Search

The immunosuppressive tumor microenvironment (TME) is a formidable barrier to the success of adoptive cell therapies for solid tumors. Oncolytic immunotherapy with engineered adenoviruses (OAd) may disrupt the TME by infecting tumor cells, as well as surrounding stroma, to improve the functionality of tumor-directed chimeric antigen receptor (CAR)-T cells, yet efficient delivery of OAds to solid tumors has been challenging. Here we describe how mesenchymal stromal cells (MSCs) can be used to systemically deliver a binary vector containing an OAd together with a helper-dependent Ad (HDAd; combinatorial Ad vector [CAd]) that expresses interleukin-12 (IL-12) and checkpoint PD-L1 (programmed death-ligand 1) blocker. CAd-infected MSCs deliver and produce functional virus to infect and lyse lung tumor cells while stimulating CAR-T cell anti-tumor activity by release of IL-12 and PD-L1 blocker. The combination of this approach with administration of HER.2-specific CAR-T cells eliminates 3D tumor spheroids in vitro and suppresses tumor growth in two orthotopic lung cancer models in vivo. Treatment with CAd MSCs increases the overall numbers of human T cells in vivo compared to CAR-T cell only treatment and enhances their polyfunctional cytokine secretion. These studies combine the predictable targeting of CAR-T cells with the advantages of cancer cell lysis and TME disruption by systemic MSC delivery of oncolytic virotherapy: incorporation of immunostimulation by cytokine and checkpoint inhibitor production through the HDAd further enhances anti-tumor activity.

The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world's great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

The Y-chromosomal genetic landscape of South America is relatively homogenous. The majority of native Amerindian people are assigned to haplogroup Q and only a small percentage belongs to haplogroup C. With the aim of further differentiating the major Q lineages and thus obtaining new insights into the population history of South America, two individuals, both belonging to the sub-haplogroup Q-M3, were analyzed with next-generation sequencing. Several new candidate SNPs were evaluated and four were confirmed to be new, haplogroup Q-specific, and variable. One of the new SNPs, named MG2, identifies a new sub-haplogroup downstream of Q-M3; the other three (MG11, MG13, MG15) are upstream of Q-M3 but downstream of M242, and describe branches at the same phylogenetic positions as previously known SNPs in the samples tested. These four SNPs were typed in 100 individuals belonging to haplogroup Q.

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6–23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

We have assessed the numbers of potentially deleterious variants in the genomes of apparently healthy humans by using (1) low-coverage whole-genome sequence data from 179 individuals in the 1000 Genomes Pilot Project and (2) current predictions and databases of deleterious variants. Each individual carried 281–515 missense substitutions, 40–85 of which were homozygous, predicted to be highly damaging. They also carried 40–110 variants classified by the Human Gene Mutation Database (HGMD) as disease-causing mutations (DMs), 3–24 variants in the homozygous state, and many polymorphisms putatively associated with disease. Whereas many of these DMs are likely to represent disease-allele-annotation errors, between 0 and 8 DMs (0–1 homozygous) per individual are predicted to be highly damaging, and some of them provide information of medical relevance. These analyses emphasize the need for improved annotation of disease alleles both in mutation databases and in the primary literature; some HGMD mutation data have been recategorized on the basis of the present findings, an iterative process that is both necessary and ongoing. Our estimates of deleterious-allele numbers are likely to be subject to both overcounting and undercounting. However, our current best mean estimates of ∼400 damaging variants and ∼2 bona fide disease mutations per individual are likely to increase rather than decrease as sequencing studies ascertain rare variants more effectively and as additional disease alleles are discovered.

Structural variation includes many different types of chromosomal rearrangement and encompasses millions of bases in every human genome. Over the past three years the extent and complexity of structural variation has become better appreciated. Diverse approaches have been adopted to explore the functional impact of this class of variation. As disparate indications of the important biological consequences of genome dynamism are accumulating rapidly, we review the evidence that structural variation has an appreciable impact on cellular phenotypes, disease and human evolution.

Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography. We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture. We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11(th)-13(th) centuries CE introduced western European lineages into Lebanese Christians.

We have identified a Y-chromosomal lineage that is unusually frequent in northeastern China and Mongolia, in which a haplotype cluster defined by 15 Y short tandem repeats was carried by approximately 3.3% of the males sampled from East Asia. The most recent common ancestor of this lineage lived 590 +/- 340 years ago (mean +/- SD), and it was detected in Mongolians and six Chinese minority populations. We suggest that the lineage was spread by Qing Dynasty (1644-1912) nobility, who were a privileged elite sharing patrilineal descent from Giocangga (died 1582), the grandfather of Manchu leader Nurhaci, and whose documented members formed approximately 0.4% of the minority population by the end of the dynasty.

We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic–speaking pastoralists from the Middle East.

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a refinement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.

Y-chromosome diversity has been analyzed at a micro-geographical level, examining 10 binary polymorphisms and 7 short tandem repeats (STRs) in 443 samples belonging to 11 populations from two regions of Northern Spain, Galicia and Cantabria. Both regions, as a whole, cluster with other Iberian populations. However, some individual populations, particularly that from the Pas Valley in Cantabria, depart markedly from this general pattern, with higher genetic distances and reduced diversity. This unusual population is even more distinct than the Basques from their Iberian neighbors. Genetic drift in a small isolated population could explain this special behavior, and in addition to its anthropological interest, this finding has important forensic implications.

Sixteen Y-chromosomal microsatellites and 16 binary markers have been used to analyze DNA variation in 408 male subjects from 15 populations in Central Asia. Large genetic differences were found between populations, but these did not display an obvious geographical or linguistic pattern like that usually seen for Y-chromosomal variation. Nevertheless, an underlying east-west clinal pattern could be detected by the Autocorrelation Index for DNA Analysis and admixture analysis, and this pattern was interpreted as being derived from the ancient peopling of the area, reinforced by subsequent migrations. Two particularly striking features were seen: an extremely high level of Y-chromosomal differentiation between geographically close populations, accompanied by low diversity within some populations. These were due to the presence of high-frequency population-specific lineages and suggested the occurrence of several recent bottlenecks or founder events. Such events could account for the lack of a clear overall pattern and emphasize the importance of multiple recent events in reshaping this genetic landscape.

A recently published study has used next-gen sequencing technology to resequence two Y chromosomes separated by 13 generations and discovered four single-base differences in approximately 10Mb DNA, suggesting that the Y chromosome euchromatin accumulates around one mutation per generation. Y-SNPs therefore now offer the best resolution of Y haplotypes and promise to distinguish almost every Y chromosome. This work illustrates the promise of current sequencing technology for forensically relevant applications.

During the past few years the DNA commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area, namely Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.

16 Y-specific STR loci have been analysed in 711 males from 12 populations in Pakistan. Individual loci showed between 4 and 10 alleles, and diversities ranged from 0.07 to 0.77. A total of 527 different haplotypes were found and the haplotype diversity ranged from 0.92 to 0.99 for the different populations. 446 haplotypes occurred in single individuals, and only 19 haplotypes were present in more than three males, but two striking examples of haplotype sharing were found, one involving 13 individuals, and the other 17. The 13 individuals were all Parsis, and 16 of the 17 were Brahuis, providing evidence for population substructuring.

The origins and dispersal of farming and pastoral nomadism in southwestern Asia are complex, and there is controversy about whether they were associated with cultural transmission or demic diffusion. In addition, the spread of these technological innovations has been associated with the dispersal of Dravidian and Indo-Iranian languages in southwestern Asia. Here we present genetic evidence for the occurrence of two major population movements, supporting a model of demic diffusion of early farmers from southwestern Iran—and of pastoral nomads from western and central Asia—into India, associated with Dravidian and Indo-European–language dispersals, respectively.

