Using Phylogenetic and Coalescent Methods to Understand the Species Diversity in the Cladia aggregata Complex (Ascomycota, Lecanorales)

Parnmen, Sittiporn; Rangsiruji, Achariya; Mongkolsuk, Pachara; Boonpragob, Kansri; Nutakki, Aparna; Lumbsch, H. Thorsten

doi:10.1371/journal.pone.0052245

Cited by 58 publications

(54 citation statements)

References 107 publications

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“…[MW3]All but one of the studied phenotypic characters that were previously used for species circumscription in the C. furcata complex have here been shown to be highly homoplasious ( Table 2). This is consistent with previous studies that had also found high homoplasy levels for phenotypic characters within Cladoniaceae (Pino-Bodas et al 2011;Parnmen et al 2012). For example, the presence of scyphi (Pino-Bodas et al 2011), or the presence of soredia (Stenroos et al 2002) were shown to be highly homoplasious in other groups of Cladoniaceae.…”

Section: Discussionsupporting

confidence: 92%

The phenotypic features used for distinguishing species within theCladonia furcatacomplex are highly homoplasious

et al. 2015

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The phenotypic features used for distinguishing species within the Cladonia furcata complex are highly homoplasious.The Lichenologist, http://dx.doi.org/10.1017/S0024282915000225Access to the published version may require subscription. Abstract:The Cladonia furcata complex here treated comprises C. farinacea, C. furcata, C. multiformis, C. scabriuscula, C. stereoclada, and C. subrangiformis. The well known taxonomic complexity of this group is caused by wide phenotypic variation within and high morphological similarity among the species. Here, we investigated the evolution of the phenotypic characters traditionally used to distinguish the species in this complex. A phylogenetic analysis of the C. furcata complex is presented here, based on three loci (ITS rDNA, IGS rDNA and rpb2), representing specimens from a broad geographical range (Europe, North America and New Zealand). The phylogenetic reconstructions were performed using Maximum Likelihood and Bayesian analyses. In addition, 14 features traditionally used for species delimitation within this complex were mapped onto the Bayesian phylogeny. All the species currently accepted, with the exception of C. stereoclada, turned out to be polyphyletic. Most of the phenotypical characters studied are highly homoplasious with the exception of the podetium type.The solid podetia represent a diagnostic character of C. stereoclada.

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Section: Discussionsupporting

confidence: 92%

The phenotypic features used for distinguishing species within theCladonia furcatacomplex are highly homoplasious

et al. 2015

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“…A likelihood ratio test (LRT) was used to evaluate whether the null model was to be rejected or not. If the GMYC model fits the data significantly better than the null model, the threshold T allows estimation of the number of species present in the dataset (Parnmen et al 2012). The GMYC method requires an ultrametric tree without identical sequences to avoid zero length terminal branches that hamper the likelihood estimation (Fujisawa and Barraclough 2013).…”

Section: Species Delimitationmentioning

confidence: 99%

Evolutionary history and species delimitations: a case study of the hazel dormouse, Muscardinus avellanarius

Mouton

Mortelliti

Grill³

et al. 2016

Conserv Genet

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Robust identification of species and significant evolutionary units (ESUs) is essential to implement appropriate conservation strategies for endangered species. However, definitions of species or ESUs are numerous and sometimes controversial, which might lead to biased conclusions, with serious consequences for the management of endangered species. The hazel dormouse, an arboreal rodent of conservation concern throughout Europe is an ideal model species to investigate the relevance of species identification for conservation purposes. This species is a member of the Gliridae family, which is protected in Europe and seriously threatened in the northern part of its range. We assessed the extent of genetic subdivision in the hazel dormouse by sequencing one mitochondrial gene (cytb) and two nuclear genes (BFIBR, APOB) and genotyping 10 autosomal microsatellites. These data were analysed using a combination of phylogenetic analyses and species delimitation methods. Multilocus analyses revealed the presence of two genetically distinct lineages (approximately 11 % cytb genetic divergence, no nuclear alleles shared) for the hazel dormouse in Europe, which presumably diverged during the Late Miocene. The phylogenetic patterns suggests that Muscardinus avellanarius populations could be split into two cryptic species respectively distributed in western and central-eastern Europe and Accession numbers are available at the ''European Nucleotide Archive'' browser at the address http://www.ebi.ac.uk/ena/data/view/ LT614830-LT614893 and in Supplementary Anatolia. However, the comparison of several species definitions and methods estimated the number of species between 1 and 10. Our results revealed the difficulty in choosing and applying an appropriate criterion and markers to identify species and highlight the fact that consensus guidelines are essential for species delimitation in the future. In addition, this study contributes to a better knowledge about the evolutionary history of the species.

