A Primer to Molecular Phylogenetic Analysis in Plants

Critical Reviews in Plant Sciences

Volumn 34, Issue 4, 2015, Pages 454-468

  Uncu, Ayse Ozgur ^a   Uncu, Ali Tevfik ^a   Celık, İbrahim ^a   Doganlar, Sami ^a   Frary, Anne ^a  

^a IZMIR INSTITUTE OF TECHNOLOGY   (Turkey)

Author keywords

Bayesian methods; distance methods; maximum likelihood methods; maximum parsimony methods; molecular evolution

Indexed keywords

EID: 84938545137     PISSN: 07352689     EISSN: 15497836     Source Type: Journal    
DOI: 10.1080/07352689.2015.1047712     Document Type: Article

References (133)

1. I.Alvarez,, and J.F.Wendel, 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet. Evol. 29: 417–434.
2. T.J.Barkman,, G.Chenery,, J.R.McNeal,, J.Lyons-Weiler,, W.J.Ellisens,, G.Moore,, A.D.Wolfe,, and C.W.dePamphilis, 2000. Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. PNAS 97: 13166–13171.
3. A.Barriere,, K.L.Gordon,, and I.Ruvinsky, 2011. Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet. 7: e1002095. doi:10.1371/journal.pgen.1002095.
4. D.A.Benson,, M.Cavanaugh,, K.Clark,, I.Karsch-Mizrachi,, D.J.Lipman,, J.Ostell,, and E.W.Sayers, 2013. GenBank. Nucleic Acids Res. 41: D36–D42.
5. U.Bergthorsson,, K.L.Adams,, B.Thomason,, and J.D.Palmer, 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424: 197–201.
6. C.Blouin,, Y.Boucher,, and A.Roger, 2003. Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information. Nucleic Acids Res. 31: 790–797.
7. A.Bombarely,, N.Menda,, I.Y.Tecle,, R.M.Buels,, S.Strickler,, T.Fischer-York,, A.Pujar,, J.Leto,, J.Gosselin,, and L.A.Mueller, 2011. The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 39: D1149–D1155.
8. L.Bromham, 2008. Reading the story in DNA. Oxford University Press Inc., New York.
9. W.J.Bruno,, N.D.Socci,, and A.L.Halpern, 2000. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17: 189–197.
10. E.S.Buckler,, A.Ippolito,, and T.P.Holtsford, 1997. The evolution of ribosomal DNA: divergent paralogues and phylogenetic implications. Genetics 145: 821–832.
11. J.G.Burleigh,, M.S.Bansal,, O.Eulenstein,, S.Hartmann,, A.Wehe,, and T.J.Vision, 2011. Genome-scale phylogenetics: Inferring the plant tree of life from 18,896 gene trees. Syst. Biol. 60: 117–125.
12. L.L.Cavalli-Sforza,, and W.F.Edwards, 1967. Phylogenetic analysis Models and Estimation Procedures. Am. J. Hum. Genet. 19: 233–257.
13. CBOL Plant Working Group. 2009. A DNA barcode for land plants. PNAS 106: 12794–12797.
14. M.W.Chase,, S.Cowan,, P.M.Hollingsworth,, C.van den Berg,, S.Madrinan,, G.Petersen,, O.Seberg,, T.Jorgsensen,, K.M.Cameron,, M.Carine,, P.Niklas,, T.A.J.Hedderson,, F.Conrad,, G.A.Salazar,, J.E.Richardson,, M.L.Hollingsworth,, T.G.Barraclough,, L.Kelly,, and M.Wilkinson, 2007. A proposal for a standardized protocol to barcode all land plants. Taxon 56: 295–299.
15. M.W.Chase,, N.Salamin,, M.Wilkinson,, J.M.Dunwell,, R.P.Kesanakurthi,, N.Haidar,, and V.Savolainen, 2005. Land plants and DNA barcodes: short-term and long-term goals. Philos. T. Roy. Soc. B. 360: 1889–1895.
16. J.J.Clarkson,, L.J.Kelly,, A.R.Leitch,, S.Knapp,, and M.W.Chase, 2010. Nuclear glutamine synthetase evolution in Nicotiana: phylogenetics and the origins of allotetraploid and homoploid (diploid) hybrids. Mol. Phylogenet. Evol. 55: 99–112.