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift. Z.H.R. was supported by a BBSRC Studentship, T.Z. by a Wellcome Trust Bioarchaeology Studentship, M.E.H. by an MRC Studentship, F.R.S. by the Leverhulme Trust, and L.P. by Ph.D. grant PRAXIS XXI/BD/13632/97 from Fundacao para a Ciencia e a Tecnologia. D.C.R. is a Glaxo Wellcome Research Fellow. C.T.-S. is supported by the CRC, and M.A.J. is a Wellcome Trust Senior Fellow in Basic Biomedical Science, supported by grant 057559. Iberian sample collection was partially funded by multidisciplinary project grant PR182/96 6745 from Complutense University.

Recent discoveries of many new genes have made it clear that there is more to the human Y chromosome than a heap of evolutionary debris, hooked up to a sequence that happens to endow its bearer with testes. Coupled with the recent development of new polymorphic markers on the Y, making it the best-characterized haplotypic system in the genome, this gives us new opportunities to assess its role in disease and selection, through association studies with phenotypes such as infertility and cancers. However, the peculiar genetics of this bizarre chromosome means that we should interpret such studies particularly cautiously.

We present the second human Y-specific minisatellite, MSY2 ( DYS440 ). It consists of three or four copies of a 99–110 bp repeat unit and is located about 1 kb upstream of the DBY gene. The most common allele contains four units, but a three-unit allele has arisen on at least four occasions; in chimpanzees and orangutans, MSY2 contains only two units. It is therefore evolving slowly and provides a particularly useful polymorphic marker for Chinese populations.

Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations—that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit.

SummaryWe have examined the worldwide distribution of a Y-chromosomal base-substitution polymorphism, the T/C transition at SRY-2627, where the T allele defines haplogroup 22; sequencing of primate homologues shows that the ancestral state cannot be determined unambiguously but is probably the C allele. Of 1,191 human Y chromosomes analyzed, 33 belong to haplogroup 22. Twenty-nine come from Iberia, and the highest frequencies are in Basques (11%; n=117) and Catalans (22%; n=32). Microsatellite and minisatellite (MSY1) diversity analysis shows that non-Iberian haplogroup-22 chromosomes are not significantly different from Iberian ones. The simplest interpretation of these data is that haplogroup 22 arose in Iberia and that non-Iberian cases reflect Iberian emigrants. Several different methods were used to date the origin of the polymorphism: microsatellite data gave ages of 1,650, 2,700, 3,100, or 3,450 years, and MSY1 gave ages of 1,000, 2,300, or 2,650 years, although 95% confidence intervals on all of these figures are wide. The age of the split between Basque and Catalan haplogroup-22 chromosomes was calculated as only 20% of the age of the lineage as a whole. This study thus provides evidence for direct or indirect gene flow over the substantial linguistic barrier between the Indo-European and non–Indo-European–speaking populations of the Catalans and the Basques, during the past few thousand years.

An unusual Y chromosome with a primary constriction inside the long-arm heterochromatin was found in the amniocytes of a 38-year-old woman. The same Y chromosome was found in her husband and brother-in-law, thus proving that it was already present in the father. FISH with alphoid DNA showed hybridization signals at the usual position of the Y centromere but not at the primary constriction. Centromere proteins (CENP)-A, CENP-C, and CENP-E could not be detected at the site of the canonic centromere but were present at the new constriction, whereas CENP-B was not detected on this Y chromosome. Experiments with 82 Y-specific loci distributed throughout the chromosome confirmed that no gross deletion or rearrangement had taken place, and that the Y chromosome belonged to a haplogroup whose members have a mean alphoid array of 770 kb (range 430-1,600 kb), whereas that of this case was approximately 250 kb. Thus, this Y chromosome appeared to be deleted for part of the alphoid DNA. It seems likely that this deletion was responsible for the silencing of the normal centromere and that the activation of the neocentromere prevented the loss of this chromosome. Alternatively, neocentromere activation could have occurred first and stimulated inactivation of the normal centromere by partial deletion. Whatever the mechanism, the presence of this chromosome in three generations demonstrates that it functions sufficiently well in mitosis for male sex determination and fertility and that neocentromeres can be transmitted normally at meiosis.

