BMC Evolutionary Biology | |
Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae) | |
Thomas J Givnish2  Elizabeth A Zimmer1  Emily B Sessa2  | |
[1] Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA;Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA | |
关键词: Polyploidy; Phylogeny; Introgression; Hybridization; Genetic distances; Divergence time estimates; Ferns; | |
Others : 1140960 DOI : 10.1186/1471-2148-12-104 |
|
received in 2012-02-08, accepted in 2012-06-14, 发布年份 2012 | |
【 摘 要 】
Background
The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called “semicristata” hypothesis, contention over the group’s history has continued in several recent, conflicting studies.
Results
Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the “semicristata” hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid “D. semicristata” x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors.
Conclusions
This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the “semicristata” hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
【 授权许可】
2012 Sessa et al.; licensee BioMed Central Ltd.
【 预 览 】
Files | Size | Format | View |
---|---|---|---|
20150325161931776.pdf | 2672KB | download | |
Figure 8. | 115KB | Image | download |
Figure 7. | 25KB | Image | download |
Figure 6. | 67KB | Image | download |
Figure 5. | 62KB | Image | download |
Figure 4. | 95KB | Image | download |
Figure 3. | 139KB | Image | download |
Figure 2. | 106KB | Image | download |
Figure 1. | 54KB | Image | download |
【 图 表 】
Figure 1.
Figure 2.
Figure 3.
Figure 4.
Figure 5.
Figure 6.
Figure 7.
Figure 8.
【 参考文献 】
- [1]Otto SP, Whitton J: Polyploid incidence and evolution. Annu Rev Genet 2000, 34:401-437.
- [2]Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH: The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci U S A 2009, 106:13875-13879.
- [3]Leitch AR, Leitch IJ: Genome plasticity and the diversity of polyploid plants. Science 2008, 320:481-483.
- [4]Linder CR, Rieseberg LH: Reconstructing patterns of reticulate evolution in plants. Am J Bot 2004, 91:1700-1708.
- [5]Schneller J: Evidence for intergeneric incompatibility in ferns. Plant Syst Evol 1981, 137:45-56.
- [6]Barrington DS, Haufler CH, Werth C: Hybridization, reticulation, and species concepts in the ferns. Am Fern J 1989, 79:55-64.
- [7]Haufler CH: Species concepts and speciation in pteridophytes. In Pteridology in Perspective 1996; Royal Botanic Gardens, Kew. Edited by Camus JM, Gibby M, Johns RJ. Royal Botanic Gardens, Kew; 1996:291-305.
- [8]Werth CR, Guttman SI, Eshbaugh WH: Electrophoretic evidence of reticulate evolution in the Appalachian Asplenium complex. Syst Bot 1985, 10:184-192.
- [9]Bennert W, Lubienski M, Korner S, Steinberg M: Triploidy in Equisetum subgenus Hippochaete (Equisetaceae, Pteridophyta). Ann Bot Lond 2005, 95:807-815.
- [10]Beck J, Windham MD, Yatskievych G, Pryer KM: A diploids-first approach to species delimitation and interpreting polyploid evolution in the fern genus Astrolepis (Pteridaceae). Syst Bot 2010, 35:223-234.
- [11]Fraser-Jenkins CR: A classification of the genus Dryopteris (Pteridophyta: Dryopteridaceae). Bull Br Mus 1986, 14:183-218.
- [12]Montgomery J, Wagner WH: Dryopteris. In Flora of North America North of Mexico. Volume 2. Oxford University Press, New York, New York; 1993::1-3.
- [13]Walker S: Cytogenetic studies in the Dryopteris spinulosa complex I. Watsonia 1955, 3:193-209.
- [14]Wagner WH: Evolution of Dryopteris in Relation to the Appalachians. In Distributional History of the Biota of the Southern Appalachians, Part II: Flora: 26–28 June 1969; Blacksburg, Virginia. Edited by Holt PC. Virginia Polytechnic Institute and State University, Blacksburg, Virginia; 1971:147-192.
