From gene trees to a dated allopolyploid network: Insights from the angiosperm genus viola (violaceae)

Systematic Biology

Volumn 64, Issue 1, 2015, Pages 84-101

  Marcussen, Thomas ^a,b   Heier, Lise ^a   Brysting, Anne K ^a   Oxelman, Bengt ^b   Jakobsen, Kjetill S ^a  

^a UNIVERSITY OF OSLO   (Norway)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Dating; Low copy nuclear gene; Polyploidy; Species network; Viola; Violaceae

Indexed keywords

CLASSIFICATION; FOSSIL; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; POLYPLOIDY; TIME; VIOLA;

EVOLUTION, MOLECULAR; FOSSILS; PHYLOGENY; POLYPLOIDY; TIME; VIOLA;

EID: 84965114132     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu071     Document Type: Article

References (112)

1. Abbott R., Albach D., Ansell S., Arntzen J.W., Baird S.J.E, Bierne N., Boughman J., Brelsford A., Buerkle C.A., Buggs R., Butlin R.K., Dieckmann U., Eroukhmanoff F., Grill A., Cahan S.H., Hermansen J.S., Hewitt G., Hudson A.G., Jiggins C., Jones J., Keller B., Marczewski T., Mallet J., Martinez-Rodriguez P., Möst M., Mullen S., Nichols R., Nolte A.W., Parisod C., Pfennig K., Rice A.M., Ritchie M.G., Seifert B., Smadja C.M., Stelkens R., Szymura J.M., Väinölä R., Wolf J.B.W., Zinner D. 2013. Hybridization and speciation. J. Evol. Biol. 26:229-246.
2. Álvarez I., Wendel J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogen. EVol. 29:417-434.
3. Arrigoni P.V., Mori B. 1980. Numeri cromosomici per la Flora Italiana: 722-727. Infor. Bot. Ital. 12:145-148.
4. Ballard H.E., Sytsma K.J. 2000. Evolution and biogeography of the woody Hawaiian violets (Viola, Violaceae): arctic origins, herbaceous ancestry and bird dispersal. Evolution 54:1521-1532.
5. Ballard H.E., Sytsma K.J., Kowal R.R. 1999. Shrinking the violets: phylogenetic relationships of infrageneric groups in Viola (Violaceae) based on internal transcribed spacer DNA sequences. Syst. Bot. 23:439-458.
6. Bartoszek K., Jones G., Oxelman B., Sagitov S. 2013. Time to a single hybridization event in a group of species with unknown ancestral history. J. Theor. Biol. 322:1-6.
7. Becker W. 1925. Viola L. In: Engler A., editor. Die natürlichen Pflanzenfamilien. Parietales und Opuntiales. Leipzig: Wilhelm Engelmann. pp. 363-376.
8. Bell C.D., Soltis D.E., Soltis P.S. 2010. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 97:1296-1303.
9. Brizicky G.K. 1961. The genera of Violaceae in the southeastern United States. J. Arnold Arboretum 42:321-333.
10. Burgess K.S., Fazekas A.J., Kesanakurti P.R., Graham S.W., Husband B.C, Newmaster S.G., Percy D.M., Hajibabaei M., Barrett S.C.H. 2011. Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode. Meth. Ecol. EVol. 2:333-340.
11. Brysting A.K., Mathiesen C., Marcussen T. 2011. Challenges in polyploid phylogenetic reconstruction: a case story from the arcticalpine Cerastium alpinum complex. Taxon 60:333-347.
12. Cai D., Rodríguez F., Teng Y., Ané C., Bonierbale M., Mueller L.A., Spooner D.M. 2012. Single copy nuclear gene analysis of polyploidy inwildpotatoes (Solanumsection Petota). BMCEvol. Biol. 12:70.
13. Chen Z.-Z., Wang L. 2010. Hybridnet: a tool for constructing hybridization networks. Bioinformatics 26:2912-2913.
14. Chen Z.-Z., Wang L. 2012. Algorithms for reticulate networks of multiple phylogenetic trees. IEEE/ACM Trans. Comput. Biol. Bioinform. 9:372-384.
15. Clausen J. 1929. Chromosome number and relationship of some North American species of Viola. Ann. Bot. 63:741-764.
16. Clausen J. 1964. Cytotaxonomy and distributional ecology of western North American violets. Madroño 17:173-197.
17. Couvreur T.L.P, Franzke A., Al-Shehbaz I.A., Bakker F.T., Koch M.A., Mummenhoff K. 2010. Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol. Biol. EVol. 27:55-71.
