Y chromosome sequence variation and the history of human populations

  title={Y chromosome sequence variation and the history of human populations},
  author={Peter A. Underhill and Peidong Shen and Alice A. Lin and Li Jin and Giuseppe Passarino and Wei Hai Yang and Erin Kauffman and Batsheva Bonn{\'e}‐Tamir and Jaume Bertranpetit and Paolo Francalacci and Muntaser E. Ibrahim and Trefor Jenkins and Judith R. Kidd and Syed Qasim Mehdi and Mark Seielstad and R. Spencer Wells and Alberto Piazza and Ronald W. Davis and Marcus W. Feldman and Luca L. Cavalli-Sforza and Peter J. Oefner},
  journal={Nature Genetics},
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… 

The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

A set of unique event polymorphisms associated with the non‐recombining portion of the Y‐chromosome (NRY) addresses this issue by providing evidence concerning successful migrations originating from Africa, which can be interpreted as subsequent colonizations, differentiations and migrations overlaid upon previous population ranges.

History and geography of human Y-chromosome in Europe: a SNP perspective.

The distribution of distinctive Y-chromosome lineages can also display a correspondence with geography, thus providing patterns of affinity and clues concerning past human movements, and it is therefore possible to recognize the effect of the colonization of Europe following the Last Glacial Maximum.

Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation.

The population genetic history of a 10.1-kbp noncoding region of the human X chromosome was studied using the males of the HGDP-CEPH Human Genome Diversity Panel to address the presence of hX in Africa.

The Eurasian Heartland: A continental perspective on Y-chromosome diversity

This study reports the frequencies of 23 Y-chromosome biallelic polymorphism haplotypes in 1,935 men from 49 Eurasian populations, with a particular focus on Central Asia.

Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers.

Variation at di-, tri-, and tetranucleotide repeat loci is distributed differently, although each class of markers exhibits a decrease of within-population genetic variation in the following order: sub-Saharan Africa, Eurasia, East Asia, Oceania, and America.

Use of y chromosome and mitochondrial DNA population structure in tracing human migrations.

This work compares and contrast uniparentally inherited loci for patterns of continuity and discreteness and discusses how their phylogenetic diversity and progression provide means to disentangle ancient colonization events by pioneering migrants from subsequent overlying migrations.

Reconstruction of human evolutionary tree using polymorphic autosomal microsatellites.

It is shown that the microsatellite allelic diversity and the number of unique alleles were highest in sub-Saharan Africans, and that the San are the first branch of the human tree before the branch leading to all other Africans.

Maori origins, Y‐chromosome haplotypes and implications for human history in the Pacific

The Y‐chromosome results support a pattern of complex interrelationships between Southeast Asia, Melanesia, and Polynesia, in contrast to mtDNA and linguistic data, which uphold a rapid and homogeneous Austronesian expansion.

A new haplogroup pattern displayed in Fujian Han in China

The results indicated that the M9G marker was highly prevalent (96.20%), suggesting a significant genetic drift, and the distinctive haplogroups frequencies imply that the haplogroup pattern is a relatively ancestral and interim type.

A Recent Shift from Polygyny to Monogamy in Humans Is Suggested by the Analysis of Worldwide Y-Chromosome Diversity

It is shown that mismatch distributions and tests of mutation/drift equilibrium based on up to 166 Y-chromosome SNPs, in 46 samples from all continents, also fail to support an increase of the male effective population size.



The role of the Y chromosome in human evolutionary studies

The addition of DNA sequencining survey data to the rapidly growing RFLP data base made it feasible for the first time to determine the exact number of nucleotide substitutions between different alleles, as well as to construct gene trees and reconstruct the phylogenetic history of populations.

Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations.

A 565-bp chromosome 21 region near the MX1 gene, which contains nine sites frequently polymorphic in human populations, has been found, unaffected by recombination and recurrent mutation and thus reflects only migratory history, genetic drift, and possibly selection.

Recent common ancestry of human Y chromosomes: evidence from DNA sequence data.

It is estimated that the spread of Y chromosomes out of Africa is much more recent than previously was thought, and the data indicate substantial population growth in the effective number of human Y chromosomes.

The geographic distribution of human Y chromosome variation.

Variation on the nonrecombining portion of the human Y chromosome is examined to investigate human evolution during the last 200,000 years, compatible with a variety of hypotheses, including multiple human migrations and range expansions.

The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data.

Analysis of worldwide genetic variation among 255 individuals by using autosomal, mitochondrial, and Y-chromosome polymorphisms reveals substantial congruity among this diverse array of genetic systems and offers broad support for an African origin of modern human populations.

Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis.

The Y chromosome provides both information about population relationships in Asia and evidence for a substantial paternal genetic contribution of Asians to northern European populations such as the Finns.

Y chromosomal DNA variation and the peopling of Japan.

Four loci mapping to the nonrecombining portion of the Y chromosome were genotyped in Japanese populations from Okinawa, the southernmost island of Japan; Shizuoka and Aomori on the main island of Honshu; and a small sample of Taiwanese, confirming the irregular distribution of this polymorphism in Asia.

Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition.

An apparently African Y chromosome which seems to have entered a Mexican Mayan population several generations ago is analyzed and how the chromosome's haplotype information might be used to answer questions of human origins and migrations is discussed.

Population genetic implications from sequence variation in four Y chromosome genes.

  • P. ShenF. Wang P. Oefner
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
Analysis of the frequencies of derived alleles for all four genes showed that they more closely fit the expectation of a Luria-Delbrück distribution than a distribution expected under a constant population size model, providing evidence for exponential population growth.

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation.

It is inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model.