Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota)

Gueidan, Cécile; Roux, Claude; Lutzoni, François

doi:10.1016/j.mycres.2007.08.010

Cited by 146 publications

(171 citation statements)

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“…All isolates were subjected to a multi-gene analysis of seven genes including Apn2, EF1-α, CAL, HIS, FG1093, ACT and TUB regions, excluding the ITS region from the combined analysis. Individual datasets were tested for congruency using the 70 % reciprocal bootstrap (BS) threshold method as described by Gueidan et al (2007). Evolutionary models for phylogenetic analyses were selected independently for each locus using MrModeltest 2.3 (Nylander 2004) under the Akaike Information Criterion (AIC) implemented in both PAUP v.4.and MrBayes v3.…”

Section: Sequence Alignment and Phylogenetic Analysismentioning

confidence: 99%

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

et al. 2014

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The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1-α (EF1-α), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence of sequence heterogeneity of ITS within D. eres is observed, which complicates the analysis and may lead to overestimation of the species diversity. The strict criteria of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS. We accept nine distinct phylogenetic species including helicis and D. pulla. Modern descriptions and illustrations are provided for these species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA-lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.

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Section: Sequence Alignment and Phylogenetic Analysismentioning

confidence: 99%

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

et al. 2014

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Section: Introductionmentioning

confidence: 99%

“…Recently, the study of character evolution has dramatically increased our knowledge of how morphological and ecological traits evolve in lichens, and how these reflect phylogenetic relationships (Blanco et al, 2006;Gueidan et al, 2007;Ekman et al, 2008;Schmitt et al, 2009a;Muggia et al, 2011). In the Collemataceae, many of the easily observable and ecologically significant traits traditionally used for taxon circumscription are clearly not characterizing monophyletic groups.…”

Section: Introductionmentioning

confidence: 99%

“…These and other studies have provided strong evidence that many commonly used morphological and anatomical characters traditionally utilized to classify lichenized fungal taxa often are poor predictors of monophyletic groups. By contrast, traits traditionally considered less important in taxonomy are often better indicators of phylogenetic relationships in lichens Blanco et al, 2006;Gueidan et al, 2007; Schmitt et al, 2009a;Rivas-Plata et al, 2011).The Peltigerales is a group of fungi forming symbioses with cyanobacteria, and which earlier often were viewed as "ancient" and featuring many presumably "old" traits (Hawksworth, 1982; Galloway, 1994). These lichens have potentially a substantial impact on the ecosystems they inhabit by fixating atmospheric nitrogen (Cornelissen et al, 2007;Nash, 2008) and many species are rare and threatened by forestry management practices and air pollution.…”

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Cardinal characters on a slippery slope – A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str)

Otálora

Aragón

Martínez

et al. 2013

Molecular Phylogenetics and Evolution

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PostprintThis is the accepted version of a paper published in Molecular Phylogenetics and Evolution. This paper has been peer-reviewed but does not include the final publisher proof-corrections or journal pagination. Citation for the original published paper (version of record):Otálora, M., Aragón, G., Martínez, I., Wedin, M. (2013) Cardinal characters on a slippery slope -A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str.). Evolution, http://dx.doi.org/10. 1016/j.ympev.2013.04.004 Access to the published version may require subscription. Here we reconstruct the phylogeny of Collemataceae using Bayesian and maximum likelihood analyses based on mitochondrial (mtSSU rDNA) and nuclear (nuLSU rDNA, Betatubulin and MCM7) markers of 70 Collemataceae species. We studied the evolution of four morphological and ecological characters traditionally used to delimit genera and infra-generic Molecular Phylogenetics andgroups. Finally, we tested if differences in branch-lengths between clades are due to differences in rates of molecular evolution. Eleven strongly supported groups were recovered in the resulting well-resolved and well-supported phylogeny. The presence/absence of a eucortex, which is currently used as the cardinal character to define genera in the group, does not characterize monophyletic groups corresponding to the genera as currently circumscribed.Ancestral state reconstruction indicates that the most recent common ancestor of the jelly lichens most likely was saxicolous/terricolous, lacked a tomentum, and had transversally septate ascospores. Although the cortex state could not be reconstructed for the ancestor of the family, our observations indicate that a lack of cortex may have an evolutionary advantage in saxicolous/terricolous species in semi-arid environments, as non-corticate species tends to be larger and occur in higher frequency and abundance in such regions, compared to corticate species. A significant evidence for faster evolutionary rates was found in a lineage mainly including taxa that occur in the wet tropics and humid temperate regions, compared to other lineages. We suggest that this can explain the greater diversity of Collemataceae in tropical and humid areas.Key words: Accelerated evolutionary rates, ancestral state reconstruction, Collemataceae, cortex, habitat, lichen-forming fungi. 4 IntroductionLichens are fungi utilizing photosynthetic algae or cyanobacteria for the exploitation of carbohydrates. The symbiotic association allows both the fungal and algal partners to colonize a range of habitats which otherwise would be inhabitable to them. Molecular phylogenetic studies have recently led to significant advances in the understanding of relationships between fungal groups including lichen fungi (Lutzoni et al., 2004; Miadlikowska et al., 2006;Hibbett et al., 2007; Ekman et al., 2008). These and other studies have provided strong evidence that many commonly used morphological and anatomical characters traditionally...

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“…Recientes estudios moleculares han modificado sustancialmente la nomenclatura de algunos géneros tales como Aspicilia, Caloplaca, Melanelia, Phaeosporobolus, Verrucaria y Xanthoria (Arup et al 2013, Divakar et al 2012, Ertz et al 2013, Gueidan et al 2007, Sohrabi et al 2013a. Hemos considerado estas actualizaciones, pero mantenemos entre paréntesis la combinación anterior.…”

Section: Materiales Y Métodosunclassified

Hongos liquenizados y liquenícolas de la Sierra de Albarracín (Teruel, España)

et al. 2014

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INTRODUCCIÓNLa Sierra de Albarracín, situada en el suroeste de la provincia de Teruel (Aragón), es uno de los conjuntos más sorprendentes del Sistema Ibérico tanto por sus paisajes como por su flora y su fauna. El conocimiento que existe sobre la flora de líquenes epifíticos en la provincia de Teruel no es completo, aunque si lo comparamos con otras provincias peninsulares puede considerarse bastante avanzado. Hasta principios del siglo XX las primeras aportaciones a la flora provincial fueron realizadas por Asso (1779), Colmeiro (1867a, b;1889 ) y Loscos (1876 -1877. Posteriormente Lázaro Ibiza (1898), Navás (1901, 1910), Pardo Sastrón (1901 Se presenta un catálogo de 462 hongos liquenizados y liquenícolas de la Sierra de Albarracín (Teruel, Aragón, España), como resultado de la IV Campaña de Recolección organizada por la Sociedad Española de Liquenología (SEL). Diplotomma hedinii es novedad para la Península Ibé-rica y Lepraria leuckertiana constituye una segunda cita peninsular, 69 taxones son novedad para Aragón y 86 lo son para la provincia de Teruel.

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Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota)

Cited by 146 publications

References 70 publications

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

Cardinal characters on a slippery slope – A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str)

Hongos liquenizados y liquenícolas de la Sierra de Albarracín (Teruel, España)

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