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Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.

Publication ,  Journal Article
Gaya, E; Redelings, BD; Navarro-Rosinés, P; Llimona, X; De Cáceres, M; Lutzoni, F
Published in: Mycologia
March 2011

The Caloplaca saxicola group is the main group of saxicolous, lobed-effigurate species within genus Caloplaca (Teloschistaceae, lichen-forming Ascomycota). A recent monographic revision by the first author detected a wide range of morphological variation. To confront the phenotypically based circumscription of these taxa and to resolve their relationships morphological and ITS rDNA data were obtained for 56 individuals representing eight Caloplaca species belonging to the C. saxicola group. We tested the monophyly of these eight morphospecies by performing maximum parsimony, maximum likelihood and two different types of Bayesian analyses (with and without a priori alignments). Restricting phylogenetic analyses to unambiguously aligned portions of ITS was sufficient to resolve, with high bootstrap support, five of the eight previously recognized species within the C. saxicola group. However, phylogenetic resolution of all or most of the eight species currently included as two distinct subgroups within the C. saxicola group was possible only by combining morphological characters and signal from ambiguously aligned regions with the unambiguously aligned ITS sites or when the entire ITS1 and 2 regions were not aligned a priori and included as an integral component of a Bayesian analysis (BAli-Phy). The C. arnoldii subgroup includes C. arnoldii, comprising four subspecies, and the C. saxicola subgroup encompasses seven species. Contrary to the C. saxicola subgroup, monophyly of taxa included within the C. arnoldii subgroup and their relationships could not be resolved with combined ITS and morphological data. Unequivocal morphological synapomorphies for all species except C. arnoldii and C. pusilla are recognized and presented.

Duke Scholars

Published In

Mycologia

DOI

EISSN

1557-2536

ISSN

0027-5514

Publication Date

March 2011

Volume

103

Issue

2

Start / End Page

361 / 378

Related Subject Headings

  • Phylogeny
  • Mycology & Parasitology
  • Molecular Sequence Data
  • DNA, Ribosomal
  • DNA, Fungal
  • Bayes Theorem
  • Ascomycota
  • 3108 Plant biology
  • 3107 Microbiology
  • 3104 Evolutionary biology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Gaya, E., Redelings, B. D., Navarro-Rosinés, P., Llimona, X., De Cáceres, M., & Lutzoni, F. (2011). Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. Mycologia, 103(2), 361–378. https://doi.org/10.3852/10-120
Gaya, Ester, Benjamin D. Redelings, Pere Navarro-Rosinés, Xavier Llimona, Miquel De Cáceres, and François Lutzoni. “Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.Mycologia 103, no. 2 (March 2011): 361–78. https://doi.org/10.3852/10-120.
Gaya E, Redelings BD, Navarro-Rosinés P, Llimona X, De Cáceres M, Lutzoni F. Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. Mycologia. 2011 Mar;103(2):361–78.
Gaya, Ester, et al. “Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.Mycologia, vol. 103, no. 2, Mar. 2011, pp. 361–78. Epmc, doi:10.3852/10-120.
Gaya E, Redelings BD, Navarro-Rosinés P, Llimona X, De Cáceres M, Lutzoni F. Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study. Mycologia. 2011 Mar;103(2):361–378.

Published In

Mycologia

DOI

EISSN

1557-2536

ISSN

0027-5514

Publication Date

March 2011

Volume

103

Issue

2

Start / End Page

361 / 378

Related Subject Headings

  • Phylogeny
  • Mycology & Parasitology
  • Molecular Sequence Data
  • DNA, Ribosomal
  • DNA, Fungal
  • Bayes Theorem
  • Ascomycota
  • 3108 Plant biology
  • 3107 Microbiology
  • 3104 Evolutionary biology