DNA analysis is making a valuable contribution to the understanding of human evolution [1]. Much attention has focused on mitochondrial DNA (mtDNA) [2] and the Y chromosome [3] and [4], both of which escape recombination and so provide information on maternal and paternal lineages, respectively. It is often assumed that the polymorphisms observed at loci on mtDNA and the Y chromosome are selectively neutral and, therefore, that existing patterns of molecular variation can be used to deduce the histories of populations in terms of drift, population movements, and cultural practices. The coalescence of the molecular phylogenies of mtDNA and the Y chromosome to recent common ancestors in Africa [5] and [6], for example, has been taken to reflect a recent origin of modern human populations in Africa. An alternative explanation, though, could be the recent selective spread of mtDNA and Y chromosome haplotypes from Africa in a population with a more complex history [7]. It is therefore important to establish whether there are selective differences between classes (haplotypes) of mtDNA and Y chromosomes and, if so, whether these differences could have been sufficient to influence the distributions of haplotypes in existing populations. A precedent for this hypothesis has been established for mtDNA in that one mtDNA background increases susceptibility to Leber hereditary optic neuropathy [8]. Although studies of nucleotide diversity in global samples of Y chromosomes have suggested an absence of recent selective sweeps or bottlenecks [9], selection may, in principle, be very important for the Y chromosome because it carries several loci affecting male fertility [10] and [11] and as many as 5% of males are infertile [11] and [12]. Here, we show that one class of infertile males, PRKX/PRKY translocation XX males, arises predominantly on a particular Y haplotypic background. Selection is, therefore, acting on Y haplotype distributions in the population.

The DNA sequences that are necessary for the formation of a functional mammalian chromosome are thought to be the origins of replication, the telomeres and the centromere. Telomere structure is now well understood, with the functional element characterized as the motif (TTAGGG)n. The structures of the DNA regions that contain origins of replication and a centromere are known, but the functionally important elements within these regions are still only poorly defined.

Eighteen yeast artificial chromosome (YAC) clones containing alphoid satellite DNA and adjacent sequences from the human Y chromosome have been identified from three different YAC libraries. Restriction site mapping of the genomic alphoid arrays and the YACs has allowed seven of the alphoid clones to be positioned on the arrays. Three clones extend into flanking sequences. At one edge the alphoid DNA is highly diverged and is flanked by a small block of the 48 base-pair satellite, dispersed moderately repeated sequences and a separate short alphoid array. More distal sequences are Y -specific. At the other edge there is much less divergence and the alphoid DNA is flanked by an Alu sequence and the five base-pair satellite.

We have analysed the sequence organization of the DNA in the pericentric region of the long arm of the human Y chromosome. The structures of one cosmid and three yeast artificial chromosome clones were determined. The region consists of a mosaic of the known 5, 48 and 68 base-pair tandemly repeated sequences and at least five novel repeated sequence families. A long range-map of approximately 3.5 x 10(6) base-pairs of genomic DNA was constructed that placed the clones between about 500 x 10(3) and 850 x 10(3) base-pairs from the long arm edge of the centromeric alphoid DNA array.

The possibility of introducing new sequencing technologies into forensic genetics raises questions that go beyond the choice between SNPs and STRs as the preferred genetic markers. We suggest that many of the novel methodological and technical issues could be incorporated into the likelihood ratio frameworks currently used by forensic scientists. However, changes to ethical and legal structures may be needed before the new information could be used.