18. Cui L., Wall P.K., Leebens-Mack J.H., Lindsay B.G., Soltis D.E, Doyle J.J., Soltis P.S., Carlson J.E., Arumuganathan K., Barakat A., Albert V.A., Ma H., dePamphilis C.W. 2006. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16:738-749.
19. Degnan J.H., Rosenberg N.A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. EVol. 24:332-340.
20. Dehal P., Boore J.L. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3:1701-1708.
21. Diosdado J.C., Ojeda F., Pastor J. 1993. IOPB chromosome data 5. Int. Organ. Plant Biosyst. Newsl. 20:6-7.
22. Dorofeev P.I. 1963. Tretichnye flory zapadnoi Sibiri (The Tertiary floras of western Siberia). Moscow: Izdatel'stvo Akademii Nauk SSSR.
23. Doyle J.J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:144-163.
24. Doyle J.J., Doyle J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15.
25. Doyle J.J., Egan A.N. 2010. Dating the origins of polyploidy events. New Phytol. 186:73-85.
26. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
27. Drummond A.J., Ho S.Y.W, Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
28. Erben M. 1996. The significance of hybridization on the forming of species in the genus Viola. Bocconea 5:113-118.
29. Escobar J.S., Scornavacca C., Cenci A., Guilhaumon C., Santoni S., Douzery E.J.P, Ranwez V., Glémin S., David J. 2011. Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae). BMC Evol. Biol. 11:181-198.
30. Fawcett J.A., Maere S., Van de Peer Y. 2009. Plants with double genomes might have had a better chance to survive the Cretaceous-tertiary extinction event. Proc. Natl. Acad. Sci. USA 106:5737-5742.
31. Forest F. 2009. Calibrating the tree of life: fossils, molecules and evolutionary timescales. Ann. Bot. 104:789-794.
32. Galland N. 1985. Chromosome number reports LXXXVII. Taxon 34:346-351.
33. Galland N. 1988. Recherche sur l'origine de la flore orophile du Maroc, étude caryologique et cytogéographique. Trav. Inst. Sci., Univ. Mohammed V. Sér. Bot. 35:1-168.
34. George E.I., McCulloch R.E. 1993. Variable selection via Gibbs sampling. J. Am. Stat. Assoc. 88:881-889.
35. Gerard D., Gibbs H.L., Kubatko L. 2011. Estimating hybridization inthe presence of coalescence using phylogenetic intraspecific sampling. BMC Evol. Biol. 11:291-303.
36. Gingins de la Sarraz F.C.J. 1823. Mémoire sur la famille des Violacées. Mém. Soc. Phys. Hist. Nat. Genève 2:1-27.
37. Gingins de la Sarraz F.C.J. 1824. Viola. In: De Candolle A.P., editor. Prodromus systematis naturalis regni vegetabilis. München: Michelsen.
38. Gong Q., Zhou J.S., Zhang Y.X., Liang G.X., Chen H.F, Xing F.W. 2010. Molecular systematics of genus Viola L. in China. J. Trop. Subtrop. Bot. 18:633-642.
39. Gregory T.R., Mable B.K. 2005. Polyploidy In animals. In: Gregory T.R., editor. The evolution of the genome. San Diego: Elsevier Academic Press. p. 428-501.
40. Hearn D.J. 2006. Adenia (Passifloraceae) and its adaptive radiation: phylogeny and growth form diversification. Syst. Bot. 31:805-821.
41. Hedrén M. 1996. Genetic differentiation, polyploidization and hybridization in northern European Dactylorhiza (Orchidaceae): evidence from allozyme markers. Plant Syst. EVol. 201:31-55.
42. Heilborn O. 1926. Bidrag til Violaceernas cytologi. Sven. Bot. Tidskr. 20:414-419.
43. Herrera C.M. 1990. The adaptedness of the floral phenotype in a relict endemic, hawkmoth-pollinated violet. 2. Patterns of variation among disjunct populations. Biol. J. Linn. Soc. 40:275-291.
44. Huber K.T., Oxelman B., Lott M., Moulton V. 2006. Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol. Biol. EVol. 23:1784-1791.
45. Huson D.H., Scornavacca C. 2012. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61:1061-1067.
