1. Using the Y chromosome to infer ethnicity and regional identification
Bram Bekaert
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YCC Nomenclature
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What is ethnicity?
SKIN COLOUR
CULTURE
GEOGRAPHICAL AREA
LANGUAGE
RELIGION
RACE
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4. Compact Oxford English dictionary
Ethnic
1 relating to a group of people having a common national or cultural tradition.
2 referring to origin by birth rather than by present nationality: ethnic Albanians.
3 relating to a non-Western cultural tradition: ethnic music.
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Ethnicity
But can someone with a white skin have African mtDNA, an Asian Y-chromosome, speak English, be Jewish and live in Belgium?
Of course.
How will we be able to infer ethnicity from an individual such as this one?
What markers can we use to determine that he is in fact a white Caucasian for forensic purposes?
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Ethnicity
Ethnicity = race
Ethnicity = geographical location
Ethnicity = language …
What we need is a phenotypical characteristic marker which is genetically determinable.
Ethnicity: population studies
Determining to which population an individual probably belongs
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History
Private alleles (Neel 1973)
Ideal alleles (Reed 1973)
Unique alleles (Chakraborty 1991)
Population-specific alleles (Shriver 1997)
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Shriver et al. 1997
PSAs or AIMs
Genetic markers with large allele-frequency differentials (δ)
δ = px – qy = qy – qx
px and qy frequencies of one allele in population X and Y and qy and qx are the frequencies of the other allele
‘large’ frequency differential is >50%
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PSAs RFLP loci
FY-null
RV2300
LPL
CKMM
PV92
DRD2
High African/European
and African/ Amerindian δ levels
Amerindian/African
and Amerindian/European δ levels
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PSAs STRs
D7S657 has a δ of .745 between European Americans ad African Americans
D1S255 has a δ of .524 between European Americans and Hispanic Americans
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Why the Y-chromosome?
High degree of geographic differentiation compared with other parts of the genome
Lower sequence diversity
Drift
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Why Y-chromosome?
Greater effective migration of women
(70% Patrilocality)
Mutation, not recombination.
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13. C’est quoi la cause? Les langues?
Do genetic barriers occur because of language barriers?
Not the primary force according Rosser (2000)
Analysed 3,616 men from 47 populations to study the Y-chromosomal diversity
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If everybody is different from everyone (has different haplotypes) or nearly so, population affiliation is likely to have become obscured
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15. Other conclusions by Rosser (2000)
The effects of drift on Y-chromosome diversity are likely to be great
But it has not erased the patterns of variation established by past population movement
HG 3 chromosomes are absent from Africa and the Americas but have wide distribution within Asia as well as in Europe
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Roewer et al. 1996
First to demonstrate informativeness of Y-STRs.
With 4 out of 7 they could differentiate between a German or a Dutch sample.
77 haplotypes were observed among 159 males tested
Don’t forget: only 6 SNPs were identified by then
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De Knijff et al.
Y-STR profiles on 200 males from 4 Dutch regions
7 STRs
Only 4 out of 150 different Y-STR haplotypes were shared between all 4 regions
DYS389 revealed marked differences between some populations
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De Knijff et al. cont.
Concludes that Y-STRs are ideal markers for comparing populations at a micro-geographic scale
Caution: not uncommon to observe Y-haplotype of African origin combined with Asian mtDNA-lineage in the same phenotypical white Caucasian male
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Butler J.M. 2003
Separation of populations with Y-SNPs is possible
Example:
AA derived at M2 and are in E3a haplogroup
US Caucasians derived at M207 and fall into haplogroup R
Even though there is a degree of admixture, Y-SNPs can be used for inferring population of origin.
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Naito E. et al. 2004
3 SNPs:
SRY
YAP M9
Sample size
130 Germans
130 Japanese
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Jobling M.A. 2001
World population
HG % of sub-Saharan African Ys
Only found in 2 cases out of ~3600 European Ys
HG % of African Ys but not found anywhere else in the world
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Jobling M.A. 2001
Within Europe, specificity less marked, but still present
FST values still significant
41% of Ys from Baltic states
and 12% of Ys from Scandinavia belong to HG16
HG16 only present in 1% of the rest of Europe
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Jobling M.A. 2001
Conclusion:
More marker sub-division of haplogroups increased population specificity
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Ploski R. (2002)
Used 9 Y-STR, n = 1,273
Observed tight clustering of Polish populations separated from non-Polish groups
Russian and Polish populations displayed non-significant differences, German and Polish populations displayed significant differences.
European populations can be differentiated from each other if suitable markers can be found.
