R. Spencer Wells

Y chromosome sequence variation and the history of human populations

Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.

The dawn of human matrilineal diversity.

The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000-70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.

The Genetic Legacy of the Mongols

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: approximately 8% of the men in this region carry it, and it thus makes up approximately 0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia approximately 1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

A Genetic Landscape Reshaped by Recent Events: Y-Chromosomal Insights into Central Asia

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.

Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages

Mitochondrial DNA (mtDNA) lineages of 232 individuals from 12 Central Asian populations were sequenced for both control region hypervariable segments, and additional informative sites in the coding region were also determined. Most of the mtDNA lineages belong to branches of the haplogroups with an eastern Eurasian (A, B, C, D, F, G, Y, and M haplogroups) or a western Eurasian (HV, JT, UK, I, W, and N haplogroups) origin, with a small fraction of Indian M lineages. This suggests that the extant genetic variation found in Central Asia is the result of admixture of already differentiated populations from eastern and western Eurasia. Nonetheless, two groups of lineages, D4c and G2a, seem to have expanded from Central Asia and might have their Y-chromosome counterpart in lineages belonging to haplotype P(xR1a). The present results suggest that the mtDNA found out of Africa might be the result of a maturation phase, presumably in the Middle East or eastern Africa, that led to haplogroups M and N, and subsequently expanded into Eurasia, yielding a geographically structured group of external branches of these two haplogroups in western and eastern Eurasia, Central Asia being a contact zone between two differentiated groups of peoples.

The Genographic Project public participation mitochondrial DNA database.

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.

Y-Chromosomal Diversity in Lebanon Is Structured by Recent Historical Events

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 11th–13th centuries CE introduced western European lineages into Lebanese Christians.

Parallel Evolution of Genes and Languages in the Caucasus Region

We analyzed 40 single nucleotide polymorphism and 19 short tandem repeat Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation, and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language coevolution occurred within geographically isolated populations, probably due to its mountainous terrain.

A Novel Y-Chromosome Variant Puts an Upper Limit on the Timing of First Entry into the Americas