46. Jaillon O., Aury J.-M., Noel B., Policriti A., Clepet C., Casagrande A., Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F., Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J., Bruyère C., Billault A., Segurens B., Gouyvenoux M., Ugarte E., Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M., Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M., Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E., Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M., Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pè M.E., Valle G., Morgante M., Caboche M., Adam-Blondon A.-F., Weissenbach J., Quétier F., Wincker P. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-468.
47. Jiao Y., Wickett N.L., Ayyampalayam S., Chanderbali A.S., Landherr L., Ralph P.E., Tomsho L.P., Hu Y., Liang H., Soltis P.S., Soltis D.E., Clifton S.W., Schlarbaum S.E, Schuster S.C., Ma H., Leebens-Mack J., dePamphilis C.W. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473:97-100.
48. Jobb G., von Haeseler A., Strimmer K. 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4:9 pp.
49. Jones G., Sagitov S., Oxelman B. 2013. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Syst. Biol. 62:1-12.
50. Khatoon S., Ali S.I. 1993. Chromosome atlas of the angiosperms of Pakistan. Karachi: Department of Botany, University of Karachi.
51. Kingman J.F.C. 1982. On the genealogy of large populations. J. Appl. Probab. 19A:27-43.
52. Kovar-Eder J., Kvaček Z., Meller B. 2001. Comparing Early to Middle Miocene floras and probable vegetation types of Oberdorf N Voitsberg (Austria), Bohemia (Czech Republic), and Wackersdorf (Germany). Rev. Palaeobot. Palynol. 114:83-125.
53. Kubatko L.S. 2009. Identifying hybridization events in the presence of coalescence via model selection. Syst. Biol. 58:478-488.
54. Leal Perez-chao J., Valbuena A.O., Sotomayor S.P., Pascual M.L.R. 1980. Numeros cromosomicos para la flora Española 121-182. Lagascalia 9.
55. Leitch I.J., Bennett M.D. 2004. Genome downsizing in polyploid plants. Biol. J. Linn. Soc. 82:651-663.
56. Levin D.A. 2002. The role of chromosomal change in plant evolution. New York: Oxford University Press.
57. Liang G.X., Xing F.W. 2010. Infrageneric phylogeny of the genus Viola (Violaceae) based on trnL-trnF, psbA-trnH, rpL16, ITS sequences, cytological and morphological data. Acta Bot. Yunn. 32:477-488.
58. Liu Z., Pagani M., Zinniker D., DeConto R., Huber M., Brinkhuis H., Shah S.R., Leckie R.M., Pearson A. 2009. Global cooling during the Eocene-Oligocene climate transition. Science 323:1187-1190.
59. Lunn D.J., Thomas A., Best N., Spiegelhalter D. 2000. WinBUGS - a Bayesian modelling framework: concepts, structure, and extensibility. Stat. Comp. 10:325-337.
60. Ma X.-F., Gustafson J.P. 2005. Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogen. Genome Res. 109:236-249.
61. Maddison W.P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
62. Mandáková T., Joly S., Krzywinski M., Mummenhoff K., Lysak M.A. 2010. Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22:2277-2290.
63. Marcussen T., Nordal I. 1998. Viola suavis, a new species in the Nordic flora, with analyses of the relation to other species in the subsection Viola (Violaceae). Nord. J. Bot. 18:221-237.
64. Marcussen T., Oxelman B., Skog A., Jakobsen K.S. 2010. Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae). BMC Evol. Biol. 10:45.
65. Marcussen T., Blaxland K., Windham M.D., Haskins K.E., Armstrong F. 2011. Establishing the phylogenetic origin, history and age of the narrow endemic Viola guadalupensis (Violaceae). Am. J. Bot. 98:1978-1988.
66. Marcussen T., Jakobsen K.S., Danihelka J., Ballard H.E., Blaxland K., Brysting A.K., Oxelman B. 2012. Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae). Syst. Biol. 61:107-126.
67. Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., IWGSC, Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.A. 2014. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345:1250092.
