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Abstract
Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and Hypoxylon, however. The URL http://tinyurl.com/spouge-barcode contains computer programs and other supplementary material relevant to this article.
Highlights
Reliable species identification is fundamental to assessing biodiversity, geographical variation, and environmental changes, as well as to discovering novel drugs and many other experimental enterprises
(1) Multiple sequence alignment of Internal Transcribed Spacer of nrDNA (ITS) sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly with at least some other non-protein barcode markers
By comparing the probability of correct identification (PCI) derived from local sequence alignment, to the PCI derived from alignment methods more appropriate to species identification, we explore biases that inappropriate alignment methods introduce into conclusions about barcode efficacy
Summary
Reliable species identification is fundamental to assessing biodiversity, geographical variation, and environmental changes, as well as to discovering novel drugs and many other experimental enterprises. Species identification in fungi is challenging, because of their ephemeral nature. Fungal diversity in the tropics is difficult to assess, because both taxonomic specialists and a complete understanding of the reliability of many taxonomic characters are lacking [1]. Based on our extended studies of fungi in Thailand, we assess the geographical distribution of the Xylariaceae, a family of the Ascomycota. The Ascomycota are less ephemeral than the fleshy fungi of the Basidiomycota, so the estimates of fungal diversity based on them are more robust than estimates based on Basidiomycota. The delimitation of Xylariaceae from other related pyrenomycete families has always been problematic [2,3], so we improved protocols for species identification within them [3,4,5,6,7]
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