- [15]Montgomery JD, Paulton EM: Dryopteris in North America. Fiddlehead Forum 1981, 8:25-31.
- [16]Sessa EB, Zimmer EA, Givnish TJ: Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). Am J Bot 2012, 99:730-750.
- [17]Sessa EB, Zimmer EA, Givnish TJ: Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae). Mol Phylogenet Evol 2012, 64:563-581.
- [18]Wagner WH, Wagner FS, Hagenah DJ: The log fern (Dryopteris celsa) and its hybrids in Michigan - a preliminary report. Mich Bot 1969, 8:1-5.
- [19]Fraser-Jenkins CR, Widen C-J: Phloroglucinol derivatives in Dryopteris filix-mas and its putative ancestors (Dryopteridaceae). In Advances in Forestry Research in India. Edited by Mukherjee SK. International Book Distributors, Uttaranchal, India; 2006:139-160.
- [20]Crane FW: Spore studies in Dryopteris, I. Am Fern J 1953, 43:159-169.
- [21]Manton I, Walker S: Cytology of the Dryopteris spinulosa complex in Eastern North America. Nature 1953, 171:1116-1117.
- [22]Walker S: Cytotaxonomic studies of some American species of Dryopteris. Am Fern J 1959, 49:104-112.
- [23]Walker S: Cytogenetic studies in the Dryopteris spinulosa complex II. Am J Bot 1961, 48:607-614.
- [24]Walker S: Further studies in the genus Dryopteris: the origin of D. clintoniana, D. celsa, and related taxa. Am J Bot 1962, 49:497-503.
- [25]Wagner WH, Hagenah D: Dryopteris in the Huron Mountain Club Area of Michigan. Brittonia 1962, 14:90-100.
- [26]Wagner WH: Pteridophytes of the Mountain Lake Area, Giles County, Virginia, including Notes from Whitetop Mountain. Castanea 1963, 28:113-150.
- [27]Widen C-J, Britton DM: A chromatographic and cytological study of Dryopteris dilatata in eastern North America. Can J Bot 1969, 47:1337-1344.
- [28]Walker S: Identification of a diploid ancestral genome in the Dryopteris spinulosa complex. Br Fern Gaz 1969, 10:97-99.
- [29]Widen C-J, Sorsa V: On the intraspecific variability of Dryopteris assimilis S. Walker and Dryopteris spinulosa Watt – A chromatographic and cytological study. Hereditas 1969, 62:1-13.
- [30]Widen C-J, Vida G, von Euw J, Reichstein T: Die Phloroglucide von Dryopteris villarii (Bell.) Woynar und anderer Farne der Gattung Dryopteris sowie die mogliche Abstammung von D. filix-mas (L.) Schott. Helv Chim Acta 1971, 54:2824-2850.
- [31]Widen C-J, Britton DM: A chromatographic and cytological study of Dryopteris dilatata in North America and eastern Asia. Can J Bot 1971, 49:247-258.
- [32]Widen C-J, Britton DM: Chemotaxonomic investigations on the Dryopteris cristata complex in North America. Can J Bot 1971, 49:1141-1153.
- [33]Widen C-J, Britton DM: A chromatographic and cytological study of Dryopteris filix-mas and related taxa in North America. Can J Bot 1971, 49:1589-1600.
- [34]Britton DM: The spores of Dryopteris clintoniana and its relatives. Can J Bot 1972, 50:2027-2029.
- [35]Fraser-Jenkins CR, Corley HV: Dryopteris caucasica - an ancestral diploid in the male fern aggregate. Br Fern Gaz 1972, 10:221-231.
- [36]Britton DM, Widen C-J: Chemotaxonomic studies on Dryopteris from Quebec and eastern North America. Can J Bot 1974, 52:627-637.
- [37]Hickok LG, Klekowski EJ: Chromosome behavior in hybrid ferns: a reinterpretation of Appalachian Dryopteris. Am J Bot 1975, 62:560-569.