The structure of a repeated DNA sequence located on the short arm of the human Y chromosome is described. Genomic mapping and cloning in lambda or cosmid vectors show that the repeated sequence consists of units 20·3 × 10 3 base-pairs long that contain the three previously described DNA sequences: Y-156, Y-190 and Y-223a. Analysis of male genomic DNA by pulsed-field gel electrophoresis shows that the units are tandemly arranged and are organized into two blocks. The major block is hypervariable in size and alleles in the range approximately 540 × 10 3 to 800 × 10 3 base-pairs were detected. The minor block is not variable in size and is approximately 60 × 10 3 base-pairs long. Analysis of rearranged Y chromosomes shows that both blocks are located on the short arm of the chromosome. Most commonly, the major block is distal to the minor block, but the opposite arrangement is also found.

In 1995, much to the delight of mitochondrial Eve (Cann et al. 1987), the search for a suitable partner resulted in the discovery of Y-chromosomal Adam (Dorit et al. 1995; Paabo 1995). Like Eve, he was traced back to sub-Saharan Africa, although with a date of 270,000 years ago, he seems a bit older than she. On the basis of the absence of sequence variation in a part of the ZFY gene in 38 globally dispersed male subjects, this date was not undisputed (Donnelly et al. 1996; Fu and Li 1996; Rogers et al. 1996; Weiss and von Haeseler 1996). Later in the same year, two additional studies did reveal a limited number of sequence variants on other parts of the Y chromosome. Because of these variants, estimates were obtained of the times back to our most recent common (male) ancestor of 37,000–49,000 years ago (Whitfield et al. 1995) and of 51,000–411,000 years ago (Hammer 1994). Now, just 5 years later, with simple PCR strategies, ⩾250 polymorphic loci scattered over the entire nonrecombining part of the human Y chromosome can be identified. Among these polymorphisms are (1) biallelic markers with a low mutation rate representing unique (or near-unique) mutation events (UMEs) in human evolution, such as single base-pair substitutions (Underhill et al. 1997), an ALU insertion/deletion polymorphism (Hammer 1994), or a LINE insertion (Santos et al. 2000); (2) moderately fast-evolving microsatellites or simple-tandem repeats (STRs), with an average mutation frequency of ∼.2% per generation (Heyer et al. 1997; Jobling et al. 1999; Kayser et al. 2000); and (3) fast-evolving loci, such as the minisatellite locus MSY1 (Jobling et al. 1998) with a mutation frequency of 6%–11% per generation. With the exception of the two pseudoautosomal regions, the almost 60–Mb nonrecombining part of the Y chromosome is transmitted strictly from father to son without recombination (Jobling and Tyler-Smith 1995). This renders the Y chromosome probably the most versatile haplotypic genotyping system of the human genome. It is thus not surprising that chromosome-Y polymorphisms have been used to follow the migration patterns of our male ancestors from the recent past (Heyer et al. 1997; Foster et al. 1998) through historical times (Skorecki et al. 1997; Hammer et al. 2000), to the origins of modern humans (Hammer et al. 1998). Recently, two excellent review articles featuring the Y chromosome were published. The first (Bertranpetit 2000) addresses the difficulties of reliably tracing back human origins solely on the basis of Y-chromosomal UMEs. The second (Jobling and Tyler-Smith 2000) gives a detailed discussion of many genetic aspects of the Y chromosome in the context of disease and selection. This editorial will be restricted to the combined use of UMEs and STRs on the Y chromosome to reconstruct our genetic history. This application has received considerable attention in recent articles published in this journal and elsewhere (see, e.g., Zerjal et al. 1997; Bianchi et al. 1998; Hurles et al. 1998, 1999; Kittles et al. 1998; Bosch et al. 1999; Karafet et al. 1999; Lahermo et al. 1999; Ruiz-Linares et al. 1999; Helgason et al. 2000b; Hill et al. 2000; Santos et al. 2000). That the combined use of Y-chromosomal UMEs and STRs is not without any caveats will be explained below.