17. M.G.Conte,, S.Gaillard,, N.Lanau,, M.Rouard,, and C.Perin, 2008. GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res. 36: D991–D998.
18. R.Cronn,, A.Liston,, M.Parks,, D.S.Gernandt,, R.Shen,, and T.Mockler, 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing by synthesis technology. Nucleic Acids Res. 36: 1–11.
19. R.Cronn,, B.J.Knaus,, A.Liston,, P.J.Maughan,, M.Parks,, J.V.Syring,, and J.Udall, 2012. Targeted enrichment strategies for next-generation plant biology. Am. J. Bot. 99: 291–311.
20. C.C.Davis,, Z.Xi,, and S.Mathews, 2014. Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there. BMC Biol. 12: 11.
21. M.O.Dayhoff, 1972. Atlas of protein sequence and structure. National Biomedical Research Foundation, Silver Springs, MD.
22. M.O.Dayhoff,, R.M.Schwartz,, and B.C.Orcutt, 1978. A model of evolutionary change in proteins. In: Atlas of Protein Sequence and Structure. pp. 345–352. M.O.Dayhoff,, Eds., National Biomedical Research Foundation, Silver Springs, MD.
23. J.Doebley,, M.L.Durbin,, E.M.Golenberg,, M.T.Clegg,, and D.P.Ma, 1990. Evolutionary analysis of the large subunit of carboxylase (rbcL) nucleotide sequence among the grasses (Graminae). Evolution 44: 1097–1108.
24. W.Dong,, J.Liu,, J.Yu,, L.Wang,, and S.Zhou, 2012. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7: e35071.
25. G.Drouin,, H.Daoud,, and J.Xia, 2008. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol. Phylogenet. Evol. 49: 827–831.
26. J.M.Duarte,, P.K.Wall,, P.P.Edger,, L.L.Landherr,, H.Ma,, J.C.Pires,, J.Leebens-Mack,, and C.W.de Pamphilis, 2011. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol. Biol. 10: 61.
27. R.J.Duff,, and D.L.Nickrent,, 1999. Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences. Am. J. Bot. 86: 372–386.
28. R.V.Eck,, and M.O.Dayhoff, 1966. Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Springs, MD.
29. R.C.Edgar, 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 51792–1797.
30. J.Felsenstein, 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol. Evol. 17: 368–376.
31. W.M.Fitch, 1971. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20: 406–416.
32. W.M.Fitch,, and E.Margoliash, 1967. Construction of phylogenetic trees. Science 155: 279–284.
33. T.Fukuda,, J.Yokoyama,, T.Nakamura,, I.J.Song,, T.Ito,, T.Ochiai,, A.Kanno,, T.Kameya,, and M.Maki, 2005. Molecular phylogeny and evolution of alcohol dehydrogenase (Adh) genes in legumes. BMC Plant Biol. 5: 6.
34. J.D.Futuyma, 2005. Evolution. Sinauer Associates Inc., Sunderland, MA.
35. N.Galtier, 2011. The intriguing evolutionary dynamics of plant mitochondrial DNA. BMC Biol. 9: 61.
36. B.S.Gaut,, S.V.Muse,, W.D.Clark,, and M.T.Clegg, 1992. Relative rates of nucleotide substitutions at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35: 292–303.
37. L.Gielly,, and P.Taberlet, 1994. The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol. Biol. Evol. 11: 769–777.
38. M.D.Gonzales,, E.Archuleta,, A.Farmer,, K.Gajendran,, D.Grant,, R.Shoemaker,, W.D.Beavis,, and M.E.Waugh, 2005. The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res. 33: D660–D665.
39. D.M.Goodstein,, S.Shu,, R.Howson,, R.Neupane,, R.D.Hayes,, J.Fazo,, T.Mitros,, W.Dirks,, U.Hellsten,, N.Putnam,, and D.S.Rokhsar, 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40: D1178–1186.
40. D.Graur,, and W.H.Li, 2000. Fundamentals of Molecular Evolution. 2nd ed., Sinauer Associates Inc., Sunderland, MA.
41. F.Grewe,, P.P.Edger,, I.Keren,, L.Sultan,, J.C.Pires,, O.Ostersetzer-Biran,, and J.P.Mower, 2014. Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Mitochondrion 19: 135–143.
