Análisis de supermatrices demuestran la importancia del muestreo de grupos externos, genes y taxones en la filogenética de Onosma (Boraginaceae)
DOI:
https://doi.org/10.3989/ajbm.2630Palabras clave:
Cystostemon, Lithospermeae, filogenia, grupo externo, Maharanga, muestreo de taxones/genes, OnosmaResumen
La tribu Lithospermeae (Boraginaceae) consta de ca. 26 géneros y 470 especies, en las que Onosma constituye aproximadamente un tercio de las especies (~150). Si bien la tribu ha sido fuertemente apoyada como monofilética, los límites taxonómicos a nivel de género y especie son todavía ambiguos. Entre ellos, no solo la posición filogenética de las especies de Onosma de Asia oriental, sino también la delimitación del género son confusas. Si Onosma de Asia oriental es monofilético o si el género debe ampliarse para incluir a Maharanga y tal vez Cystostemon son todavía cuestiones por resolver. Por estas razones, realicé 16 análisis filogenéticos con diferentes coberturas de taxones, alineamientos, regiones de genes y grupos externos, con hasta 746 taxones de la tribu Lithospermeae y con cinco regiones de ADN, usando datos de GenBank. Los resultados, con la cobertura taxonómica más amplia hasta la fecha, demuestran que si bien el género Onosma no resultó monofilético en ninguno de los análisis, las relaciones filogenéticas entre Onosma s.s., Onosma de Asia oriental, Maharanga y Cystostemon difieren entre análisis. Sin embargo, el test AU (“approximately unbiased”) mostró que la topología (((Onosma-Asia Oriental+Maharanga) Cystostemon) Onosma s.s.) es ampliamente compatible. Por lo tanto, este trabajo destaca la importancia del muestreo de taxones, genes y grupos externos en la filogenética de Onosma.
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Álvarez I. & Wendel J.F. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434. https://doi.org/10.1016/S1055-7903(03)00208-2 PMid:14615184
Aygoren Uluer D., Hawkins J.A. & Forest F. 2020a. Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd 1 and 26S rDNA. Plant Systematics and Evolution 306: 1-14. https://doi.org/10.1007/s00606-020-01691-7
Aygoren Uluer D., Forest F. & Hawkins J.A. 2020b. Supermatrix analyses and molecular clock rooting of Fabales: Exploring the effects of outgroup choice and long branch attraction on topology. Botany 98: 231-247. https://doi.org/10.1139/cjb-2019-0109
Barrett R.L., Clugston J.A., Cook L.G., Crisp M.D., Jobson P.C., Lepschi B.J., Renner M.A. & Weston P.H. 2021. Understanding Diversity and Systematics in Australian Fabaceae Tribe Mirbelieae. Diversity 13: 391. https://doi.org/10.3390/d13080391
Cecchi L. & Selvi F. 2009. Phylogenetic relationships of the monotypic genera Halacsya and Paramoltkia and the origins of serpentine adaptation in circum-mediterranean Lithospermeae (Boraginaceae): insights from ITS and matK DNA sequences. Taxon 58: 700-714. https://doi.org/10.1002/tax.583002
Cecchi L., Coppi A. & Selvi F. 2011. Evolutionary dynamics of serpentine adaptation in Onosma (Boraginaceae) as revealed by ITS sequence data. Plant Systematics and Evolution 297: 185-199. https://doi.org/10.1007/s00606-011-0506-3
Cecchi L., Coppi A., Hilger H.H. & Selvi F. 2014. Non-monophyly of Buglossoides (Boraginaceae: Lithospermeae): Phylogenetic and morphological evidence for the expansion of Glandora and reappraisal of Aegonychon. Taxon 63: 1065-1078. https://doi.org/10.12705/635.4
Chacón J., Luebert F. & Weigend M. 2017. Biogeographic events are not correlated with diaspore dispersal modes in Boraginaceae. Frontiers in Ecology and Evolution 5: 26. https://doi.org/10.3389/fevo.2017.00026
Chacón J., Luebert F., Selvi F., Cecchi L. & Weigend M. 2019. Phylogeny and historical biogeography of Lithospermeae (Boraginaceae): Disentangling the possible causes of Miocene diversifications. Molecular Phylogenetics and Evolution 14: 106626. https://doi.org/10.1016/j.ympev.2019.106626 PMid:31526848
Cohen J.I. & Davis J.I. 2009. Nomenclatural changes in Lithospermum (Boraginaceae) and related taxa following a reassessment of phylogenetic relationships. Brittonia 61: 101-111. https://doi.org/10.1007/s12228-009-9082-z
Cohen J.I. 2011. A phylogenetic analysis of morphological and molecular characters of Lithospermum L. (Boraginaceae) and related taxa: evolutionary relationships and character evolution. Cladistics 27: 559-580. https://doi.org/10.1111/j.1096-0031.2011.00352.x PMid:34875811
Cohen J.I. 2014. A phylogenetic analysis of morphological and molecular characters of Boraginaceae: evolutionary relationships, taxonomy, and patterns of character evolution. Cladistics 30: 139-169. https://doi.org/10.1111/cla.12036 PMid:34784688
Coppi A., Cecchi L., Nocentini D. & Selvi F. 2015. Arnebia purpurea: a new member of formerly monotypic genus Huynhia (Boraginaceae-Lithospermeae). Phytotaxa 204: 123-136. https://doi.org/10.11646/phytotaxa.204.2.3
Darriba D., Taboada G.L., Doallo R. & Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772. https://doi.org/10.1038/nmeth.2109 PMid:22847109 PMCid:PMC4594756
Guindon S. & Gascuel O. 2003 A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696-704. https://doi.org/10.1080/10635150390235520 PMid:14530136
Heath T.A., Hedtke S.M. & Hillis D.M. 2008. Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution 46: 239-257.
