MycoKeys , or why we need a new journal in mycology ?

A personal synopsis of the decisions made at the Nomenclature Section meeting of the International Botanical Congress in Melbourne in July 2011 is provided, with an emphasis on those which will affect the working practices of, or will otherwise be of interest to, mycologists. The topics covered include the re-naming of the Code, the acceptance of English as an alternative to Latin for validating diagnoses, conditions for permitting electronic publication of names, mandatory deposit of key nomenclatural information in a recognized repository for the valid publication of fungal names, the discontinuance of dual nomenclature for pleomorphic fungi, clarification of the typification of sanctioned names, and acceptability of names originally published under the zoological code. Collectively, these changes are the most fundamental to have been enacted at a single Congress since the 1950s, and herald the dawn of a new era in the practice of fungal nomenclature.

markup of published texts permit unprecedented increase of visibility, citations and re-use of the biodiversity information (Penev et al. 2010b).
There are also other exciting and novel advances in biodiversity science that change the field with a speed never seen before. Electronic media helps not only in fast and efficient publication and communication between researchers but becomes themselves tools and platforms for indexing, aggregating and retrieval of information, providing unique opportunities to accelerate biodiversity research and understanding. The research process itself is accelerated by methods to increase the speed and efficiency of sampling and discovery of new taxa, as well as with their identification through an array of new techniques such as DNA sequencing.
MycoKeys is launched to respond to the challenges described above through a transformative publishing model with innovative approaches to publication and dissemination. The journal will publish papers across all disciplines dealing with taxonomy, systematics, evolution, phylogeny, biogeography, taxon-based ecology, and conservation of the monophyletic kingdom Fungi. MycoKeys will publish taxonomic or ecological data on any taxon of any geological age from any part of the world with no limit to manuscript size. Special attention will be paid to works offering integrative and inter-disciplinary approaches that promote innovative ways of presenting the research information.
Mycokeys will consider publishing works on the following topics: • Descriptions of new taxa, if they are accompanied with proper diagnoses and/or keys to distinguish them from close relatives or similar taxa, and if DNA sequence data are deposited in Genbank prior to publication. All new taxa need to be registered at Mycobank and Mycobank numbers indicated in the manuscript. New taxa should ideally be described in connection with a phylogenetic analysis or evidence that the barcode gene (ITS) is unique for the new taxon.  Pensoft Taxon Profile (PTP) for the genus Aspergillus (Eurotiomycetes) obtained dynamically from external web resources. The profile is generated by clicking on any taxon name published in a MycoKeys paper, in this case in the paper by Raja et al. (2011). The links on the left bar, if in bold font, lead to various biodiversity platforms where information on this taxon is available; links in normal font indicate that there is no information on the taxon in the particular platform. The PTP tool is available also as standalone application at http://www.ptp.pensoft.eu pected discoveries. Regular contributions may eventually be published in special issues devoted to a region/country.
In addition MycoKeys will respond to the present-day cultural and technological shift in scholarly publishing and communication through: • Mandatory open access to all journal articles, providing an unlimited and barrier-free distribution of published content • Pre-publication recording of all new names in Mycobank as well as rapid postpublication registration in Index Fungorum and LIAS • Inclusion of the Mycobank registration numbers in the original descriptions (protologues) • All new taxa and other taxon descriptions and associated images are provided to the Encylopedia of Life on the day of publication • All taxon treatments are provided to the Plazi treatment repository • All new taxa are exported to the Wiki environment (Species-Id) on the day of publication; the link to the Wiki version of a treatment is included in the protologue and citation of the original description is always explicitly shown in the Wiki version • An established infrastructure for data publishing in cooperation with the GBIF, the Consortium for Barcode of Life, and Dryad Data Repository • Data matrices and primary data files for interactive keys (e.g., Lucid, Intkey, MX, and others) can be published as supplementary files to facilitate use and reuse by future workers • Immediate alert service on new publications through email, RSS, Twitter, Facebook, Mendeley, and other networks • Immediate distribution and dissemination of your publication to scientific databases, indices and search engines (ISI Web of Knowledge, Google Scholar, CABI Abstracts, DOAJ, and others) • Archiving of your publication, electronically and in print, in trusted (e-) archives and libraries, in the first case PubMedCentral • Continuous development and implementation of cutting-edge publishing technologies: XML-based editorial work flow and mark up process, data publication and various semantic enhancements to published texts to ensure a pleasant and efficient reading process as well as a wide dissemination of separate parts of a logically 'atomised' article's content • Automated cross-linking of any taxon mentioned in the MycoKeys papers through the Pensoft Taxon Profile ( Fig. 1) with major indexing and aggregation platforms such as the GBIF, EOL, MycoBank, Index Fungorum, the International Plant Name Index (IPNI), ZooBank, the National Center for Biodiversity Information (NCBI), Genbank, Barcode of Life, the Biodiversity Heritage Library (BHL), PubMed, PubMedCentral, and others • Publication of identical content in four different formats to serve different target user groups: (1) full-colour, high-resolution print version; (2) PDF for reference to the printed version and easy archiving; (3) HTML for easy reading, browsing and applying semantic enhancements to the text; and (4) XML to provide a machine-readable file for archiving and data mining • Quick turnaround time; papers published within one to three weeks time after acceptance • No restrictions and no charges for colour either in the online or in the printed version On behalf of its authors, MycoKeys will place special effort on increasing public awareness of published scientific discoveries through an established system of press releases to science news distributors, mass media, blogs, social networks and others.
A new journal can only succeed when it is appreciated by an enthusiastic community of authors, reviewers, editors and readers. We are confident that the new opportunities offered by MycoKeys will be embraced and warmly welcomed by all mycologosts to the great benefit of scientists, research funders and society in general.
Semantic tagging of and semantic enhancements to systematics papers. ZooKeys working example.

