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Mark Stoneking

Publications and source records attributed to Mark Stoneking.

At least 37 records · Page 2Linked to original sources
PubMed2004

Independent origins of Indian caste and tribal paternal lineages.

The origins of the nearly one billion people inhabiting the Indian subcontinent and following the customs of the Hindu caste system are controversial: are they largely derived from Indian local populations (i.e. tribal groups) or from recent immigrants to India? Archaeological and linguistic evidence support the latter hypothesis, whereas recent genetic data seem to favor the former hypothesis. Here, we analyze the most extensive dataset of Indian caste and tribal Y chromosomes to date. We find that caste and tribal groups differ significantly in their haplogroup frequency distributions; caste groups are homogeneous for Y chromosome variation and more closely related to each other and to central Asian groups than to Indian tribal or any other Eurasian groups. We conclude that paternal lineages of Indian caste groups are primarily descended from Indo-European speakers who migrated from central Asia approximately 3,500 years ago. Conversely, paternal lineages of tribal groups are predominantly derived from the original Indian gene pool. We also provide evidence for bidirectional male gene flow between caste and tribal groups. In comparison, caste and tribal groups are homogeneous with respect to mitochondrial DNA variation, which may reflect the sociocultural characteristics of the Indian caste society.

Analysis of Variance↗
PubMed2004

A comprehensive survey of human Y-chromosomal microsatellites.

We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.

Chromosomes, Human, Y↗
PubMed2004

Development of Y-chromosomal microsatellite markers for nonhuman primates.

We have analysed 136 newly identified human Y-chromosomal microsatellites in five (sub)species of nonhuman primates. We identified 83 male-specific loci for central chimpanzees, 82 for western chimpanzees, 67 for gorillas, 45 for orangutans and 19 loci for mandrills. Polymorphism was detected at 56 loci in central chimpanzees, 29 in western chimpanzees, 24 in western gorillas, 17 in orangutans and at three in mandrills. Success in male-specific amplification of human Y-chromosomal microsatellites in nonhuman primates was significantly negatively correlated with divergence time from the human lineage. We observed significantly more Y-chromosomal microsatellite diversity in central chimpanzees than in western chimpanzees. There were significantly more male-specific loci with longer alleles in humans than with longer alleles in the nonhuman primates; however, this significant difference disappeared when only the loci which are polymorphic in nonhuman primates were analysed, suggesting that ascertainment bias is responsible. This study provides primatologists with a large number of polymorphic, male-specific microsatellite markers that will be valuable for investigating relevant questions in behavioural ecology such as male reproductive strategies, kin-based cooperation among males and male-specific dispersal patterns in wild groups of nonhuman primates.

Animals↗
PubMed2004

Y-STR haplotypes from eight south Indian groups based on five loci.

Five Y-chromosome short tandem repeat (STR) loci (DYS389I, DYS389II, DYS390, DYS391, and DYS393) were typed in 81 males from seven tribal populations of south India, including 30 Koragas, 23 Yeravas, 5 Mullukurunan, 2 Mullukurumba, 4 Paniya, 3 Kuruchian and 3 Bettakurumba; and 11 south Indian caste individuals of mixed origins.

Chromosomes, Human, Y↗
PubMed2003

Molecular evolution of Pediculus humanus and the origin of clothing.

The human head louse (Pediculus humanus capitis) and body louse (P. humanus corporis or P. h. humanus) are strict, obligate human ectoparasites that differ mainly in their habitat on the host : the head louse lives and feeds exclusively on the scalp, whereas the body louse feeds on the body but lives in clothing. This ecological differentiation probably arose when humans adopted frequent use of clothing, an important event in human evolution for which there is no direct archaeological evidence. We therefore used a molecular clock approach to date the origin of body lice, assuming that this should correspond with the frequent use of clothing. Sequences were obtained from two mtDNA and two nuclear DNA segments from a global sample of 40 head and body lice, and from a chimpanzee louse to use as an outgroup. The results indicate greater diversity in African than non-African lice, suggesting an African origin of human lice. A molecular clock analysis indicates that body lice originated not more than about 72,000 +/- 42,000 years ago; the mtDNA sequences also indicate a demographic expansion of body lice that correlates with the spread of modern humans out of Africa. These results suggest that clothing was a surprisingly recent innovation in human evolution.