Jian S., Soltis P.S., Gitzendanner M.A., Moore M.J., Li R., Hendry T.A., Qiu Y.L., Dhingra A., Bell C.D. & Soltis D.E. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57: 38-57. https://doi.org/10.1080/10635150801888871 PMid:18275001
Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C. & Thierer T. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28. 1647-1649. https://doi.org/10.1093/bioinformatics/bts199 PMid:22543367 PMCid:PMC3371832
Koyuncu O., Yaylacı Ö.K., Özgişi K., Sezer O. & Öztürk D. 2013. A new Onosma (Boraginaceae) species from central Anatolia, Turkey. Plant Systematics and Evolution 299: 1839-1847. https://doi.org/10.1007/s00606-013-0839-1
Letunic I. & Bork P. 2016. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research 44: W242-W245. https://doi.org/10.1093/nar/gkw290 PMid:27095192 PMCid:PMC4987883
Mehrabian A.R., Sheidai M., Noormohammadi Z., Asrei Y. & Mozafarian V. 2011. Inter-simple sequence repeats (ISSR) and morphological diversity in Onosma L. (Boraginaceae) species in Iran. African Journal of Biotechnology 10: 10831-10838. https://doi.org/10.5897/AJB11.1910
Miller M.A., Pfeiffer W. & Schwartz T. 2011. The CIPRES science gateway: a community resource for phylogenetic analyses. In: Proceedings of the Gateway Computing Environments Workshop (GCE). New Orleans, Louisiana. https://doi.org/10.1145/2016741.2016785
Nasrollahi F., Kazempour-Osaloo S., Saadati N., Mozaffarian V. & Zare-Maivan H. 2019. Molecular phylogeny and divergence times of Onosma (Boraginaceae ss) based on nrDNA ITS and plastid rpl32-trnL (UAG) and trnH-psbA sequences. Nordic Journal of Botany 37: e02060. https://doi.org/10.1111/njb.02060
Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.H. & Kõljalg U. 2006. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PloS ONE 1: e59. https://doi.org/10.1371/journal.pone.0000059 PMid:17183689 PMCid:PMC1762357
Qiu Y.L., Lee J., Whitlock B.A., Bernasconi-Quadroni F. & Dombrovska O. 2001. Was the ANITA rooting of the angiosperm phylogeny affected by long-branch attraction? Molecular Biology and Evolution 18: 1745-1753. https://doi.org/10.1093/oxfordjournals.molbev.a003962 PMid:11504854
Rambaut A. & Drummond A.J. 2007. Tracer v1. 4. Website:https://beast.community/tracer [accessed: 23 Mar. 2022].
Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574. https://doi.org/10.1093/bioinformatics/btg180 PMid:12912839
Selvi F., Cecchi L., Hilger H.H. & Coppi A. 2017. A reappraisal of the genus Megacaryon (Boraginaceae, Lithospermeae) based on molecular, morphological, and karyological evidence. Systematics and Biodiversity 15: 552-563. https://doi.org/10.1080/14772000.2017.1290707
Shimodaira H. & Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114. https://doi.org/10.1093/oxfordjournals.molbev.a026201
Smith A.B. 1994. Rooting molecular trees: problems and strategies. Biological Journal of the Linnean Society 51: 279-292. https://doi.org/10.1111/j.1095-8312.1994.tb00962.x
Solís-Lemus C. & Ané C. 2016. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics 12: e1005896. https://doi.org/10.1371/journal.pgen.1005896 PMid:26950302 PMCid:PMC4780787
Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313 https://doi.org/10.1093/bioinformatics/btu033 PMid:24451623 PMCid:PMC3998144
Thomas D.C., Weigend M. & Hilger H.H. 2008. Phylogeny and systematics of Lithodora (Boraginaceae-Lithospermeae) and its affinities to the monotypic genera Mairetis, Halacsya and Paramoltkia based on ITS1 and trnLUAA-sequence data and morphology. Taxon 57: 79-97.
Trifinopoulos J., Nguyen L.T., von Haeseler A. & Minh B.Q. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44: W232-W235. https://doi.org/10.1093/nar/gkw256 PMid:27084950 PMCid:PMC4987875
Weigend M., Gottschling M., Selvi F. & Hilger H.H. 2009. Marbleseeds are gromwells-Systematics and evolution of Lithospermum and allies (Boraginaceae tribe Lithospermeae) based on molecular and morphological data. Molecular Phylogenetics and Evolution 52: 755-768. https://doi.org/10.1016/j.ympev.2009.05.013 PMid:19464377
Wu H.Y., Chan K.T., But G.W.C. & Shaw P.C. 2021. Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification. Scientific Reports 11: 1-9. https://doi.org/10.1038/s41598-021-82385-z PMid:33564041 PMCid:PMC7873228
Yang H.M., Zhang Y.X., Yang J.B. & Li D.Z. 2013. The monophyly of Chimonocalamus and conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers. Molecular Phylogenetics and Evolution 68: 340-356. https://doi.org/10.1016/j.ympev.2013.04.002 PMid:23583782
Zeng L., Zhang N., Zhang Q., Endress P.K., Huang J. & Ma H. 2017. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. New Phytologist 214: 1338-1354. https://doi.org/10.1111/nph.14503 PMid:28294342
Zhu G.L., Harald R. & Rudolf K. 1995. Boraginaceae. In: Wu Z. Y. & Raven P. H. (eds), Flora of China 16: 329-427. Science Press, Beijing, & Missouri Botanical Garden Press, St. Louis.
Zwickl D.J. & Hillis D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51: 588-598. https://doi.org/10.1080/10635150290102339 PMid:12228001
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