Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae)

Heredity

Volumn 110, Issue 2, 2013, Pages 138-151

  Krak, K ^a   Caklova P ^a   Chrtek, J ^a,b   Fehrer, J ^a  

^a INSTITUTE OF BOTANY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

Author keywords

apomixis; gene tree incongruence; Hieracium; hybridization; incomplete lineage sorting; low copy nuclear markers

Indexed keywords

CHLOROPLAST DNA; RIBOSOMAL SPACER DNA; SQUALENE SYNTHASE; VEGETABLE PROTEIN;

APOMIXIS; DATA SET; DICOTYLEDON; EVOLUTIONARY BIOLOGY; GENETIC MARKER; HYBRID; HYBRIDIZATION; PHYLOGENETICS; PHYLOGENY; POLYMORPHISM; POLYPLOIDY; RECONSTRUCTION; SPECIATION (BIOLOGY);

ARTICLE; ASTERACEAE; BIOLOGICAL MODEL; CROSS BREEDING; DNA SEQUENCE; GENETIC MARKER; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENTIATION;

ASTERACEAE; CROSSES, GENETIC; DNA, CHLOROPLAST; DNA, RIBOSOMAL SPACER; FARNESYL-DIPHOSPHATE FARNESYLTRANSFERASE; GENETIC MARKERS; GENETIC SPECIATION; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA;

ASTERACEAE; HIERACIUM;

EID: 84872599723     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2012.100     Document Type: Article

References (49)

