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Human population structure and its effects on sampling Y chromosome sequence variation.

Michael F Hammer1, Felisa Blackmer, Dan Garrigan

  • 1Genomic Analysis and Technology Core, Division of Biotechnology, Biosciences West Building, University of Arizona, Tucson, AZ 85721, USA. mhammer@u.arizona.edu

Genetics
|August 22, 2003
PubMed
Summary

Global Y chromosome studies may overestimate human population expansion due to geographical sampling biases. Rare variants on the nonrecombining portion of the Y chromosome (NRY) show patterns influenced by sampling, questioning previous demographic inferences.

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Area of Science:

  • Human evolutionary genetics
  • Population genetics
  • Genomics

Background:

  • Global sequencing studies of the nonrecombining Y chromosome (NRY) suggest human demographic expansion.
  • However, NRY polymorphisms are often geographically localized, and the impact of sampling strategy on variation patterns is unclear.

Purpose of the Study:

  • To investigate the influence of geographical sampling designs on patterns of human NRY polymorphism.
  • To assess whether population structure, independent of demographic expansion, can explain observed NRY variation.

Main Methods:

  • Sequencing of 26.5 kb of noncoding Y chromosome DNA from 92 males across 35 global populations.
  • Sequencing the same region in 73 males from 3 distinct populations.
  • Coalescent simulations to model population structure effects.

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Main Results:

  • The number of singleton variants positively correlated with the number of populations sampled globally.
  • Tajima's D and Fu and Li's D statistics showed significant negative correlations with the number of pooled populations in global samples.
  • TD and FD values were less negative in samples from 3 distinct populations compared to the global sample.
  • Coalescent simulations indicated that population splitting alone can generate negative TD values.

Conclusions:

  • Observed NRY population structure can create an upward bias in singleton variants in global surveys.
  • Inferences of human demographic expansion based on global NRY sampling strategies may be unreliable.
  • Geographical sampling design significantly impacts the interpretation of human NRY variation data.