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

被引：19

作者：

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
]}

机构：

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

来源：

PLOS ONE | 2018年 / 13卷 / 04期

基金：

巴西圣保罗研究基金会;

关键词：

HOMOZYGOSITY; RUNS;

D O I：

10.1371/journal.pone.0196360

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：14

共 31 条

[1] Educational Attainment Influences Levels of Homozygosity through Migration and Assortative Mating [J].

Abdellaoul, Abdel ;

Hottenga, Jouke-Jan ;

Willemsen, Gonneke ;

Bartels, Meike ;

van Beijsterveldt, Toos ;

Ehli, Erik A. ;

Davies, Gareth E. ;

Brooks, Andrew ;

Sullivan, Patrick F. ;

Penninx, Brenda W. J. H. ;

de Geus, Eco J. ;

Boomsma, Dorret I. .

PLOS ONE, 2015, 10 (03)

[2] The Role of Inbreeding in the Extinction of a European Royal Dynasty [J].

Alvarez, Gonzalo ;

Ceballos, Francisco C. ;

Quinteiro, Celsa .

PLOS ONE, 2009, 4 (04)

[3] Genetics of population isolates [J].

Arcos-Burgos, M ;

Muenke, M .

CLINICAL GENETICS, 2002, 61 (04) :233-247

[4]

Auricchio MTBDM, 2007, HUM BIOL, V79, P667

[5] Estimation of Recent and Ancient Inbreeding in a Small Endogamous Tunisian Community Through Genomic Runs of Homozygosity [J].

Ben Halim, Nizar ;

Nagara, Majdi ;

Regnault, Be'atrice ;

Hsouna, Sana ;

Lasram, Khaled ;

Kefi, Rym ;

Azaiez, Hela ;

Khemira, Laroussi ;

Saidane, Rachid ;

Ben Ammar, Slim ;

Besbes, Ghazi ;

Weil, Dominique ;

Petit, Christine ;

Abdelhak, Sonia ;

Romdhane, Lilia .

ANNALS OF HUMAN GENETICS, 2015, 79 (06) :402-417

[6] Estimating human inbreeding coefficients: Comparison of genealogical and marker heterozygosity approaches [J].

Carothers, A. D. ;

Rudan, I. ;

Kolcic, I. ;

Polasek, O. ;

Hayward, C. ;

Wright, A. F. ;

Campbell, H. ;

Teague, P. ;

Hastie, N. D. ;

Weber, J. L. .

ANNALS OF HUMAN GENETICS, 2006, 70 :666-676

[7] Royal dynasties as human inbreeding laboratories: the Habsburgs [J].

Ceballos, F. C. ;

Alvarez, G. .

HEREDITY, 2013, 111 (02) :114-121

[8] Runs of homozygosity: windows into population history and trait architecture [J].

Ceballos, Francisco C. ;

Joshi, Peter K. ;

Clark, David W. ;

Ramsay, Michele ;

Wilson, James F. .

NATURE REVIEWS GENETICS, 2018, 19 (04) :220-+

[9] Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data [J].

Ceballos, Francisco C. ;

Hazelhurst, Scott ;

Ramsay, Michele .

BMC GENOMICS, 2018, 19

[10]

CURIECOHEN M, 1982, GENETICS, V100, P339

← 1 2 3 4 →