68. Maureira-Butler I.J., Pfeil B.E., Muangprom A., Osborn T.C., Doyle J.J. 2008. The reticulate history of Medicago (Fabaceae). Syst. Biol. 57:466-482.
69. Mayrose I., Zhan S.H., Rothfels C.J., Magnuson-Ford K., Barker M.S., Rieseberg L.H, Otto S.P. 2011. Recently formed polyploid plants diversify at lower rates. Science 333:1257.
70. Meseguer A.S., Aldasoro J.J., Sanmartín I. 2013. Bayesian inference of phylogeny, morphology and range evolution reveals a complex evolutionary history in St. John's wort (Hypericum). Mol. Phylogen. EVol. 67:379-403.
71. Mohammadi Shahrestani M. 2013. Biosystematical investigation of sect. Sclerosium of genus Viola in Iran. M.Sc. thesis. Rasht: University of Rasht. 1-164 (In Persian, with English abstract).
72. Moore D.M. 1967. Chromosome numbers of Falkland islands angiosperms. Brit. Antarct. Surv. Bull. 14:69-82.
73. Morton J.K. 1993. Chromosome numbers and polyploidy in the flora of Cameroon mountain. Opera Bot. 121:159-172.
74. Müntzing A. 1932. Cytogenetic investigations on synthetic Galeopsis tetrahit. Hereditas 16:105-154.
75. Nakamura K., Denda T., Kokubugata G., Huang C.-J., Peng C.-I., Yokota M. 2014. Phylogeny and biogeography of the Viola iwagawae-tashiroi species complex (Violaceae, section Plagiostigma) endemic to the Ryukyu Archipelago, Japan. Plant Syst. Evol.: in press.
76. Nichols R. 2001. Gene trees and species trees are not the same. Trends Ecol. EVol. 16:358-364.
77. Otto S.P. 2007. The evolutionary consequences of polyploidy. Cell 131:452-462.
78. Ownbey M. 1950. Natural hybridization and amphiploidyinthegenus Tragopogon. Am. J. Bot. 37:489-499.
79. Parham J.F., Donoghue P.C.J, Bell C.J., Calway T.D., Head J.J., Holroyd P.A, Inoue J.G., Irmis R.B., Joyce W.G., Ksepka D.T, Patané J.S.L., Smith N.D., Tarver J.E., van Tuinen M., Yang Z., Angielczyk K.D., Greenwood J.M., Hipsley C.A., Jacobs L., Makovicky P.J., Müller J., Smith K.T., Theodor J.M., Warnock R.C.M., Benton M.J. 2012. Best practices for justifying fossil calibrations. Syst. Biol. 61:346-359.
80. Rambaut A., Drummond A.J. 2009. Tracer v1.5. Available from: http://beast.bio.ed.ac.uk/Tracer.
81. Renoult J.P., Kjellberg F., Grout C., Santoni S., Khadari B. 2009. Cytonuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations. BMC Evol. Biol. 9:248-266.
82. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. 2011. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61:539-542.
83. Roquet C., Sanmartín I., Garcia-Jacas N., Sáez L., Susanna A., Wikström N., Aldasoro J.J. 2009. Reconstructing the history of Campanulaceae with a Bayesian approach to molecular dating and dispersalvicariance analyses. Mol. Phylogen. EVol. 52:575-587.
84. Rosenberg N.A., Feldman M.W. 2002. Chapter 9. The relationship between coalescence times and population divergence times. In: Slatkin M., Veuille M., editors. Modern Developments in Theoretical Population Genetics. Oxford: Oxford University Press, p. 130-164.
85. Rutschmann F. 2006. Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Divers. Distrib. 12:35-48.
86. Sanso A.M., Seo M.N. 2005. Chromosomes of some Argentine angiosperms and their taxonomic significance. Caryologia 58:171-177.
87. Sauquet H., Ho S.Y.W, Gandolfo M.A., Jordan G.J., Wilf P., Cantrill D.J., Bayly M.J., Bromham L., Brown G.K., Carpenter R.J., Lee D.M., Murphy D.J, Sniderman J.M.K, Udovicic F. 2012. Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales) Syst. Biol. 61:289-313.
88. Scheen A.C., Pfeil B.E., Petri A., Heidari N., Nylinder S., Oxelman B. 2012. Use of allele-specific sequencing primers is an efficient alternative to PCR subcloning of low-copy nuclear genes. Mol. Ecol. Resour. 12:128-135.
89. Schmidt A. 1964. Zur Systematischen Stellung von Viola chelmea Boiss. et Heldr. ssp. chelmea und V. delphinantha Boiss. Ber. deut. bot. Ges. 77:256-261.