- [38]Fraser-Jenkins CR: Dryopteris caucasica, and the cytology of its hybrids. Fern Gaz 1976, 11:263-267.
- [39]Gibby M: The origin of Dryopteris campyloptera. Can J Bot 1977, 55:1419-1428.
- [40]Gibby M, Walker S: Further cytogenetic studies and a reappraisal of the diploid ancestry in the Dryopteris carthusiana complex. Fern Gazette 1977, 11:315-324.
- [41]Gibby M, Widen C-J, Widen HK: Cytogenetic and phytochemical investigations in hybrids of Macaronesian Dryopteris (Pteridophyta: Aspidiaceae). Plant Syst Evol 1978, 130:235-252.
- [42]Petersen RL, Fairbrothers DE: Flavonols of the fern genus Dryopteris: systematic and morphological implications. Bot Gaz 1983, 144:104-109.
- [43]Widen C-J, Britton DM: Phloroglucinol derivates of Dryopteris tokyoensis and the missing genome in D. cristata and D. carthusiana (Dryopteridaceae). Ann Bot Fenn 1985, 22:213-218.
- [44]Viane RLL: Taxonomical significance of the leaf indument in Dryopteris: I. Some North American, Macaronesian, and European Taxa. Plant Syst Evol 1986, 153:77-105.
- [45]Werth CR: Isozyme evidence on the origin of Dryopteris cristata and D. carthusiana. Am J Bot 1989, 76:208.
- [46]Werth CR: Isozyme studies on the Dryopteris “spinulosa” complex, I: The origin of the log fern Dryopteris celsa. Syst Bot 1991, 16:446-461.
- [47]Hutton C: The common ancestor of the allotetraploid ferns Dryopteris carthusiana and D. cristata: a chloroplast DNA analysis. M.A. thesis. Mt. Holyoke College, Massachusetts, USA; 1992.
- [48]Stein DB, Hutton C, Conant DS, Haufler CH, Werth CR: Reconstructing Dryopteris “semicristata” (Dryopteridaceae): Molecular profiles of tetraploids verify their undiscovered diploid ancestor. Am J Bot 2010, 97:998-1004.
- [49]Juslen A, Vare H, Wikstrom N: Relationships and evolutionary origins of polyploid Dryopteris (Dryopteridaceae) from Europe inferred using nuclear pgiC and plastid trnL-F sequence data. Taxon 2011, 60:1284-1294.
- [50]Britton DM, Jermy AC: The spores of Dryopteris filix-mas and related taxa in North America. Can J Bot 1974, 52:1923-1926.
- [51]Manton I: Problems of Cytology and Evolution in the Pteridophyta. Cambridge University Press, Cambridge; 1950.
- [52]Gastony GJ, Yatskievych G: Maternal inheritance of the chloroplast and mitochondrial genomes in Cheilanthoid ferns. Am J Bot 1992, 79:716-722.
- [53]Vogel JC, Russell SJ, Rumsey FJ, Barrett JA, Gibby M: Evidence for maternal transmission of chloroplast DNA in the genus Asplenium (Aspleniaceae, Pteridophyta). Bot Acta 1998, 111:247-249.
- [54]Stein DB, Barrington DS: Recurring hybrid formation in a population of Polystichum x potteri: evidence from chloroplast DNA comparisons. Ann Mo Bot Gard 1990, 77:334-339.
- [55]Miller MA, Pfeiffer W, Schwartz T: Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop 2010, 1-8.
- [56]Fraser-Jenkins CR: Dryopteris affinis: A new treatment for a complex species in the European pteridophyte flora. Willdenowia 1980, 10:107-115.
- [57]Xiang JY: Chromosome numbers of 13 species in the genus Dryopteris (Dryopteridaceae) from Yunnan, China. Acta Phytotax Sin 2006, 44:304-319.
- [58]Hoshizaki BJ, Wilson KA: The cultivated species of the fern genus Dryopteris in the United States. Am Fern J 1999, 89:1-98.