42. N.V.Grishin, 1995. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 41: 675–679.
43. B.G.Hall, 2008. Phylogenetic trees made easy. 3rd ed., Sinauer Associates Inc., Sunderland, MA.
44. J.A.Hartigan, 1973. Minimum evolution fits to a given tree. Biometrics 29: 53–65.
45. D.L.Hartl,, and A.G.Clark, 1997. Principles of Population Genetics. Sinauer Associates Inc., Sunderland, MA.
46. M.Hasegawa,, Y.Lida,, T.Yano,, F.Takaiwa,, and M.Iwabuchi, 1985. Phylogenetic relationships among eukaryotic kingdoms inferred from ribosomal RNA sequences. J. Mol. Evol. 22: 32–38.
47. M.D.Hendy,, and D.Penny, 1982. Branch and bound algorithms to determine minimal evolutionary trees. Math. Biosci. 59: 277–290.
48. R.Hiesel,, A.von Haeseler,, and A.Brennicke, 1994. Plant mitochondrial nucleic acid sequences as a tool for phylogenetic analysis. PNAS 91: 634–638.
49. K.W.Hilu,, T.Borsch,, K.Muller,, D.E.Soltis,, P.S.Soltis,, V.Savolainen,, M.W.Chase,, M.Powell,, L.A.Alice,, R.Evans,, H.Sauquet,, C.Neinhus,, T.A.B.Slotta,, J.G.Rohwer,, C.S.Campbell,, and L.W.Chatrou, 2003. Angiosperm phylogeny based on matK sequence information. Am. J. Bot. 90: 1758–1776.
50. P.M.Hollingsworth,, S.W.Graham,, and D.P.Little, 2011. Choosing and using a plant DNA barcode. PLoS ONE 6: e19254.
51. H.Huang,, C.Shi,, Y.Liu,, S.Y.Mao,, and L.Z.Gao, 2014. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol. Biol. 14: 151.
52. J.P.Huelsenbeck,, and F.Ronquist, 2011. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755.
53. L.A.Inda,, M.Pimentel,, and M.W.Chase, 2010. Chalcone synthase variation and phylogenetic relationships in Dactylorhiza (Orchidaceae). Bot. J. Linn. Soc. 163: 155–165.
54. V.M.Ingram, 1963. The Hemoglobins in Genetics and Evolution. Columbia University Press, New York.
55. R.K.Jansen,, C.Kaittanis,, C.Saski,, S.B.Lee,, J.Tomkins,, A.J.Alverson,, and H.Daniell, 2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol. Biol. 6: 32.
56. R.K.Jansen,, Z.Cai,, L.A.Raubeson,, H.Daniell,, C.W.dePamphilis,, J.Leebens-Mack,, K.F.Muller,, M.Guisinger-Bellian,, R.C.Haberle,, A.K.Hansen,, T.W.Chumley,, S.B.Lee,, R.Peery,, J.R.McNeal,, J.V.Kuehl,, and J.L.Boore, 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. PNAS 104: 19369–19374.
57. T.H.Jukes,, and C.R.Cantor, 1969. Evolution of protein molecules. In: Mammalian Protein Metabolism. pp. 21–132. H.N.Munro,, Eds., Academic Press, New York.
58. S.Jung,, M.Staton,, T.Lee,, A.Blenda,, R.Svancara,, A.Abbott,, and D.Main, 2008. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res. 36: D1034–D1040.
59. M.Kearse,, R.Moir,, A.Wilson,, S.Stones-Havas,, M.Cheung,, S.Sturrock,, S.Buxton,, A.Cooper,, S.Markowitz,, C.Duran,, T.Thierer,, B.Ashton,, P.Mentjies,, and A.Drummond, 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649.
60. C.Kim,, H.Shin,, Y.T.Chang,, and H.K.Choi, 2010. Speciation pathway of Isoetes (Isoetaceae) in East Asia inferred from molecular phylogenetic relationships. Am. J. Bot. 97: 958–969.
61. M.Kimura, 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111–120.
62. M.Kimura, 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
63. H.Kishino,, T.Miyata,, and M.Hasegawa, 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31: 151–160.
64. V.Knoop, 2004. The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr. Genet. 46: 123–139.
65. V.Knoop, 2011. When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol. Life Sci. 68: 567–586.
66. V.Knoop,, U.Volkmar,, J.Hecht,, and F.Grewe, 2011. Mitochondrial genome evolution in the plant lineage. In: Plant Mitochondria. pp. 3–29. F.Kempken,, Eds., Springer, New York.
