Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene

Crespo, Ana; Lumbsch, H. Thorsten; Mattsson, Jan-Eric; Blanco, Óscar; Divakar, Pradeep K.; Articus, Kristina; Wiklund, Elisabeth; Bawingan, Paulina A.; Wedin, Mats

doi:10.1016/j.ympev.2006.11.029

Cited by 134 publications

(195 citation statements)

References 60 publications

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“…forms a well-supported monophyletic group, confirming the results of earlier studies (Mattsson and Wedin 1999, Persoh and Rambold 2002, Arup et al 2007, Crespo et al 2007. Our analyses showed that two representatives of the genus Protoparmelia, P. badia and P. picea, form the sister-group to Parmeliaceae s.…”

Section: Discussionsupporting

confidence: 90%

“…However, these authors suggested their data were not sufficient to differentiate between the scenario where Protoparmelia was sister to Parmeliaceae, and where (Protoparmelia+Gypsoplaca) was the sister. Crespo et al (2007) likewise showed a supported relationship of Protoparmelia badia as a close relative to Parmeliaceae, but here Gypsoplacaceae was not included. Furthermore, "Lecidea" rubrocastanea was proposed to be close to Protoparmelia (Spribille and Printzen 2007) but there was no support for this relationship.…”

Section: Parmelia Sulcata and Flavoparmelia Caperatamentioning

confidence: 81%

“…Recently, a number of phylogenetic studies enhanced our knowledge of evolution and phylogenetic relationships within Parmeliaceae (Crespo et al 2010(Crespo et al , 2011Thell et al 2012). All genera currently accepted in Parmeliaceae in a wide sense (including the sometimes recognized Anziaceae, Alectoriaceae, Hypogymniaceae and Usneaceae) form a well-supported monophyletic group in all major published analyses (Persoh and Rambold 2002;Crespo et al 2007Arup et al 2007). However, the relationships of Parmeliaceae with other groups in Lecanorales are poorly known.…”

Section: Parmelia Sulcata and Flavoparmelia Caperatamentioning

confidence: 99%

“…Members of the Cladoniaceae were selected as outgroup for the analysis because previous studies suggested that these families are closely related to Parmeliaceae (Miadlikowska et al 2006;Crespo et al 2007). Details of the studied material, including GenBank accession numbers are shown in Table 1.…”

Section: Samplingmentioning

confidence: 99%

“…The data sets include 118 sequences from previous publications by PARSYS working group (Crespo et al 2007) and 13 downloaded from GenBank. A total of 54 taxa were analyzed including 36 representatives of the family Parmeliaceae s.…”

Section: Dna Sequencesmentioning

confidence: 99%

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The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota)

et al. 2013

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Section: Discussionsupporting

confidence: 90%

Section: Parmelia Sulcata and Flavoparmelia Caperatamentioning

confidence: 81%

Section: Parmelia Sulcata and Flavoparmelia Caperatamentioning

confidence: 99%

Section: Samplingmentioning

confidence: 99%

Section: Dna Sequencesmentioning

confidence: 99%

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The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota)

et al. 2013

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Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Pogoda

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Nadiadi

et al. 2019

Ecology and Evolution

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Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha‐proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1 gene always contained the highest number of introns out of all the mitochondrial protein‐coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome‐wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensis and Graphis lineola . Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum ), even between closely related sister species (e.g., Cladonia ). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad‐scale genome streamlining via loss of protein‐coding genes as well as noncoding, parasitic DNA elements.

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Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence

Crespo

Kauff

Divakar

et al. 2010

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Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re‐circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.

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Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene

Cited by 134 publications

References 60 publications

The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota)

The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota)

Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence

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