Artículo

Denham, S.S.; Brignone, N.F.; Johnson, L.A.; Pozner, R.E."Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae)" (2019) Molecular Phylogenetics and Evolution. 130:211-226
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

The Calyceraceae (47 spp.) is a small family of plants that is sister to the Asteraceae (∼ 25,000 spp.), one of the largest families of angiosperms. Most members of Calyceraceae are endemic to the Andes and Patagonia, representing an excellent model within which to study diversification patterns in these regions. The single phylogenetic study of Calyceraceae conducted to date revealed that the boundaries of most genera and several species of this family require further analyses, especially the “Nastanthus–Gamocarpha” clade. In this study, we reconstructed the phylogeny of the “Nastanthus–Gamocarpha” clade using multispecies coalescent models under BPP and StarBeast2 programs, sampling 63 individuals from 13 of the 14 species recognized to date. We then used this phylogenetic framework to delimit species using BFD and the A11 method implemented in BPP. Species limits suggested through a coalescent approach were then re-evaluated in the light of morphology, geography, and phenology. Coalescent-based methods indicated that most putative lineages could be recognized as distinct species. Morphological, geographical, ecological, and phenological data further supported species delimitation. Necessary taxonomic changes are proposed. Namely, the paraphyletic Nastanthus is synonymized under Gamocarpha, while five species of Boopis are transferred into Gamocarpha. We used an integrative taxonomic approach to recognize 13 species and one subspecies within the newly circumscribed genus Gamocarpha. © 2018 Elsevier Inc.

Registro:

Documento: Artículo
Título:Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae)
Autor:Denham, S.S.; Brignone, N.F.; Johnson, L.A.; Pozner, R.E.
Filiación:Instituto de Botánica Darwinion (Consejo Nacional de Investigaciones Científicas y Técnicas, Academia Nacional de Ciencias Exactas, Físicas y Naturales), casilla de correo 22, B1642HYD San Isidro, Buenos Aires, Argentina
Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Avenida 122 y 60, La Plata, Buenos Aires, Argentina
Department of Biology and M. L. Bean Life Science Museum, 4102 LSB, Brigham Young University, Provo, UT 84602, United States
Palabras clave:Andean plants; Coalescent models; Morphology; Phenology; Species delimitation; Species tree
Año:2019
Volumen:130
Página de inicio:211
Página de fin:226
DOI: http://dx.doi.org/10.1016/j.ympev.2018.10.015
Handle:http://hdl.handle.net/20.500.12110/paper_10557903_v130_n_p211_Denham
Título revista:Molecular Phylogenetics and Evolution
Título revista abreviado:Mol. Phylogenet. Evol.
ISSN:10557903
CODEN:MPEVE
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10557903_v130_n_p211_Denham

Referencias:

  • APG, III, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III (2009) Bot. J. Linn. Soc., 161, pp. 105-121
  • Baldwin, B.G., Markos, S., Phylogenetic utility of the external transcribed spacer (ETS) of 18S–26S nrDNA: congruence of ETS and ITS trees of Calycadenia (Compositae) (1998) Mol. Phylogenet. Evol., 10, pp. 449-463
  • Bandelt, H.J., Forster, P., Röhl, A., Median-joining networks for inferring intraspecies phylogenies (1999) Mol. Biol. Evol., 16, pp. 37-48
  • Bayer, R.J., Greber, D.G., Bagnall, N.H., Phylogeny of Australian Gnaphalieae (Asteraceae) Based on Chloroplast and Nuclear Sequences, the trnL Intron, trnL/trnF Intergenic Spacer, matK, and ETS (2002) Syst. Bot., 27, pp. 801-814
  • Bortolus, A., Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology (2008) AMBIO: J. Human Environ., 37, pp. 114-118
  • Bouckaert, R.R., Drummond, A.J., Bmodeltest: bayesian phylogenetic site model averaging and model comparison (2017) BMC Evol. Biol., 17, pp. 42-111
  • Cabrera, A.L., Willink, A., Biogeografía de América Latina. Serie de Biología 13 (1973), Secretaría General de la Organización de los Estados Americanos Washington, D.C., USA; Carstens, B.C., Dewey, T.A., Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats (2010) Syst. Biol., 59, pp. 400-414
  • Carstens, B.C., Pelletier, T.A., Reid, N.M., Satler, J.D., How to fail at species delimitation (2013) Mol. Ecol., 22, pp. 4369-4383
  • Caviedes-Solis, I.W., Bouzid, N.M., Banbury, B.L., Leaché, A.D., Uprooting phylogenetic uncertainty in coalescent species delimitation: a meta-analysis of empirical studies (2015) Curr. Zool., 61, pp. 866-873
  • Darriba, D., Tabeada, G.L., Doallo, R., Posada, D., jModelTest2: more models, new heuristics and parallel computing (2012) Nat. Methods, 9, p. 772
  • de Queiroz, K., Species concepts and species delimitation (2007) Syst. Biol., 56, pp. 879-886
  • Demesure, B., Sodzi, N., Petit, J.R., A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants (1995) Mol. Ecol., 4, pp. 129-134
  • Denham, S.S., Zavala-Gallo, L., Pozner, R.E., Morphology and taxonomic revision of Calycera (2014) Syst. Bot., 39, pp. 1226-1249
  • Denham, S.S., Zavala-Gallo, L., Johnson, L.A., Pozner, R.E., Insights into the phylogeny and evolutionary history of Calyceraceae (2016) Taxon, 65, pp. 1328-1344. , https://doi.org/10.12705/656.7
  • DeVore, M.L., Systematic studies of Calyceraceae. Dissertation (1994), Ohio State University Columbus, USA; Di Rienzo, J.A., Casanoves, F., Balzarini, M.G., Gonzalez, L., Tablada, M., Robledo, C.W., http://www.infostat.com.ar, InfoStat versión 2017, website [accessed 12 October 2017]; Doyle, J.J., Doyle, J.L., A rapid DNA isolation procedure for small quantities of fresh leaf tissue (1987) Phytochem. Bull. Bot. Soc. Amer., 19, pp. 11-15
  • Edwards, S.V., Is a new and general theory of molecular systematics emerging? (2009) Evolution, 63, pp. 1-19
  • Erbar, C., Studies on floral development and pollen presentation in Acicarpha tribuloides with a discussion of the systematic position of the family Calyceraceae (1993) Botanische Jahrbucher für Systematik, Pflanzengeschichte und Pflanzengeographie, 115, pp. 325-350
  • Fernández, M., Ezcurra, C., Calviño, C.I., Species limits and morphometric and environmental variation within the South Andean and Patagonian Mulinum spinosum species-group (Apiaceae-Azorelloideae) (2017) Syst. Biodivers., 15, pp. 489-505
  • Gaitán, J.J., López, C.R., Bran, D.E., Vegetation composition and its relationship with the environment in mallines of north Patagonia, Argentina (2011) Wetlands Ecol. Manage., 19, pp. 121-130
  • Goloboff, P.A., Catalano, S.A., TNT version 1.5, including a full implementation of phylogenetic morphometrics (2016) Cladistics, 32, pp. 221-238