67. S.Kumar,, K.Tamura,, and M.Nei, 1993. Manual for MEGA: Molecular Evolutionary Genetics Analysis software. Pennsylvania State University, University Park, PA.
68. E.K.Lee,, A.Cibrian-Jaramillo,, S.O.Kolokotronis,, M.S.Katari,, A.Stamatakis,, M.Ott,, J.C.Chiu,, D.P.Little,, D.Wm. Stevenson,, R.McCombie,, R.A.Martienssen,, G.Coruzzi,, and R.DeSalle, 2011. A functional phylogenomic view of the seed plants. PLoS Genet. 7: e1002411.
69. C.Liang,, P.Jaiswal,, C.Hebbard,, S.Avraham,, E.S.Buckler,, T.Casstevens,, B.Hurwitz,, S.McCouch,, J.Ni,, A.Pujar,, D.Ravenscroft,, L.Ren,, W.Spooner,, I.Tecle,, J.Thomason,, C.W.Tung,, X.Wei,, I.Yap,, K.Youens-Clark,, D.Ware,, and L.Stein, 2008. Gramene: a growing plant comparative genomics resource. Nucleic Acids Res. 36: D947–D953.
70. J.Q.Liao,, L.Ross,, X.Fan,, L.N.Sha,, H.Y.Kang,, H.Q.Zhang,, Y.Wang,, J.Liu,, X.L.Wang,, X.F.Yu,, R.W.Yang,, C.B.Ding,, L.Zhang,, and Y.H.Zhou, 2013. Phylogeny and maternal donors of the tetraploid species with St genome (Poaceae: Triticeae) inferred from CoxII and ITS sequences. Biochem. Syst. Ecol. 50: 277–285.
71. Y.Liu,, C.J.Cox,, W.Wang,, and B.Goffinet, 2014. Mitochondrial phylogenomics of early land plants: Mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Syst. Biol. 63: 862–878.
72. D.R.Maddison, 1991. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Biol. 40: 315–328.
73. O.Malek,, K.Lattig,, R.Hiesel,, A.Brennicke,. and V.Knoop, 1996. RNA editing in bryophytes and a molecular phylogeny of land plants. The EMBO Journal 15: 1403–1411.
74. E.Margoliash, 1963. Primary structure and evolution cytochrome c. PNAS 50: 672–679.
75. S.Marten-Rodriguez,, C.B.Fenster,, I.Agnarsson,, L.E.Skog,, and E.A.Zimmer, 2010. Evolutionary breakdown of pollination specialization in a Caribbean plant radiation. New Phytol. 188: 403–417.
76. R.J.Mason Gamer, 2008. Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae). Mol. Phylogenet. Evol. 47: 598–611.
77. B.Mau,, and M.Newton, 1997. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6: 122–131.
78. B.Mau,, M.Newton,, and B.Larget, 1999. Bayesian phylogenetic inference via Markov chain Monte carlo methods. Biometrics 55: 1–12.
79. R.Messeguer,, M.W.Ganal,, J.C.Steffens,, and S.D.Tanksley, 1991. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol. Biol. 16: 753–770.
80. M.J.Moore,, C.D.Bell,, P.S.Soltis,, and D.E.Soltis, 2007. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. PNAS 104: 19363–19368.
81. M.J.Moore,, P.S.Soltis,, C.D.Bell,, J.G.Burleigh,, and D.E.Soltis, 2010. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. PNAS 107: 4623–4628.
82. M.Nei, 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
83. M.Nei, 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30: 371–403.
84. M.Nei,, and S.Kumar, 2000. Molecular Evolution and Phylogenetics. Oxford University Press Inc., New York.
85. S.V.Nikiforova,, D.Cavalieri,, R.Velasco,, and V.Goremykin, 2013. Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line. Mol. Biol. Evol. 30: 1751–1760.
86. S.Ohno, 1970. Evolution by Gene Duplication. Springer-Verlag, Berlin.
87. B.Oldenkott,, K.Yamaguchi,, S.T.Tsukinoki,, N.Knie,, and V.Knoop, 2014. Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata. RNA doi: 10.1261/rna.045575.114.
88. T.Ota,, and M.Nei, 1994. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 38: 542–643.
89. F.Pardi,, and O.Gascuel, 2012. Combinatorics of distance-based tree inference. PNAS 109: 16443–16448.
90. C.L.Parkinson,, K.L.Adams,, and J.D.Palmer, 1999. Multigene analyses identify the three earliest lineages of extant flowering plants. Curr. Biol. 9: 1485–1488.