To the Editor:Tarazona-Santos et al. (2001xGenetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome. Tarazona-Santos, E, Carvalho-Silva, DR, Pettener, D, Luiselli, D, De Stefano, GF, Martinez Labarga, C, Richards, O, Tyler-Smith, C, Pena, SDJ, and Santos, F. Am J Hum Genet. 2001; 68: 1485–1496Abstract | Full Text | Full Text PDF | PubMed | Scopus (108)See all References2001) compute estimates of within- and among-group genetic variability for South Amerindian Y-chromosome samples that are thought to represent tribal populations living in various major geoecological regions of South America: the Andean highlands, the Brazilian plateau, the Chaco region, the Argentinian pampa, and the Chilean rain forest.The samples are agglomerated into two groups, one representing populations from the Andean highlands and the other representing populations from Amazonia, the Brazilian plateau, and the Chaco. Variability estimates are computed for both subdivisions and are consequently compared, with the Andean group exhibiting higher values. For apparently unjustified reasons, a sample from the tropical forest of Ecuador that has an Amazonian origin and exhibits the highest within-group variability is excluded from the analysis, unfortunately casting doubt on the reliability of the results.Various among-group variability estimates and their association with distances among map locations of places where samples were presumably collected are computed next. We are aware of the difficulties in obtaining Amerindian samples, but the extremely small size of some samples used in this study (the central Brazilian plateau is represented by five individuals) precludes the possibility that among-group variability statistics are unbiased estimators of population relationships. The lack of association between genetic and geographic distances may be a reflection of this shortcoming.On the basis of their results, Tarazona-Santos et al. (2001xGenetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome. Tarazona-Santos, E, Carvalho-Silva, DR, Pettener, D, Luiselli, D, De Stefano, GF, Martinez Labarga, C, Richards, O, Tyler-Smith, C, Pena, SDJ, and Santos, F. Am J Hum Genet. 2001; 68: 1485–1496Abstract | Full Text | Full Text PDF | PubMed | Scopus (108)See all References2001) conclude that two Y-chromosome microevolutionary models that involve differential patterns of genetic drift and gene flow characterize South Amerindians. Andean populations exhibit low rates of genetic drift and high rates of gene flow, whereas populations from Amazonia, the Brazilian plateau, and the Chaco exhibit high rates of drift and low rates of gene flow. It seems to us that this is a rash generalization, if it is based on the variability estimates presented in this study. Furthermore, it presupposes that non-Andean South Amerindian tribes living far apart, in markedly different geoecological areas, can be agglomerated and treated as one homogeneous group sharing the same population structure. We are not convinced that this is a realistic assumption.

Eight Y chromosome short tandem repeats (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II) were used to assess haplotype distribution in non-selected, unrelated Bantu males living in Central Africa [N. Mathias, M. Bayes, C. Tyler-Smith, Highly informative compound haplotypes for the human Y chromosome, Hum. Mol. Genet. 3 (1994) 115-123; L. Roewer, J. Arnemann, N.K. Spurr, K.H. Grzeschik, J.T. Epplen, Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts, Hum. Genet. 89 (1992) 389-394; P. De Knijff, M. Kayser, A. Caglia, D. Corach, N. Fretwel, C. Gehrig, G. Graziosi, F. Heidorn, S. Herrmann, B. Herzog, M. Hidding, K. Honda, M. Jobling, M. Krawczak, K. Leim, S. Meuser, E. Meyer, W. Oesterreich, A. Pandya, W. Parson, G. Penacino, A. Perez-Lezaun, A. Piccini, M. Prinz, C. Schmitt, P. M. Schneider, R. Szibor, J. Teifel-Greding, G. Weishold, L. Rower, Chromosome Y microsatellites: population genetic and evolutionary aspects, Int. J. Legal Med. 110 (1997) 134-149; M. Kayser, A. Caglia, D. Corach, N. Fretwel, C. Gehrig, G. Graziosi, F. Heidorn, S. Herrmann, B. Herzog, M. Hidding, K. Honda, M. Jobling, M. Krawczak, K. Leim, S. Meuser, E. Meyer, W. Oesterreich, A. Pandya, W. Parson, G. Penacino, A. Perez-Lezaun, A. Piccini, M. Prinz, C. Schmitt, P. M. Schneider, R. Szibor, J. Teifel-Greding, G. Weishold, P. de Knijff, L. Rower, Evaluation of Y chromosome STRs: a multicenter study, Int. J. Legal Med. 110 (1997) 125-133, 141-149]. One hundred and sixty-five full haplotypes were obtained from Bantu males. The most common haplotype (DYS19-15, DYS389I-13, DYS389II-30, DYS390-21, DYS391-10, DYS392-11, DYS393-13, DYS385I/II-15,17) was shared by 5.5% of individuals. In the Bantu population in Central Africa, the haplotype diversity and the discrimination capacity of Y-STR may be estimated at 99.14% and 0.5333, respectively.

