Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate

Author(s)

Lemes, Renan B. ^[1] ; Nunes, Kelly ^[1] ; Carnavalli, Juliana E. P. ^[1] ; Kimura, Lilian ^[1] ; Mingroni-Netto, Regina C. ^[1] ; Meyer, Diogo ^[1] ; Otto, Paulo A. ^[1]

Affiliation

^[1] Univ Sao Paulo, Inst Biociencias, Dept Genet & Evolutionary Biol, Sao Paulo, SP - Brazil

• Document type: Journal article
• Source: PLoS One; v. 13, n. 4 APR 24 2018.
• Web of Science Citations: 4

Abstract

The analysis of genomic data (similar to 400,000 autosomal SNPs) enabled the reliable estimation of inbreeding levels in a sample of 541 individuals sampled from a highly admixed Brazilian population isolate (an African-derived quilombo in the State of Sao Paulo). To achieve this, different methods were applied to the joint information of two sets of markers (one complete and another excluding loci in patent linkage disequilibrium). This strategy allowed the detection and exclusion of markers that biased the estimation of the average population inbreeding coefficient (Wright's fixation index FIS), which value was eventually estimated as around 1% using any of the methods we applied. Quilombo demographic inferences were made by analyzing the structure of runs of homozygosity (ROH), which were adapted to cope with a highly admixed population with a complex foundation history. Our results suggest that the amount of ROH <2Mb of admixed populations should be somehow proportional to the genetic contribution from each parental population. (AU)

• FAPESP's process: 12/18010-0 - Balancing selection in the human genome: detection, causes and consequences
• Grantee: Diogo Meyer
• Support Opportunities: Regular Research Grants
• FAPESP's process: 12/09950-9 - Evolution of HLA genes: population differentiation and signatures of recent selection in native and admixed populations from Brazil
• Grantee: Kelly Nunes
• Support Opportunities: Scholarships in Brazil - Post-Doctoral