Africa↗
PubMed2003

A genome scan to detect candidate regions influenced by local natural selection in human populations.

As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic variation. A potential approach for detecting local selection is to screen random loci across the genome; those loci that exhibit unusually large genetic distances between human populations are then potential markers of genomic regions under local selection. We investigated this approach by genotyping 332 short tandem repeat (STR) loci in Africans and Europeans and calculating the genetic differentiation for each locus. Patterns of genetic diversity at these loci were consistent with greater variation in Africa and with local selection operating on populations as they moved out of Africa. For 11 loci exhibiting the largest genetic differences, we genotyped an additional STR locus located nearby; the genetic distances for these nearby loci were significantly larger than average. These genomic regions therefore reproducibly exhibit larger genetic distances between populations than the "average" genomic region, consistent with local selection. Our results demonstrate that genome scans are a promising means of identifying candidate regions that have been subjected to local selection.

Genetics, Population↗
PubMed2003

Mitochondrial DNA evidence for admixed origins of central Siberian populations.

The Yakuts of northeastern Siberia are a Turkic-speaking population of horse- and cattle-breeders surrounded by Tungusic-speaking reindeer-herders and hunter-gatherers. Archaeological and ethnohistorical data suggest that Yakuts stem from a common ancestral population with the Buryats living near Lake Baikal. To address this hypothesis, we obtained sequences of the first hypervariable segment (HV1) of the mitochondrial DNA control region from Yakuts and Buryats and compared these with sequences from other Eurasian populations. The mtDNA results show that the Buryats have close affinities with both Central Asian Turkic groups and Mongols, while the Yakuts have close affinities with northeastern Siberian, Tungusic-speaking Evenks and south Siberian, Turkic-speaking Tuvans. This different ancestry of the Yakuts and the Tuvans (compared with other Turkic-speaking groups) most likely reflects extensive admixture that occurred between Turkic-speaking steppe groups and Evenks as the former migrated into Siberia. Moreover, the Yakuts are unique among Siberian populations in having a high number of haplotypes shared exclusively with Europeans, suggesting, contrary to the historical record, that occasionally Yakut men took Russian women as wives.

Base Sequence↗
PubMed2003

Mitochondrial DNA analysis reveals diverse histories of tribal populations from India.

We analyzed 370 bp of the first hypervariable region of the mitochondrial DNA (mtDNA) control region in 752 individuals from 17 tribal and four nontribal groups from the Indian subcontinent, to address questions concerning the origins, genetic structure and relationships of these groups. Southern Indian tribes showed reduced diversity and large genetic distances, both among themselves and when compared with other groups, and no signal of prehistoric demographic expansions. These results probably reflect enhanced genetic drift because of small population sizes and/or bottlenecks in these groups. By contrast, northern groups exhibited more diversity and signals of prehistoric demographic expansions. Phylogenetic analyses revealed that southern and northern groups (except northeastern ones) have related mtDNA sequences albeit at different frequencies, further supporting the larger impact of drift on the genetic structure of southern groups. The Indian mtDNA gene pool appears to be more closely related to the east Eurasian gene pool (including central, east and southeast Asian populations) than the west Eurasian one (including European and Caucasian populations). Within India, northeastern tribes are quite distinct from other groups; they are more closely related to east Asians than to other Indians. This is consistent with linguistic evidence in that these populations speak Tibeto-Burman languages of east Asian origin. Otherwise, analyses of molecular variance suggested that caste and tribal groups are genetically similar with respect to mtDNA variation.

Cluster Analysis↗
PubMed2003

Apparent intrachromosomal exchange on the human Y chromosome explained by population history.