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Which polymorphisms?
STR
SNP
Which ones?
Search the literature
Research
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Y-SNPs vs. Y-STRs
It is now accepted that SNPs have more value to determine the ethnicity of an individual (or to which population he/she belongs) because of the slow mutation rate compared to the high mutation rate of STRs which are more powerful for the individualization of samples.
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Y-SNPs vs. Y-STRs
Y-SNPs
Population differences
Older history
Slower mutation rates
2 x 10-8
Y-STRs
Inter-population differences
More recent history
Faster mutation rates
2 x 10-3
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28. Combining Y-SNPs with Y-STRs
Determining the ethnicity of an individual
Regional identification
Identifying the individual
Three for the price of one!
Hammer and Narveson’s funded study by the US National Institute of Justice
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Hammer and Narveson 2000
Devised two Y-STR pentaplexes
And examined a set of 18Y-SNPs to determine their population specificity
FST values were used to calculate the variance between haplotypes of different populations
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FST
FST value using Y-SNPs obtained for 28 populations was 0.356
FST value for Y-STR haplotypes determined from 1 pentaplex was 0.069
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Combined haplotypes
18 Y-SNPS and 1 pentaplex were combined and tested on 1141 chromosomes
Revealed the individualization properties of Y-STRs
While retaining the geographic and evolutionary information of the SNPs
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Final Conclusion
Possible to use Y-SNPs to infer ethnicity
Possible to use Y-STRs to infer ethnicity, regional identification and identity
Mix of the two where Y-SNPs infer ethnicity and Y-STRs infer identity would be ideal
What is needed?
More comparative studies
Multiplex assays
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References
Shriver, M.D. and Kittles, R.A. (2004) Genetic ancestry and the search for personalized genetic histories. Nature Reviews Vol. 5
Parra, E.J., Kittles, R.A., Shriver, M.D. (2004) Implications of correlations between skin colour and genetic ancestry for biomedical research. Nature Genetics Vol.36 nr.11
Hammer, M. and Narveson, S. (2000) Development of the human Y chromosome as a forensic tool. National institute of Justice
Roewer, L. et al. (1996) Analysis of molecular variance (AMOVA) of Y-chromosome-specific microsatellites in two closely related human populations. HMG Vol.5 Nr.7 pp
De Knijff, P. et al. Towards a reliable forensic an population genetic use of chromosome y microsatellites. Avaliable at
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Shriver, M.D. et al. (1997) Ethnic-affiliation estimation by use of population-specific DNA markers. Am. J. Hum. Genet. Vol.60 pp
Rosser, Z. et al. (2000) Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am. J. Hum. Genet. Vol.67 pp
Kittler, R. et al. (2003) Apparent intrachromosomal exchange on the human Y chromosome explained by population history. Eur. J. Hum. Genet. Vol.11 pp
Shriver, M.D. et al. (2004) The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Human genomics Vol.1 Nr.4 pp
Tyler-Smith, C. and Jobling, M.A. (2003) The human Y chromosome: an evolutionary marker comes of age. Nature Genetics Vol. 4 pp
References
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References
Ploski, (2002) Homogeneity and distinctiveness of Polish paternal lineages revealed by Y chromosome microsatellite haplotype analysis. Hum Genet. Vol.110 Nr.6 pp
Butler, J.M. (2003) Recent developments in Y-STR analysis. Forensic Science Review Vol.15 Nr.2
Jobling, M.A. (2001) Y chromosomal SNP haplotype diversity in forensic analysis. For. Sc. Int. Vol.118 pp
Underhill, P.A. (2003) Inferring Human History: Clues from Y chromosome haplotypes. Cold Spring Harbor Symposia on Quantitative Biology Vol. LXVIII pp
Naito, E. et al. (2001) A novel dimorphism in the human SRY gene: usefulness in human migration studies. Int. J. Legal Med. Vol.114 pp
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References
Kashyap, V.K. (2004) Genetic structure and affinity among eight ethnic populations of Eastern India: Based on 22 polymorphic DNA loci. J. of Human Biology Vol.16 pp
Nassidze, I. (2004) Mitochondrial DNA and Y chromosome variation in the Caucasus. Annals of Human Genetics Vol. 68 pp
Underhill, P.A. et al. (2001) Maori origins, Y chromosome haplotypes and implications for human history in the Pacific. Human Mutation Vol.17 pp
Brion, M. et al. (2004) Hierarchical analysis of 30 Y-chromosome SNPs in European populations. Int. J. Legal Med. Vol.119 pp.10-15
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Questions?
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