- [59]Gibby M, Jermy AC, Rasbach H, Rasbach K, Reichstein T, Vida G: The genus Dryopteris in the Canary Islands and Azores and the description of two new tetraploid species. Bot J Linn Soc 1977, 74:251-277.
- [60]Gibby M: Hybridization and speciation in the genus Dryopteris (Pteridophyta: Dryotperidaceae) on Pico Island in the Azores. Plant Syst Evol 1985, 149:241-252.
- [61]Smith AR: New species and new combinations of ferns from Chiapas, Mexico. Proc Calif Acad Sci 1975, 40:209-230.
- [62]Reyes-Jaramillo I, Camargo-Ricalde SL, Aquiahuatl-Ramos MA: Mycorrhizal-like interaction between gametophytes and young sporophytes of the fern Dryopteris muenchii (Filicales) and its fungal endophyte. Rev Trop Biol 2008, 56:1101-1107.
- [63]Widen C-J, Fraser-Jenkins CR, Reichstein T, Gibby M, Sarvela J: Phloroglucinol derivatives in Dryopteris sect. Fibrillosae and related taxa (Pteridophyta, Dryopteridaceae). Ann Bot Fenn 1996, 33:69-100.
- [64]Geiger JMO, Ranker T: Molecular phylogenetics and historical biogeography of Hawaiian Dryopteris (Dryopteridaceae). Mol Phylogenet Evol 2005, 34:392-407.
- [65]Korall P, Pryer KM, Metzgar JS, Schneider H, Conant DS: Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci. Mol Phylogenet Evol 2006, 39:830-845.
- [66]Korall P, Conant DS, Metzgar JS, Schneider H, Pryer KM: A molecular phylogeny of scaly tree ferns (Cyatheaceae). Am J Bot 2007, 94:873-886.
- [67]Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH: Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 2005, 102(23):8369-8374.
- [68]Small R, Lickey E, Shaw J, Hauk WD: Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae. Mol Phylogenet Evol 2005, 36:509-522.
- [69]Rouhan G, Dubuisson JY, Rakotondrainibe F, Motley TJ, Mickel JT, Labat J, Moran RC: Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: contributions of species from the Indian Ocean area. Mol Phylogenet Evol 2004, 33:745-763.
- [70]Taberlet P, Gielly L, Pautau G, Bouvet J: Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 1991, 17:1105-1109.
- [71]Duffy AM, Kelchner SA, Wolf PG: Conservation of selection on matK following an ancient loss of its flanking intron. Gene 2009, 438:17-25.
- [72]Ishikawa H, Watano Y, Kano K, Ito M, Kurita S: Development of primer sets for PCR amplification of the PgiC gene in ferns. J Plant Res 2002, 115:65-70.
- [73]Schuettpelz E, Grusz AL, Windham M, Pryer K: Utility of nuclear gapCp in resolving polyploid fern origins. Syst Bot 2008, 33:621-629.
- [74]Fraser-Jenkins CR: Dryopteris stanley-walkeri Fras.-Jenk., the missing diploid common-ancestor of D. carthusiana and D. cristata. In Plant Diversity of the Himalaya. Edited by Pande PC, Samant SS. Gyanodaya Prakashan, Nainital, India; 2001:119-152.
- [75]Widen C-J, Sorsa V, Sarvela J: Dryopteris dilatata s.lat. in Europe and the island of Madeira: a chromatographic and cytological study. Acta Bot Fenn 1970, 91:2-30.
- [76]Schneller JJ, Holderegger R: Lack of isozyme variation in the agamosporous fern Dryopteris remota. Am Fern J 1994, 84:94-98.
- [77]Carlson TM, Wagner WH: The North American distribution of the genus Dryopteris. Contrib Univ Mich Herb 1982, 15:141-162.
- [78]Sigel E: Polyphyly of a polyploid species: an inquiry into the origin of Dryopteris campyloptera and Dryopteris dilatata (Dryopteridaceae). M.Sc. thesis. The University of Vermont, USA; 2008.
