Limits...
Ancestry, admixture and fitness in Colombian genomes.

Rishishwar L, Conley AB, Wigington CH, Wang L, Valderrama-Aguirre A, Jordan IK - Sci Rep (2015)

Bottom Line: The primary ancestry component for the population is European (average = 74.6%, range = 45.0%-96.7%), followed by Native American (average = 18.1%, range = 2.1%-33.3%) and African (average = 7.3%, range = 0.2%-38.6%).Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns.These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.

View Article: PubMed Central - PubMed

Affiliation: 1] School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA [2] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [3] BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia.

ABSTRACT
The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%-96.7%), followed by Native American (average = 18.1%, range = 2.1%-33.3%) and African (average = 7.3%, range = 0.2%-38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.

No MeSH data available.


Related in: MedlinePlus

Ancestry and admixture patterns for Colombian genomes.(A) PCA of pairwise allele sharing distances among admixed Colombian genomes from Medellin compared with putative ancestral populations from Africa, the Americas, Asia and Europe. (B) Admixture plots showing ancestry proportions for three putative ancestral populations and the admixed Colombian genomes. (C) The lower panel shows only the Colombian genomes. (D) Ancestral admixture proportion distributions and averages for the Colombian genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4508918&req=5

f1: Ancestry and admixture patterns for Colombian genomes.(A) PCA of pairwise allele sharing distances among admixed Colombian genomes from Medellin compared with putative ancestral populations from Africa, the Americas, Asia and Europe. (B) Admixture plots showing ancestry proportions for three putative ancestral populations and the admixed Colombian genomes. (C) The lower panel shows only the Colombian genomes. (D) Ancestral admixture proportion distributions and averages for the Colombian genomes.

Mentions: Admixed Colombian genome sequences from Medellin were compared with a number of world-wide populations that are likely to be closely related to Colombian ancestral source populations (Supplementary Fig. S1). To do this, pairwise allele (SNP) sharing distances were computed between all genomes and principal component analysis (PCA) was used to project the resulting pairwise distances (Fig. 1A and Supplementary Fig. S2). The first principal component (81.1% of the variation) shows clear separation between the African ancestral population and all other populations, whereas the Native American, East Asian and European ancestral populations are separated along the second principal component (10.5% of the variation). The Colombian genomes from Medellin appear most closely related to the European ancestral population, but extend outward along both principal component axes consistent with African and Native American admixture. The East Asian population is most closely related to the Totonac Native American population from Mexico followed by the Bolivian population, which shows higher levels of apparent European admixture.


Ancestry, admixture and fitness in Colombian genomes.

Rishishwar L, Conley AB, Wigington CH, Wang L, Valderrama-Aguirre A, Jordan IK - Sci Rep (2015)

Ancestry and admixture patterns for Colombian genomes.(A) PCA of pairwise allele sharing distances among admixed Colombian genomes from Medellin compared with putative ancestral populations from Africa, the Americas, Asia and Europe. (B) Admixture plots showing ancestry proportions for three putative ancestral populations and the admixed Colombian genomes. (C) The lower panel shows only the Colombian genomes. (D) Ancestral admixture proportion distributions and averages for the Colombian genomes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508918&req=5

f1: Ancestry and admixture patterns for Colombian genomes.(A) PCA of pairwise allele sharing distances among admixed Colombian genomes from Medellin compared with putative ancestral populations from Africa, the Americas, Asia and Europe. (B) Admixture plots showing ancestry proportions for three putative ancestral populations and the admixed Colombian genomes. (C) The lower panel shows only the Colombian genomes. (D) Ancestral admixture proportion distributions and averages for the Colombian genomes.
Mentions: Admixed Colombian genome sequences from Medellin were compared with a number of world-wide populations that are likely to be closely related to Colombian ancestral source populations (Supplementary Fig. S1). To do this, pairwise allele (SNP) sharing distances were computed between all genomes and principal component analysis (PCA) was used to project the resulting pairwise distances (Fig. 1A and Supplementary Fig. S2). The first principal component (81.1% of the variation) shows clear separation between the African ancestral population and all other populations, whereas the Native American, East Asian and European ancestral populations are separated along the second principal component (10.5% of the variation). The Colombian genomes from Medellin appear most closely related to the European ancestral population, but extend outward along both principal component axes consistent with African and Native American admixture. The East Asian population is most closely related to the Totonac Native American population from Mexico followed by the Bolivian population, which shows higher levels of apparent European admixture.

Bottom Line: The primary ancestry component for the population is European (average = 74.6%, range = 45.0%-96.7%), followed by Native American (average = 18.1%, range = 2.1%-33.3%) and African (average = 7.3%, range = 0.2%-38.6%).Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns.These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.

View Article: PubMed Central - PubMed

Affiliation: 1] School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA [2] PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia [3] BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia.

ABSTRACT
The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%-96.7%), followed by Native American (average = 18.1%, range = 2.1%-33.3%) and African (average = 7.3%, range = 0.2%-38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.

No MeSH data available.


Related in: MedlinePlus