Introduction
The internationally agreed rules that regulate how fungi are named are examined and revised at each International Botanical Congress, the last published being those re-sulting from the Vienna Congress in 2005(McNeill et al. 2006). These Congresses are now held every six years, and the subsequent one in Melbourne in July 2011 was faced with a staggering 338 proposals made to modify the Vienna edition of the International Code of Botanical Nomenclature (McNeill and Turland 2011). This was the largest number to have confronted any Congress since that held in Paris in 1954. The issues that the Melbourne Congress had to address included topics as fundamental as the language required for the valid publication of names, the acceptability of electronic publication, and the unease amongst mycologists on how decisions were made. It may seem weird to 21 st century biological science students that fungi are embraced in a Code with just "botanical" in the title. However, the actual remit was all organisms traditionally studied in departments of botany in museums and universities, regardless of their current classification in the kingdoms of Life -even all bacteria were covered until the Montreal Congress of 1959. Some rules are, nevertheless, applicable only to particular systematic groups or categories, and since the Brussels Congress of 1910 there have been special regulations which only apply to the names of fungi. Foremost amongst these have been issues related to: (1) the date at which the nomenclature of fungi was deemed to commence; (2) the status of living cultures as name-bearing types; and (3) the separate naming of morphs in pleomorphic fungi. Any proposed changes in the rules relating to particular groups or categories (e.g. fossils) are discussed by a series of permanent committees, the members of which are elected at the end of each Congress and serve to the next. In the case of the fungi, the permanent committee is now called the Nomenclature Committee for Fungi (NCF). A valuable synopsis of how the current system operates is given by McNeill and Greuter (1986), while Nicolson (1991) provides an authoritative historical account of the development of the Code.
During recent decades, and especially in the 2000s, many mycologists had become increasingly dissatisfied with various aspects of the rules concerning the naming of fungi. This was reflected in sessions and debates at various national, regional, and international meetings, culminating in three Nomenclature Sessions held as a part of the IXth International Mycological Congress (IMC9) in Edinburgh in August 2010. During those sessions, various already published proposals for change were discussed, and in addition all delegates to the Congress were invited to complete a questionnaire to canvass their views on key issues and possible ways forward; a report of those Sessions and the results of the questionnaires are provided by Norvell et al. (2010).
The decisions taken at the Melbourne Congress were so fundamental, with respect to both "botanical" nomenclature as a whole, and especially with specific topics that concerned fungi, that these need to be widely promulgated. A formal report of those decisions is provided by McNeill et al. (2011), and more detailed information of those pertaining to fungi is presented by Norvell (2011). Those reports include the new approved wordings, though they may still undergo some fine-tuning by the Editorial Committee appointed by the Congress. The Editorial Committee is to meet in London in December 2011, and it is anticipated that the finalized Melbourne Code will be printed in mid-2012. However, changes effected at an International Botanical Congress come into effect immediately they are approved by the Plenary Session of the Congress unless specifically limited by date. It is, therefore, essential that all mycologists involved in the naming of fungi are made aware of both the changes made that come into force before the Code is printed, and those that are to be anticipated from 1 January 2013.
The purpose of the present article is to alert mycologists as a whole to the fundamental changes made at the Melbourne Congress, a package which represents a paradigm shift in how fungi are now to be named, and to indicate the implications of those changes for working practices. It is not, however, to be considered authoritative, and the final version of the Melbourne Code should be consulted as soon as it becomes available.

Name of the Code changed
Mycologists, tired of appearing subservient to botanists, and for mycology to be treated as a part of botany (Hawksworth 1997, Minter 2011) made proposals for the name of the Code to be changed to reflect their independence (Hawksworth et al. 2009). This view had been supported at IMC9 , and the Melbourne Congress agreed that the new Code should be called the International Code of Nomenclature for algae, fungi, and plants. The lower case letters used for the words "algae", "fungi", and "plants" are employed to make clear these terms are being used in a colloquial sense, for instance the inclusion of cyanobacteria in algae, and chromistan fungal analogues, slime moulds, and lichens in "fungi".
The Congress further agreed that editorial changes should be made throughout the text so that it referred to "organisms" governed by the Code, and no longer used "plants" where fungi were included in the concept.
Governance of fungal nomenclature to be considered Proposals to transfer decision-making on issues concerning fungi from International Botanical to International Mycological Congresses (Hawksworth et al. 2009), and which had been strongly supported at IMC9 (Norvell et al. 2009) were not accepted. However, a Subcommittee on governance of the Code with respect to fungi was established under a Special Committee mandated with examining how the Nomenclature Section operated. That Committee (and Subcommittee) are to report to the next International Botanical Congress in 2017. In view of this move, mycologists will now have to consider whether to put on hold the question of the need for an independent Code for fungi (see below) pending that report. The matter needs to be placed on the agenda for Nomenclature Sessions to be convened during IMC10 in 2014.

English or Latin validating diagnoses permitted
The issue of whether to discontinue the requirement for validating diagnoses or descriptions in Latin has been raised at almost all International Botanical Congresses since this requirement was first introduced in 1935. The Melbourne Congress was presented with proposals from botanists to allow any language, as is the practice in zoology, and some alternative ones, including one by mycologists to require Latin or English for fungi , Demoulin 2010. There was a precedent in that the alternative of Latin or English was already allowed for fossils in the Vienna Code. The Congress not only supported the mycological proposal, but also decided that it should apply not just to fungi but to all organisms treated under the Code. Further, so enthusiastic was the meeting, that it was agreed that this provision should operate from 1 January 2012, not 1 January 2013. Consequently, mycologists no longer need to struggle with coining a few sentences of pseudo-Latin when describing new fungi. However, in consequence, I personally see value in presenting both a diagnosis (i.e. a short statement of how the fungus differs from others) and a separate description (i.e. a detailed account of all the features of the fungus) when describing a new fungus. If a diagnosis were in Latin or English, the description could then continue to be in any language of the author's choice. A diagnosis has been required for the introduction of new scientific names in zoology since 1930 (International Commission on Zoological Nomenclature 1999: Art. 13), and the practice has much to commend it.

Electronic publication permitted (but with restrictions)
The issue of the acceptability of works published only electronically as a vehicle for the effective publication of scientific names has been the subject of a series of Special Committees established by successive International Botanical Congresses since that held in Tokyo in 1993, and is also an issue currently being actively debated by zoologists (Michel et al. 2009). With the increasing proliferation of new electronic journals, and established journals also increasingly being available in both electronic and hard-copy forms, the issue was becoming increasingly urgent. A Special Committee established by the Vienna Congress in 2005, considered the matter in depth  and prepared detailed proposals for consideration by the Melbourne Congress (Special Committee on Electronic Publication 2010). The Melbourne Congress accepted many of these proposals, and the pertinent revised texts and guidelines as to best practice are given by Knapp et al. (2011). The key points agreed were that from 1 January 2012, works published in electronic form on the worldwide web in an unchangeable Portable Document Format (PDF) are to be treated as effectively published, provided that they have either an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN). However, non-final versions made available online in advance of a definitive version (e.g. accepted papers as yet unedited or proof-read) are not treated as effectively published. Where both electronic and hard-copy versions of a work are made available, the date of effective publication of both is treated as being the same. Guidance as to how copies can be differentiated is included in Knapp et al. (2011).
It is important to appreciate that the new provisions do not mean that material placed on or available through websites and lacking ISSN or ISBN numbers constitutes effective publication. Authors considering submitting to an electronic journal, should therefore first check that it has an ISSN number. It is also recommended that electroniconly works containing new taxa are drawn to the attention of appropriate indexing centres, and mycologists should endeavour to do that until the requirement for the prior deposit of key nomenclatural information becomes mandatory on 1 January 2013.

