An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

PLoS Computational Biology

Volumn 10, Issue 6, 2014, Pages

  Liu, Kevin J ^a,b   Dai, Jingxuan ^a   Truong, Kathy ^a   Song, Ying ^c   Kohn, Michael H ^b   Nakhleh, Luay ^a,b  

^a Rice University   (United States)

^b RICE UNIVERSITY   (United States)

^c INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENES;

COMPARATIVE GENOMICS; EUKARYOTIC SPECIES; EVOLUTIONARY HISTORY; GENETIC MATERIALS; HIDDEN-MARKOV MODELS; HYBRIDISATION; INTERSPECIFIC HYBRIDIZATION; MODEL-BASED OPC; MUS MUSCULUS; PHYLOGENETIC NETWORKS;

HIDDEN MARKOV MODELS;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHROMOSOME 7; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER PROGRAM; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DATA ANALYSIS; EUKARYOTE; GENE IDENTIFICATION; GENE LOCUS; GENOME ANALYSIS; HIDDEN MARKOV MODEL; INTROGRESSION; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MOUSE; NONHUMAN; PROCESS DEVELOPMENT; PROCESS MODEL; PROMOTER REGION; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CHROMOSOME MAP; COMPUTER SIMULATION; GENETIC DATABASE; GENOMICS; PHYLOGENY; POPULATION GENETICS; PROBABILITY;

ALGORITHMS; ANIMALS; CHROMOSOME MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOMICS; MARKOV CHAINS; MICE; MODELS, GENETIC; PHYLOGENY;

EID: 84903386054     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003649     Document Type: Article

References (44)

1. Mallet J, (2005) Hybridization as an invasion of the genome. Trends in Ecology & Evolution 20: 229-237.
2. Song Y, Endepols S, Klemann N, Richter D, Matuschka FR, et al. (2011) Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. Current Biology 21: 1296-1301.
3. The Heliconious Genome Consortium, (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487: 94-98.
4. Maddison W, (1997) Gene trees in species trees. Systematic Biology 46: 523-536.
5. Yu Y, Degnan JH, Nakhleh L, (2012) The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genet 8: e1002660.
6. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722.
7. Eriksson A, Manica A, (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominids. Proceedings of the National Academy of Sciences 109: 13956-13960.
8. Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, et al. (2012) Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genet 8: e1002891.
9. Moody M, Rieseberg L, (2012) Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect helianthus). Molecular Phylogenetics And Evolution 64: 145-155.
10. Nakhleh L, (2013) Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution 28: 719-728.
11. Durand EY, Patterson N, Reich D, Slatkin M, (2011) Testing for ancient admixture between closely related populations. Molecular Biology and Evolution 28: 2239-2252.
12. Hobolth A, Christensen OF, Mailund T, Schierup MH, (2007) Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet 3: e7.
13. Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, et al. (2009) Ancestral population genomics: The coalescent hidden Markov model approach. Genetics 183: 259-274.
14. Mailund T, Dutheil JY, Hobolth A, Lunter G, Schierup MH, (2011) Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet 7: e1001319.
15. Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, et al. (2012) A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet 8: e1003125.
16. Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JR, et al. (2013) Unsupervised genome-wide recognition of local relationship patterns. BMC Genomics 14: 347.
17. Rabiner LR, (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77: 257-286.
18. Brent RP (1973) Algorithms for Minimization without Derivatives. Mineola, New York: Dover Publications, 1-208 pp.
19. Than C, Ruths D, Nakhleh L, (2008) PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9: 322.
20. Felsenstein J (2004) Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.
21. Westesson O, Holmes I, (2009) Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput Biol 5: e1000318.
22. Hein J, Schierup MH, Wiuf C (2005) Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory. Oxford University Press, 95-169 pp.
23. Li H, Durbin R, (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
24. Degnan JH, Salter LA, (2005) Gene tree distributions under the coalescent process. Evolution 59: 24-37.
25. Rodriguez F, Oliver J, Marin A, Medina J, (1990) The general stochastic model of nucleotide substitution. Journal of Theoretical Biology 142: 485-501.
26. Yu Y, Than C, Degnan J, Nakhleh L, (2011) Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60: 138-149.
27. Huber K, Oxelman B, Lott M, Moulton V, (2006) Reconstructing the evolutionary history of polyploids from multilabeled trees. Molecular Biology and Evolution 23: 1784-1791.
28. Wu Y, (2012) Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66: 763-775.
29. Kingman JFC (1982) On the genealogy of large populations. Journal of Applied Probability 19pp. 27-43.
30. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
31. Guénet JL, Bonhomme F, (2003) Wild mice: an ever-increasing contribution to a popular mammalian model. Trends in Genetics 19: 24-31.
32. Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, et al. (2004) Comparative recombination rates in the rat, mouse, and human genomes. Genome Research 14: 528-538.
33. Mouse Genome Sequencing Consortium, (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
34. Rambaut A, Grassly NC, (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 13: 235-238.
35. Jukes T, Cantor C (1969) Evolution of protein molecules. In: Munro H, editor, Mammalian Protein Metabolism, Academic Press, NY. pp. 21-132.
36. Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, et al. (2009) A customized and versatile high-density genotyping array for the mouse. Nat Meth 6: 663-666.
37. Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, et al. (2011) Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 43: 648-655.
38. Didion J, Yang H, Sheppard K, Fu CP, McMillan L, et al. (2012) Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics 13: 34.
39. Scheet P, Stephens M, (2006) A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics 78: 629-644.
40. Yu Y, Barnett RM, Nakhleh L, (2013) Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology 62: 738-751.
41. Salcedo T, Geraldes A, Nachman MW, (2007) Nucleotide variation in wild and inbred mice. Genetics 177: 2277-2291.
42. Geraldes A, Basset P, Smith KL, Nachman MW, (2011) Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination. Molecular Ecology 20: 4722-4736.
43. Geraldes A, Basset P, Gibson B, Smith KL, Harr B, et al. (2008) Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Molecular Ecology 17: 5349-5363.
44. Baines JF, Harr B, (2007) Reduced X-linked diversity in derived populations of house mice. Genetics 175: 1911-1921.