To the Editor: The Americas were the last continents to be settled by humans, yet many details of the earliest occupation remain poorly understood. Proposals for the date of first entry fall into two ranges, one suggesting a very early occupation ∼30,000–40,000 years before present (BP), and the other favoring dates ∼13,000 years BP, when the polar climate was again hospitable. We present Y-chromosomal data that support strongly the latter dates. Recent activity in archeology has prompted a reinterpretation of the economy and culture of the earliest Americans (Dillehay 2000). Although this has revolutionized thinking about American prehistory, it has not pushed dates for the earliest human entry substantially backward in time. Indeed, the paucity of sites and skeletal material credibly dated to >14,000 years BP has been a consistent puzzle for those who would posit an extremely ancient history of human occupation in the Americas. Only two Y-chromosome haplotypes seem to have reached the Americas from Asia before colonial contacts began in the 15th century. The most frequent haplotype—reaching a frequency of 100% in some populations—was identified by hypervariable markers (Pena et al. 1995) and was later confirmed by the discovery of two SNPs known as “M3” and “M45” (Underhill et al. 1996, 2000). A second haplotype, marked by a nucleotide substitution in the RPS4Y gene, was subsequently discovered at lower frequencies (Bergen et al. 1999), presumably reaching the Americas more recently. This pattern of limited haplotype diversity has also been observed in mtDNA (Torroni et al. 1994). Putting a date on the earliest human entry into the continent has been hampered by the absence of a known mutation occurring before—but very close to—the time that the resulting haplotype entered the Americas. The M3/DYS199 polymorphism occurred after the first populations entered the Americas (Underhill et al. 1996), so knowing when it arose would not put an upper bound on the time of first colonization. Here, we describe a novel Y-chromosome SNP that can be reliably dated and that occurred before—but sufficiently close in time to—the initial human radiation into the Americas, so as to provide a meaningful upper bound on the time of entry. The polymorphism, which we call “M242” in the framework established by Underhill et al. (2000) (dbSNP accession number ss9805824), is a C→T transition residing in intron 1 (IVS-866) of the DBY gene. The M242-T allele is found only on chromosomes bearing the derived alleles at M45 and M74 (fig. 1). In addition, the derived allele (M242-T) is found on every chromosome bearing the M3 mutation, but not exclusively. Thus, as shown in figure 1, the M242 mutation arose after the M45/M74 mutations but before M3. This places it within a crucial gap that is very close in time to the entry of the first modern humans into the American continents. In the standard nomenclatural system of the Y Chromosome Consortium (2002), chromosomes bearing this polymorphism would be denoted as Q* in the absence of the Qa-defining mutation. The derived allele of M242 occurs at a frequency of 100% in indigenous Y chromosomes that do not carry the RPS4Y mutation (Bortolini et al. 2003 [in this issue]; P.U., unpublished data). It also occurs at a low but appreciable frequency (0%–17%; average ∼5%) in central Asian, Indian, and Siberian populations (table 1). On the basis of its widespread Eurasian distribution and its position within the Y-chromosome phylogeny (fig. 1), it is clear that the M242 mutation occurred before the first migration into the Americas. Thus, determining its age in Asian populations will establish the earliest time at which the first migrants could have reached the Americas. Figure 1 Partial revision of the Y-chromosome phylogeny presented by Underhill et al. (2000), indicating the placement of M242 relative to other Y-chromosome polymorphisms in haplogroups IX and X, arising in central Asia and the Americas. As can be seen, M242 ... Table 1 Frequency of M242 in 49 Populations Examined[Note] We applied several approaches to dating this mutation in 69 Eurasian samples—out of a total 1,935 individuals tested—observed to have the M242-T allele (table 2 and Wells et al. 2001). These methods are based on the accumulation of variation at 15 microsatellite loci. One approach is a widely used, model-based technique (Su et al. 1999), which was corroborated independently by a technique less dependent on assumptions about a population’s demographic history (Stumpf and Goldstein 2001). Guided by the original description of the method (Su et al. 1999), the initial effective population size (Ne) for the Asian male population was assumed to fall between a low of 1,111 and a high of 1,500. If a Y-chromosome microsatellite mutation rate of 0.18% and a human generation time (g) of 25 years are used, this leads to an estimate of 9,200–9,700 years BP, when the average variance across all microsatellite loci is taken (0.589). Although a male generation time of 25 years is frequently assumed, there is now compelling evidence that the male generation time—at least within modern times—is closer to 32 or 35 years (Tremblay and Vezina 2000; Helgason et al. 2003). When a generation time of 35 years is applied, the age estimates range from 13,000 to 14,000 years BP (table 3). As can be seen from the table, the estimates of effective population size have a relatively minor effect on age estimates, whereas mutation rates have a somewhat greater impact. A solid consensus regarding an average Y-chromosome microsatellite mutation rate, for mostly the same loci used in the present study, is developing around a rate of 0.18%–0.20% per generation (Heyer et al. 1997; Kayser et al. 2000). The best estimates of the age of the M242 mutation when this method is used appear to center on the 14,000–15,000-year range. A significant drawback of this method is its lack of a clear approach for calculating standard errors. Table 2 Microsatellite Genotypes for 69 M242-Bearing Chromosomes Identified in the Populations Listed in Table 1 Table 3 Estimated Ages of M242 for a Range of Male Generation Times, Y-Chromosome Microsatellite Mutation Rates, and Effective Population Sizes, Calculated Using the Method of Su et al. (1999) Although this method is now well established for a range of demographic scenarios, we wanted to compare these estimates with those from an entirely different method—one that is insensitive to assumptions of Ne and population growth rate (Stumpf and Goldstein 2001). This approach relies on an inference of the ancestral microsatellite haplotype, which we identified as the haplotype with the most frequent allele at each locus. Again using a mutation rate of 0.18% per generation, we estimate the age of the M242 mutation to be 15,000 years BP, averaged over each of the 15 loci (table 4). The SD for this average estimate is only 1,700 years, which definitively precludes an arrival time of ⩾30,000 years BP. Table 4 shows the results obtained when a variety of mutation rates and generation times are used, and here, too, our best estimate of the mutation’s age is ∼18,000 years BP. This establishes a fairly solid upper bound on the time of first entry into the Americas that seems to preclude a time of entry >20,000 years BP, and our best guess would be closer to 15,000–18,000 years BP. Since our estimate derives solely from the ancestral Asian populations, it is unaffected by changes of diversity occurring after European conquest of the Americas. Even demographic changes that occurred in central Asia and Siberia after Russians established greater sway in the region are likely to have had a minor effect, because we have sampled haplotype diversity over such a huge geographic area. Furthermore, microsatellite diversity on the M242-bearing haplotype in several Native American populations (Bortolini et al. 2003 [in this issue]) is nearly the same as in our Asian sample, substantiating our result and suggesting that the M242-T haplotype entered the Americas very soon after it arose. Table 4 Estimated Age of M242 for a Range of Male Generation Times and Y-Chromosome Microsatellite Mutation Rates, Calculated Using the Method of Stumpf and Goldstein (2001) This discovery, which indicates a rather more recent entry into the Americas than suggested by previous genetic studies (Cavalli-Sforza et al. 1994; Torroni et al. 1994), places the DNA evidence more in line with archeological data, which is characterized by a clear dearth of sites credibly dated beyond 14,000 years BP. Our results do not contradict earlier studies of mtDNA (Torroni et al. 1994) and the autosomes (Cavalli-Sforza et al. 1994), whose standard errors were large and whose authors noted several reasons to expect their dates to overestimate the timing of the first human arrivals to the Americas. In addition, a more recent time of entry into the continent makes the proposal of the Amerind language family more plausible; or, conversely—given the rapidity of linguistic change—the existence of a unified Amerind family would itself imply a fairly recent settling of the Americas, as we have suggested here.

Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean

The Phoenicians were the dominant traders in the Mediterranean Sea two thousand to three thousand years ago and expanded from their homeland in the Levant to establish colonies and trading posts throughout the Mediterranean, but then they disappeared from history. We wished to identify their male genetic traces in modern populations. Therefore, we chose Phoenician-influenced sites on the basis of well-documented historical records and collected new Y-chromosomal data from 1330 men from six such sites, as well as comparative data from the literature. We then developed an analytical strategy to distinguish between lineages specifically associated with the Phoenicians and those spread by geographically similar but historically distinct events, such as the Neolithic, Greek, and Jewish expansions. This involved comparing historically documented Phoenician sites with neighboring non-Phoenician sites for the identification of weak but systematic signatures shared by the Phoenician sites that could not readily be explained by chance or by other expansions. From these comparisons, we found that haplogroup J2, in general, and six Y-STR haplotypes, in particular, exhibited a Phoenician signature that contributed > 6% to the modern Phoenician-influenced populations examined. Our methodology can be applied to any historically documented expansion in which contact and noncontact sites can be identified.