Deposit of key nomenclatural information made mandatory for fungi
The concept of some form of obligatory registration of newly proposed scientific names for fungi goes back to the 1950s (Ainsworth and Ciferri 1955). Following the establishment of a Special Committee on Registration at the Berlin Congress in 1987, and a series of subsequent workshops, a provision to make this a requirement for all groups of organisms covered by the Code was accepted by the Tokyo Congress in 1993 -but then rejected at the St Louis Congress in 1999 despite successful trials (Greuter 2009). The development of the worldwide web, however, has made it possible to devise much-improved systems from those that were possible in the 1980s and early 1990s. Following informal discussions during the 2002 International Mycological Congress (IMC7) in Oslo, in 2004 the CBS-KNAW Fungal Biodiversity Centre in Utrecht established an online system for the deposit of key information on newly proposed names of fungi -MycoBank. This voluntary system proved popular with mycologists, and also with mycological journals, as a way of rapidly expediting information on nomenclatural novelties. Since 2007 Mycobank has operated under the auspices of the International Mycological Association (IMA) which now has long-term responsibility fot its continuance.
Formal proposals to make the deposit of key nomenclatural information in a recognized online repository a mandatory requirement for valid publication of new scientific names in fungi at all taxonomic ranks (including new combinations and replacement names) were then developed (Hawksworth et al. 2010). Those proposals were overwhelming endorsed by the International Mycological Congress in Edinburgh later in the same year . The Melbourne Congress approved the formal proposals with some "friendly" amendments, mainly based on suggestions for avoiding unnecessary inflation of names in the repositories (Morris et al. 2011). In addition a recommendation that information on choices made between competing names or honomyms, spelling or gender also be deposited (Gams 2010) was approved.
The new requirement comes into force on 1 January 2013, after which date scientific names of fungi which are published without a unique identifier by a recognized repository will not be considered as validly published; i.e. they will not exist for nomenclatural purposes and need not be considered when determining the correct name for a taxon under the Code. While the requirement is only for information required by the rules of the Code, such as the diagnosis and information as to the nomenclatural type or a basionym, as appropriate, there is no objection to databases also including additional information and the prospects are enormously exciting (Lumbsch et al. 2011).
The responsibility of appointing online depositaries was given to the Nomenclature Committee for Fungi, which will need to advise mycologists as to which are approved. No single repository was specified in the proposals, thus leaving the possibilities open in the rapidly-moving electronic age. At present it is deposit in MycoBank which is now required by almost all mycological journals.
Mycologists should note that the prudent way to proceed is to make the online deposit of the required data, and obtain the numerical identifier, only after their work has been accepted for publication. This is to ensure that the information included agrees in every detail that which will appear in the publication which establishes the name. This will not affect the priority of the name as the effective date of publication will be that of the electronic or hard-copy publication and not the date information is deposited. The lodging of a name and associated details in a repository such as MycoBank will not in itself establish a name.
This exciting move means that, for the first time ever, mycologists will have immediate and free online access to the key nomenclatural and diagnostic information on newly proposed fungal names. It also means that it is the authors of new names which will now have the responsibility of ensuring that names they propose are incorporated into international indexing repositories.

Dual nomenclature of pleomorphic fungi discontinued
The concept of permitting separate names for anamorphs of fungi with a pleomorphic life-cycle has been an issue of debate since the phenomenon was recognized in the mid-19 th century. This was even before the first international rules for "botanical" nomenclature were issued in 1867 (Weresub andPirozynski 1979, Taylor 2011). Special provisions are to be found in the earliest Codes, which were then modified several times, and often substantially (Weresub and Pirozynski 1979). The rules became increasingly complex, and by the mid-1970s they were being interpreted in different ways by different mycologists -even ones working on the same genus. Following intensive discussions under the auspices of the International Mycological Association (IMA), drastic changes were made at the Sydney Congress in 1981 to clarify and simplify the procedures -and the now familiar terms anamorph, teleomorph, and holomorph entered general use. An unfortunate effect of the simplification was that many name changes had to be made as a consequence, including ones of some well-known and economically important species; at that date, the conservation of species names was not allowed under the Code.
Unforeseen in the 1970s, when the 1981 provisions were crafted, was the impact of molecular systematics. A decade later, it was starting to become obvious that fungi with no known sexual stage could confidently be placed in genera which were typified by species in which the sexual stage was known (Reynolds and Taylor 1991), and the issue of the abandonment of the dual nomenclatural system was posited (Reynolds and Taylor 1992). This possibility was debated at subsequent International Mycological Congresses, and on other occasions (e.g. Seifert et al. 2000, Seifert 2003, and the need for change was increasingly recognized. Cannon and Kirk (2000) regarded deletion as inevitable in the long-term, and further calls for deleting the provision followed (e.g. Rossman and Samuels 2005). At the International Botanical Congress in Vienna in 2005, some minor modifications were made which allowed anamorph-typified names to be epitypified by material showing the sexual stage when it was discovered, and for that name or epithet to continue to be used where there was no previously sexuallytypified name available.
More importantly, the Vienna Congress established a Special Committee to investigate the issue further, but unfortunately it was unable to reach a consensus . Matters were becoming increasingly desperate as mycologists using molecular phylogenetic approaches started to ignore the provisions, or interpret them in different ways (Rossman and Seifert 2010). The view that emerged from the International Mycological Congress in Edinburgh the same year, was that mycologists, as a whole, favoured gradual progress towards a single nomenclature ). In the meantime, various proposals were made to improve the situation, but the situation was becoming so complex that few mycologists were likely to take the time to understand them fully and implement them correctly. In order to progress the matter, an international symposium was held in Amsterdam in April 2011, under the auspices of the International Commission on the Taxonomy of Fungi (ICTF), to explore ways to obtain a solution. If a solution could not be reached at the Melbourne Congress, the prospect was for no substantive change to be made until after the 2017 International Botanical Congress. This situation would then have become intolerable as mycologists increasingly ignore the rules.
The Amsterdam symposium prepared a declaration of principles which, it was hoped, would be accommodated in any change made to Article 59 (Hawksworth et al. 2011). In effect these amounted to the ending of dual nomenclature, but with safeguards to minimize changes in familiar names. The "Amsterdam Declaration" prompted a critical response from some other mycologists who perceived difficulties in aspects of the declaration, and wished to continue allowing dual nomenclature (Gams et al. 2011). Both these documents were made available to delegates at the Melbourne Congress. In order to ensure some resolution of the issue, proposals for three possible options were developed by Redhead, in consultation with various mycologists, for presentation at the meeting. Following extensive discussions at the Congress, the option to discontinue the dual nomenclature system was approved, but with some safeguards to limit resultant instability (Norvell 2011, McNeill et al. 2011. After 1 January 2013, one fungus can only have one name; the system of permitting separate names to be used for anamorphs then ends. This means that all legitimate names proposed for a species, regardless of what stage they are typified by, can serve as the correct name for that species. All names now compete on an equal footing for priority regardless of the stage represented by the name-bearing type. In order not to render names that had been introduced in the past for separate morphs as illegitimate, it was agreed that these should not be treated as superfluous alternative names in the sense of the Code. It was further decided that anamorph-typified names should not be taken up to displace widely used teleomorph-typified names until the case has been considered by the General Committee established by the Congress 1 . Recognizing that there were cases in some groups of fungi where there could be many names that might merit formal retention or rejection, a new provision was introduced. It was decided that lists of names can be submitted to the General Committee and, after due scrutiny, names accepted on those lists are to be treated as conserved over competing synonyms (and listed as Appendices to the Code). Lichen-forming fungi (but not lichenicolous fungi) were always excluded from the provisions permitting dual nomenclature; the new Code will include a paragraph to make it explicit that lichen-forming fungi are excluded from the newly accepted provisions.
Mycologists need now to work to implement this major change. In cases where a later teleomorph-typified name is not widely used, it can be anticipated that mycologists will now simply adopt the earlier anamorph-typified name. If others consider a decision inappropriate, a proposal for the conservation of the teleomorph-typified name over the earlier anamorph-typified name can be made to the Nomenclature Committee for Fungi (NCF). Although no detailed arrangements were made at the Congress, it is anticipated that, where specialist working groups on particular fungal genera or families exist, as is the case for subcommissions of the International Commission on the Taxonomy of Fungi (ICTF), draft lists of names for possible approval will be prepared by them. In my personal view, there could also be some advantage in endeavouring to have one list covering all potentially affected generic names, if mechanisms to achieve that could be put in place. In the early part of 2012, the NCF is to work closely with the ICTF and other groups where they exist (e.g. within the International Union of Microbiological Societies, IUMS) to develop processes for the preparation of lists on particular groups. Draft lists will need to be made available for comment by mycologists at large (e.g. through the IMA and ICTF web sites), and they will then require revising them in the light of comments received. Lists received by the NCF would, after due consideration by that Committee, then be forwarded to the General Committee for approval.
Where mycologists wish still to refer to anamorphs separately, the new provisions do not prohibit informal usages, such as "acremonium-state" or "acremonium-like", ideally with a small initial letter and normal not italic type as suggested by Cannon and Kirk (2000). This form of typography makes clear that the designations are not scientific names governed by the Code. 1 The General Committee is elected at each International Botanical Congress, and is responsible for receiving, considering, and approving reports from the various permanent nomenclature committees, such as the Nomenclature Committee for Fungi, for the period up to the next Congress..