- [79]Brysting AK, Mathiesen C, Marcussen T: Challenges in polyploid phylogenetic reconstruction: a case story from the arctic-alpine Cerastium alpinum complex. Taxon 2011, 60:333-347.
- [80]Trewick SA, Morgan-Richards M, Russell SJ, Henderson S, Rumsey FJ, Pinter I, Barrett JA, Gibby M, Vogel JC: Polyploidy, phylogeography and Pleistocene refugia of the rockfern Asplenium ceterach: evidence from chloroplast DNA. Mol Ecol 2002, 11:2003-2012.
- [81]Huber KT, Oxelman B, Lott M, Moulton V: Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol Biol Evol 2006, 23:1784-1791.
- [82]Werth CR: The origin of the Log Fern Dryopteris celsa: Allozyme evidence. Am J Bot 1985, 72:929.
- [83]Ane C, Larget B, Baum DA, Smith SD, Rokas A: Bayesian estimation of concordance among gene trees. Mol Biol Evol 2007, 24:412-426.
- [84]Larget BR, Kotha SK, Dewey CN, Ane C: BUCKy: Gene tree/species tree reconciliation with Bayesian Concordance Analysis. Bioinformatics 2010, 26:2910-2911.
- [85]Fraser-Jenkins CR, Jermy AC: Nomenclatural notes on Dryopteris Adans. Taxon 1976, 25:659-665.
- [86]Soltis DE, Soltis PS: Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 1999, 14:348-352.
- [87]Soltis DE, Soltis PS, Tate JA: Advances in the study of polyploidy since Plant speciation. New Phytol 2004, 161:173-191.
- [88]Perrie LR, Shepherd LD, De Lange PJ, Brownsey PJ: Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns. Mol Ecol 2010, 19:2916-2932.
- [89]Hunt HV, Ansell SW, Russell SJ, Schneider H, Vogel JC: Dynamics of polyploid formation and establishment in the allotetraploid rock fern Asplenium majoricum. Ann Bot-Lond 2011, 108:143-157.
- [90]Beck J, Windham MD, Pryer KM: Do asexual polyploid lineages lead short evolutionary lives? A case study from the fern genus Astrolepis. Evolution 2011, 65:3217-3229.
- [91]Soltis DE, Soltis PS: Molecular data and the dynamic nature of polyploidy. Crit Rev Plant Sci 1993, 12:243-273.
- [92]Husband BC: The role of triploid hybrids in the evolutionary dynamics of mixed-ploidy populations. Biol J Linn Soc 2004, 82:537-546.
- [93]Symonds VV, Soltis PS, Soltis DE: Dynamics of polyploid formation in Tragopogon (Asteraceae): Recurrent formation, gene flow, and population structure. Evolution 2010, 64:1984-2003.
- [94]Kodandaramaiah U, Peña C, Braby MF, Grund R, Müller CJ, Nylin S, Wahlberg N: Phylogenetics of Coenonymphina (Nymphalidae: Satyrinae) and the problem of rooting rapid radiations. Mol Phylogenet Evol 2009, 1-9.
- [95]Marcussen T, Blaxland K, Windham MD, Haskins KE, Armstrong F: Establishing the phylogenetic origin, history, and age of the narrow endemic Viola guadalupensis (Violaceae). Am J Bot 2011, 98:1978-1988.
- [96]Raynor GS, Ogden EC, Hayes JV: Dispersion of fern spores into and within a forest. Rhodora 1976, 78:1-15.
- [97]Hewitt G: The genetic legacy of the Quaternary ice ages. Nature 2000, 405:907-913.
- [98]Davis MB, Shaw RG: Range shifts and adaptive responses to quaternary climate change. Science 2001, 292:673-679.
- [99]Chapman MA, Burke JM: Genetic divergence and hybrid speciation. Evolution 2007, 61:1773-1780.
- [100]Paun O, Forest F, Fay MF, Chase MW: Hybrid speciation in angiosperms: parental divergence drives ploidy. New Phytol 2009, 182:507-518.
- [101]Stelkens R, Seehausen O: Genetic distance between species predicts novel trait expression in their hybrids. Evolution 2009, 63:884-897.