91. M.Parks,, R.Cronn,, and A.Liston, 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol. 7: 84.
92. P.Poczai,, and, J.Hyvonen, 2010. Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol. Biol. Rep. 37: 1897–1912.
93. A.A.Popescu,, K.T.Huber,, and E.Paradis, 2012. Ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics 28: 1536–1537.
94. S.Proost,, M.van Bel,, L.Sterck,, K.Billiau,, T.van Parys,, van Y.de Peer,, and K.Vandepoele, 2009. PLAZA: A comparative genomics resource to study gene and genome evolution in plants. The Plant Cell 21: 3718–3731.
95. Y.L.Qiu,, J.Lee,, F.Bernasconi-Quadroni,, D.E.Soltis,, P.S.Soltis,, M.Zanis,, E.A.Zimmer,, Z.Chen,, V.Savolainen,, and M.W.Chase, 1999. The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402: 404–407.
96. S.Rajapakse,, S.Nilmalgoda,, M.Molnar,, R.Ballard,, D.Austin,, and J.Bohac, 2004. Phylogenetic relationships of the sweet potato in Ipomoea series Batatas (Convolvulaceae) based on nuclear beta-amylase gene sequences. Mol. Phylogenet. Evol. 30: 623–632.
97. B.Rannala,, and Z.Yang, 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43: 304–311.
98. B.R.Ruhfel,, M.A.Gitzendanner,, P.S.Soltis,, D.E.Soltis,, and J.G.Burleigh, 2014. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol. Biol. 14: 23.
99. A.Rzhetsky,, and M.Nei, 1992. A simple method for estimating and testing minimum evolution trees. Mol. Biol. Evol. 9: 945–967.
100. A.Rzhetsky,, and M.Nei, 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10: 1073–1095.
101. N.Saitou,, and M.Nei, 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
102. M.V.Sanchez-Puerta,, C.C.Abbona,, S.Zhuo,, E.J.Tepe,, L.Bohs,, R.G.Olmstead,, and J.D.Palmer, 2011. Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons. BMC Evol. Biol. 11: 277.
103. M.V.Sanchez-Puerta,, Y.Cho,, J.P.Mower,, A.J.Alverson,, and J.D.Palmer, 2008. Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria. Mol. Biol. Evol. 25: 1762–1777.
104. F.Sanger,, S.Nicklen,, and A.R.Coulson, 1977. DNA Sequencing with chain-terminating inhibitors. PNAS 74: 5463–5467.
105. O.I.Sanjur,, D.R.Piperno,, T.C.Andres,, and L.Wessel-Beaver, 2002. Phylogenetic relationships among domesticated and wild species of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene: Implications for a crop plant evolution and areas of origin. PNAS 99: 535–540.
106. O.Seberg,, G.Petersen,, J.I.Davis,, J.C.Pires,, D.W.Stevenson,, M.W.Chase,, M.F.Fay,, D.S.Devey,, T.Jorgensen,, K.J.Sytsma,, and Y.Pillon, 2012. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. Am. J. Bot. 99:875–889.
107. L.N.Sha,, X.Fan,, H.Q.Zhang,, H.Y.Kang,, Y.Wang,, X.L.Wang,, L.Zhang,, C.B.Ding,, R.W.Yang,, and Y.H.Zhou, 2014. Phylogenetic relationships in Leymus (Triticeae; Poaceae): Evidence from chloroplast trn-H-psbA and mitochondrial coxII intron sequences. J. Syst. Evol. 52: 722–734.
108. J.Shaw,, E.B.Lickey,, E.E.Schilling,, and R.L.Small, 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The tortoise and the hare III. Am. J. Bot. 94: 275–288.
109. P.H.A.Sneath,, and R.R.Sokal, 1973. Numerical Taxonomy. Freeman Publishers, San Francisco, CA.
110. R.R.Sokal,, and C.D.Michener, 1958. A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 28: 1409–1438.
111. D.E.Soltis,, P.S.Soltis,, M.W.Chase,, M.E.Mort,, D.C.Albach,, M.Zanis,, V.Savolainen,, W.H.Hahn,, S.B.Hoot,, M.F.Fay,, M.Axtell,, S.M.Swensen,, L.M.Prince,, W.J.Kress,, K.C.Nixon,, and J.S.Farris, 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133: 381–461.
