DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?

Forno, Manuela Dal; Lawrey, James D.; Moncada, Bibiana; Bungartz, Frank; Grube, Martín; Schuettpelz, Eric; Lücking, Robert

doi:10.3390/d14040284

Cited by 8 publications

(14 citation statements)

References 134 publications

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“…PhyloKey could therefore be a useful tool in 'non-molecular museomics', the quantitative assessment of phenotype characters and their integration with molecular data, by scoring a large number of herbarium samples and evaluating their placement on a reference tree. While DNA barcoding of older herbarium samples is partially feasible and has been shown to work in Cora (Dal Forno et al 2022), it depends on the condition of the underlying sample and is often unsuccessful, so PhyloKey could be a non-molecular complement to this approach.…”

Section: Charactermentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…We illustrate this approach using the basidiolichen genus Cora, which was recently shown to contain hundreds of species (Lücking et al 2014(Lücking et al , 2017Dal Forno et al 2022). Currently, around 265 species are distinguished using a combination of molecular and morphological data (Dal Forno et al 2022). A total of 105 species has been formally described (Lücking et al 2013(Lücking et al , 2015a(Lücking et al , 2017(Lücking et al , 2020cVargas et al 2014;Ariyawansa et al 2015;Moncada et al 2019) and 87 of these have molecular and comprehensive phenotype data available.…”

Section: Introductionmentioning

confidence: 99%

“…2014, 2017; Dal Forno et al . 2022). Currently, around 265 species are distinguished using a combination of molecular and morphological data (Dal Forno et al .…”

Section: Introductionmentioning

confidence: 99%

“…Characters used to score Cora species and samples. For visual character definitions, see Fig.1, and for additional details on character definitions, seeDal Forno et al (2022).…”

mentioning

confidence: 99%

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PhyloKey: a novel method to rapidly and reliably identify species in complex, species-rich genera, and an opportunity for ‘non-molecular museomics’

Lücking,

Moncada,

Dal Forno

2023

The Lichenologist

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We present a novel identification tool called PhyloKey, based on the method of morphology-based, phylogenetic binning developed within the software package RAxML. This method takes a reference data set of species for which both molecular and morphological data are available, computes a molecular reference tree, maps the morphological characters on the tree, and computes weights based on their level of consistency versus homoplasy using maximum likelihood (ML) and maximum parsimony (MP). Additional units for which only morphological data are known are then binned onto the reference tree, calculating bootstrap support values for alternative placements. This approach is modified here to work as an identification tool which uses the same character coding approach as interactive keys. However, rather than identifying individual samples through a progressive filtering process when entering or selecting characters, query samples are binned in batch mode to all possible alternative species in the tree, with each placement receiving a bootstrap support adding to 100% for all alternative placements. In addition to the fact that, after scoring a character matrix, a large number of specimens can be identified at once in short time, all possible alternative identifications are immediately apparent and can be evaluated based on their bootstrap support values. We illustrate this approach using the basidiolichen genus Cora, which was recently shown to contain hundreds of species. We also demonstrate how the PhyloKey approach can aid the restudying of herbarium samples, adding further value to these collections and contributing with large quantitative data matrices to ‘non-molecular museomics’. Our analysis showed that PhyloKey identifies species correctly with as low as 50% of the characters sampled, depending on the nature of the reference tree and the character weighting scheme. Overall, a molecular reference tree worked best, but a randomized reference tree gave more consistent results, whereas a morphological reference tree performed less well. Surprisingly, even character weighting gave the best results, followed by parsimony weighting and then maximum likelihood weighting.

