Aberrant time to most recent common ancestor as a signature of natural selection

Molecular Biology and Evolution

Volumn 32, Issue 10, 2015, Pages 2784-2797

  Hunter Zinck, Haley ^a   Clark, Andrew G ^a  

^a Cornell University ^*  (United States)

Author keywords

anomaly detection; natural selection; time to most recent common ancestor

Indexed keywords

ALGORITHM; ARTICLE; BALANCING SELECTION; DEMOGRAPHY; GENE LOCUS; GENE SEQUENCE; GENEALOGY; GENOME; GENOMICS; HUMAN; NATURAL SELECTION; ORGANISMS BY PHYLOGENETIC POSITION; TIME TO MOST RECENT COMMON ANCESTOR; GENETIC SELECTION; PHYLOGENY; POPULATION DENSITY; TIME FACTOR;

ALGORITHMS; DEMOGRAPHY; GENETIC LOCI; GENOMICS; HUMANS; PHYLOGENY; POPULATION DENSITY; SELECTION, GENETIC; TIME FACTORS;

EID: 84943421547     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv142     Document Type: Article

References (32)

1. Akey JM. (2009). Constructing genomic maps of positive selection in humans: where do we go from here? Genet Res. 19(5): 711-722
2. Albrechtsen A, Moltke I, Nielsen R. (2010). Natural selection and the distribution of identity-by-descent in the human genome. Genetics. 186(1): 295-308
3. Arbiza L, Zhong E, Keinan A. (2012). NRE: a tool for exploring neutral loci in the human genome. BMC Bioinformatics 13: 301
4. Bamshad M, Wooding SP. (2003). Signatures of natural selection in the human genome. Nat Rev Genet. 4(2): 99-111
5. Bishop CM. (2006). Pattern recognition and machine learning (Information Science and Statistics). Secaucus (NJ): Springer-Verlag New York, Inc
6. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, et al. (2010). Human genome sequencing using unchained base reads on self-Assembling DNA nanoarrays. Science 327(5961): 78-81
7. Ewing G, Hermisson J. (2010). MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26(16): 2064-2065
8. Fay JC, Wu CI. (2000). Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413
9. Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R. (2014). On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol. 31(5): 1275-1291
10. Garud NR, Messer PW, Buzbas EO, Petrov DA. (2015). Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLOS Genet. 11(2): 1-32
11. Gautier M, Vitalis R. (2012). rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28(8): 1176-1177
12. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. (2011). Bayesian inference of ancient human demography from individual genome sequences. Nat Genet. 43(10): 1031-1034
13. Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, et al. (2013). Identifying recent adaptations in large-scale genomic data. Cell 152(4): 703-713
14. Grossman SR, Shlyakhter I, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, et al. (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327(5967): 883-886
15. Han L, Abney M. (2013). Using identity by descent estimation with dense genotype data to detect positive selection. Eur J Hum Genet. 21: 205-211
16. He X, Cai D, Niyogi P. (2005). Laplacian score for feature selection. In: Weiss Y, Scholkopf B, Platt JC, editors. Advances in Neural Information Processing Systems. Cambridge (MA): MIT Press.p. 507-514
17. Hudson R, Kreitman M, Aguadé M. (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159
18. Leffler EM, Gao Z, Pfeifer S, Ségurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G, et al. (2013). Multiple instances of ancient balancing selection shared between humans and chimpanzees. Science 339(6127): 1578-1582
19. Li H, Durbin R. (2011). Inference of human population history from individual whole-genome sequences. Nature 475(7357): 493-496
20. Li H, Wiehe T. (2013). Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Comput Biol. 9(5): e1003060
21. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. (2010). GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 28(5): 495-501
22. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. (2007). Recent and ongoing selection in the human genome. Nat Rev Genet. 8(11): 857-868
23. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. 2005. Genomic scans for selective sweeps using SNP data. Genome Res. 15(11): 1566-1575
24. Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. (2014). Genome-wide inference of ancestral recombination graphs. PLoS Genet. 10(5): e1004342
25. Ribeiro PJ Jr, Diggle PJ. (2001). geoR: a package for geostatistical analysis. RNEWS. 1(2): 14-18
26. Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328(5978): 636-639
27. Sabeti P, Schaffner S, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen T, Altshuler D, Lander E. (2006). Positive natural selection in the human lineage. Science. 312(5780): 1614
28. Sheehan S, Harris K, Song Y. (2013). Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194: 647-662
29. Sing T, Sander O, Beerenwinkel N, Lengauer T. (2005). ROCR: visualizing classifier performance in R. Bioinformatics 21(20): 3940-3941
30. Tajima F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 595(3): 585-595
31. Voight B, Kudaravalli S, Wen X, Pritchard J. (2006) A map of recent positive selection in the human genome. PLoS Biol. 4(3): 446-458
32. Zhao Q, Okada K, Rosenbaum K, Kehoe L, Zand DJ, Sze R, Summar M, LinguraruMG. (2014). Digital facial dysmorphology for genetic screening: hierarchical constrained localmodel using ICA.Med Image Anal. 18(5): 699-710