Ancestry-specific recent effective population size in the Americas

PLoS Genetics

Volumn 14, Issue 5, 2018, Pages

  Browning, Sharon R ^a   Browning, Brian L ^b   Daviglus, Martha L ^c   Durazo Arvizu, Ramon A ^d   Schneiderman, Neil ^e   Kaplan, Robert C ^f   Laurie, Cathy C ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^d LOYOLA UNIVERSITY CHICAGO   (United States)

^e Department of Biology   (United States)

^f ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ALGORITHM; AMERICAN; ANCESTRY GROUP; ARTICLE; BOOTSTRAPPING; BOTTLENECK POPULATION; CONFIDENCE INTERVAL; DATA ANALYSIS; EFFECTIVE POPULATION SIZE; EUROPEAN AMERICAN; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPE; HISPANIC; HUMAN; IMMIGRATION; MEASUREMENT ACCURACY; POPULATION GENETIC PHENOMENA AND FUNCTIONS; POPULATION GROWTH ESTIMATION; POPULATION STRUCTURE; PUERTO RICO; RELATIVE; SIMULATION; UNITED STATES; WESTERN HEMISPHERE; CAUCASIAN; CLINICAL TRIAL; COMPUTER SIMULATION; GENETIC ASSOCIATION STUDY; GENETICS; HUMAN GENOME; MULTICENTER STUDY; POPULATION DENSITY; POPULATION GENETICS; PROCEDURES; STATISTICS AND NUMERICAL DATA;

AFRICAN AMERICANS; AMERICAS; COMPUTER SIMULATION; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; GENOME, HUMAN; HAPLOTYPES; HISPANIC AMERICANS; HUMANS; POPULATION DENSITY; UNITED STATES;

EID: 85048224392     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1007385     Document Type: Article

References (30)

1. Henn BM, Botigue LR, Bustamante CD, Clark AG, Gravel S, Estimating the mutation load in human genomes. Nat Rev Genet. 2015;16: 333–43. doi: 10.1038/nrg3931 25963372
2. Lim ET, Wurtz P, Havulinna AS, Palta P, Tukiainen T, Rehnstrom K, et al. Distribution and medical impact of loss-of-function variants in the Finnish founder population. Plos Genetics. 2014;10: e1004494. doi: 10.1371/journal.pgen.1004494 25078778
3. Keinan A, Clark AG, Recent explosive human population growth has resulted in an excess of rare genetic variants. Science. 2012;336: 740–3. doi: 10.1126/science.1217283 22582263
4. Coventry A, Bull-Otterson LM, Liu X, Clark AG, Maxwell TJ, Crosby J, et al. Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun. 2010;1: 131. doi: 10.1038/ncomms1130 21119644
5. Schultz TP, Human-capital, family-planning, and their effects on population-growth. Am Econ Rev. 1994;84: 255–60.
6. Wright S, Evolution in Mendelian populations. Genetics. 1931;16: 97–159. 17246615
7. Frankham R, Effective population size/adult population size ratios in wildlife: a review. Genetical Research. 1995;66: 95–107.
8. Maples BK, Gravel S, Kenny EE, Bustamante CD, RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am J Hum Genet. 2013;93: 278–88. doi: 10.1016/j.ajhg.2013.06.020 23910464
9. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, et al. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009;5: e1000519. doi: 10.1371/journal.pgen.1000519 19543370
10. Sankararaman S, Sridhar S, Kimmel G, Halperin E, Estimating local ancestry in admixed populations. Am J Hum Genet. 2008;82: 290–303. doi: 10.1016/j.ajhg.2007.09.022 18252211
11. Baran Y, Pasaniuc B, Sankararaman S, Torgerson DG, Gignoux C, Eng C, et al. Fast and accurate inference of local ancestry in Latino populations. Bioinformatics. 2012;28: 1359–67. doi: 10.1093/bioinformatics/bts144 22495753
12. Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK, Gignoux CR, et al. Reconstructing the population genetic history of the Caribbean. PLoS Genet. 2013;9: e1003925. doi: 10.1371/journal.pgen.1003925 24244192
13. Browning SR, Grinde K, Plantinga A, Gogarten SM, Stilp AM, Kaplan RC, et al. Local ancestry inference in a large US-Based Hispanic/Latino study: Hispanic Community Health Study/Study of Latinos (HCHS/SOL). G3: Genes|Genomes|Genetics. 2016;6: 1525–34. doi: 10.1534/g3.116.028779 27172203
14. Browning SR, Browning BL, Accurate non-parametric estimation of recent effective population size from segments of identity by descent. Am J Hum Genet. 2015;97: 404–18. doi: 10.1016/j.ajhg.2015.07.012 26299365
15. Palamara PF, Lencz T, Darvasi A, Pe'er I, Length distributions of identity by descent reveal fine-scale demographic history. American Journal of Human Genetics. 2012;91: 809–22. doi: 10.1016/j.ajhg.2012.08.030 23103233
16. Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, et al. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet. 2013;9: e1004023. doi: 10.1371/journal.pgen.1004023 24385924
17. Browning BL, Browning SR, Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics. 2013;194: 459–71. doi: 10.1534/genetics.113.150029 23535385
18. Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, et al. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci U S A. 2011;108: 11983–8. doi: 10.1073/pnas.1019276108 21730125
19. Baharian S, Barakatt M, Gignoux CR, Shringarpure S, Errington J, Blot WJ, et al. The Great Migration and African-American Genomic Diversity. PLoS Genet. 2016;12: e1006059. doi: 10.1371/journal.pgen.1006059 27232753
20. Gibson C, Population of the 100 largest cities and other urban places in the United States: 1790 to 1990. U.S. Census Bureau, Population Division; 1998.
21. Dyck CJ, An introduction to Mennonite history: a popular history of the Anabaptists and Mennonites. Scottdate, PA: Herald Press; 1981.
22. Fortes-Lima C, Gessain A, Ruiz-Linares A, Bortolini M-C, Migot-Nabias F, Bellis G, et al. Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname. The American Journal of Human Genetics. 2017;101: 725–36. doi: 10.1016/j.ajhg.2017.09.021 29100086
23. Eltis D, Was the slave trade dominated by men?The Journal of Interdisciplinary History. 1992;23: 237–57.
24. Felsenstein J, Inbreeding and variance effective numbers in populations with overlapping generations. Genetics. 1971;68: 581–97. 5166069
25. Kristiansson K, Naukkarinen J, Peltonen L, Isolated populations and complex disease gene identification. Genome Biol. 2008;9: 109. doi: 10.1186/gb-2008-9-8-109 18771588
26. Kelleher J, Etheridge AM, McVean G, Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes. PLoS Comput Biol. 2016;12: e1004842. doi: 10.1371/journal.pcbi.1004842 27145223
27. Browning BL, Browning SR, Detecting identity by descent and estimating genotype error rates in sequence data. Am J Hum Genet. 2013;93: 840–51. doi: 10.1016/j.ajhg.2013.09.014 24207118
28. The International HapMap ConsortiumIntegrating common and rare genetic variation in diverse human populations. Nature. 2010;467: 52–8. doi: 10.1038/nature09298 20811451
29. The International HapMap ConsortiumA second generation human haplotype map of over 3.1 million SNPs. Nature. 2007;449: 851–61. doi: 10.1038/nature06258 17943122
30. Simonsick EM, Newman AB, Nevitt MC, Kritchevsky SB, Ferrucci L, Guralnik JM, et al. Measuring higher level physical function in well-functioning older adults: expanding familiar approaches in the Health ABC study. J Gerontol A Biol Sci Med Sci. 2001;56: 644–9.