The rush to get publishable units of raw data to consumers in human population genetics often translates into symposium papers that fail the test of time. However, this volume contains some gems within the field of anthropological genetics that connect historical accounts of human diversity that are based on serum protein electrophoresis with a deeper understanding of hybrid populations that emerges from the application of new technologies, including single-nucleotide polymorphisms (SNPs) and simple tandem repeats (STRs), to augment RFLPs, VNTRs, mtDNA, and Y haplotypes. What follows is a comprehensive and complementary set of essays that focus on genome systems in humans dispersed by geography and language. However, anyone expecting unanimity in interpretation of the signals that these different genetic systems yield for a given population may be surprised by a continued difficulty in assembling the final synthesis. If we compare two groups and discount the Y haplotypes, which conflict with the mtDNA, microsatellite data, and the SNPs, what are we left with? A final appeal to linguistics and archaeology for help documenting sexual selection or differential migration rates? The problem of discordant signals quickly surfaces in a comparative genetic study of five Brazilian tribal populations summarized by Hutz et al. Most geneticists, I suspect, prefer well-defended arguments based on extensive and appropriate sampling, relevant mathematical models, and deep understanding of molecular biology. Using this logic, we can discover whether the source of disparity unmasked with different molecular markers is truly a feature rooted in the history of the population examined or simply a peculiar and predictable genetic feature of the system targeted.For this reason, some of the most useful chapters (one on trinucleotide repeats, by Deka and Chakraborty; one on Y haplotypes, by Tyler-Smith; one on ancient DNA work, by Kolman; one on interspersed repeats, by Deininger et al.; and one on microsatellite statistics, by Chakraborty) do not focus on particular populations but reflect knowledge and judgment about particular systems with their advantages and shortcomings. I would wish for a cohort of beginning graduate students to routinely read these chapters before preparing theses proposals, so that expectations of advisor and student about the level of resolution possible with a given system more closely matches the experience of these experts in their respective fields. These particular chapters are also a valuable reminder to senior researchers about the need for healthy skepticism when it comes to evaluating fantastic media reports of new breakthroughs in human evolutionary biology. There are many unanswered questions in these chapters suggesting how chromatin architecture, recombination rates in haplotypes spanning similar lengths of sequence but drawn from different genomic regions, and responses to drift in uniparental systems possibly contribute to the disparity documented for American Indians of Brazil and other populations highlighted later in the volume.One case study illustrating the tough choices investigators must make when interpreting discordant data is seen in the very first chapter, by Papiha and Mastana. They explored the origins of the Sinhalese of Sri Lanka. Previous classical studies with protein markers suggested this population might be closely related to Bengalis from northeastern India, following oral traditions. However, this account was later disputed by additional protein studies showing that their closest relationship was actually with the Tamils of Southern India. Noteworthy in this dispute was the fact that the second study drew on Sinhalese and Tamil populations sampled from Singapore, not from Sri Lanka. VNTRs now support the original assertion of a migration from northeastern India, but six STRs from the three southern Indian tribal groups also examined indicate that populations in the south are strongly differentiated from each other. Equivalent STRs for Sinhalese or Tamils are not presented. Is this an instance of sex-biased dispersal coupled with simple genetic drift? Or does suspected disparity in sampling a gene pool from two nonequivalent sources now allow us to dismiss the dispute? The authors don’t state that they will be testing Y and mtDNA markers for a complete