A maximum pseudo-likelihood approach for phylogenetic networks

BMC Genomics

Volumn 16, Issue , 2015, Pages 1-10

  Yu, Yun ^a   Nakhleh, Luay ^a,b  

^a Rice University   (United States)

^b RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; FEASIBILITY STUDY; HYBRIDIZATION; INCOMPLETE LINEAGE SORTING; MAXIMUM PSEUDO LIKELIHOOD METHOD; PHYLOGENY; POPULATION GENETICS; SIMULATION; STATISTICAL ANALYSIS; YEAST; ALGORITHM; BIOLOGY; MOLECULAR EVOLUTION; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; PHYLOGENY;

EID: 84944739954     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-16-S10-S10     Document Type: Article

References (46)

1. Nakhleh L: Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution 2013, 28(12):719-728.
2. Pollard DA, Iyer VN, Moses AM, Eisen MB: Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet 2006, 2:1634-1647.
3. Kuo CH, Wares JP, Kissinger JC: The Apicomplexan whole-genome phylogeny: An analysis of incongruence among gene trees. Mol Biol Evol 2008, 25(12):2689-2698.
4. White MA, Ane C, Dewey CN, Larget BR, Payseur BA: Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genetics 2009, 5:1000729.
5. Arnold ML: Natural Hybridization and Evolution Oxford University Press, Oxford; 1997.
6. Barton NH: The role of hybridization in evolution. Molecular Ecology 2001, 10(3):551-568.
7. Mallet J: Hybridization as an invasion of the genome. Trends Ecol Evol 2005, 20(5):229-237.
8. Mallet J: Hybrid speciation. Nature 2007, 446:279-283.
9. Rieseberg LH: Hybrid origins of plant species. Annu Rev Ecol Syst 1997, 28:359-389.
10. 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 2012, 109(35):13956-13960[http://www.pnas.org/content/109/35/13956.full.pdf+html], doi:10.1073/pnas.1200567109.
11. Staubach F, Lorenc A, Messer PW, Tang K, Petrov DA, Tautz D: Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (mus musculus). PLoS Genet 2012, 8(8):1002891.
12. Consortium THG: Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 2012, 487(7405):94-98.
13. Moody ML, Rieseberg LH: Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect Helianthus). Molecular Phylogenetics And Evolution 2012, 64:145-155.
14. Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ: Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 2015, 347(6217):1258524.
15. Than C, Ruths D, Innan H, Nakhleh L: Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions. J Comput Biol 2007, 14:517-535.
16. Holland BR, Benthin S, Lockhart PJ, Moulton V, Huber KT: Using supernetworks to distinguish hybridization from lineage-sorting. BMC Evol Biol 2008, 8:202.
17. Meng C, Kubatko LS: Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. Theor Popul Biol 2009, 75(1):35-45.
18. Kubatko LS: Identifying hybridization events in the presence of coalescence via model selection. Syst Biol 2009, 58(5):478-488.
19. Joly S, McLenachan PA, Lockhart PJ: A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am Nat 2009, 174(2):54-70.
20. Yu Y, Than C, Degnan JH, Nakhleh L: Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 2011, 60:138-149.
21. Yu Y, Ristic N, Nakhleh L: Fast algorithms and heuristics for phylogenomics under ils and hybridization. BMC Bioinformatics 2013, 14:6, Chap. S6.
22. Yu Y, Degnan JH, Nakhleh L: The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics 2012, 8:1002660.
23. Yu Y, Barnett RM, Nakhleh L: Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology 2013, 62:738-751, Chap. 738.
24. Yu Y, Dong J, Liu K, Nakhleh L: Maximum likelihood inference of reticulate evolutionary histories. Proceedings of the National Academy of Sciences 2014, 111:16448-16453, Chap. 16448.
25. Yu Y, Nakhleh L: A distance-based method for inferring phylogenetic networks in the presence of incomplete lineage sorting. International Symposium on Bioinformatics Research and Applications (ISBRA) Lecture Notes in Bioinformatics 2015, 9096:378-389.
26. Liu L, Yu L, Edwards SV: A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evolutionary Biology 2010, 10(302).
27. Than C, Ruths D, Nakhleh L: PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 2008, 9:322.
28. Nakhleh L: PhyloNet 2008 [http://bioinfo.cs.rice.edu/phylonet].
29. Nakhleh L: Evolutionary phylogenetic networks: models and issues. In The Problem Solving Handbook for Computational Biology and Bioinformatics. Springer, New York;Heath, L., Ramakrishnan, N 2010:125-158.
30. Feller W: In An Introduction to Probability Theory and Its Applications. Volume 1. 3 edition. Wiley, New York; 1968.
31. Dress A, Huber KT, Koolen J, Moulton V, Spillner A: Basic phylogenetic combinatorics Cambridge University Press; 2012.
32. Gambette P, Huber KT: On encodings of phylogenetic networks of bounded level. Journal of Molecular Biology 2012, 65(1):157-180.
33. Salter LA, Pearl DK: Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Systematic Biology 2001, 50(1):7-17.
34. Kubatko LS, Carstens BC, Knowles LL: STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25(7):971-973.
35. Salichos L, Rokas A: Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 2013, 497:327-331.
36. Yu Y, Warnow T, Nakhleh L: Algorithms for MDC-based multi-locus phylogeny inference. The 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB) LNBI 6577 2011, 531-545.
37. Yu Y, Warnow T, Nakhleh L: Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles. Journal of Computational Biology 2011, 18:1543-1559.
38. Hudson RR: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338.
39. Rambaut A, Grassly NC: Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp Appl Biosci 1997, 13:235-238.
40. Stamatakis A: Raxml version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies. Bioinformatics 2014, 30(9):1312-1313.
41. Than C, Nakhleh L: Species tree inference by minimizing deep coalescences. PLoS Computational Biology 2009, 5(9):1000501.
42. Rambaut A: Phylogen v1.1 2012 [http://tree.bio.ed.ac.uk/software/phylogen/].
43. Clark AG, Messer PW: Conundrum of jumbled mosquito genomes. Science 2015, 347(6217):27-28.
44. Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitefield J: Networks: expanding evolutionary thinking. Trends in Genetics 2013, 29(8):439-441.
45. van Iersel L, Moulton V: Trinets encode tree-child and level-2 phylogenetic networks. Journal of mathematical biology 2014, 68(7):1707-1729.
46. Pardi F, Scornavacca C: Reconstructible phylogenetic networks: Do not distinguish the indistinguishable. PLoS Comput Biol 2015, 11(4):1004135.