The human Y chromosome displays an unusual content of repetitive sequences. Y-chromosomal repeats are potential targets for intrachromosomal recombination, which is thought to be involved in a number of Y-associated defects, such as male infertility. Such rearrangements could potentially be investigated by the use of highly polymorphic DNA markers located within the repeat units, such as microsatellites. Here we analyse the two copies of the Y-chromosomal microsatellite DYS385, which we identified and localized to an approximately 190 kb duplicated and inverted fragment at Yq11.223. We found a highly significant correlation (r=0.853, P&<0.001) and a nonsignificant difference in a chi(2)-test (chi(2)=15.45, P>0.05) between the allele frequency distributions at both copies of the Y-STR in a German population sample (n=70). Such nearly identical allele frequency distribution between two copies of a duplicated highly polymorphic microsatellite cannot be explained by the independent mutational process that creates microsatellite alleles. Instead, this might be interpreted as evidence for a reciprocal intrachromosomal exchange process between the duplicated fragments. However, more detailed analyses using additional human populations as well as additional Y chromosome markers revealed that this phenomenon is highly population-specific and disappears completely when Y-STR diversity is analysed in association with two Y-SNP haplogroups. We found that the diversity of the two DYS385 loci (and other Y-STRs) is highly depending on the haplogroup background, and that equal proportions of both haplogroups in the German sample explains the nearly identical allele frequency distributions at the two DYS385 loci. Thus, we demonstrate here that allele frequency distributions at duplicate loci that are suggestive of intrachromosomal recombination can be explained solely by population history.

Chromosome Mapping↗
PubMed2003

Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry.

To investigate geographic structure within U.S. ethnic populations, we analyzed 1705 haplotypes on the basis of 9 short tandem repeat (STR) loci on the Y-chromosome from 9-11 groups each of African-Americans, European-Americans, and Hispanics. There were no significant differences in the distribution of Y-STR haplotypes among African-American groups, whereas European-American and Hispanic groups did exhibit significant geographic heterogeneity. However, the significant heterogeneity resulted from one sample; removal of that sample in each case eliminated the significant heterogeneity. Multidimensional scaling analysis of R(ST) values indicated that African-American groups formed a distinct cluster, whereas there was some intermingling of European-American and Hispanic groups. MtDNA data exist for many of these same groups; estimates of the European-American genetic contribution to the African-American gene pool were 27.5%-33.6% for the Y-STR haplotypes and 9%-15.4% for the mtDNA types. The lack of significant geographic heterogeneity among Y-STR and mtDNA haplotypes in U.S ethnic groups means that forensic DNA databases do not need to be constructed for separate geographic regions of the U.S. Moreover, absence of significant geographic heterogeneity for these two loci means that regional variation in disease susceptibility within ethnic groups is more likely to reflect cultural/environmental factors, rather than any underlying genetic heterogeneity.

Africa↗
PubMed2002

Testing hypotheses of language replacement in the Caucasus: evidence from the Y-chromosome.

A previous analysis of mtDNA variation in the Caucasus found that Indo-European-speaking Armenians and Turkic-speaking Azerbaijanians were more closely related genetically to other Caucasus populations (who speak Caucasian languages) than to other Indo-European or Turkic groups, respectively. Armenian and Azerbaijanian therefore represent language replacements, possibly via elite dominance involving primarily male migrants, in which case genetic relationships of Armenians and Azerbaijanians based on the Y-chromosome should more closely reflect their linguistic relationships. We therefore analyzed 11 bi-allelic Y-chromosome markers in 389 males from eight populations, representing all major linguistic groups in the Caucasus. As with the mtDNA study, based on the Y-chromosome Armenians and Azerbaijanians are more closely-related genetically to their geographic neighbors in the Caucasus than to their linguistic neighbors elsewhere. However, whereas the mtDNA results show that Caucasian groups are more closely related genetically to European than to Near Eastern groups, by contrast the Y-chromosome shows a closer genetic relationship with the Near East than with Europe.

Adult↗
PubMed2002

Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea.

