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Am J Hum Genet. 2018 Nov 1;103(5):707-726. doi: 10.1016/j.ajhg.2018.09.013. Epub 2018 Oct 25.

Understanding the Hidden Complexity of Latin American Population Isolates.

Author information

1
Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
2
Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA.
3
Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA.
4
Department of Psychiatry and Biobehavioral Sciences, Semel Center for Informatics and Personalized Genomics, University of California Los Angeles, Los Angeles, CA 90095, USA.
5
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
6
Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Statistics, Stanford University, Stanford, CA 94305, USA.
7
Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China; Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France.
8
Genética Molecular (GENMOL), Universidad de Antioquia, Medellín, Colombia.
9
Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA. Electronic address: klohmueller@ucla.edu.

Abstract

Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36×. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.

KEYWORDS:

deleterious mutations; identity by descent; linkage disequilibrium; pedigree; population genetics; population isolate

PMID:
30401458
PMCID:
PMC6218714
[Available on 2019-05-01]
DOI:
10.1016/j.ajhg.2018.09.013

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