- [102]Liu HM, Zhang XC, Wang W, Qiu YL, Chen ZD: Molecular phylogeny of the fern family Dryopteridaceae Inferred from chloroplast rbcL and atpB genes. Int J Plant Sci 2007, 168:1311-1323.
- [103]Schuettpelz E, Pryer KM: Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy. Proc Natl Acad Sci U S A 2009, 106:11200-11205.
- [104]Russell A, Samuel R, Klejna V, Barfuss MHJ, Rupp B, Chase MW: Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann Bot-Lond 2010, 106:37-56.
- [105]Grusz AL, Windham MD, Pryer KM: Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae). Am J Bot 2009, 96:1636-1645.
- [106]Katoh K, Asimenos G, Toh H: Multiple alignment of DNA sequences with MAFFT. In Bioinformatics for DNA sequence analysis. Edited by Posada D. Humana Press, New York, New York; 2009:39-64.
- [107]Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A: Geneious. Version 5.4. 2012.
- [108]Simmons MP, Ochoterena H: Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 2000, 49:369-381.
- [109]Borschenius F: Fastgap. Version 1.2. Distributed by the author. 2009.
- [110]Farris JS, Kallersjo M, Kluge AG, Bult C: Testing significance of incongruence. Cladistics 1996, 10:315-319.
- [111]Swofford DL: PAUP*. Phylogenetic Analysis Using Parismony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachussetts; 2002.
- [112]Hipp A, Hall J, Sytsma K: Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst Biol 2004, 53:81-89.
- [113]Darlu P, Lecointre G: When does the incongruence length difference test fail? Mol Biol Evol 2002, 19:432-437.
- [114]Sikes DS, Lewis PO: Software manual for PAUPRat: A tool to implement Parsimony Ratchet searches using PAUP*. Distributed by the authors. 2001.
- [115]Zwickl DJ: Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Doctoral thesis. The University of Texas at Austin, Texas, USA; 2006.
- [116]Stamatakis A: RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
- [117]Stamatakis A, Hoover P, Rougemont J: A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 2008, 57:758-771.
- [118]Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
- [119]Givnish TJ, Sytsma KJ: Consistency, characters, and the likelihood of correct phylogenetic inference. Mol Phylogenet Evol 1997, 7:320-330.
- [120]Nixon KC: The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
- [121]Sundue MA: A morphological cladistic analysis of Terpsichore (Polypodiaceae). Syst Bot 2010, 35:716-729.
- [122]Nylander JAA: MrModeltest. Version 2. Distributed by the author. 2004.
- [123]Rambaut A, Drummond AJ: Tracer. Version 1.5. 2007. Available from: http://tree.bio.ed.ac.uk/software/tracer/ webcite
- [124]Drummond AJ, Ho SYW, Phillips MJ, Rambaut A: Relaxed phylogenies and dating with confidence. PLoS Biol 2006, 4:699-710.
- [125]Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214-222. BioMed Central Full Text
- [126]Sauquet H, Ho SYW, Gandolfo MA, Jordan GJ, Wilf P, Cantrill DJ, Bayly MJ, Bromham L, Brown GK, Carpenter RJ, Lee DM, Murphy DJ, Sniderman JMK, Udovicic F: Testing the impact of calibration of molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). Syst Biol 2012, 61:289-313.
- [127]Ho SYW, Phillips MJ: Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 2009, 58:367-380.
- [128]Pirie MD, Doyle JA: Dating clades with fossils and molecules: the case of Annonaceae. Bot J Linn Soc 2012, 169:84-116.
- [129]Lott M, Spillner A, Huber KT, Petri A, Oxelman B, Moulton V: Inferring polyploid phylogenies from multiply-labeled gene trees. BMC Evol Biol 2009, 9:216. BioMed Central Full Text
- [130]Lott M, Spillner A, Huber KT, Moulton V: PADRE: a package for analyzing and displaying reticulate evolution. Bioinformatics 2009, 25:1199-1200.