90. Smith-White S. 1959. Cytological evolutionin the Australian flora. Cold Spring Harb. Sym. Quant. Biol. 24:273-289.
91. Soltis D.E., Salcedo M.C.S, Thaden I.J., Majure L.M., Miles N.M., Mavrodiev E.V, Mei W., Cortez M.B., Soltis P.S., Gitzendanner M.A. 2014. Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. (2011). New Phytol. 202:1105-1117.
92. Soltis D.E., Soltis P.S. 1993. Molecular data and the dynamic nature of polyploidy. Crit. Rev. Plant Sci. 12:243-273.
93. Tang H., Bowers J.E., Wang X., Paterson A.H. 2010. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc. Natl. Acad. Sci. USA 107:472-477.
94. Tate J., Soltis D.E., Soltis P.S. 2005. Polyploidy In plants. In: Gregory T.R., editor. The evolution of the genome. San Diego: Elsevier Academic Press. pp. 371-426.
95. Tokuoka T. 2008. Molecular phylogenetic analysis of Violaceae (Malpighiales)basedonplastid and nuclear DNA sequences. J. Plant Res. 121:253-260.
96. Tokuoka T., Tobe H. 2006. Phylogenetic analyses of Malpighiales using plastid and nuclear DNA sequences, with particular reference to the embryology of Euphorbiaceae sens. str. J. Plant Res. 119:599-616.
97. Twyford A.D., Ennos R.A. 2012. Next-generation hybridization and introgression. Heredity 108:179-189.
98. van den Hof K., van den Berg R.G., Gravendeel B. 2008. Chalcone synthase gene lineage diversification confirms allopolyploid evolutionary relationships of European rostrate violets. Mol. Biol. EVol. 25:2099-2108.
99. Verlaque R., Espeut M. 2007. Violaceae. In: Marhold K., editor. IAPT/IOPT chromosome data 3. Taxon 56:E1.
100. Wahlert G.A., Marcussen T., de Paula-Souza J., Feng M., Ballard H.E. 2014. A phylogeny of the Violaceae (Malpighiales) inferred from plastid DNA sequences: implications for generic diversity and intrafamilial taxonomy. Syst. Bot. 39:239-252.
101. Wang H., Moore M.J., Soltis P.S., Belle C.D., Brockington S.F, Alexandre R., Davis C.C., Latvis M., Manchester S.R., Soltis D.E. 2009. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc. Natl. Acad. Sci. USA 106:3853-3858.
102. Wendel J.F., Doyle J.J. 2005. Polyploidy and evolution In plants. In: Henry R., editor. Diversity and evolution in plants. Oxon: CABI Publishing. pp. 97-117.
103. Wolfe K.H. 2001. Yesterday's polyploidization and mystery of diploidization. Nat. Rev. Genet. 2:333-341.
104. Wood T.E., Takebayashi N., Barker M.S., Mayrose I., Greenspoon P.B., Rieseberg L.H. 2009. The frequency of polyploid speciation in vascular plants. Proc. Natl. Acad. Sci. USA 106:13875-13879.
105. Xi Z., Ruhfel B.R., Schaefer H., Amorim A.M., Sugumarane M., Wurdack K.J., Endress P.K., Matthews M.L., Stevens P.F, Mathews S., Davis C.C. 2012. Phylogenomicsanda posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proc. Natl. Acad. Sci. USA 109:17519-17524.
106. Yang Z., Rannala B. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656.
107. Yockteng R., Ballard H.E., Mansion G., Dajoz I., Nadot S. 2003. Phylogenetic relationships among pansies (Viola section Melanium) investigated using ITS and ISSR markers. Plant Syst. EVol. 241:153-170.
108. Yoo K.-O., Jang S.-K. 2010. Infrageneric relationships of Korean Viola based on eight chloroplast markers. J. Syst. EVol. 48:474-481.
109. Yoo K.-O., Jang S.-K., Lee W.-T. 2005. Phylogeny of Korean Viola based on ITS sequences. Korean J. Plant Taxon. (Sigmul Bunryu Hag-hoeji) 35:7-23 (in Korean).
110. Yu Y., Than C., Degnan J., Nakhleh L. 2011. Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Syst. Biol. 60:138-149.
111. Yu Y., Barnett R.M., Nakhleh L. 2013. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Syst. Biol. 62:738-751.
112. Zwickl D.J., Stein J.C., Wing R.A., Ware D., Sanderson M.J. 2014. Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Syst. Biol. 63:645-659.