  • Gratton, P., Trucchi, E., Trasatti, A., Riccarducci, G., Marta, S., Allegrucci, G., Cesaroni, D., Sbordoni, V., Testing classical species properties with contemporary data: how “Bad Species” in the brassy ringlets (Erebia tyndarus complex, Lepidoptera) turned good (2016) Syst. Biol., 65, pp. 292-303
  • Grummer, J.A., Bryson, R.W., Reeder, T.W., Species delimitation using bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae) (2014) Syst. Biol., 63, pp. 119-133
  • Hall, T.A., BioEdit: a user-friendly biological sequence aligment editor and analysis program for Windows 95/98/NT (1999) Nucleic Acids Symp. Ser., 41, pp. 95-98
  • Hedin, M., Carlson, D., Coyle, F., Sky island diversification meets the multispecies coalescent divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia (2015) Mol. Ecol., 24, pp. 3467-3484
  • Heled, J., Drummond, A.J., Bayesian inference of specie trees from multilocus data (2010) Mol. Biol. Evol., 27, pp. 570-580
  • Hellwig, F.H., Calyceraceae (2007) The families and genera of vascular plants. Flowering plants, , Eudicots. Asterales, 19–25 K. Kubitzki J.W. Kadereit C. Jeffrey Berlin Heidelberg, Springer-Verlag
  • Huson, D.H., Bryant, D., Application of phylogenetic networks in evolutionary studies (2006) Mol. Biol. Evol., 23, pp. 254-267
  • Isaac, N.J.B., Mallet, J., Mace, G.M., Taxonomic inflation: its influence on macroecology and conservation (2004) Trends Ecol. Evol., 19, pp. 464-469
  • Kass, R.E., Raftery, A.E., Bayes factors (1995) J. Am. Stat. Assoc., 90, pp. 773-795
  • Knowles, L.L., Carstens, B.C., Delimiting species without monophyletic gene trees (2007) Syst. Biol., 56, pp. 887-895
  • Leaché, A.D., Fujita, M.K., Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus) (2010) Proc. R. Soc. B, 277 (1697), pp. 3071-3077
  • Leins, P., Erbar, C., Flower and Fruit: Morphology, Ontogeny, Phylogeny, Function and Ecology (2010), Schweizerbart Science Publishers Stuttgart, Baden-Wurtemberg, Germany; Liu, L., Yu, L., Kubatko, L., Pearl, D.K., Edwards, S.V., Coalescent methods for estimating phylogenetic trees (2009) Mol. Phylogenet. Evol., 53, pp. 320-328
  • Lundberg, J., Bremer, K., A phylogenetic study of the order Asterales using one morphological and three molecular data sets (2003) Int. J. Plant Sci., 164, pp. 553-578
  • Matsumoto, T., Yasumoto, A.A., Nitta, K., Yahara, T., Tachida, H., Difference in flowering time as an isolating barrier (2013) J. Theor. Biol., 317, pp. 161-167
  • Moore, D.M., Further records for the vascular flora of the Falkland Islands (1967) Bot. Notiser, 120, pp. 17-25
  • Moore, D.M., The flora of the Fuego-Patagonia Cordillera: its origins and affinities (1983) Rev. Chil. Hist. Nat., 56, pp. 123-136
  • Morrison, D.A., Introduction to Phylogenetic Networks (2011), RJR Productions Uppsala, Sweden; Niemiller, M.L., Near, T.J., Fitzpatrick, B.M., Delimiting species using multilocus data: diagnosing cryptic diversity in the Southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae) (2012) Evolution, 66, pp. 846-866
  • O'Meara, B.C., New heuristic methods for joint species delimitation and species tree inference (2010) Syst. Biol., 59, pp. 59-73
  • Ogilvie, H.A., Bouckaert, R., Drummond, A.J., StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates (2017) Mol. Biol. Evol., 34, pp. 2101-2114
  • Pozner, R., Zanotti, C., Johnson, L.A., Evolutionary origin of the Asteraceae capitulum: insights from Calyceraceae (2012) Am. J. Bot., 99, pp. 1-13
  • Rahn, K., Chromosome numbers in some South American angiosperms (1960) Botanisk Tidsskrift, 56, pp. 117-127
  • Rannala, B., Yang, Z., Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci (2003) Genetics, 164, pp. 1645-1656
  • Rannala, B., Yang, Z., Improved reversible jump algorithms for Bayesian species delimitation (2013) Genetics, 194, pp. 245-253
  • Reitz, R., (1988), Flora ilustrada Catarinense, I Parte, As plantas, fasc. Calic: Caliceráceas. Herbário “Barbosa Rodrigues”. Itajaí. Brazil; Sang, T., Crawford, D.J., Stuessy, T.F., Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae) (1997) Am. J. Botany, 84, pp. 1120-1136
