Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae)

Abstract

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 group 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.

The contribution of the edaphic factor as a driver of recent plant diversification in a Mediterranean biodiversity hotspot

“…Superrosids include some clades with well‐documented recent radiations consisting of many neoendemics in eastern and particularly south‐eastern Iberia (e.g. Helianthemum , Martín‐Hernanz et al., 2019; Erodium , Fiz‐Palacios et al., 2010), as well as lineages that are highly diversified in other Iberian regions (e.g. Genisteae in the west; Saxifraga in northern mountains).…”

Systematic implications from a robust phylogenetic reconstruction of the genus Helianthemum (Cistaceae) based on genotyping-by-sequencing (GBS) data

“…2016). Overall, these findings emphasize that, beyond the systematic implications, studies at microevolutionary scale are necessary to evaluate diversification dynamics in these complexes and to understand why most species of Helianthemum are endemic or have very restricted distribution ranges (Martín-Hernanz & al. 2019a, 2019b.…”

“…1984;López-González 1992;Raynaud 1999). To date, two comprehensive molecular phylogenetic reconstructions of the genus Helianthemum have been attempted, one based on the analyses of nrDNA (ITS) plus cpDNA (ndhF, psbA-trnH, trnL-trnF) concatenated Sanger sequences , the other based on GBS data (Martín-Hernanz & al. 2019a).…”

“…Conversely, the phylogenetic analyses of GBS data (Martín-Hernanz & al. 2019a) (i) provided highly resolved phylogenetic trees with very strong support even at the most external nodes, (ii) robustly confirmed the three clades previously identified by , and (iii) showed striking similar topologies among them, each one consisting of one species-rich subclade that corresponded with one of the three largest sections in the genus (H. sects.…”

“…The biological and taxonomic complexity of these species is also reflected in the low statistical support retrieved for their intraspecific relationships as well as in the existence of topological incongruences for some nodes of the phylogenetic trees (see Fig. 4 in Martín-Hernanz & al. 2019a), further revealing that trait convergence, incomplete lineage sorting or hybridization and introgression could be playing an essential role in the differentiation of these lineages (Soubani & al.…”