Untangling the phylogeny of Leandra s.str. (Melastomataceae, Miconieae)

Molecular Phylogenetics and Evolution

Volumn 96, Issue , 2016, Pages 17-32

  Reginato, Marcelo ^a,b   Michelangeli, Fabián A ^a  

^a INSTITUTE OF SYSTEMATIC BOTANY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

*BEAST; Hybridization; Leandra; Melastomataceae; Multispecies coalescent; Rogues

Indexed keywords

BRAZIL; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; HYBRIDIZATION; MELASTOMATACEAE; MOLECULAR EVOLUTION; PHYLOGENY;

BRAZIL; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HYBRIDIZATION, GENETIC; MELASTOMATACEAE; PHYLOGENY;

EID: 84951335723     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2015.11.015     Document Type: Article

References (66)

1. Aberer A.J., Krompass D., Stamatakis A. Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Syst. Biol. 2013, 62(1):162-166.
2. Alexander P.J., Rajanikanth G., Bacon C.D., Bailey C.D. Rapid inexpensive recovery of high quality plant DNA using a reciprocating saw and silica-based columns. Mol. Ecol. Notes 2007, 7:5-9.
3. Arthofer W., Schueler S., Steiner F.M., Schlick-Steiner B.C. Chloroplast DNA-based studies in molecular ecology may be compromised by nuclear-encoded plastid sequence. Mol. Ecol. 2010, 19(18):3853-3856.
4. Baumgratz J.F.A., Souza M.L.D. Melastomataceae na Reserva Ecológica de Macaé de Cima, Nova Friburgo, Rio de Janeiro, Brasil. II - Leandra (Miconieae). Rodriguésia 2011, 62(3):629-662.
5. Bécquer-Granados E.R., Neubig K.M., Judd W.S., Michelangeli F.A., Abbott J.R., Penneys D.S. Preliminary molecular phylogenetic studies in Pachyanthus (Miconieae, Melastomataceae). Bot. Rev. 2008, 74(1):37-52.
6. Blanco-Pastor J.L., Vargas P., Pfeil B.E. Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria. PLoS One 2012, 7(6):1-16.
7. Camargo E.A., Goldenberg R. Two new species of Leandra from Espírito Santo, Brazil. Brittonia 2011, 63(2):220-226.
8. Camargo E.A., Souza C.M.F., Caddah M.K., Goldenberg R. O gênero Leandra, seções Carassanae, Chaetodon, Niangae, Oxymeris e Secundiflorae (Melastomataceae) no estado do Paraná. Rodriguésia 2009, 60(3):595-631.
9. Clausing G., Renner S.S. Molecular phylogenetics of Melastomataceae and Memecylaceae: implications for character evolution. Am. J. Bot. 2001, 88(3):486-498.
10. Cogniaux A. Melastomataceae. Monographiae Phanerogamarum 1891, vol. 7:1-1256. G. Masson, Paris.
11. Darriba D., Taboada G.L., Doallo R., Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 2012, 9(8):772.
12. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24(6):332-340.
13. Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29(8):1969-1973.
14. Farris J.S. The retention index and homoplasy excess. Syst. Biol. 1989, 38(4):406-407.
15. Fehrer J., Gemeinholzer B., Chrtek J., Bräutigam S. Incongruent plastid and nuclear DNA phylogenies reveal ancient intergeneric hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae). Mol. Phylogenet. Evol. 2007, 42(2):347-361.
16. Garrick R.C., Meadows C.A., Nicolas A.N., Nason J.D., Dyer R.J. A set of polymorphic nuclear intron markers for conservation genetics and phylogeography of Euphorbia species (Pedilanthus clade). Conserv. Genet. 2008, 9(6):1673-1676.
17. Gehrke B., Bräuchler C., Romoleroux K., Lundberg M., Heubl G., Eriksson T. Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification. Mol. Phylogenet. Evol. 2008, 47(3):1030-1044.