112. S.C.K.Straub,, M.Parks,, K.Weitemier,, M.Fishbein,, R.C.Cronn,, and A.Liston, 2012. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am. J. Bot. 99: 349–364.
113. D.Swarbreck,, C.Wilks,, P.Lamesch,, T.Z.Berardini,, M.Garcia-Hernandez,, H.Foerster,, D.Li,, T.Meyer,, R.Muller,, L.Ploetz,, A.Radenbaugh,, S.Singh,, V.Swing,, C.Tissier,, P.Zhang,, and E.Huala, 2008. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36: D1009–D1014.
114. D.L.Swofford, and D.P.Begle, 1993. PAUP: Phylogenetic Analysis Using Parsimony, Version 3.1. User's Manual. Illinois Natural History Survey, Champaign, IL.
115. G.Sun,, M.Pourkheirandish,, and T.Komatsuda, 2010. Molecular evolution and phylogeny of the rpb2 gene in the genus Hordeum. Ann. Bot. 103: 975–983.
116. P.Taberlet,, E.Coissac,, F.Pompanon,, L.Gielly,, C.Miquel,, A.Valentini,, T.Vermat,, G.Corthier,, C.Brochmann,, and E.Willerslev, 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35: e14.
117. P.Taberlet,, L.Gielly,, G.Pautou,, and J.Bouvet, 1991. Universal primers for Amplification of three non-coding regions of chloroplast DNA. Plant. Mol. Biol. 17: 1105–1109.
118. K.Tamura, 1992. The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol. Biol. Evol. 9: 814–825.
119. K.Tamura,, and M.Nei, 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10: 512–526.
120. K.Tamura,, G.Stecher,, D.Peterson,, A.Filipski,, and S.Kumar, 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6. 0. Mol. Biol. Evol. 30: 2725–2729.
121. J.D.Thompson,, D.G.Higgins,, and T.J.Gibson, 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucleic Acids Res. 22: 4673–4680.
122. W.Wang,, H.L.Li,, and Z.D.Chen, 2014. Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement. Sci. China Life Sci. 57: 280–286.
123. J.D.Watson,, T.A.Baker,, S.P.Bell,, A.Gann,, M.Levine,, and R.Oosick, 2008. Molecular Biology of the Gene. 6th ed., Pearson/Benjamin Cummings, San Francisco, CA.
124. K.H.Wolfe,, W.H.Li,, and P.M.Sharp, 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. PNAS 84: 9054–9058.
125. Z.Xi,, Y.Wang,, R.K.Bradley,, M.Sugumaran,, C.J.Marx,, J.S.Rest,, and C.C.Davis, 2013. Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet. 9: e1003265.
126. Z.Yang, 1996. Among-site rate variation and its impact on phylogenetic analyses. TREE 11: 367–372.
127. Z.Yang,, N.Goldman,, and A.E.Friday, 1995. Maximum likelihood trees from DNA sequences: A peculiar statistic estimation problem. Syst. Biol. 44: 384–399.
128. Z.Yang,, and B.Rannala, 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte carlo method. Mol. Biol. Evol. 14: 717–724.
129. Z.Yang,, and B.Rannala, 2012. Molecular phylogenetics: principles and practice. Nat. Rev. Genet. 13: 303–314.
130. J.Zeng,, X.Fan,, L.Zhang,, X.Wang,, H.Zhang,, H.Kang,, and Y.Zhou, 2010. Molecular phylogeny and maternal progenitor implication in the genus Kengyilia (Triticeae: Poaceae): Evidence from COXII intron sequences. Biochem. Syst. Ecol. 38: 202–209.
131. E.A.Zimmer,, and J.Wen, 2013. Reprint of: Using nuclear gene data for plant phylogenetics: Progress and prospects. Molecular Phylogenet. Evol. 66: 539–550.
132. E.Zuckerkandl,, and L.B.Pauling, 1962. Molecular disease, evolution, and genic heterogeneity. In: Horizons in Biochemistry. pp. 189–225. M.Kasha, and B.Pullman,, Eds., Academic Press, New York.
133. E.Zuckerkandl,, and L.B.Pauling, 1965. Evolutionary divergence and convergence in proteins. In: Evolving Genes and Proteins. pp. 97–166. V.Bryson,, and H.J.Vogel,, Eds., Academic Press, New York.