DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?
Abstract
:1. Introduction
2. Materials and Methods
2.1. Newly Generated Sequence Data from Fresh and Historical Collections
2.1.1. Sampling
2.1.2. DNA Extractions
2.1.3. PCR, ITS Sanger Sequencing and Assembly
2.1.4. PCR, ITS Illumina Sequencing and Bioinformatic Analyses
2.1.5. Microfluidics PCR, Multi-Marker Illumina Sequencing and Bioinformatic Analyses
2.2. Phylogenetic Analyses
2.2.1. ITS-Based Phylogeny
2.2.2. Six-Marker Phylogeny
2.3. Quantitative Species Delimitation
2.3.1. Single-Locus Tree-Based Methods
2.3.2. Distance-Based Methods and Barcoding Gap Analyses
2.3.3. ITS-Based BLAST Performance
2.4. Phenotypic Assessment
3. Results
3.1. Comparison of Sequence Performance between Fresh and Historical Collections
- Run 01 (Plates 1 and 2): 331.6 MB (I1 or Indexes), 3.35 GB (R1 or forward reads) and 3.94 GB (R2 or reverse reads) (samples: NSF-001–106 and US-001–086); 8417853 total sequences;
- Run 02 (Plates 3 and 4): 289 MB (I1 or Indexes), 3.06 GB (R1 or forward reads) and 3.55 GB (R2 or reverse reads) (samples: US-087–278); 11250308 total sequences.
3.2. ITS-Based Phylogeny
3.3. Comparison between ITS and Astral Six-Marker Tree
3.4. Quantitative Species Delimitation Methods
3.5. ITS-Based BLAST Performance
3.6. Phenotype Assessment
3.7. Intragenomic ITS Variation
4. Discussion
4.1. Use of Archival Specimens
4.2. Assessment of ITS as a Barcoding Marker and Intragenomic Variation within ITS
4.3. Accurate Assessment of Phylogenetic Diversity in Cora and Corella
4.4. Level of Cryptic Speciation and Potential Taxonomic Inflation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Character\State | 0 | 1 | 2 | 3 | 4 | 5 | ? | |
---|---|---|---|---|---|---|---|---|
1 | Substrate a | — | rock | soil | ground | epiphytic | — | — |
2 | Size | — | small (lobes > 1 cm) | 10édium (lobes 1–3 cm) | large (lobes > 3cm) | — | — | — |
3 | Sutures b | absent | short | long | — | — | — | — |
4 | Color c | — | grey | (grey-) brown | olive (-green) | green | aeruginous | — |
5 | Surface | even | granular- rugose | pitted | broadly undulate | narrowly undulate | — | — |
6 | Trichomes d | absent | present (felty) | present (setose) | present (strigose) | — | — | — |
7 | Margin | glabrous | pilose | granular | granular-pilose | — | — | — |
8 | Soredia | absent | present | — | — | — | — | — |
9 | Cortex | absent | viaduct- shaped | collapsed | compacted | prosoplecten- chymatous | paraplecten- chymatous | — |
10 | Papillae | absent | present | — | — | — | — | — |
11 | Hymenophore | — | rounded- confluent | concentric | resupinate- cyphelloid | cyphelloid | — | not observed |
12 | Bleeding pigment | absent | present | — | — | — | — | — |
13 | Central America | absent | present | — | — | — | — | — |
14 | Caribbean | absent | present | — | — | — | — | — |
15 | Galapagos | absent | present | — | — | — | — | — |
16 | Northern Andes | absent | present | — | — | — | — | — |
17 | Central Andes | absent | present | — | — | — | — | — |
18 | Southern Andes | absent | present | — | — | — | — | — |
19 | Eastern Brazil | absent | present | — | — | — | — | — |
20 | Asia | absent | present | — | — | — | — | — |
Proposed Term | Etymology | Phenotype Distance | Phylogenetic Relationship | Distribution |
---|---|---|---|---|
Eu-(phylo-)cryptic (“cryptic”) | Greek: eús, eû = good | zero (same phenotype) | closely related or sister species | sympatric |
Kapo-(phylo-)cryptic (“near-cryptic”) | Greek: kápos = somewhat | very low (similar phenotype) | closely related or sister species | sympatric |
Allo-(phylo-)cryptic (“semi-cryptic”) | Greek: állos = other | zero or very low (same or similar phenotype) | closely related or sister species | allopatric |
Pseudo-(phylo-)cryptic (“homoplasic”) | Greek: pseudḗs = false | zero or very low (same or similar phenotype) | unrelated or distantly related | sympatric or allopatric |
Dataset | Method | Settings | Estimate | Other Metrics: | |||
---|---|---|---|---|---|---|---|
Cora 1325 Terminals | bPTP | min | 791 (mean) | 708 (min) | 889 (max) | ||
Cora 1325 Terminals | GMYC | single | 189 | 145–237 (confidence interval) | 36.02878 (likelihood ratio) | 1.50E-08 (LR Test) | |
Cora 1325 Terminals | ad hoc | 265 | |||||
Extrapolated | Barcode gap/threshold distance | ||||||
Cora 716 Terminals | ad hoc | 175 | 265 | N/A | |||
Cora 716 Terminals | DNADIST | 171 | 259 | 0.0060 | |||
Prior maximal distance | Barcode gap/threshold distance | ||||||
Cora 716 Terminals | ABGD | Partition 2 | 231 | 350 | 0.001668 | 0.0040 | |
Cora 716 Terminals | ABGD | Partition 3 | 231 | 350 | 0.002783 | 0.0040 | |
Cora 716 Terminals | ABGD | Partition 4 | 147 | 223 | 0.004642 | 0.0110 | |
ASAP score | p-value | Barcode gap/threshold distance | |||||
Cora 716 Terminals | ASAP | K80-2 | 161 | 244 | 11.0 | 0.1620 | 0.0086 |
Cora 716 Terminals | ASAP | K80-2 | 128 | 194 | 13.5 | 0.0025 | 0.0130 |
Cora 716 Terminals | ASAP | K80-2 | 205 | 310 | 17.5 | 0.2020 | 0.0046 |
Cora 716 Terminals | ASAP | JC69 | 161 | 244 | 9.5 | 0.1300 | 0.0086 |
Cora 716 Terminals | ASAP | JC69 | 143 | 217 | 18.5 | 0.0796 | 0.0102 |
Cora 716 Terminals | ASAP | JC69 | 205 | 310 | 18.5 | 0.246 | 0.0046 |
Cora 716 Terminals | ASAP | Simple | 161 | 244 | 8.5 | 0.1400 | 0.0086 |
Cora 716 Terminals | ASAP | Simple | 205 | 310 | 17.0 | 0.2260 | 0.0046 |
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Dal Forno, M.; Lawrey, J.D.; Moncada, B.; Bungartz, F.; Grube, M.; Schuettpelz, E.; Lücking, R. DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story? Diversity 2022, 14, 284. https://doi.org/10.3390/d14040284
Dal Forno M, Lawrey JD, Moncada B, Bungartz F, Grube M, Schuettpelz E, Lücking R. DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story? Diversity. 2022; 14(4):284. https://doi.org/10.3390/d14040284
Chicago/Turabian StyleDal Forno, Manuela, James D. Lawrey, Bibiana Moncada, Frank Bungartz, Martin Grube, Eric Schuettpelz, and Robert Lücking. 2022. "DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?" Diversity 14, no. 4: 284. https://doi.org/10.3390/d14040284