18. Glaziou A.F.M. Plantae Brasiliae centralis a Glaziou lectae - Liste des plantes du Brésil Central recueillies en 1861-1895: Mélastomacées. Mém. Soc. Bot. France 1908, 1(3):201-296.
19. Goldenberg R., Shepherd G.J. Studies on the reproductive biology of Melastomataceae in "cerrado" vegetation. Plant Syst. Evol. 1998, 211:13-29.
20. Goldenberg R., Fraga C.N., Fontana A.P., Nicolas A.N., Michelangeli F.A. Taxonomy and phylogeny of Merianthera (Melastomataceae). Taxon 2012, 61(5):1040-1056.
21. Goldenberg R., Penneys D.S., Almeda F., Judd W.S., Michelangeli F.A. Phylogeny of Miconia (Melastomataceae): patterns of stamen diversification in a megadiverse neotropical genus. Int. J. Plant Sci. 2008, 24:315-327.
22. Guindon S., Gascuel O. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst. Biol. 2003, 52:696-704.
23. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27(3):570-580.
24. Heled, J., 2013. biopy - a Library for Phylogenetic Exploration. figshare. doi: doi:10.6084/m9.figshare.761224.
25. Heled J., Bouckaert R.R. Looking for trees in the forest: summary tree from posterior samples. BMC Evol. Biol. 2013, 13:221.
26. Hojsgaard D., Klatt S., Baier R., Carman J.G., Hörandl E. Taxonomy and biogeography of apomixis in angiosperms and associated biodiversity characteristics. Crit. Rev. Plant Sci. 2014, 33(5):414-427.
27. Hörandl E., Paun O. Patterns and sources of genetic diversity in apomictic plants: implications for evolutionary potentials. Apomixis: Evolution, Mechanisms and Perspectives 2007, International Association for Plant Taxonomy, Ruggel. E. Hörandl, U. Grossniklaus, P.J. Van Dijk, T. Sharbel (Eds.).
28. Hörandl E., Paun O., Johansson J.T., Lehnebach C., Armstrong T., Chen L., Lockhart P. Phylogenetic relationships and evolutionary traits in Ranunculus s.l. (Ranunculaceae) inferred from ITS sequence analysis. Mol. Phylogenet. Evol. 2005, 36(2):305-327.
29. Joly S. JML: testing hybridization from species trees. Mol. Ecol. Resour. 2012, 12(1):179-184.
30. Joly S., McLenachan P.A., Lockhart P.J. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am. Nat. 2009, 174(2):E54-E70.
31. Judd W.S., Bécquer E.R., Majure L.C. Taxonomic studies in the Miconieae (Melastomataceae). XI. A revision of Miconia sect. Calycopteris on Hispaniola. Brittonia 2014, 66(3):216-249.
32. Katoh S. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 2013, 30:772-780.
33. Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
34. Leaché A.D., Harris R.B., Rannala B., Yang Z. The influence of gene flow on species tree estimation: a simulation study. Syst. Biol. 2014, 63(1):17-30.
35. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
36. Maia, F.R., 2013. Sistemas reprodutivos e visitantes florais em Melastomataceae dos Campos Rupestres no limite sul do Cerrado, Tibagi, Paraná. Master Thesis, UFPR, 86p.
37. Martin C.V., Little D.P., Goldenberg R., Michelangeli F.A. A phylogenetic evaluation of Leandra (Miconieae, Melastomataceae): a polyphyletic genus where the seeds tell the story, not the petals. Cladistics 2008, 24(3):315-327.
38. Michelangeli F.A., Guimarães P.J., Penneys D.S., Almeda F., Kriebel R. Phylogenetic relationships and distribution of New World Melastomeae (Melastomataceae). Bot. J. Linn. Soc. 2013, 171(1):38-60.
39. Michelangeli F.A., Penneys D.S., Giza J., Soltis D., Hils M.H., Skean J.D. A preliminary phylogeny of the tribe Miconieae (Melastomataceae) based on nrITS sequence data and its implications on inflorescence position. Taxon 2004, 53:279-290.
