Tropico
01-30-2014, 01:15 AM
A study done on Puerto Ricans, Mexicans and Colombians. Check it out. Focused on our Native ancestry but delved a little into the Euro and African ones as well. Very interesting. I wonder why they didn't use DR... :bored::roll eyes:
http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004023.g002&representation=PNG_M
- Using ADMIXTURE, we find Native American proportions being 12.8% in PUR (Puerto Rico), 25.6% in CLM (Colombia), and 47.6% in MXL (Mexican Americans) (Figure 2a). RFMIX finds values falling within percentage points of these values, and within one percentage point of the values inferred in the 1000 Genomes project through related methods [1]. Estimates of African ancestry showed a larger difference across methods, with ADMIXTURE (RFMIX) estimates at 14.8%(11.7%) in PUR, 8.9%(7.8%) in CLM, and 5.4%(4.2%) in MXL.
- The inferred Native American ancestry proportions are in good agreement with results from the GALA study [49], which reported proportions of 12.4% in Puerto Rico and 49.6% in Mexico. The PUR result is also comparable to the 15.2% of Native ancestry inferred in a different Puerto Rican sample.
Ancestry by Generations:
http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004023.g003&representation=PNG_M
Puerto Rico:
In PUR, we found evidence for two periods of European and African migration, the first 14.9 GA (generations ago) and the most recent period at 6.8 GA. This model is in excellent agreement with historical records, which suggest that isolated Native populations contributed little gene flow to the colony after the initial contact period, and that substantial slave trade and European immigration continued until the second half of the 19th century. We do not mean to imply that migrations actually occurred in exactly two distinct pulses-we do not have the resolution to distinguish more than two pulses per population. However, the inference of a migration pulse 6.8 GA indicates that migrations occurred during a period spanning this date. This complex scenario, with multiple waves of migration from African and European individuals, is consistent with the observation that European and African ancestries vary across the island, whereas no evidence of such variation was found in Native ancestry.
The inferred onset of ADMIXTURE in CLM is 13.0 ga ( CI ), significantly later than that in both MXL and PUR and consistent with later European settlement in western Colombia compared to Mexico and Puerto Rico. We also find evidence for a small but statistically significant second wave of Native American migration, 4.8 ga ( CI 4–6). As above, this does not necessarily indicate a single, punctual event, but probable contact between an admixed population and Native American individuals during that period. By contrast, we find no evidence for continuing African gene flow in CLM.
FULL ARTICLE:
Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004023)
http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004023.g002&representation=PNG_M
- Using ADMIXTURE, we find Native American proportions being 12.8% in PUR (Puerto Rico), 25.6% in CLM (Colombia), and 47.6% in MXL (Mexican Americans) (Figure 2a). RFMIX finds values falling within percentage points of these values, and within one percentage point of the values inferred in the 1000 Genomes project through related methods [1]. Estimates of African ancestry showed a larger difference across methods, with ADMIXTURE (RFMIX) estimates at 14.8%(11.7%) in PUR, 8.9%(7.8%) in CLM, and 5.4%(4.2%) in MXL.
- The inferred Native American ancestry proportions are in good agreement with results from the GALA study [49], which reported proportions of 12.4% in Puerto Rico and 49.6% in Mexico. The PUR result is also comparable to the 15.2% of Native ancestry inferred in a different Puerto Rican sample.
Ancestry by Generations:
http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004023.g003&representation=PNG_M
Puerto Rico:
In PUR, we found evidence for two periods of European and African migration, the first 14.9 GA (generations ago) and the most recent period at 6.8 GA. This model is in excellent agreement with historical records, which suggest that isolated Native populations contributed little gene flow to the colony after the initial contact period, and that substantial slave trade and European immigration continued until the second half of the 19th century. We do not mean to imply that migrations actually occurred in exactly two distinct pulses-we do not have the resolution to distinguish more than two pulses per population. However, the inference of a migration pulse 6.8 GA indicates that migrations occurred during a period spanning this date. This complex scenario, with multiple waves of migration from African and European individuals, is consistent with the observation that European and African ancestries vary across the island, whereas no evidence of such variation was found in Native ancestry.
The inferred onset of ADMIXTURE in CLM is 13.0 ga ( CI ), significantly later than that in both MXL and PUR and consistent with later European settlement in western Colombia compared to Mexico and Puerto Rico. We also find evidence for a small but statistically significant second wave of Native American migration, 4.8 ga ( CI 4–6). As above, this does not necessarily indicate a single, punctual event, but probable contact between an admixed population and Native American individuals during that period. By contrast, we find no evidence for continuing African gene flow in CLM.
FULL ARTICLE:
Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004023)