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“…This has been shown in other cases as well (see e.g. Parmelia barrenoae, ; Physconia thorstenii, Divakar et al (2007); Caloplaca citrina group Vondrák et al (2009); Melanelixia californica, ; Parmelia mayi, Molina et al (2011a); Cladia aggregata group, Parnmen et al (2012); Parmotrema perforatum group, Widhelm et al in press) and demonstrates the importance of careful re-analysis of morphological and chemical characters in order to phenotypically circumscribe species. Further, the species-level lineages uncovered in this widely distributed isidiate taxon showed biogeographic structure in what was previously believed to be a pantropical species.…”

Section: Resultsmentioning

confidence: 54%

“…Further, the species-level lineages uncovered in this widely distributed isidiate taxon showed biogeographic structure in what was previously believed to be a pantropical species. Although geographical structure of species detection using molecular data has recently been shown to be a common phenomenon in lichenized fungi (Argüello et al 2007;Divakar et al 2010a;Otalara et al 2010;Amo de Paz et al 2012;Parnmen et al 2012;Moncada et al 2014;Leaviit et al 2015b;Alors et al 2016); caution must be taken to generalizing for all isidate lichen taxa (Leavitt et al 2013a;Roca-Valiente et al 2013;Divakar et al 2016). Etymology.…”

Section: Resultsmentioning

confidence: 99%

“…Molecular sequence data have led to the circumscription of previously overlooked species-level lineages and a number of taxonomic re-evaluations of widely distributed species in lichenized fungi. Diverse examples of widely distributed nominal taxa masking multiple, species-level diversity include: Cladia aggregata (Parnmen et al 2012), Melanelixia glabra (Divakar et al 2010a), Melanelixia fuliginosa/M. glabratula , Melanohalea elegantula, M. exasperata (Leavitt et al 2013a), Montanelia tominii (Leavitt et al 2015b), Parmelia saxatilis (Molina et al 2011a), P. sulcata , Molina et al 2011b, Parmelina quercina (Argüello et al 2007), P. tiliacea (Nuñez-Zapata et al 2011), Protoparmelia badia , Physconia distorta , Rhizoplaca melanophthalma (Leavitt et al 2013b), and Sphaerophorus globosus (Högnabba and Wedin 2003).…”

Section: Introductionmentioning

confidence: 99%

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Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species

Kirika¹,

Divakar²,

Crespo³

et al. 2016

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Citation: Kirika PM, Divakar PK, Crespo A, Mugambi G, Orock EA, Leavitt SD, Gatheri GW, Lumbsch HT (2016) Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species. MycoKeys 14: 1-16. doi: 10.3897/mycokeys.14.8971 Abstract A number of lichen-forming fungal species are widely distributed. Here, we investigate biogeographic patterns in a widely distributed isidiate taxon -Parmelinella wallichiana -using molecular sequence data. Our results revealed that Parmelinella wallichina, as currently circumscribed, is not monophyletic but falls into four clades, two of them represented by a sample only. A third clade, occurring in Africa and southern India is described as a new species, Parmelinella schimperiana Kirika & Divakar, sp. nov. Our study adds a further example of previously overlooked, geographically distinct, lineages that were discovered using molecular data.

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Using Phylogenetic and Coalescent Methods to Understand the Species Diversity in the Cladia aggregata Complex (Ascomycota, Lecanorales)

Cited by 58 publications

References 107 publications

The phenotypic features used for distinguishing species within theCladonia furcatacomplex are highly homoplasious

The phenotypic features used for distinguishing species within theCladonia furcatacomplex are highly homoplasious

Evolutionary history and species delimitations: a case study of the hazel dormouse, Muscardinus avellanarius

Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species

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