40. Michelangeli, F.A., Nicolas, A.N., Ocampo, G., Goldenberg, R., Almeda, F., Judd, W., Becquer-Granados, E.R., Skean, J.D., Kriebel, R., Sosa, K., Caddah, M.K., Ionta, G.M., Penneys, D.S., Alvear, M., Burke, J.M., Majure, L.C., Reginato, M., in preparation. Historical Biogeography of the Neotropical tribe Miconieae (Melastomataceae) reveals a pattern of progressive colonization from Amazonia to other Neotropical forests.
41. Nixon K. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 1999, 15:407-414.
42. Penneys D.S., Judd W.S. Combined molecular and morphological phylogenetic analyses of the Blakeeae (Melastomataceae). Int. J. Plant Sci. 2013, 174(5):802-817.
43. Penneys D.S., Michelangeli F.A., Judd W.S., Almeda F. Henrietteeae (Melastomataceae): a new neotropical berry-fruited tribe. Syst. Bot. 2010, 35(4):783-800.
44. R Core Team, 2014. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
45. Rambaut, A., Drummond, A.J., 2007. Tracer.
46. Rambaut A., Grassly N.C. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1997, 13:235-238.
47. Rannala B., Yang Z. Bayesian estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 2003, 164:1645-1656.
48. Reginato, M., in preparation. Taxonomic revision of Leandra sect. Leandra (Melastomataceae, Miconieae).
49. Reginato M., Goldenberg R. Two new species of Leandra s. str. (Melastomataceae) from the Atlantic Forest in Espírito Santo, Brazil. Blumea 2013, 57(3):210-214.
50. Reginato M., Baumgratz J.F.A., Goldenberg R. A taxonomic revision of Pleiochiton (Melastomataceae, Miconieae). Brittonia 2013, 65(1):16-41.
51. Reginato M., Michelangeli F.A., Goldenberg R. Phylogeny of Pleiochiton (Melastomataceae, Miconieae): total evidence. Bot. J. Linn. Soc. 2010, 162(3):423-434.
52. Reid N.M., Hird S.M., Brown J.M., Pelletier T.A., McVay J.D., Satler J.D., Carstens B.C. Poor fit to the multispecies coalescent is widely detectable in empirical data. Syst. Biol. 2013, 63(3):322-333.
53. Renner S.S. Phylogeny and classification of the Melastomataceae and Memecylaceae. Nordic J. Bot. 1993, 13(5):519-540.
54. Saraiva L.C., Cesar O., Monteiro R. Breeding systems of shrubs and trees of a Brazilian Savanna. Arq. Biol. Tecnol. 1996, 39:751-763.
55. Schliep K.P. phangorn: phylogenetic analysis in R. Bioinformatics 2011, 27(4):592-593.
56. Scornavacca C., Berry V., Lefort V., Douzery E.J., Ranwez V. PhySIC_IST: cleaning source trees to infer more informative supertrees. BMC Bioinformatics 2008, 9(1):413.
57. Seehausen O. Hybridization and adaptive radiation. Trends Ecol. Evol. 2004, 19:198-207.
58. Soltis P.S., Soltis D.E. The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 2009, 60:561-588.
59. Steel M.A., Penny P. Distributions of tree comparison metrics - some new results. Syst. Biol. 1993, 42(2):126-141.
60. Stehmann, J.R., Forzza, R., Salino, A., Sobral, M., Costa, D.P., Kamino, L.H.Y., 2009. Plantas da Floresta Atlântica. Rio de Janeiro, vol. 1, pp. 1-500.
61. Straub S.C., Fishbein M., Livshultz T., Foster Z., Parks M., Weitemier K., Liston A. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 2011, 12(1):211.
62. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
63. Tamura K., Stecher G., Peterson D., Filipski A., Sudhir K. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013, 30:2725-2729.
64. Triana J. Les Mélastomacées. Trans. Linn. Soc. London 1871, 28:1-188.
65. Wurdack J.J. Melastomataceae of Santa Catarina. Sellowia 1962, 14:109-208.
66. Yang Z. MCMCcoal: Markov Chain Monte Carlo Coalescent Program 2007, University College London, London.