picture but imply that their four VNTR loci are a better predictor of dispersal than 15 classical protein markers. This will be an interesting case to follow.Hope that resolution will ultimately come stems from an exhaustive study of six STRs located on the Y chromosome in Turkish subjects (Rolf et al.). This report confirms that both Y and mtDNA haplotypes reveal the same percentage and source of admixture from East Asia, stemming from medieval times. Linguistic and historical records predicted such a result, but it was difficult to show with classical genetic markers and contributed to a general muddling of the picture concerning farmers and their origins in the Middle East, recalling the old dispute about Neolithic demic diffusion versus localized Paleolithic gene pools (which is more fully the subject of the highly informative but difficult-to-follow chapter on mtDNAs of the trans-Caucasus, by Metspalu et al.)Microsatellite analysis is the subject of an additional chapter examining the relationships between indigenous populations of Columbia and admixture with blacks and whites in the region. How many loci are necessary to dissect admixture and identify its sources? Guarino et al. show that nine are too few—or did they simply show that ABI's Profiler Plus PCR Multiplex System loci were the wrong nine to test? Understanding the location of these loci and the mutational forces to which they respond may be important for quantification of allelic truncation rates.Uniparental genome scenarios involving Y haplotypes included in this volume range from a localized focus (Pakistani men) to a more global view (using primarily haplogroups 3 [or M9-G] and 7 [or 92R-7 C]). Zerjal et al.’s male-focused worldview, combined with microsatellite analysis, helps flesh out the recent expansion of certain male lineages in haplogroup 3. However, the chapter by Mehdi et al. discussing present-day Pakistani populations contains a figure that may potentially cause dismay. It portrays genetic relationships as distances for 35 microsatellite loci and depicts African Pygmies in a trifurcation with other all human groups and chimpanzees. I am all for recognizing an African origin of modern humans, but this is an insensitive way to portray that hypothesis.The uniparental focus also extends to chapters on mtDNA. An attempt by Francalacci et al. to standardize the mtDNA world database is presented for haplogroups, but control-region sequences are restricted to HV1. This is useful for African, European, and some Asian populations but is of limited relevance for tribal populations of southeast Asia and Oceania, as well as for some American Indians. Europeans and central Asians are the primary subject of the contribution of Metspalau et al. on maternal markers. Finally, the chapter by Merriwether et al. on the mtDNAs of the southwest Pacific is a model of clarity and shows just how much information can still be extracted from a single, well-characterized genetic locus.To complete this set of chapters, Antunez-de Mayolo et al. explore the use of a unique Alu insertion in intron G of the progesterone-receptor gene to mark migrations in recent times. Sub-Saharan Africans and most East Asians lack this insertion, which is more common in Europeans and tribal populations from northern and western Asia. When the Americas are assayed, the Maya Campeche of Central America show frequencies comparable to those in modern Germans (.063 vs. .069), which the authors consider evidence of some Caucasian component to American Indian founder populations. This suggestion corroborates the finding of lineage X mtDNA haplotypes in both groups and our inability to map Siberian gene genealogies directly with American Indian ones.How does this volume stand up to others? It does not give a single worldview on the biogenetic basis of human diversity, as does the recent translation Genes, People, and Languages by L. L. Cavalli-Sforza (North Point Press, 2000). However, it is more detailed in many respects and is clearly meant for a different audience. With the recent explosion of haplotypes from the Y chromosome, we have more powerful means of examining who moves where and why. For the next 2 years, however, Genomic Diversity will be an excellent place to begin, with signposts to the past for those who seek to learn from the mistakes of others.