1. Alvarez I, Wendel JF (2003). Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29: 417-434. (Pubitemid 37491888)
2. Arnold ML (1997). Natural Hybridization and Evolution. Oxford University Press: New York.
3. Asker SE, Jerling L (1992). Apomixis in Plants. CRC Press: Boca Raton, Florida.
4. Brysting AK, Oxelman B, Huber KT, Moulton V, Brochmann C (2007). Untangling complex histories of genome mergings in high polyploids. Syst Biol 56: 467-476.
5. Campbell CS, Wojciechowski MF, Baldwin BG, Alice LA, Donoghue MJ (1997). Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol Biol Evol 14: 81-90. (Pubitemid 27024431)
6. Chrtek J, Mráz P, Sennikov AN (2006). Hieracium grofae-A rediscovered diploid hybrid from the Ukrainian Carpathians. Biologia 61: 365-373. (Pubitemid 44682229)
7. Chrtek J, Zahradńiček J, Krak K, Fehrer J (2009). Genome size in Hieracium subgenus Hieracium (Asteraceae) is strongly correlated with major phylogenetic groups. Ann Bot 104: 161-178.
8. Degnan JH, Rosenberg NA (2009). Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 24: 332-340.
9. Degnan JH, Salter LA (2005). Gene tree distributions under the coalescent process. Evolution 59: 24-37. (Pubitemid 40181296)
10. Doyle JJ, Doyle JL, Rauscher JT, Brown AHD (2003). Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytol 161: 121-132. (Pubitemid 38047053)
11. Evans RC, Campbell CS (2002). The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes. Amer J Bot 89: 1478-1484.
12. Fehrer J, Gemeinholzer B, Chrtek J, Bräutigam S (2007). Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae). Mol Phylogenet Evol 42: 347-361. (Pubitemid 44751511)
13. Fehrer J, Krak K, Chrtek J (2009). Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise. BMC Evol Biol 9: 239.
14. Feliner GN, Rosselló JA (2007). Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 44: 911-919. (Pubitemid 47048931)
15. Funk DJ, Omland KE (2003). Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34: 397-423. (Pubitemid 38171425)
16. Grusz AL, Windham MD, Pryer KM (2009). Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae). Amer J Bot 96: 1636-1645.
17. Hall TA (1999). BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Series 41: 95-98.
18. Holder MT, Anderson JA, Holloway AK (2001). Difficulties in detecting hybridization. Syst Biol 50: 978-982.
19. Hörandl E (2009). Geographical parthenogenesis: opportunities for asexuality. In: Schön I, Martens K, van Dijk P (eds). Lost Sex-The Evolutionary Biology of Parthenogenesis. Springer: Dordrecht, Heidelberg, London, New York, pp 161-186.
20. Huson DH, Bryant D (2006). Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267. (Pubitemid 43100040)
21. Joly S, Starr JR, Lewis WH, Bruneau A (2006). Polyploid and hybrid evolution in roses east of the Rocky Mountains. Amer J Bot 93: 412-425. (Pubitemid 43346721)
22. Kaplan Z, Fehrer J (2007). Molecular evidence for a natural primary triple hybrid in plants revealed from direct sequencing. Ann Bot 99: 1213-1222. (Pubitemid 47355835)
23. Krak K, Álvarez I, Caklová P, Costa A, Chrtek J, Fehrer J (2012). Development of novel low-copy nuclear markers for Hieraciinae (Asteraceae) and their perspective for other tribes. Amer J Bot 99: e74-e77.
24. Linder CR, Rieseberg LH (2004). Reconstructing patterns of reticulate evolution in plants. Amer J Bot 91: 1700-1708. (Pubitemid 43193727)
25. Lo EYY, Stefanovic S, Dickinson TA (2010). Reconstructing reticulation history in a phylogenetic framework and potential of allopatric speciation driven by polyploidy in an agamic complex in Crataegus (Rosaceae). Evolution 64: 3593-3608.
26. Merxmüller H (1975). Diploide Hieracien. Anales del Instituto Botánico A. J. Cavanilles 32: 189-196.
27. Mráz P, Chrtek J, Fehrer J, Plačková I (2005). Rare recent natural hybridization in the genus Hieracium s.str.-evidence from morphology, allozymes and chloroplast DNA. Plant Syst Evol 255: 177-192. (Pubitemid 41504201)
28. Mráz P, Paule J (2006). Experimental hybridization in the genus Hieracium s. str.: crosses between diploid taxa. Preslia 78: 1-26. (Pubitemid 44110813)
29. Müller K (2005). SeqState: Primer design and sequence statistics for phylogenetic DNA datasets. Appl Bioinf 4: 65-69. (Pubitemid 41043903)
30. Nylander JAA (2004). MrModeltest v2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University.
31. Olmstead RG, Palmer JD (1994). Chloroplast DNA systematics: a review of methods and data analysis. Amer J Bot 81: 1205-1224. (Pubitemid 2138969)
32. Rieseberg LH (1998). Molecular ecology of hybridization. In: Carvalho GR (ed). Advances in Molecular Ecology. IOS Press: Burke, Virginia, pp 243-265.
33. Rieseberg LH, Willis JH (2007). Plant speciation. Science 317: 910-914. (Pubitemid 47301311)
34. Rokas A, Carroll SB (2006). Bushes in the tree of life. PLoS Biol 4: 1899-1904. (Pubitemid 44760005)
35. Ronquist F, Huelsenbeck JP (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574. (Pubitemid 37038874)
36. Russell A, Samuel R, Klenja V, Barfuss MHJ, Rupp B, Chase MW (2010). Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann Bot 106: 37-56.
37. Sang T (2002). Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit Rev Biochem Mol Biol 37: 121-147. (Pubitemid 34779349)
38. Schuhwerk F (1996). Published chromosome counts in Hieracium. http://www. botanischestaatssammlung.de/projects/chrzlit.html.
39. Shaw J, Lickey EB, Schilling EE, Small RL (2007). Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angios-perms: the tortoise and the hare III. Amer J Bot 94: 275-288. (Pubitemid 46955026)
40. Silvestro D, Michalak I (2010). raxmlGUI: a graphical front-end for RAxML. Available at http://sourceforge.net/projects/raxmlgui/.
41. Simmons MP, Ochoterena H (2000). Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49: 369-381.
42. Small RL, Cronn RC, Wendel JF (2004). Use of nuclear genes for phylogenetic reconstruction. Aust Syst Bot 17: 145-170. (Pubitemid 38600714)
43. Speksnijder AGCL, Kowalchuk GA, De Jong S, Kline E, Stephen JR, Laanbroek HJ (2001). Microvariant artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl Environ Microbiol 67: 469-472. (Pubitemid 32044454)
44. Stace CA (1998). Sectional names in the genus Hieracium (Asteraceae) sensu stricto. Edinb J Bot 55: 469-472.
45. Stamatakis A (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690. (Pubitemid 44642609)
46. Swofford DL (2002). PAUP&z.ast;. Phylogenetic Analysis Using Parsimony (&z.ast;and other methods). Version 4 Sinauer: Sunderland, Massachusetts.
47. Wagner A, Blackstone N, Cartwright P, Dick M, Misof B, Snow P et al. (1994). Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst Biol 43: 250-261. (Pubitemid 24977978)
48. Whitfield JB, Lockhart PJ (2007). Deciphering ancient rapid radiations. Trends Ecol Evol 22: 258-265. (Pubitemid 46590495)
49. Zahn KH (1921-1923). Hieracium L. In: Engler HGA (ed). Das Pflanzenreich IV(280). Compositae-Hieracium. Wilhelm Engelmann: Leipzig. Vol. 76, pp 1-32.