Tables and Figures from the Anthropology and Human diversity component of the 13th IHW
For additional information see: Meyer, Single et al. (2004). Single locus polymorphism of
classical HLA genes. In "HLA 2004: Immunobiology of the Human MHC". Hansen, J. and Dupont, B. (Eds). IHWG Press, Seattle.
Figures
- Each file contains 4 graphs, for all populations surveyed at that locus.
These plots depict: (a) the number of alleles [k] per sample; (b) the normalized
deviate of the homozygosity [Fnd]; (c) the expected heterozygosity [Hetz];
(d) the degree of allele sharing among regions. For each region there are
two columns. The first depicts the fraction of alleles in a region which
are either exclusively found in that region (black), shared by two (dark
gray), three (light gray), or more than three regions (white) regions. The
second column shows the contribution of the alleles in each category to the
overall alleles frequency in that region (i.e., a frequency weighted version
of the first column). The total number of alleles is indicated at the top
of each set of columns.
AF-plots_A.pdf (pdf document)
AF-plots_C.pdf (pdf document)
AF-plots_B.pdf (pdf document)
AF-plots_DRB1.pdf (pdf document)
AF-plots_DQA1.pdf (pdf document)
AF-plots_DQB1.pdf (pdf document)
AF-plots_DPA1.pdf (pdf document)
AF-plots_DPB1.pdf (pdf document)
Tables
- Summary tables (Table 2 in Meyer et al. (2004)). These contain statistics
that summarize the distribution of alleles by region and across all regions.
Each locus is presented in a separate worksheet, and the legends are provided
in the first worksheet.
AF-summary.xls (excel document)
Go to detailed description of Summary tables
- Regional tables (Table 3 in Meyer et al. (2004)). These allow an
assessment of the degree of sharing of specific alleles found at or above the
threshold frequency of 0.05 in at least one population sample (regionally
frequent alleles). The statistic reported in the tables is the maximum
frequency for that allele in samples from the region.
Each locus is presented in a separate worksheet. The legend is provided
in the first worksheet.
AF-regional.xls (excel document)
Go to detailed description of Regional tables
- Population tables (Table 4 in Meyer et al. (2004)). These provide
frequencies for all observed alleles, in each population surveyed, grouped by
world region. Each locus is in a separate file, and within each file
each region is is presented in a separate worksheet. The legend is is provided in
the first worksheet.
AF-population_A.xls (excel document)
AF-population_C.xls (excel document)
AF-population_B.xls (excel document)
AF-population_DRB1.xls (excel document)
AF-population_DQA1.xls (excel document)
AF-population_DQB1.xls (excel document)
AF-population_DPA1.xls (excel document)
AF-population_DPB1.xls (excel document)
- Population genetic analyses detail tables (these tables are not published in
Meyer et al. (2004)). Each locus is presented in a separate worksheet. The legend is
provided in the first worksheet.
AF-detail.xls (excel document)
Detailed description of table contents
- Summary table.
The summary table contains statistics that summarize the distribution of
alleles by region and across all regions. The first
column corresponds to all regions combined and is followed by a separate column
for each region. In this table we report sample-size weighted averages over all
population samples in each region for the statistics indicated with an asterisk
below. Due to the presence of a few very large samples for certain loci, the
following procedure was used to modify the weights. If the maximum sample size
in a region was more than 1.5 times the next largest in that region, the weight
used for the largest population was 1.5 times that of the next largest. In this
way, the large samples maintain a proportionally larger contribution to the
weighted mean without overwhelming the contribution of the smaller samples.
For example, in European populations typed at the DRB1 locus, the Irish
population has a sample size of 1,000. The next largest population in this
region has a sample size of 103. So, the adjusted weight assigned to the Irish
population sample is 1.5*103 = 154.5. The statistics in the summary table are
the following:
- Number of population samples typed
- Expected heterozygosity (gene diversity)*
- Locus-level Fst* (defined in the chapter ``Population genetic analyses'')
- Number of different alleles (k) per region
- Range of values for k per population: The minimum and maximum values of
k for population samples in the region are reported.
- Number of different alleles needed to reach a frequency of 0.5*: The
minimum number of different alleles necessary to account for 50% of the allele
frequency. Small values correspond to samples where a few alleles are observed
at high frequencies; high values correspond to cases where allele frequencies
are more even, with several alleles at similar frequencies having the high end
of the spectrum.
- Range of values for k per population: The minimum and maximum
values of k for population samples in the region are reported.
- Number of different alleles needed to reach a frequency of 0.5*:
The minimum number of different alleles necessary to account for 50% of the
allele frequency. Small values correspond to samples where a few alleles are
observed at high frequencies; high values correspond to cases where allele
frequencies are more even, with several alleles at similar frequencies having
the high end of the spectrum.
- Number of regionally frequent alleles: Alleles with a frequency
of 0.05 or more in at least one population sample.
- Regionally frequent alleles that are frequent in only one
region: For each region, this specifies how many of the frequent alleles have
a frequency at or above the threshold exclusively in that region.
- Regionally frequent alleles observed in only one region: For each
region, this specifies how many of the frequent alleles are exclusive to that
region, regardless of their frequency.
- Regional Table.
This table allows an assessment of the degree of sharing of specific alleles
found at or above the threshold frequency of 0.05 in at least one population
sample regionally frequent alleles). The statistic reported in the
tables is the maximum frequency for that allele in samples from the region.
While other statistics could have been used for these tables (mean, median,
etc.), we chose the maximum to highlight the sharing (and absence from some
regions) of specific high frequency alleles.
Alleles that were observed in only one population sample in that region are
marked with an asterisk, in order to highlight regionally frequent alleles that
were not shared within the region. This table facilitates the identification of specific
alleles responsible for the patterns seen in the summary table. The number of
alleles listed is equal to the total number of regionally frequent alleles
indicated in the summary table.