  • Schlick-Steiner, B.C., Steiner, F.M., Seifert, B., Stauffer, C., Christian, E., Crozier, R.H., Integrative taxonomy: a multisource approach to exploring biodiversity (2010) Annu. Rev. Entomol., 55, pp. 421-438
  • Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Siripun, K.C., Small, R.L., The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis (2005) Am. J. Bot., 92, pp. 142-166
  • Sukumaran, J., Knowles, L.L., Multispecies coalescent delimits structure, not species (2017) Proc. Natl. Acad. Sci. USA, 114, pp. 1607-1612
  • Tate, J.A., Simpson, B.B., Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species (2003) Syst. Bot., 28, pp. 723-737
  • Thiers, B., (2018), http://sweetgum.nybg.org/ih, Index Herbariorum: a Global Directory of Public Herbaria and Associated Staff. New York Botanical Garden's Virtual Herbarium. (last accessed June 2018); Venning, F.D., Manual of Advanced Plant Microtechnique (1953), Wm. C. Brown Company Publishers Dubuque, Iowa, USA; Weins, J.J., Penkrot, T.A., Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus) (2002) Syst. Biol., 51, pp. 69-91
  • White, T.J., Bruns, T., Lee, S., Taylor, J., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics (1990) PCR Protocols: A Guide to Methods and Applications, pp. 315-322. , M.A. Innis D.H. Gelfand J.J. Sninsky T.J. White Academic Press San Diego, California, USA
  • Willis, C.G., Ellwood, E.R., Primack, R.B., Davis, C.C., Pearson, K.D., Gallinat, A.S., Yost, J.M., Soltis, P.S., Old plants, new tricks: phenological research using herbarium specimens (2017) Trends Ecol. Evol., 32, pp. 531-546
  • Xie, W., Lewis, P.O., Fan, Y., Kuo, L., Chen, M., Improving marginal likelihood estimation for bayesian phylogenetic model selection (2011) Syst. Biol., 60, pp. 150-160
  • Yang, Z., The BPP program for species tree estimation and species delimitation (2015) Curr. Zool., 61, pp. 854-865
  • Yang, Z., Rannala, B., Bayesian species delimitation using multilocus sequence data (2010) Proc. Natl. Acad. Sci. USA, 107, pp. 9264-9269
  • Yang, Z., Rannala, B., Unguided species delimitation using DNA sequence data from multiple loci (2014) Mol. Biol. Evol., 31, pp. 3125-3135
  • Zavala-Gallo, L., Evaluación de los límites genéricos y evolución morfológica de las Calyceraceae sobre la base de un análisis filogenético combinado (molecular-morfológico). PhD Dissertation (2013), Universidad Nacional de La Plata Buenos Aires, Argentina; Zavala-Gallo, L., Denham, S., Pozner, R., Revision of Nastanthus (Calyceraceae) (2010) Gayana Botanica, 67, pp. 158-175
  • Zhang, C., Zhang, D.X., Zhu, T., Yang, Z., Evaluation of a Bayesian coalescent method of species delimitation (2011) Syst. Biol., 60, pp. 747-761

Citas:

---------- APA ----------
Denham, S.S., Brignone, N.F., Johnson, L.A. & Pozner, R.E. (2019) . Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae). Molecular Phylogenetics and Evolution, 130, 211-226.
http://dx.doi.org/10.1016/j.ympev.2018.10.015
---------- CHICAGO ----------
Denham, S.S., Brignone, N.F., Johnson, L.A., Pozner, R.E. "Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae)" . Molecular Phylogenetics and Evolution 130 (2019) : 211-226.
http://dx.doi.org/10.1016/j.ympev.2018.10.015
---------- MLA ----------
Denham, S.S., Brignone, N.F., Johnson, L.A., Pozner, R.E. "Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae)" . Molecular Phylogenetics and Evolution, vol. 130, 2019, pp. 211-226.
http://dx.doi.org/10.1016/j.ympev.2018.10.015
---------- VANCOUVER ----------
Denham, S.S., Brignone, N.F., Johnson, L.A., Pozner, R.E. Using integrative taxonomy and multispecies coalescent models for phylogeny reconstruction and species delimitation within the “Nastanthus–Gamocarpha” clade (Calyceraceae). Mol. Phylogenet. Evol. 2019;130:211-226.
http://dx.doi.org/10.1016/j.ympev.2018.10.015