Italy) and in a random sample of about 350 individuals from two Italian regions, Latium and Sardinia. 1. The SAHH1 enzyme product provided another interesting example of a change in the electrophoretic pattern brought about by the haemolysate ageing. In vitro storage of SAHH 1 red cell lysates leads to the production of a pattern similar to that expected from a heterozygote SAHH 2-1. This change has been shown to be abolished by pretreating the sample with mercaptoethanol. The results indicate that the systematic use of sulphydril reducing agents can provide a more reliable means of analysing the SAHH polymorphism if differently stored samples are to be compared by starch gel electrophoresis. 2. Evidence against complete linkage of the SAHH and ADA loci has been obtained from two informative SAHH/ADA matings encountered in this study. 3. The SAHH allele frequencies observed in the two samples analysed were: SAHH1 = 0.969, SAHH2 = 0.024, SAHH3 = 0.007 (Latium) and SAHH1 = 0.973, SAHH2 = 0.011, SAHH3 = 0.016 (Sardinia). 4. The ADA2 allele frequency estimates were: 0.083 (Latium) and 0.059 (Sardinia). These figures are almost identical to those already reported for the same two regions.

Mitochondrial DNA polymorphisms in Italy. I. Population data from Sardinia and Rome

The polymorphisms of human mitochondrial DNA were studied in about 150 Sardinians from Cagliari and 100 other Italians living in Rome, using total blood cell DNA and the following restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII and HincII. 1. Seven different new morphs have been identified, one for HaeII, four for AvaII and two for HincII. 2. 16 and 17 mtDNA types were observed in the Sardinian and Roman samples, respectively. Of these only seven were shared by both groups. The morphs BamHI-3, MspI-4 and AvaII-9 were found associated at a frequency (10.0%) much higher than expected (0.17%). 3. Sardinians can be differentiated from the other Italians for a higher frequency of both morph AvaII-1 (P less than 0.05) and type 1 (2-1-1-1-1) (P approximately less than 0.03), and for a lower intragroup heterogeneity (0.52 v. 0.61). 4. The Italian sample on the whole can also be differentiated from the Caucasian group previously examined for a lower frequency of BamHI morph 2 (P Yates less than 0.01), a higher frequency of HaeII morph 1 (P Yates less than 0.02) and for the presence at a non-negligible incidence (5 individuals out of 229) of the new type 57-2 (2-3-1-4-13-2). The data indicate that mtDNA polymorphisms have not only proved to be a useful tool in detecting differences among major human groups but they can also differentiate populations within the same major ethnic division.

Phosphoglycolate phosphatase polymorphism: gene frequencies in three Italian samples

The electrophoretic polymorphism of the PGP locus has been studied in about 1,700 Italians. The sample consisted of individuals from Viareggio (North-Central Italy), Rome (Central Italy) and Cagliari (Sardinia, Southern Italy). Comparison among the three groups showed a high degree of heterogeneity. The Sardinian sample was well differentiated from the other two concerning the frequencies of both the PGP3 and of PGP2 alleles. The frequency of the PGP1 allele varied from 0.900 (Viareggio) to 0.987 (Cagliari). The gene frequencies, together with those available for other European populations were plotted against the latitudes of the different localities sampled and fitted to a North-South cline.

Population studies on human phosphoglucomutase-1 thermostability polymorphism

The electrophoretic and thermostability polymorphisms of the PGM1 locus were examined in about 700 Czechoslovakians (Prague) and 3000 Italians. The Italian sample consisted of individuals from Pavia (Northern Italy), Viareggio and Rome (Central Italy) and Naples (Southern Italy). The eight PGM1 alleles, PGM1Str1, PGM1Sts1, PGM1Ftr1, PGM1Fts1, PGM2Str1, PGM2Sts1, PGM2Ftr1, PGM2Fts1, have been considered as combinations of mutations at three different sites, 1/2, S/F and tr/ts, within the PGM1 gene and their frequencies discussed in terms of linkage disequilibrium between these sites. All pairwise differences between the samples were significant except for Pavia-Viareggio and Viareggio-Rome. The frequencies of the PGMts1 alleles have been found to range from 0.0981 (Prague) to 0.0546 (Naples) and can be ordered according to a North-South cline.