Typification of sanctioned names clarified
The dates on which the nomenclature of fungi was deemed to start were changed from 1801 or 1821 to 1753 by the International Botanical Congress in Sydney in 1981. This change was made because the later-starting point system had come to be interpreted in different ways, and because of difficulties in ascertaining the first usages of already proposed names after the proscribed dates (Demoulin et al. 1981). In order to minimize the resultant name changes, the concept of "sanctioning" was introduced. Sanctioning permitted the continued use of names that had been adopted in the 1801 Synopsis Methodica Fungorum of Persoon, or the 1821-32 Systema Mycologicum of Fries over names that otherwise would have to be taken up under the normal rules of priority, homonymy, etc. However, the wording of the rule in the Sydney Code was somewhat ambiguous and, although modified slightly at the Berlin Congress in 1987, it could still be interpreted as meaning either that the typification of a sanctioned name should be made only on materials cited in the sanctioning work, or that it could be based on materials cited in the original pre-sanctioning place of publication.
Proposals to address this issue were published before the Melbourne Congress (Perry 2010, Redhead et al. 2010), but there were concerns over these. In consequence, a series of informal discussions was held in Melbourne, which involved the proposers and other concerned mycologists. Those meetings led to the formulation of a series of proposals which were adopted by the Congress (McNeill et al. 2011, Norvell 2011. The net effect of the changes made is that a name that has been sanctioned can now be lectotypified (not neotypified) by material from among the elements associated with either the original protologue of the name, the sanctioning treatment, or both. A further and welcome clarification is that in cases where in the sanctioning work elements associated with the original protologue did not include a subsequently designated type selected for the sanctioned name, the sanctioning author is considered to have introduced a later homonym that is to be retained because of its sanctioned status.
No particular date was mentioned in the adopted proposals, which means that they became operative when approved by the Melbourne Congress. They are also retroactive, and so safeguard many typifications made since the 1981 Congress which were based on material cited in the original protologue, or on material of the sanctioning author where that differed. The adoption of these clarifications is most welcome as it removes the need for many typifications made since 1981 to be revisited, something that could have had unfortunate implications for the stability of many sanctioned names.

Names of fungi first described as animals are validly published
The revelation that Microsporidia, a group traditionally studied by zoologists, belonged to kingdom Fungi posed a threat to numerous names in use in the phylum. This situation arose as, while those names had been correctly published and were available for use under the provisions of the International Code of Zoological Nomenclature, many did not meet the requirements of the botanical Code. At the Vienna Congress in 2005, it was agreed that names within Microsporidia, and other organisms that had originally been published under the zoological code, were to be treated as validly published under the botanical Code. However, in accordance with the wishes of workers on these fungi, the Melbourne Congress accepted proposals made by Redhead et al. (2009) that these organisms should be excluded from governance by the botanical Code and continue to be covered by the zoological one, despite their phylogenetic position. It was further agreed that this principle should be adopted for other groups of organisms traditionally treated under other codes.

Explicitly indicate the physiological state of type cultures
A rule in the current Code allows cultures of algae and fungi to serve as name-bearing types, provided that they are "preserved in a metabolically inactive state". In practice, the physiological state of cultures designated as types is often not stated by describing authors. In order make this explicit, it is now recommended that the phrase "permanently preserved in a metabolically inactive state", or equivalent, be used when cultures are designated as types.

Names based on fossil parts loose special provisions
In recent years there have been extensive debates in the palaeobotanical community on how to revise the provisions relating to the naming of parts of fossil organisms treated under the Code -and which applied to fungi as well as plants. Competing sets of proposals were submitted to the Melbourne Congress. As in the case of ending the separate naming of anamorphs in pleomorphic fungi, the Congress decided to abandon the practice of separately naming parts of fossils. Consequently, names of fossils which prove to be parts of a single species will now compete with each other for priority, in the same way as occurs for names not based on fossils.

