In summary, continental ancestry in the Bolivian population is mainly Native American (73.3%) followed by European (25.8%). African ancestry (0.9%), in contrast, was observed to be minimal (Figure 81). When analyzing continental ancestry by department, La Paz (81%) exhibited the highest Native American, but the lowest European contribution (18.7%). In comparison, Santa Cruzwas observed to have the lowest Native American (57.8%), but the highest European ancestry (39.4%). In all departments African ancestry was lowwith Pando showing the highest value (3%).Among ecological regions the Native American genetic contribution was highest in the Andeans (80.5%) and decreasing from the West via the Sub-Andean (71.9%) to the East in the Llanos (67%). In contrast, European ancestry was lowest in the Andeans (19.2%) rising in the Sub- Andean (27.9%) and is highest in the Llanos (31.2%). The highest African ancestry was observed in the Llanos (1.9%). Native American ancestry was almost similar in rural (77.2%) and in urban (72.1%) populations. Likewise, European (22.2%, 26.9%), and African ancestry (0.6, 0.9%) differed only slightly.
Figure 81: Average continental ancestry of the Bolivian population based on 46 AIMs. Adapted from Figure 4 published in [333], doi:10.1371/journal.pone.0058980.g004, East Asia was removed as reference population. Based on STRUCTURE results.
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Continental ancestry for each individual of the respective population is shown in STRUCTURE graphs (Figure 82, 83, 84). The optimal value of K given by Structure Harvester [327] was K=3, and thus, reflecting the three continental regions Africa, Europe, and Native America.The graphs clearly demonstrate that the Native American ancestry is prevalent in the Bolivian population with Santa Cruz exhibiting the lowest Native American, but the greatest European genetic component when compared to other departments. Likewise, a decreasing Native American and an increasing European genetic component from the Andeans via the Sub-Andeans to the Llanos can be clearly seen. In all departments, there are a few individuals with European ancestry values of >50% or slightly below that level, especially in Santa Cruz (n=22) and Pando (n=6). The highest value (69%) was found in an individual from Pando. African ancestry, in contrast, was low with the highest values found in La Paz (23.6%) and Pando (16.9%).
The Bolivian populations seem to exhibit asimilar genetic sub-structure. At K=5 all Bolivian departments show a genetic component (green) which is shared with the Native American reference group. At K=6 the Native American populations seem to share this genetic component with the European population. The African reference population, in contrast, apparently does not share a genetic component (pink) which can be observed from K=4 to K=6.
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Figure 82: Structure analysis of the Bolivian population among departments. Adapted from Figure S7 published in [333], doi:10.1371/journal.pone.0058980.g005, East Asia was removed as reference population. Based on STRUCTURE results.
Figure 83: Structure analysis of the Bolivian population among regions. Adapted from S8. published in [333], doi:10.1371/journal.pone.0058980.g005, East Asia was removed as reference population. Based on STRUCTURE results.
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Figure 84: Structure analysis of the Bolivian population among rural and urban regions. Adapted from S9 published in [333], doi:10.1371/journal.pone.0058980.g005, East Asia was removed as reference population. Based on STRUCTURE results.
In the PCA analysis the Bolivianpopulationclearly groups with the Native American reference group with only some samples that show some closer affiliations to Europe (Figure 85A). Only one individual, that is, the individual from La Paz with a relative high African ancestry (23.6%) when compared to other Bolivians shows some affinity to the African cluster. The first principal component (PC1=25.84%) separates Africa from Native America and Europe and the second (PC2=11.75%) separates Europe from Native America. It can be observed that the Andean populations are more tightly grouped into clusters whereas the Llanos populations are more dispersed (Figure 85B). The Sub-Andean populations occupy an intermediate position. This dispersion can be observed again in the standard deviation (SD) of the main ancestry genetic component in Bolivians, that is, among Native American ancestry. The mean of Native American ancestry in the Andeans reached 80.5% with a standard deviation of 8.5%. The Sub-Andeans had a mean of 71.8% and a SD of 9.9%. In contrast, the populations in the Llanos were observed with a Native American ancestry mean of 67% and a SD of 14.1%. This pattern is again observed when considering the departments. Santa Cruz and Pando (from the Llanos) seem to highly disperse (Figure 85C). No clear pattern can be observed when rural populations are compared against urban populations (Figure 85D).
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A) B)
C) D)
Figure 85: PCA of Bolivian profiles with 46 AIM indel markers. Based on Figure 6 published in [333], doi:10.1371/journal.pone.0058980.g006, East Asia was removed as reference population from figure A.
The outcome of estimating ancestries in populations depends on many decisions like the panel of SNPs, but also the number of SNPs included, the reference samples, and number of samples. Twelve of the Bolivian samples were previously genotyped with the LACE panel [259]. By comparison, Native American ancestry with the 46-AIM panel was lower, and correspondingly, led to an increased European ancestry (on average the difference is about 15% between the 46-AIM and the LACE panel). Therefore, European ancestry might be slightly overestimated with the 46-AIM panel in the Bolivian population. The mean of the European ancestry in the whole Bolivian population reached 24.6%. In a previous study with a 324 Native American-specific AIM panel European ancestry was observed to be around 12% [288].
The influence of sample size on the estimation of population ancestry was evaluated with a simulation analysis (Figure 86). When using a sample size between 30 and 70 the mean value for the ancestry proportion varies to a very low degree. For example, Native American ancestry in La Paz (n=105) reached 80.1%, 83.1% and 85.5% for a sample size of 5, 30, and 70. The respective
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values for Chuquisaca (n=73) came to 72.3%, 74.6%, and 76.3%. As shown in Figure 82, the mean values in the simulations approach the values which were obtained with the original sample size. As it was expected, the bootstrap intervals decrease as the sample sizes increase. Above a sample size of 30, the bootstrap intervals are already small. Bootstrap intervals do not overlap between continental ancestries even for sample size five.
Figure 86: Ancestry values obtained for La Paz and Chuquisaca by way of simulations. Vertical dotted bars indicate bootstrap intervals obtained from the computation of ancestry on 1000 simulations (each sample size); the central dots indicate the mean values. Published in [361].