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Section: Charactermentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…2014, 2017; Dal Forno et al . 2022). Currently, around 265 species are distinguished using a combination of molecular and morphological data (Dal Forno et al .…”

Section: Introductionmentioning

confidence: 99%

“…Characters used to score Cora species and samples. For visual character definitions, see Fig.1, and for additional details on character definitions, seeDal Forno et al (2022).…”

mentioning

confidence: 99%

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PhyloKey: a novel method to rapidly and reliably identify species in complex, species-rich genera, and an opportunity for ‘non-molecular museomics’

Lücking,

Moncada,

Dal Forno

2023

The Lichenologist

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Chemical Constituents Isolated from the Lichen Biome of Selected Species Native to North America

Rakotondraibe,

Spjut,

Addo

2024

Progress in the Chemistry of Organic Natural Products

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Towards a dynamic checklist of lichen-forming, lichenicolous and allied fungi of Ecuador – using the Consortium of Lichen Herbaria to manage fungal biodiversity in a megadiverse country

Yánez-Ayabaca,

Benítez,

Molina

et al. 2023

The Lichenologist

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A checklist of Lichen-forming, Lichenicolous and Allied Fungi of Ecuador is presented with a total of 2599 species, of which 39 are reported for the first time from the country. The names of three species, Hypotrachyna montufariensis, H. subpartita and Sticta hypoglabra, previously not validly published, are validated. Pertusaria oahuensis, originally introduced by Magnusson as ‘ad interim’, is validated as Lepra oahuensis. The form Leucodermia leucomelos f. albociliata is validated. Two new combinations, Fissurina tectigera and F. timida, are made, and Physcia mobergii is introduced as a replacement name for the illegitimate P. lobulata Moberg non (Flörke) Arnold. In an initial step, the checklist was compiled by reviewing literature records of Ecuadorian lichen biota spanning from the late 19th century to the present day. Subsequently, records were added based on vouchers from 56 collections participating in the Consortium of Lichen Herbaria, a Symbiota-based biodiversity platform with particular focus on, but not exclusive to, North and South America. Symbiota provides sophisticated tools to manage biodiversity data, such as occurrence records, a taxonomic thesaurus, and checklists. The thesaurus keeps track of frequently changing names, distinguishing taxa currently accepted from ones considered synonyms. The software also provides tools to create and manage checklists, with an emphasis on selecting vouchers based on occurrence records that can be verified for identification accuracy. Advantages and limitations of creating checklists in Symbiota versus traditional ways of compiling these lists are discussed. Traditional checklists are well suited to document current knowledge as a ‘snapshot in time’. They are important baselines, frequently used by ecologists and conservation scientists as an established naming convention for citing species reported from a country. Compiling these lists, however, requires an immense effort, only to inadequately address the dynamic nature of scientific discovery. Traditional checklists are thus quickly out of date, particularly in groups with rapidly changing taxonomy, such as lichenized fungi. Especially in megadiverse countries, where new species and new occurrences continue to be discovered, traditional checklists are not easily updated; these lists necessarily fall short of efficiently managing immense data sets, and they rely primarily on secondary evidence (i.e. literature records rather than specimens). Ideally, best practices make use of dynamic database platforms such as Symbiota to assess occurrence records based both on literature citations and voucher specimens. Using modern data management tools comes with a learning curve. Systems like Symbiota are not necessarily intuitive and their functionality can still be improved, especially when handling literature records. However, online biodiversity data platforms have much potential in more efficiently managing and assessing large biodiversity data sets, particularly when investigating the lichen biota of megadiverse countries such as Ecuador.

show abstract

DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?

Cited by 8 publications

References 134 publications

PhyloKey: a novel method to rapidly and reliably identify species in complex, species-rich genera, and an opportunity for ‘non-molecular museomics’

PhyloKey: a novel method to rapidly and reliably identify species in complex, species-rich genera, and an opportunity for ‘non-molecular museomics’

Chemical Constituents Isolated from the Lichen Biome of Selected Species Native to North America

Towards a dynamic checklist of lichen-forming, lichenicolous and allied fungi of Ecuador – using the Consortium of Lichen Herbaria to manage fungal biodiversity in a megadiverse country

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