The Draft BioCode and MycoCode need to be revisited
Moves towards increased harmonization between the various codes of nomenclature were initiated in 1985. However, the prospect, in the long-term, of having a set of rules governing the future nomenclature of all organisms was developed in the early 1990s (Hawksworth 1995). This culminated in the publication of a Draft BioCode in 1996 which had been prepared by the IUBS 2 /IUMS International Committee on Bio-nomenclature (ICB) 3 . Little progress was made in taking the initiative further as the mechanisms and resources to develop the prerequisite lists of names to be considered available were not forthcoming. The project was subsequently revived as a scientific programme of IUBS in 2009, and an updated Draft BioCode was prepared and released for further discussion in January 2011 (Greuter et al. 2011). That draft was the subject of a session and debate at Biosystematics 2011 (which incorporated the International Congress of Systematic and Evolutionary Biology) in Berlin in February 2011. This initiative was mentioned briefly in the final session of the Nomenclature Section meetings in Melbourne, but was not considered in any depth. A suggestion that the Section establish a Special Committee to liaise with those involved in the revision of the draft was not approved.
The possibility of having an independent code for mycology was raised and received considerable vocal support at the International Mycological Congress (IMC8) in Cairns in 2006. However, the option of renaming and revising the botanical Code was the one favoured at the subsequent Congress in Edinburgh in 2010 . The issue was also raised at the Amsterdam symposium in April 2011 which was primarily convened to address the issue of dual nomenclature. At that symposium it was suggested that the BioCode model could provide a framework for the future regulation of the nomenclature of fungi (Hawksworth et al. 2011). Key to any movement in this direction, was seen as the extent to which the botanical Code would change to meet the needs of mycologists (Taylor 2011). In view of the major changes made at the Melbourne Congress, the issue of whether an independent MycoCode is really now required needs to be debated at the International Mycological Congress (IMC10) in Bangkok in 2014.

Discussion
I have participated in all International Botanical Congresses since that held in St Petersburg in 1975, and served on the Editorial Committee of the botanical Code since 1987. The progress made in adapting the rules to the needs of both user and practitioner mycologists over that period has been considerable. These have included, for example, the change in starting point, the conservation and rejection of species names, the designatation of interpretive types ("epitypes"), and allowing living metabolically inactive cultures to be nomenclatural types. The powers of the permanent Nomenclature Committees have also been enhanced over the years, so that they can now recommend rejection of any name whose adoption is regarded as disadvantageous.
Even against this background of increasing adaptation, the raft of changes effected at the Melbourne Congress in 2011, has to be seen as the dawn of a new era for botani- 3 The IUBS/IUMS International Committee on Bionomenclature comprises representatives of the five internationally mandated organismal codes of nomenclature: botanical, cultivated plant, prokaryote, viral, and zoological; it was formally established in 1994. cal and mycological nomenclature, truly bringing it into the modern age. The decisions made with respect to the name of the Code, its coverage, electronic publication, and the requirement for the deposition of key information in a recognized depositary as a requirement for the publication of fungal names, place the Melbourne Code ahead of what zoologists are currently endeavouring to do.
There is still much to be achieved by mycologists, especially with respect to the implementation of the consequences of the end of dual nomenclature for pleomorphic fungi, although the regulatory mechanisms are now in place. A major issue that remains is how best to designate taxa only known from molecular studies of environmental samples, and to consider whether that requires any changes in the Code (Hawksworth et al. 2011, Hibbett et al. 2011, Taylor 2011. Finally, I must stress that the views and interpretations presented in this overview are personal, and that mycologists should check the decisions and verify actual wordings agreed in Melbourne for themselves, especially in the official report of the Nomenclature Section meetings (McNeill et al. 2011), and then the edited published version of the International Code of Nomenclature for algae, fungi, and plants when it becomes available in mid-2012. Greuter

Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne -
what does e-publication mean for you?

Introduction
At the XVIII International Botanical Congress in Melbourne, Australia, in July 2011, two important changes were made to the International Code of Botanical Nomenclature (now the International Code of Nomenclature for algae, fungi, and plants) that will take effect from 1 January 2012. These changes will affect everyone who publishes names governed by this Code. As the Melbourne Code will not be published until approximately mid-2012, we felt it would be helpful to outline these changes, particularly those concerning effective publication in electronic media (in Articles 29, 30, and 31). For a concise report on all the changes to the Code accepted in Melbourne, see McNeill et al. (2011). A draft wording of the revised Articles, Notes, and Recommendations on effective publication is provided to aid editors and publishers in establishing best practice for implementing this aspect of the Code. We also outline here what these changes do not mean, to guide those wishing to publish new names and typifications by electronic means. We urge readers to consult the report of the Special Committee on Electronic Publication accompanying the changes proposed before the Congress , wherein the reasoning for the changes now accepted into the Code is set out.

Draft wording of revised Articles 29, 30, and 31 and Recommendations 29A, 30A, and 31A
Here we reproduce the wording of all of the relevant Articles, Notes, and Recommendations (omitting the Examples), with the changes highlighted in bold. The wording here is provisional, pending the meeting of the Editorial Committee in December 2011 to finalize the printed version of the Melbourne Code.

Article 29
29.1. Publication is effected, under this Code, by distribution of printed matter (through sale, exchange or gift) to the general public or at least to botanical institutions with libraries accessible to botanists generally. Publication is also effected by electronic distribution of material in Portable Document Format (PDF; see also Art. 29.3 and Rec. 29A.1) in an online publication with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN). Publication is not effected by communication of new names at a public meeting, by the placing of names in collections or gardens open to the public, by the issue of microfilm made from manuscripts, typescripts or other unpublished material, or by distribution electronically other than as described above.
29.2. For the purpose of this Article, "online" is defined as accessible electronically via the World Wide Web.

Should Portable Document Format (PDF) be succeeded, a successor international standard format communicated by the General Committee (see Div. III) is acceptable.
29.4. The content of a particular electronic publication must not be altered after it is first issued. Any such alterations are not themselves effectively published. Corrections or revisions must be issued separately to be effectively published.

Recommendation 29A
[Existing Recommendation replaced by the following:]

29A.1. Publication electronically in Portable Document Format (PDF) should comply with the PDF/A archival standard (ISO 19005).
29A.2. Authors should preferably publish in publications that are archived, satisfying the following criteria as far as is practical (see also Rec. 29A.1): (a) The material should be placed in multiple trusted online digital repositories, e.g. an ISO-certified repository; (b) Digital repositories should be in more than one area of the world and preferably on different continents; (c) Deposition of printed copies in libraries in more than one area of the world and preferably on different continents is also advisable.

Article 30
30.1. Publication by distribution of electronic material does not constitute effective publication before 1 January 2012.

An electronic publication is not effectively published if there is evidence associated with or within the publication that it is merely a preliminary version that was, or is to be, replaced by a version that the publisher considers final, in which case only that final version is effectively published.
30.3. Publication by indelible autograph before 1 January 1953 is effective. Indelible autograph produced at a later date is not effectively published.
30.4. For the purpose of this Article, indelible autograph is handwritten material reproduced by some mechanical or graphic process (such as lithography, offset, or metallic etching).
30.5. Publication on or after 1 January 1953 in trade catalogues or non-scientific newspapers, and on or after 1 January 1973 in seed-exchange lists, does not constitute effective publication.
30.6. The distribution on or after 1 January 1953 of printed matter accompanying exsiccatae does not constitute effective publication. Note 1. If the printed matter is also distributed independently of the exsiccata, it is effectively published. 30.7. Publication on or after 1 January 1953 of an independent non-serial work stated to be a thesis submitted to a university or other institute of education for the purpose of obtaining a degree is not effectively published unless it includes an explicit statement (referring to the requirements of the Code for effective publication) or other internal evidence that it is regarded as an effective publication by its author or publisher.
Note 2. The presence of an International Standard Book Number (ISBN) or a statement of the name of the printer, publisher, or distributor in the original printed version is regarded as internal evidence that the work was intended to be effectively published.

