A distance-based method for inferring phylogenetic networks in the presence of incomplete lineage sorting

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 9096, Issue , 2015, Pages 378-389

  Yu, Yun ^a   Nakhleh, Luay ^a  

^a Rice University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGY;

DISTANCE-BASED METHODS; EVOLUTIONARY HISTORY; EVOLUTIONARY PROCESS; INFERRED NETWORKS; PAIRWISE DISTANCES; PHYLOGENETIC NETWORKS; SIMULATION STUDIES; VERY LARGE DATUM;

SORTING;

EID: 84944538210     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-19048-8_32     Document Type: Conference Paper

References (38)

1. Arnold, M.L.: Natural Hybridization and Evolution. Oxford University Press, Oxford (1997)
2. Barton, N.H.: The role of hybridization in evolution. Molecular Ecology 10(3), 551–568 (2001)
3. The Heliconius Genome Consortium: Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487(7405), 94–98 (2012)
4. Cranston, K.A., Hurwitz, B., Ware, D., Stein, L., Wing, R.A.: Species trees from highly incongruent gene trees in rice. Syst. Biol. 58, 489–500 (2009)
5. Degnan, J.H., Rosenberg, N.A.: Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24(6), 332–340 (2009)
6. Eriksson, A., Manica, A.: Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proceedings of the National Academy of Sciences 109(35), 13956–13960 (2012)
7. Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.H.-Y., Hansen, N.F., Durand, E.Y., Malaspinas, A.-S., Jensen, J.D., Marques-Bonet, T., Alkan, C., Prfer, K., Meyer, M., Burbano, H.A., Good, J.M., Schultz, R., Aximu-Petri, A., Butthof, A., Hber, B., Hffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E.S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, E., Guic, I., Doronichev, V.B., Golovanova, L.V., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R.W., Johnson, P.L.F., Eichler, E.E., Falush, D., Birney, E., Mullikin, J.C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., Pbo, S.: A draft sequence of the Neandertal genome. Science 328(5979), 710–722 (2010)
8. Hobolth, A., Dutheil, J., Hawks, J., Schierup, M., Mailund, T.: Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Research 21, 349–356 (2011)
9. Holland, B.R., Benthin, S., Lockhart, P.J., Moulton, V., Huber, K.T.: Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol. Biol. 8, 202 (2008)
10. Hudson, R.R.: Generating samples under aWright-Fisher neutral model of genetic variation. Bioinformatics 18, 337–338 (2002)
11. Huson, D.H., Rupp, R., Scornavacca, C.: Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, New York (2010)
12. Joly, S., McLenachan, P.A., Lockhart, P.J.: A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 174(2), E54–E70 (2009)
13. Kubatko, L.S.: Identifying hybridization events in the presence of coalescence via model selection. Syst. Biol. 58(5), 478–488 (2009)
14. Kuo, C.-H., Wares, J.P., Kissinger, J.C.: The Apicomplexan whole-genome phylogeny: An analysis of incongruence among gene trees. Mol. Biol. Evol. 25(12), 2689–2698 (2008)
15. Liu, L., Yu, L.L., Kubatko, L., Pearl, D.K., Edwards, S.V.: Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol. 53, 320–328 (2009)
16. Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46(3), 523–536 (1997)
17. Mallet, J.: Hybridization as an invasion of the genome. Trends Ecol. Evol. 20(5), 229–237 (2005)
18. Mallet, J.: Hybrid speciation. Nature 446, 279–283 (2007)
19. Meng, C., Kubatko, L.S.: Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theor. Popul. Biol. 75(1), 35–45 (2009)
20. Moody, M.L., Rieseberg, L.H.: 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 (2012)
21. Mossel, E., Roch, S.: Incomplete lineage sorting: consistent phylogeny estimation from multiple loci. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 7(1), 166–171 (2010)
22. Nakhleh, L.: Evolutionary phylogenetic networks: models and issues. In: Heath, L., Ramakrishnan, N. (eds.) The Problem Solving Handbook for Computational Biology and Bioinformatics, pp. 125–158. Springer, New York (2010)
23. Nakhleh, L.: Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution 28(12), 719–728 (2013)
24. Pollard, D.A., Iyer, V.N., Moses, A.M., Eisen, M.B.: Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet. 2(10), e173 (2006)
25. Rambaut, A.: Phylogen v1.1 (2012), http://tree.bio.ed.ac.uk/software/phylogen/
26. Rannala, B., Yang, Z.: Phylogenetic inference using whole genomes. Annu. Rev. Genomics Hum. Genet. 9, 217–231 (2008)
27. Rieseberg, L.H.: Hybrid origins of plant species. Annu. Rev. Ecol. Syst. 28, 359–389 (1997)
28. Staubach, F., Lorenc, A., Messer, P.W., Tang, K., Petrov, D.A., Tautz, D.: Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (mus musculus). PLoS Genet. 8(8), e1002891 (2012)
29. Syring, J., Willyard, A., Cronn, R., Liston, A.: Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am. J. Bot. 92, 2086–2100 (2005)
30. Takuno, S., Kado, T., Sugino, R.P., Nakhleh, L., Innan, H.: Population genomics in bacteria: A case study of staphylococcus aureus. Molecular Biology and Evolution 29(2), 797–809 (2012)
31. Than, C., Ruths, D., Innan, H., Nakhleh, L.: Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J. Comput. Biol. 14, 517–535 (2007)
32. Than, C., Sugino, R., Innan, H., Nakhleh, L.: Efficient inference of bacterial strain trees from genome-scale multi-locus data. Bioinformatics 24, i123–i131 (2008)
33. White, M.A., Ane, C., Dewey, C.N., Larget, B.R., Payseur, B.A.: Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genetics 5, e1000729 (2009)
34. Yu, Y., Barnett, R.M., Nakhleh, L.: Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology 62, 738–751 (2013)
35. Yu, Y., Degnan, J.H., Nakhleh, L.: The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics 8, e1002660 (2012)
36. Yu, Y., Dong, J., Liu, K., Nakhleh, L.: Maximum likelihood inference of reticulate evolutionary histories. Proceedings of the National Academy of Sciences 111, 16448–16453 (2014)
37. Yu, Y., Ristic, N., Nakhleh, L.: Fast algorithms and heuristics for phylogenomics under ils and hybridization. BMC Bioinformatics 14, S6 (2013)
38. Yu, Y., Than, C., Degnan, J.H., Nakhleh, L.: Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60, 138–149 (2011)