Transcript Bioquest_2007_Project_1_Poster

Click Clack – Milk Attack??
Gretchen A. Koch, Goucher College
Introduction
Lactate persistence (also known as lactose tolerance) refers to adult expression of the
lactase-phlorizin hydrolase (LPH) enzyme controlled by the LCT gene. The selection for
this trait in the human population appears to be correlated with the domestication of cattle
and utilization of milk. SNP linked alleles have been identified for European and African
populations.
Paul Mangum, Midland College
Figure 1: Distribution of Lactose Tolerance
Phenotypes Among Afro-Asiatic Speakers
Lactose
Tolerant
53%
Slight
Lactose
Intolerance
19%
Tishkoff, Sarah A, et al. 2007.Convergent adaptation of human lactase persistence in
Africa and Europe. Nature Genetics, Volume 39, Number 1, Pages 31 – 40.
Figure 4: Distribution of Lactose Tolerance
Phenotypes Among Niger-Kordofanian Speakers
Lactose Intolerant
29%
Lactose Tolerant
35%
Lactose Intolerant
44%
Lactose Tolerant
44%
Slight Lactose
Intolerance
21%
Slight Lactose
Intolerance
27%
Figure 5: Percent of Ancestral
Genotypes at -13907 bp
Figure 6: Percent of Ancestral
Genotypes at -13915 bp
4.5
Figure 7: Percent of Ancestral
Genotypes at -14010 bp
102
90
83.67
4.08
100.00
4
3.5
80
100
98.51
3.33
98.41
70
98
3
58.73
60
2
96
Percent
Percent
51.67
2.5
94
1.59
53.47
50
40
92.78
1.5
30
92
0.99
1
20
90
0.5
0
References
Knight, Alec, et al. 2003. African Y Chromosome and mtDNA Divergence Provides
Insight into the History of Click Languages. Current Biology, Volume 13, Issue 8, 15
April 2003, Page 705.
Slight Lactose
Intolerance
24%
Figure 3: Distribution of Lactose Tolerance
Phenotypes Among Khoisan Speakers
Hypotheses
1. The frequency of Lactase Non-Persistence (LNP) will be the greatest in the most
ancestral language group.
2. The percentage of ancestral genotypes will be higher in the most ancestral language
group.
Based on the results from the first analysis, we created another program in VBA that
calculated the percentage of ancestral DNA in each language group. In order to complete
this task, the number of individuals in each language group for which the genotypes were
counted. The program then looked at whether or not the individual genotypes varied from
the ancestral genotypes of CC at -13907 bp, TT at -13915 bp, and GG at -14010 bp. If the
exact genotype at the specific position on the chromosome was unknown for an individual
(indicated by “? ?”) in the data set, then that individual was not interpreted as having an
SNP from the ancestral DNA.
Lactose Intolerant
27%
Lactose Tolerant
49%
In contrast to the original paper, our analysis removed the geopolitical borders separating
the sampled individuals and combined the samples as language groups. Alec Knight et al.,
2003, used Y chromosome and mtDNA variation among African populations and
concluded that the click (including Khoisan) languages are the most ancestral of the
African languages groups.
The results from this analysis were visualized using a three-dimensional pie chart to
readily demonstrate the percentage of individuals in each language exhibiting the different
phenotypes.
Figure 2: Distribution of Lactose Tolerance
Phenotypes Among Nilo-Saharan Speakers
Lactose
Intolerant
28%
The data set presented by Tishkoff et al. 2007 contained the genotype of the SNPs at
13907, 13915, and 14010 base pairs upstream from the LCT gene for 493 individuals. The
data set further categorized each individual according to the country in which he or she
resides as well as the language spoken. Based on the raw glucose rise after lactose
digestion, each individual (for which measurements were available) was given a lactose
tolerance phenotype. Those individuals that are lactose intolerant are Type 1; Type 2
individuals show a slight intolerance to lactose. Finally, individuals of Type 3 show a
phenotype of lactose tolerance. The original research analyzed the data based on language
spoken and country of origin.
Methods
Using Microsoft Visual Basic for Applications (VBA) ©, we created a program that
grouped the individuals based on language and phenotype. For example, if the individual
was named “KEAA001” in the data set, “KE” indicates the country of origin to be Kenya,
and “AA” indicates the language spoken to be the Afro-Asiatic language. The program
surveyed all of the data presented and grouped the individuals according to the following
categories, with the designations in the individual names shown in parentheses:
Language
Lactose Tolerance Group
Afro-Asiatic (AA)
Type 1, Type 2, or Type 3
Nilo-Saharan (NS)
Type 1, Type 2, or Type 3
Niger-Kordofanian (NK)
Type 1, Type 2, or Type 3
Khoisan (SW and HZ) Type 1, Type 2, or Type 3
David Matlack, Earlham College
Results
Percent
Kristin Jenkins, NESCent
10
88
Afro-Asiatic
(AA)
Nilo-Saharan
(NS)
NigerKordofanian
(NK)
Language Spoken
Khoisan (SW
and HZ)
0
Afro-Asiatic
(AA)
Nilo-Saharan
(NS)
NigerKordofanian
(NK)
Language Spoken
Khoisan (SW
and HZ)
Afro-Asiatic
(AA)
Nilo-Saharan
(NS)
NigerKordofanian
(NK)
Khoisan (SW
and HZ)
Language Spoken
Conclusion
As evident in Figures 1-4, the Afro-Asiatic speakers tested showed a higher proportion of the population with the
lactose tolerant phenotype, and the Khoisan speakers showed a higher proportion of lactose intolerant phenotypes.
This evidence, based on phenotypes, supports the hypothesis that LNP will be the greatest in the most ancestral
language.
To further explore this relationship, the second study of genotypes was undertaken. In all three positions, the
Khoisan speakers show the highest percentage of the population possessing the ancestral genotype. The most
compelling evidence comes from Figure 7, where the three other groups are all below 60% of the population
having ancestral genotypes. In sharp contrast, nearly 84% of the Khoisan speakers have ancestral genotypes in the
position of the third SNP. This supports the hypothesis expressed by Alec Knight et al., 2003, that the click
languages are the most ancestral.
Acknowledgements
We would like to thank the organizers of the 2007 BioQUEST workshop for their dedication and support as well as
NESCent, HHMI, Dr. Claudia Neuhauser, Goucher College, and Midland College for their financial support.