Evolution of HLA genes: population differentiation and signatures of recent selection in native and admixed populations from Brazil

• Grant number: 12/09950-9
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): September 01, 2012
• Effective date (End): August 31, 2016
• Field of knowledge: Biological Sciences - Genetics
• Principal Investigator: Regina Célia Mingroni Netto
• Grantee: Kelly Nunes
• Home Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 13/08028-1 - CEGH-CEL - Human Genome and Stem Cell Research Center, AP.CEPID

Abstract

There is consensus that the HLA genes (Human Leucocyte Antigen), which encode proteins essential for adaptive immune response, evolve under balancing selection regime - which increases the genetic diversity compared to the expected under neutrality. However, questions concerning the time scale of the action of natural selection and its effects on population differentiation remain controversial, and are the subject of this project. The first question to discuss is how does balancing selection modulate population differentiation in the HLA genes. Although theoretical models suggest that the balancing selection reduces differentiation between populations, a recent study by our group showed that differentiation is greater in the MHC region (Major Histocompatibility Complex), where HLA genes are located, than in the rest of the genome. One interpretation for this result is that balancing selection favors different sets of alleles in distinct populations, resulting in a pattern of high diversity within and population differentiation between populations. However, our previous study used a reduced number of microsatellites, and had to deal with uncertainties about the mutational model of this marker. In this project we propose to analyze 700,000 SNPs (7,000 in the MHC region) in 100 individuals from five Native American populations, to test the hypothesis that differences between populations in HLA genes differs from the genomic average. The second question we will address concerns the time scale on which natural selection acts: we will test for signs of recent selection (in the order of hundreds of years) working in the HLA genes. Although several methods have detected selection in HLA genes, most are only sensitive to ancient selective (on the order of thousands of years). To test for recent selection we will use the admixture mapping approach, which searches genomic regions with atypical admixture proportions, suggesting a selective advantage of one of the ancestral components in recent evolutionary history. We propose to genotype 700,000 SNPs in 150 individuals of admixed quilombolas communities, which have tri-hybrid ancestry, so as to test if the South American environment imposes some kind of recent selective pressure in HLA genes. The two analyzes are complementary in terms of theoretical and operational. First, they try to characterize more precisely - temporal and geographically - the system of natural selection acting on HLA genes. Secondly, the data generated for Native America will be used to estimate the ancestry of the admixed population. A study using large-scale genotyping of native and admixed populations have great statistical power to test hypotheses open on the action of natural selection in HLA genes, and bring original responses on the evolution of these genes.

Scientific publications

(8)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

LEMES, RENAN B.; NUNES, KELLY; CARNAVALLI, JULIANA E. P.; KIMURA, LILIAN; MINGRONI-NETTO, REGINA C.; MEYER, DIOGO; OTTO, PAULO A. Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate. PLoS One, v. 13, n. 4 APR 24 2018. Web of Science Citations: 4.

MEYER, DIOGO; AGUIAR, VITOR R. C.; BITARELLO, BARBARA D.; BRANDT, DEBORA Y. C.; NUNES, KELLY. A genomic perspective on HLA evolution. IMMUNOGENETICS, v. 70, n. 1, p. 5-27, JAN 2018. Web of Science Citations: 17.

KIMURA, LILIAN; NUNES, KELLY; INES MACEDO-SOUZA, LUCIA; ROCHA, JORGE; MEYER, DIOGO; MINGRONI-NETTO, REGINA CELIA. Inferring paternal history of rural African-derived Brazilian populations from Y chromosomes. AMERICAN JOURNAL OF HUMAN BIOLOGY, v. 29, n. 2, SI MAR-APR 2017. Web of Science Citations: 3.

AMORIM, CARLOS EDUARDO G.; NUNES, KELLY; MEYER, DIOGO; COMAS, DAVID; BORTOLINI, MARIA CATIRA; SALZANO, FRANCISCO MAURO; HUNEMEIER, TABITA. Genetic signature of natural selection in first Americans. Proceedings of the National Academy of Sciences of the United States of America, v. 114, n. 9, p. 2195-2199, FEB 28 2017. Web of Science Citations: 17.

CANTOR, MAURICIO; PIRES, MATHIAS M.; MARQUITTI, FLAVIA M. D.; RAIMUNDO, RAFAEL L. G.; SEBASTIAN-GONZALEZ, ESTHER; COLTRI, PATRICIA P.; PEREZ, S. IVAN; BARNECHE, DIEGO R.; BRANDT, DEBORA Y. C.; NUNES, KELLY; DAURA-JORGE, FABIO G.; FLOETER, SERGIO R.; GUIMARAES, JR., PAULO R. Nestedness across biological scales. PLoS One, v. 12, n. 2 FEB 6 2017. Web of Science Citations: 11.

NUNES, KELLY; PIOVEZAN, BRUNO; TORRES, MARGARETH A.; PONTES, GERLANDIA N.; KIMURA, LILIAN; CARNAVALLI, JULIANA E. P.; MINGRONI NETTO, REGINA CELIA; MORAES, MARIA ELISA; MEYER, DIOGO. Population variation of HLA genes in rural communities in Brazil, the Quilombos from the Vale do Ribeira, Sao Paulo - Brazil. HUMAN IMMUNOLOGY, v. 77, n. 6, p. 447-448, JUN 2016. Web of Science Citations: 2.

NUNES, KELLY; ZHENG, XIUWEN; TORRES, MARGARETH; MORAES, MARIA ELISA; PIOVEZAN, BRUNO Z.; PONTES, GERLANDIA N.; KIMURA, LILIAN; CARNAVALLI, JULIANA E. P.; MINGRONI NETTO, REGINA C.; MEYER, DIOGO. HLA imputation in an admixed population: An assessment of the 1000 Genomes data as a training set. HUMAN IMMUNOLOGY, v. 77, n. 3, p. 307-312, MAR 2016. Web of Science Citations: 12.

BRANDT, DEBORA Y. C.; AGUIAR, VITOR R. C.; BITARELLO, BARBARA D.; NUNES, KELLY; GOUDET, JEROME; MEYER, DIOGO. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data. G3-GENES, GENOMES, GENETICS, v. 5, n. 5, p. 931-941, MAY 1 2015. Web of Science Citations: 33.