30A.1. Preliminary and final versions of the same electronic publication should be clearly indicated as such when they are first issued.
30A.2. It is strongly recommended that authors avoid publishing new names and descriptions or diagnoses of new taxa (nomenclatural novelties) in ephemeral printed matter of any kind, in particular printed matter that is multiplied in restricted and uncertain numbers, in which the permanence of the text may be limited, for which effective publication in terms of number of copies is not obvious, or that is unlikely to reach the general public. Authors should also avoid publishing new names and descriptions or diagnoses in popular periodicals, in abstracting journals, or on correction slips.
30A.3. To aid availability through time and place, authors publishing nomenclatural novelties should give preference to periodicals that regularly publish taxonomic articles. Otherwise, a copy of a publication (whether published as printed or electronic matter) should be sent to an indexing centre appropriate to the taxonomic group, and publications that exist only as printed matter should be deposited in at least ten, but preferably more, botanical or other generally accessible libraries throughout the world.
30A.4. Authors and editors are encouraged to mention nomenclatural novelties in the summary or abstract, or list them in an index in the publication.

Article 31
31.1. The date of effective publication is the date on which the printed or electronic matter became available as defined in Art. 29 and 30. In the absence of proof establishing some other date, the one appearing in the printed or electronic matter must be accepted as correct.
[Existing Note 1 replaced by the following:] 31.2. When a publication is issued in parallel electronic and printed versions, these must be treated as effectively published on the same date unless the dates of the versions are different according to Art. 31.1.
31.3. When separates from periodicals or other works placed on sale are issued in advance, the date on the separate is accepted as the date of effective publication unless there is evidence that it is erroneous.

Recommendation 31A
31A.1. The date on which the publisher or publisher's agent delivers printed matter to one of the usual carriers for distribution to the public should be accepted as its date of effective publication.

Best practice
Authors of new names, editors and publishers will all be interested in ensuring that the publications including new names are in accordance with the Melbourne Code, so that the names therein are effectively published. We suggest that those publishing in journals or monograph series and books that have online editions communicate with the editors so that best practice can be established across the community as quickly as possible. Many publishers have been carefully addressing the issues involved with the e-publication of novelties for some time (see Knapp and Wright 2010; guidelines in PLoS One [http://www.plosone.org/static/policies.action#taxon]) and considerable interest in making these new Code changes function effectively has been apparent.
Some practices that we feel will help with the initial stages of e-publication of novelties that are according to the Melbourne Code are: • Having each article bear the date of publication prominently (as is done in many journals, for example New Phytologist or Nature). • If an online early version is issued that is not the same as the final version (and thus not the place of effective publication), stamp each article with this fact prominently (for example American Journal of Botany). • Prominent display of the ISSN or ISBN of the publication on each article will help indexers establish effective publication. • Publication in journals (or monograph series) that participate in the CLOCKSS system (see Knapp and Wright 2010 for a description) or another international archive and preservation system will ensure long-term archiving. • Authors of new names by electronic means should alert the appropriate indexing center as recommended in Rec. 30A.3 -this will help indexers who may otherwise not be aware of electronically published names.

What these changes do not mean
Although the new Articles and Recommendations use the terms PDF and PDF/A, this does not mean that publications must be issued only in that format to be effectively published. For example, some online journals issue papers in Hypertext Markup Language (HTML) format together with a parallel PDF version. In such cases, the PDF version will be effectively published. The stipulation that the General Committee for Botanical Nomenclature will communicate the acceptability of a new international standard format, should PDF ever be succeeded, means authors of novelties and the community using the Code can remain informed as to advances in the field and that the Code will be protected from obsolescence. Use of the following means of electronic publication will not result in effective publication of novelties under the Melbourne Code: • Publication on websites or in ephemeral documents available over the Internet (there are strict criteria for granting of ISSNs [http://www.issn.org]). • Publication in journals without a registered ISSN or e-ISSN. • Publication in books without a registered ISBN or e-ISBN. The Recommendation approved to advise the deposition of a hard copy of any epublication in a library suggests to botanists an action, but it does not set out standard practice or a protocol for librarians to follow. Librarians are themselves in a complex transition zone between publication modalities (Johnson and Luther 2007), and botanists may find librarians to be unwilling or unable to accommodate single hard copy papers as individual accessions should the volume be great.

Two other important changes to the Code relating to the publication of names
The second change to the Code approved in Melbourne to take effect from 1 January 2012 is that the description or diagnosis required for valid publication of the name of a new taxon of all organisms falling under the Code may be in either English or Latin. This is the current provision for names of plant fossils, but all new non-fossil taxa have required a Latin description or diagnosis (fungi and plants from 1 January 1935; algae [including cyanobacteria, if treated under the Code] from 1 January 1958). This has no bearing on the form of scientific names, which continue to be Latin or treated as Latin. Individual journal requirements for Latin and/or English will, of course, be determined by the editors of those journals.
A third change to the Code approved in Melbourne relating to publication of names, but one not taking effect until 1 January 2013 (not 1 January 2012 as reported by Miller et al. 2011), is that all new names of organisms treated as fungi must, as an additional requirement for valid publication, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (such as MycoBank [http://www.mycobank.org/]). This will be publicized separately.
The requirement for a unique identifier for new names of fungi on or after 1 January 2013 does not apply to plants or algae; there is no need for authors of new names in these groups to request Life Science Identifiers (LSIDs) -or other identifiers -from indexing centers. Um rascunho revisado da redação dos Artigos, Notas e Recomendações sobre publicação efetiva é apresentado para auxiliar os editores e editoras no estabelecimento de boas práticas para implementação deste aspecto do Código. Nós também esboçamos aqui o que essas mudanças não significam, para guiar aqueles que desejam publicar nomes novos e tipificações por meios eletrônicos. Nós recomendamos aos leitores consultar o relatório do Comitê Especial sobre Publicação Eletrônica que acompanha as mudanças propostas anteriormente ao Congresso , onde estão as razões para estas alterações agora aceitas no Código e aqui expostas.
• Si se emite una versión en línea que no es la misma que la versión final (y por lo tanto no da lugar a una publicación efectiva) sellar cada artículo con este hecho en forma destacada (véase por ejemplo, American Journal of Botany).
• La visualización prominente del ISSN o ISBN de la publicación de cada artículo ayudará a los indizadores a establecer si el artículo está efectivamente publicado o si no lo está.
De acuerdo al Código de Melbourne el uso de los siguientes medios de publicación electrónica no resultará en una publicación efectiva de novedades.
El requisito de un identificador único para nuevos nombres de hongos desde o después del 1 de enero de 2013 no se aplica a plantas o algas; no hay necesidad para autores de nuevos nombres en estos grupos solicitar LSIDs (siglas en inglés de Life Science Identifiers, Identificadores de Ciencias de la Vida), u otros identificadores de centros de indexación.