Further genetic heterogeneity of human red cell phosphoglucomutase-1: a mon-electrophoretic polymorphism

The electrophoretic patterns of human red cell phosphoglucomutase (PGM) were determined by standard starch-gel electrophoresis on two aliquots of haemolysate, one of which was previously heat-treated. Samples from 67 families and 417 unrelated healthy subjects were examined. Heat denaturation studies combined with electrophoresis showed a greater heterogeneity of phosphoglucomutase-1 (PGM1) isozymes than that revealed by electrophoresis alone. Both PGM11 and the PGM21 isozymes turned out to be either heat-resistant (tr) or heat-sensitive (ts) and this new phenotypic property segregated along with the electrophoretic allele with which it was originally associated. Comparison of red cell PGM1 patterns of 217 PGM21-1 heterozygous individuals, analysed both as described in this paper and by acid starch-gel electrophoresis, which also distinguishes two common PGM11 (PGM1S1 and PGM1f1) and two common PGM12 (PGM2S1 and PGM2F1) allelic products, has shown that the two sets of four alleles do not coincide. Thus eight different PGM1 alleles were identified. The PGM1Str1, PGM1Sts1, PGM1Ftr1, PGM1FTSts1, PGM2Str1, PGM2Sts1, PGM2Ftr1 and PGM2Fts1 gene frequencies were estimated as 0 . 523, 0 . 066, 0 . 099, 0 . 029, 0 . 224, 0 . 012, 0 . 043, 0 . 004, respectively. Three polymorphic sites are hypothesized within the PGM1 structural gene and the observed frequencies of the eight alleles discussed in terms of 'disequilibrium' among these sites. This is the second example of a human enzyme isoelectrophoretic polymorphism revealed by research specifically aimed at detecting electrophoretically cryptic genetic variations. The technique used in this study appears to offer a reliable means of detecting isoelectrophoretic variants for proteins already known to be electrophoretically polymorphic.

Glyoxalase I polymorphism: gene frequencies in two Italian populations

The gene frequencies for human red cell glyoxalase I have been determined in 1,222 unrelated subjects from two areas of Central Italy (Rome and Viareggio). No significant difference has been found between the two samples. Therefore the data have been pooled. The cumulative GLO1 gene frequency estimate is 0.376 +/- 0.010. This gene frequency is comparable to that reported for another sample from Rome and very similar to that found in Naples while it is significantly lower than those reported for Northern Italy (Milan and Genoa) and for the Northern European Caucasian populations studied so far.

An electrophoretic polymorphism that mimics a true genetic polymorphism in Triturus cristatus carnifex (Amiphibia, Urodela)

Phosphoglucomutase electrophoretic patterns have been studied in 60 tail homogenates of Triturus cristatus carnifex. Our results show that the same sample produces a different electrophoretic pattern with homogenate ageing; a new band of intermediate mobility appears, together with the one produced by the fresh preparation. The phenomenon can mimic a true genetic polymorphism when differently stored samples are analyzed.

Dynamics of phosphoglucomutase heat sensitivity polymorphism in Culicidae

In 6 species of mosquitoes of the genera Aedes and Culiseta (Culicidae, Diptera) the frequency of phosphoglucomutase (PGM) heat sensitivity alleles is inversely correlated with the temperature of the environment where larvae develop. These data suggest that different selective values are associated with the PGM thermoresistant and thermosensitive genotypes in the different habitats.

Nonelectrophoretic genetic variability in mosquitoes: polymorphism for temperature-resistant and temperature-sensitive phosphoglucomutase alleles in Culex pipiens

Homogenates of single individuals of two natural populations and five laboratory populations of Culex pipiens were examined by combining electrophoresis and heat denaturation studies on phosphoglucomutase (PGM). All populations showed a high degree of polymorphism for isoelectrophoretic temperature-resistant (tr) and temperature-sensitive (ts) alleles. Formal genetic data on the heat stability differences of the PGM are given. If both electrophoretic and isoelectrophoretic alleles are taken into account, the mean increase in the degree of heterozygosity is quite remarkable, i.e., about 65%.--The data are considered in relation to the biological significance that this new type of variability of structural genes could have in natural populations.