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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01416

MAXIMIZE RESOLUTION OR MINIMIZE ERROR? USING GBS TO INVESTIGATE THE RECENT DIVERSIFICATION OF HELIANTHEMUM (CISTACEAE)

 SARA MARTIN HERNANZ1*,  ABELARDO APARICIO1,  MARIO FERNÁNDEZ MAZUECOS2, ENCARNACIÓN RUBIO1, ALFREDO REYES BETANCORT3, ARNOLDO SANTOS GUERRA3, MARIA OLANGUA CORRAL4 and  RAFAEL G. Albaladejo1
  • 1University of Seville, Spain
  • 2Real Jardín Botánico (RJB), Spain
  • 3Other, Spain
  • 4Jardín Botánico Canario "Viera y Clavijo", Spain

A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic genus of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS) we established a rigorous methodological workflow in which we (i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, (ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and (iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch-lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.

Keywords: Branch length, Diversification, evolutionary radiation, genotyping-by-sequencing, helianthemum, Phylogenetic resolution, phylogenomics

Received: 16 Jul 2019; Accepted: 11 Oct 2019.

Copyright: © 2019 MARTIN HERNANZ, APARICIO, FERNÁNDEZ MAZUECOS, RUBIO, REYES BETANCORT, SANTOS GUERRA, OLANGUA CORRAL and Albaladejo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Miss. SARA MARTIN HERNANZ, University of Seville, Seville, Spain, sara.martin.hernanz@gmail.com