Agradecimientos
SK recibe apoyo del programa de NSF Planetary Biodiversity Inventory programme (DEB-0316614, PBI Solanum -a worldwide treatment). La participación de JMcN y NJT a la Sección de Nomenclatura del XVIII CIB en Melbourne fue apoyada en parte por la International Association for Plant Taxonomy (IAPT). Agradecemos a Katherine Challis (Kew) por los valiosos comentarios.

Testing the phylogenetic utility of MCM7 in the Introduction
The Ascomycota, commonly referred to as the sac-fungi (Eriksson 2009), is the largest and most phylogenetically diverse group of organisms within the Kingdom Fungi and consists of an estimated 64,000 described species (Kirk et al. 2008). Currently the Ascomycota comprises three subphyla, 15 classes and 68 orders (Kirk et al. 2008). Species belonging to the Ascomycota can be found in all ecosystems where they inhabit a diverse array of ecological niches, acting as saprobes that decay dead organic matter, pathogens of plants and animals, as well as mutualists (lichen-forming fungi) and endophytes. In addition, numerous taxa within the Ascomycota are of industrial, medical and economical importance. A large proportion of taxa that reside within the Ascomycota are known only from their mitosporic or asexual states (Gams and Seifert 2008), thereby, making it difficult to determine phylogenetic and evolutionary relationships within this mega diverse group of fungi. The advent of molecular systematics has revolutionized our knowledge of the phylogenetics of the Ascomycota. Early fungal phylogenetic studies used DNA sequences from nuclear ribosomal genes such as small subunit (18S) and large subunit (28S) rDNA genes (Bruns et al. 1991, Berbee and Taylor 1995, Spatafora 1995, Tehler et al. 2000. Due to the presence of a large number of copies within the genome being subjected to concerted evolution (Zimmer et al. 1990), and due to their ease of amplification (Hills and Dixon 1991), 18S and 28S sequence data were used early on and still dominate the fungal sequence data in GenBank (Begerow et al. 2010, Lutzoni et al. 2004. Recently, however, fungal systematists have started using a number of singlecopy protein-coding genes for investigating deep phylogenetic relationships among the fungi. This has largely become possible due to the advent of fungal phylogenomics (Galagan et al. 2005). This task has been achieved due in part to the efforts of research consortiums among fungal systematists such as "Assembling the Fungal Tree of Life" , Lutzoni et al. 2004 and "Deep Hypha" (Blackwell et al. 2006).
Despite their widely accepted use in inferring evolutionary relationships among the ascomycete fungi, a number of protein-coding genes have been shown to perform variably (Aguileta et al. 2008). In fact a number of studies have attempted to use varying definitions of phylogenetic informativeness to compare various genes to one another. In addition to the aforementioned study by Aguileta et al. (2008), which compared gene based trees to an ideal tree, Townsend et al. (2007) used character rates, Graybeal et al. (1994) used empirical saturation plots and Collins et al. (2005) used base compositional stationarity, amongst others. The Townsend et al. (2007) measure of selecting genes with an optimal rate as it is projected backwards in time was applied to a taxon set comprising all major classes in the Ascomycota for DNA sequences from three ribosomal genes (two nuclear, one mitochondrial) and three protein-coding genes by Schoch et al. (2009a). These studies showed how different genes behave differently for discovering older versus younger divergences. In the majority of cases the selected protein-coding genes were more informative than the ribosomal genes over all time periods. Using different criteria, Aguileta et al. (2008) showed that several protein-coding genes used routinely in fungal phylogenetic studies were not among the best performing genes when tested against 246 single-copy orthologous genes extracted from 30 fungal genomes (see supplementary material in Aguileta et al. 2008). The authors discovered two ortholog single-copy protein coding gene loci, MS277 and MS456, which outperformed all other protein-coding genes in their study. MS456, commonly referred to as MCM7, codes for a licensing factor required for DNA replication initiation and cell proliferation. The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication (Kearsey and Labib 1998). Schmitt et al. (2009b) subsequently developed fungal-specific primers for these two loci and tested their phylogenetic utility across a wide range of classes from the Ascomycota with a majority of taxa sampled from within the lichenized fungi in the Lecanoromycetes. Notably, the large and diverse class Dothideomycetes did not have representatives in this study. Data from this study suggested that, compared to MS277 (TSR1), the MCM7 primers were able to amplify a greater number of diverse taxa within the Ascomycota. However, the authors did not compare MCM7 with any other gene commonly used for fungal phylogenies. This includes the 28S large-subunit nuclear ribosomal DNA (LSU), which is currently one of the most widely used ribosomal genes for assessing phylogenetic relationships at the class level and below for Fungi (Begerow et al. 2010, Lutzoni et al. 2004. The major objectives of this study, therefore, were to: 1) test the phylogenetic utility of MCM7 for estimating phylogenies at various taxonomic ranks (class and below) with a focus on non-lichenized ascomycetes; 2) expand use of the MCM7 gene to include taxa in the Dothideomycetes, Geoglossomycetes, Leotiomycetes, and Sordariomycetes; and, 3) compare the congruence, robustness and resolving power of MCM7-based phylogenies with that of LSU-based phylogenies for the same taxon set. Comparing the phylogenetic utility of the new gene with that of existing ones helps build robust and well-resolved phylogenies among ascomycete fungi while improving cost management of molecular studies.

Taxon sampling
Taxa used in this study are listed in Table 1, along with information on the source of the isolates as well as their country of origin, where available. The focus of our taxon sampling was to include non-lichenized ascomycetes representing terrestrial and freshwater ascomycete taxa from the Dothideomycetes, Geoglossomycetes, Leotiomycetes, and Sordariomycetes for both MCM7 and LSU genes. We assembled datasets of each gene for the same 89 taxa. Six classes from within the rankless taxon Leotiomyceta (Schoch et al. 2009b): Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes, were sampled. Based on results of previous phylogenetic analyses (James et al. 2006, Lutzoni et al. 2004, one representative each from Saccharomycotina and Taphrinomycotina was used as outgroup taxa for all analyses. For some taxa, more than one representative was sequenced for both genes to verify its identity as well as to assess the utility of MCM7 in comparison to LSU at lower taxonomic levels. Newly generated sequences are deposited in GenBank and their accession numbers are listed in Table 1.

