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 36x. 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.
[1]Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA 90095 USA;
[2]Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA;
[3]Univ Calif Los Angeles, Semel Inst Neurosci & Human Behav, Ctr Neurobehav Genet, Los Angeles, CA 90095 USA;
[4]Univ Calif Los Angeles, Semel Ctr Informat & Personalized Genom, Dept Psychiat & Biobehav Sci, Los Angeles, CA 90095 USA;
[5]Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA;
[6]Icahn Sch Med Mt Sinai, Icahn Inst Genom & Multiscale Biol, New York, NY 10029 USA;
[7]Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA;
[8]Stanford Univ, Dept Stat, Stanford, CA 94305 USA;
[9]Fudan Univ, Minist Educ, Key Lab Contemporary Anthropol, Shanghai 200438, Peoples R China;
[10]Fudan Univ, Collaborat Innovat Ctr Genet & Dev, Shanghai 200438, Peoples R China;
[11]Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France;
[12]Univ Antioquia, Genet Mol GENMOL, Medellin, Colombia
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