Alignment-of-Protoparmelia-s.str_Concated-6-loci_2015

Protoparmelia-s-sl_Concated-6-loci-Alignment_RPB1-MCM7-TSR1-NULSU-MTSSU-nrIT

Phylogeny of <i>Protoparmelia s</i>. <i>str</i>. based on six concatenated loci.

<p>Numbers above branches indicate ML BS ≥ 70%. Branches in bold indicate Bayesian posterior probabilities (PP) ≥ 0.94. Specimen indicators include country codes (see Supporting information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124625#pone.0124625.s001" target="_blank">S1 Table</a>). Taxon names refer to putative species supported by ML BS ≥ 70% or Bayesian Inference (PP ≥ 0.94), and tested for speciation probabilities using BP&P and spedeSTEM. Colored boxes indicate species supported by BP&P (left) and spedeSTEM (right), respectively.</p

SpedeSTEM validation results.

<p>spedeSTEM validation results, using θ = 0.5. The absolute difference between the AICc score for the given model and the best-fitting one is listed under the column labeled ‘‘Di” and the model weighting is listed under the column labeled “wi”.</p><p>SpedeSTEM validation results.</p

Genetic characteristics of nuclear loci used in this study.

<p>Genetic characteristics of nuclear loci used in this study, including the total number of sequences per locus, length of the alignment; and best model of evolution selected using the Akaike information criterion as suggested by jModelTest.</p><p>Genetic characteristics of nuclear loci used in this study.</p

*BEAST species trees for <i>Protoparmelia s</i>. <i>str</i>. as suggested by ML (BS ≥ 70%) or Bayesian (PP ≥ 0.94).

<p>Posterior probabilities at nodes indicate support from the *BEAST analyses. The posterior probability of each delimited species calculated by BP&P are indicated in front of each putative species. Boxes in dark grey indicate clades not supported as separate taxa by BP&P. <i>Protoparmelia badia</i> B1 & B2 were supported as separate species whereas <i>P</i>. <i>badia</i> C1 & C2 were not supported as separate species (referred to as <i>P</i>. <i>badia</i> C) by BP&P. Box in light grey indicates species not supported as separate taxa by spedeSTEM.</p