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Integral Phylogenomic Approach over Ilex L. Species from Southern South America

Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires—IEGEBA (UBA—CONICET), C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Ciudad Autónoma de Buenos Aires, Argentina
Author to whom correspondence should be addressed.
Current address: Escuela de Ciencias Agrarias, Naturales y Ambientales, Universidad del Noroeste de la Provincia de Buenos Aires (UNNOBA), Av. Pte. Dr. Arturo Frondizi N° 2650 Pergamino, Buenos Aires, Argentina.
Received: 9 October 2017 / Revised: 3 November 2017 / Accepted: 16 November 2017 / Published: 22 November 2017
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)
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The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I. paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses. We selected seven introns and nine IGSs as variable non-coding markers that were used in phylogenomic analyses. Eight extra IGSs were proposed as candidate markers. Southern South American species formed one lineage, except for I. paraguariensis, I. dumosa and I. argentina, which occupied intermediate positions among sampled taxa; Euroasiatic species formed two lineages. Some concordant relationships were retrieved from nuclear sequence data. We also conducted integral analyses, involving a supernetwork of molecular data, and a simultaneous analysis of quantitative and qualitative morphological and phytochemical characters, together with molecular data. The total evidence tree was used to study the evolution of non-molecular data, evidencing fifteen non-ambiguous synapomorphic character states and consolidating the relationships among southern South American species. More South American representatives should be incorporated to elucidate their origin. View Full-Text
Keywords: multilocus phylogenomics; networks and splits graphs; non-coding regions; plastomes; supernetwork; character evolution multilocus phylogenomics; networks and splits graphs; non-coding regions; plastomes; supernetwork; character evolution

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Cascales, J.; Bracco, M.; Garberoglio, M.J.; Poggio, L.; Gottlieb, A.M. Integral Phylogenomic Approach over Ilex L. Species from Southern South America. Life 2017, 7, 47.

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