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1 CBS Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The
Netherlands
2 Department of Microbiology, Faculty of Science and Informatics, University
of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
3 Department of Plant Pathology, Pennsylvania State University, University
Park 16802, U.S.A.
*
Correspondence: Robert A. Samson,
r.samson{at}cbs.knaw.nl
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INTRODUCTION |
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 TOP INTRODUCTION RECOMMENDATIONS |
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The following issues are described below in more detail:
1. Which and how many genes are required to delimit a species?
During the discussion, several points were dealt with. It was suggested
that genealogical concordance principles should be tested before we can answer
the question of how many genes are needed to define a species. It was agreed
that ITS sequences should be determined for later quick identification
purposes, although sequence data are not required by the International Code of
Botanical Nomenclature. For species delimitation, the polyphasic approach was
suggested as the "gold standard" using a combination of multilocus
sequence data, morphological, physiological characteristics and ecological
data. However, no one character could be used as a "gold standard"
to test the null hypothesis that this is not a new species, only applying the
whole set of characters will enable us to define new species. For species
descriptions it is recommended to examine several (2-3) gene sequences (e.g.
ITS, calmodulin, β-tubulin, actin) and submit them to recognised sequence
databases. If the description of the new species meets the current conditions
of the Botanical Code, it is not possible to reject a species. However, such
an action can be recommended in the review of manuscripts describing new
Aspergillus species. Regarding extrolites, it was suggested that a
set of 4-8 compounds to be used, rather than a single molecule - no
recommendations for which molecule. Additional points: it would be good to
have a database (DNA and other types of characters) for quick identification;
characters that are used for identification versus characters that are used to
delimit a species should be separated.
Summary: A polyphasic approach is the gold standard, but it is difficult to define a standard set of criteria that must be met. Morphological characteristics are sometimes variable and need to be combined with other characters. Some suggestions for other characters included DNA sequences, physiological and ecological data and extrolite analyses. Regarding sequence data, ITS has been suggested because it has been used widely, but ITS sequences frequently show little or no variation between otherwise easily recognised closely related species. Solid phylogenetic species recognition generally requires multiple, more variable loci such as β-tubulin, calmodulin, actin, and other intron-rich protein coding genes. Difficulties regarding sequence data include the fact that not everyone has access to PCR and sequencing facilities, it is still unknown if other genes are more informative, and sequence data are not required by the Botanical Code. Consequently the absence of sequence data is presently not ground for rejection of new species.
2. What do we do about dual nomenclature?
It was suggested to use the same species name for both the anamorph and
teleomorph, although it is not invalid to use another name according to the
Botanical Code. A single culture should have only one name, but again it is
not invalid to use a second name. Several participants suggested using
Aspergillus as the primary name and the teleomorph as a secondary
name, but experts of the International Botanical Code of Nomenclature
disagreed as the second name will be invalid. Another suggestion was to
epitypify all new species to prepare for a single name, although again, it is
not in agreement with the Botanical Code. Regarding clinical researchers who
depend on one of the names, it was suggested to use the name
"group" (or complex) if identification is based on morphology,
which cannot distinguish between closely related species. Most, although not
all participants, agreed to give preference to the teleomorph name.
Researchers working on Aspergillus genetics mentioned that in a
specific field, a name has a certain meaning, and preferred the name
Aspergillus for phylogeny and genetics. Another suggestion was to
give the name as follows: teleomorph [anamorph genus] if both exist, but it
was rejected by most participants because names should not become too long by
combining anamorph and teleomorph names. In the final vote, it was accepted by
most participants to use dual names where necessary, single name in normal
use, depending on the state that is seen, and treat it as a recommendation.
Regarding Latin description of new species, it was accepted to have a short
Latin diagnosis, followed by a more detailed English description. The
Botanical Code accepts a valid description or a diagnosis in Latin. The
majority of the workshop saw the need for a separate fungal nomenclatural code
such as the code which the bacteriologists use.
Summary: Dual nomenclature is not an ideal system, but there are several difficulties with changing this. The majority voted to keep two names, but there were dissenting opinions. According to the Botanical Code, two names are legal and changing the code is difficult. However, different research communities sometimes use different names for a single species, causing confusion. The different names signal different morphological and physiological characteristics that people are looking for. Using a terminology such as complex or group might be helpful, but not precise enough for some applications. Names should not become too long by combining anamorph and teleomorph names. Single names would simplify things now that DNA features are available and identification does not necessarily depend only on morphology. However, it is difficult to have users switch to different names, and there is no consensus on which (teleomorph or anamorph) name to use.
3. What are the standards for describing and storing type cultures?
It was proposed that ex type cultures of new species be deposited in 2-3
different culture collections, preferably located in different parts of the
world (Asia, Europe, US) to deal with import/export issues. If there is no
available type culture, the Aspergillus community has the option of
declaring it invalid. It was also suggested that at least a single locus DNA
sequence must be provided for publication. There should be a limit to the time
(e.g. six months) between publishing and depositing in collections. These
suggestions are not accommodated by the Botanical Code, but were accepted as
recommendations for good practice. New taxa should always be compared with ex
type cultures of related species.
Summary: There should be 2-3 different open sources of a type culture of a newly proposed species in order to be scientifically valid. These should be deposited in a timely manner. New descriptions that are not deposited will be considered invalid by the Aspergillus community.
4. What sorts of databases do we need?
It was agreed that different specialised databases are needed for key
identification purposes, with good links between databases. However, each
database requires funding and curation. The use of a Wikipedia approach for
the databases was questioned because of a lack of quality control, although it
is a strong possibility as a clearinghouse for general information regarding
protocols and media. It was suggested to use the Aspergillus website
as a clearing house by linking to other sites. It was accepted that links
should show the focus of each individual database, and there is a need for
links to other communities as well. The databases that are linked to the
Aspergillus website should be of high quality. Some overlap between
databases is not a real problem. Regarding a simple database for species
identification, it was suggested to include basic sequences for
identification, pictures and links to media protocols. Although such a
database already exists, it is in a more complicated form. Finally, it was
agreed that the Wikipedia approach, not suitable for databases, was a good
idea for media and protocols.
Summary: Databases are critical for identification and biology. In general, focused databases that are linked to other related databases were encouraged. The links should give an idea about the content of the database. A simple database for identification was proposed which would include basic sequences, photos, links to media/growth protocols, or the possibility to make a phylogenetic tree to get around the nomenclature problem.
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RECOMMENDATIONS |
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TOPINTRODUCTIONRECOMMENDATIONS |
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This protocol will be endorsed by the IUMS International Commission of Penicillium and Aspergillus.
This article has been cited by other articles:
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  J.I. Pitt and R.A. Samson Nomenclatural considerations in naming species of Aspergillus and its teleomorphs Stud Mycol, January 1, 2007; 59(1): 67 - 70. [Abstract] [Full Text] [PDF]
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