To investigate the paternal population history of New Guinea, 183 individuals from 11 regional populations of West New Guinea (WNG) and 131 individuals from Papua New Guinea (PNG) were analyzed at 26 binary markers and seven short-tandem-repeat loci from the nonrecombining part of the human Y chromosome and were compared with 14 populations of eastern and southeastern Asia, Polynesia, and Australia. Y-chromosomal diversity was low in WNG compared with PNG and with most other populations from Asia/Oceania; a single haplogroup (M-M4) accounts for 75% of WNG Y chromosomes, and many WNG populations have just one Y haplogroup. Four Y-chromosomal lineages (haplogroups M-M4, C-M208, C-M38, and K-M230) account for 94% of WNG Y chromosomes and 78% of all Melanesian Y chromosomes and were identified to have most likely arisen in Melanesia. Haplogroup C-M208, which in WNG is restricted to the Dani and Lani, two linguistically closely related populations from the central and western highlands of WNG, was identified as the major Polynesian Y-chromosome lineage. A network analysis of associated Y-chromosomal short-tandem-repeat haplotypes suggests two distinct population expansions involving C-M208--one in New Guinea and one in Polynesia. The observed low levels of Y-chromosome diversity in WNG contrast with high levels of mtDNA diversity reported for the same populations. This most likely reflects extreme patrilocality and/or biased male reproductive success (polygyny). Our data further provide evidence for primarily female-mediated gene flow within the highlands of New Guinea but primarily male-mediated gene flow between highland and lowland/coastal regions.

Chromosomes, Human, Y↗
PubMed2002

A whole genome amplification method to generate long fragments from low quantities of genomic DNA.

Several whole genome amplification strategies have been developed to preamplify the entire genome from minimal amounts of DNA for subsequent molecular genetic analysis. However, none of these techniques has proven to amplify long products from very low (nanogram or picogram) quantities of genomic DNA. Here we report a new whole genome amplification protocol using a degenerate primer (DOP-PCR) that generates products up to about 10 kb in length from less than 1 ng genomic template DNA. This new protocol (LL-DOP-PCR) allows in the subsequent PCR the specific amplification, with high fidelity, of DNA fragments that are more than 1 kb in length. LL-DOP-PCR provides significantly better coverage for microsatellites and unique sequences in comparison to a conventional DOP-PCR method.

DNA↗
PubMed2002

Extreme mtDNA homogeneity in continental Asian populations.

Mitochondrial DNA (mtDNA) variation in continental Asia has not been well-studied. Here, we report mtDNA HV1 sequences for 84 Xi'an and 82 Changsha Han Chinese, 89 Honshu Japanese, and 35 Vietnamese. Comparison of these sequences with other Asian mtDNA sequences reveals high variability within populations, but extremely low differentiation among Asian populations. Correlations between genetic distance and geographic distance, based on mtDNA and Y chromosome variation, indicate a higher migration rate in females than in males. This may reflect patrilocality, as suggested previously, but another plausible hypothesis is that the demographic expansion associated with the spread of agriculture in Asia may be responsible for the extreme genetic homogeneity in Asia.

Asia↗
PubMed2002

Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms.

Previous studies have reported that about 85% of human diversity at Short Tandem Repeat (STR) and Restriction Fragment Length Polymorphism (RFLP) autosomal loci is due to differences between individuals of the same population, whereas differences among continental groups account for only 10% of the overall genetic variance. These findings conflict with popular notions of distinct and relatively homogeneous human races, and may also call into question the apparent usefulness of ethnic classification in, for example, medical diagnostics. Here, we present new data on 21 Alu insertions in 32 populations. We analyze these data along with three other large, globally dispersed data sets consisting of apparently neutral biallelic nuclear markers, as well as with a beta-globin data set possibly subject to selection. We confirm the previous results for the autosomal data, and find a higher diversity among continents for Y-chromosome loci. We also extend the analyses to address two questions: (1) whether differences between continental groups, although small, are nevertheless large enough to confidently assign individuals to their continent on the basis of their genotypes; (2) whether the observed genotypes naturally cluster into continental or population groups when the sample source location is ignored. Using a range of statistical methods, we show that classification errors are at best around 30% for autosomal biallelic polymorphisms and 27% for the Y chromosome. Two data sets suggest the existence of three and four major groups of genotypes worldwide, respectively, and the two groupings are inconsistent. These results suggest that, at random biallelic loci, there is little evidence, if any, of a clear subdivision of humans into biologically defined groups.

Alleles↗