Molecular Methods (DNA extraction, primers and sequencing)
Total genomic DNA from terrestrial ascomycetes was extracted using methods outlined in Promputtha and Miller (2010), whereas DNA from freshwater ascomycete taxa was extracted from axenic cultures obtained from single-spore isolates following Campbell et al. (2007). PCR reactions were carried out using known LSU and MCM7 primers (Rehner and Samuels 1995, Schmitt et al. 2009b, Vilgalys and Hester 1990. The LSU gene was amplified using thermocycler conditions outlined in Miller and Huhndorf (2004) and MCM7 was amplified using the following thermocycler conditions: initial denaturing at 94 C for 5 min; 30 cycles of denaturing at 94 C for 45 sec, annealing at 50-56 C for 50 sec; extension at 72 C for 1 min; and a final extension step of 72 C for 5 min. For taxa which were difficult to amplify, the annealing temperature was decreased to 45 C. PCR reactions using illustra Ready-To-Go™ PCR Beads (GE Healthcare, Waukesha, WI) contained 1-5 µl genomic DNA, 2.5 µL of BSA (bovine serum albumin, New England Biolabs, Ipswich, MA) and/or 2.5 µL of DMSO (dimethyl Table 1. Species used in this study along with their source, localities and accession numbers. sulfoxide, Fisher Scientific, Pittsburgh, PA), 1 µl of each 10mM primer, and enough distilled water to bring the reaction volume to 25 µL. Purified PCR products were used in 11 µL sequencing reactions with BigDye Terminators v. 3.1 (Applied Biosystems, Foster City, CA) in combination with the following LSU primers: LROR, LR3, LR3R, LR6 and MCM7 primers: Mcm7-709for, Mcm7-1384rev. Sequences were generated on an ABI Applied Biosystems 3730XL high-throughput DNA capillary sequencer at the UIUC Keck Center for Comparative and Functional Genomics.

Sequence alignment
Each sequence fragment was subjected to an individual BLAST search to verify its identity. MCM7 sequences from the GenBank were assembled and aligned with newly obtained sequences using Sequencher 4.9 (Gene Codes Corp.), optimized by eye, and manually corrected. For the LSU data, the newly obtained sequences were aligned with sequences from GenBank using the multiple sequence alignment program, MUSCLE® (Edgar 2004), with default parameters in operation. MUSCLE® was implemented using the program Seaview v. 4.1 (Gouy et al. 2010). The LSU sequences were aligned in MUSCLE® using a previous (trusted) alignment made by eye in Sequencher v. 4.9 based on a method called "jump-starting alignment" (Morrisson 2006). The final alignment was again optimized by eye and manually corrected using MacClade v. 4.08 (Maddison and Maddison 2000) and Se-Al v. 2.0a8 (Rambaut 1996). The separate and combined alignments are available from the authors upon request.

Maximum likelihood and Bayesian search strategies for phylogenetic analyses
Maximum likelihood (ML) and Bayesian Inference (BI) methods were used in phylogenetic analyses for both the MCM7 and LSU datasets. The Akaike Information Criterion (AIC) (Posada and Buckley 2004) as implemented in Modeltest v. 3.7 (Posada and Crandall 1998) was used to determine the best-fit model of evolution for each data set for both ML and BI. For the separate and combined datasets, the best-fit model of evolution was the GTR + I + G model. Likelihood analyses were conducted using PhyML (Guindon and Gascuel 2003) under the following parameters: GTR model was implemented with six rate classes and invariable sites. Across site variations were fixed with parameter values obtained from Modeltest and 1000 bootstrap replicates were performed from a BioNJ starting tree employing the best of nearest neighbor interchange (NNI) and subtree pruning and regrafting (SPR) branch swapping. Maximum likelihood analyses were also performed using RAxML v. 7.0.4 (Stamatakis 2006) run on the CIPRES Portal v. 2.0  with the default rapid hillclimbing algorithm and GTR model employing 1000 fast bootstrap searches. Clades with bootstrap values ≥ 70% were considered significant and strongly supported (Hills and Bull 1993). Bayesian analyses employing a Markov Chain Monte Carlo (MCMC) algorithm were run with MrBayes v. 3.1 (Huelsenbeck and Ronquist 2001) on the CIPRES Portal v. 2.0 as an additional means of assessing branch support. These analyses incorporated the general time reversible model (Rodríguez et al. 1991) including an estimation of invariant sites and assuming a gamma distribution parameter (GTR + I + G) with six rate categories. Four independent chains of MCMC were run for 50 million generations to insure that the same tree space was being sampled during each analysis and that the trees were not trapped in local optima. Trees were sampled every 1000 th generation resulting in 50,000 total trees. Bayesian posterior probabilities (BPP) were determined from a consensus tree generated from the remaining 40,000 trees in PAUP * 4.0b10 (Swofford 2002) after the first 10,000 trees, which extended beyond the burn-in phase in each analysis, were discarded. Clades with posterior probability ≥ 95% were considered significant and strongly supported.

Combined analyses and test for conflict
The individual LSU and MCM7 datasets were examined for potential conflict before they were combined into a single dataset for total evidence analyses (Eernisse andKluge 1993, Kluge 1989). Since previous studies have shown that the incongruence length difference (ILD) test performs poorly (Barker and Lutzoni 2002, Dolphin et al. 2000, Dowton and Austin 2002, Yoder et al. 2001), a simple test was used for comparing and assessing the combinability of the data from individual datasets. The individual gene phylogenies were considered to be incongruent if clades with significant ML bootstrap support and BI BPP (i.e. ≥ 70% BS or ≥ 95% BPP) were conflicting in the tree topologies (Alfaro et al. 2003, Weins 1998, Lutzoni et al. 2004). Incongruent clades with < 70% BS and < 95% BPP suggest the conflict is statistically unsupported. If there is no conflict based on the above assumptions, it supports the argument that the individual genes possess similar phylogenetic histories and can be combined. Since no significant conflict was observed among clades in each of the individual datasets, they were combined to achieve maximum phylogenetic resolution and support. The combined dataset was analyzed with the same parameters as above except that the protein coding dataset was partitioned based on codon positions. For BI we used flat priors and unlinked model parameters across partitions. The combined datasets were partitioned and analyzed so as to allow separate parameter estimation for each gene as well as for each codon position for MCM7.

Substitution saturation test
All of the 89 sequences from the MCM7 alignment were used to assess transitions/ transversions (ti/tv) substitution saturation of first, second, and third-codon positions. Observed ti/tv was plotted against Jukes Cantor JC89 corrected distance (Jukes and Cantor 1969) for each codon position separately as well as combined using the program DAMBE (Xia andXia 2001, Xia 2009). Transition and transversion of each codon position can be considered saturated if the scatter points on the two-dimensional plot appear to level off with an increase in sequence divergence. In addition, the I SS statistic, which is a measure of substitution saturation in molecular phylogenetic datasets developed by Xia et al. (2003) and implemented in DAMBE, was also used to detect saturation. Nucleotide statistics for both genes were calculated in PAUP* 4.0b10 (Swofford 2002), SeqState v. 1.4.1 (Müller 2005), and Mega v. 4 (Tamura et al. 2007).

Phylogenetic Informativeness
We performed a phylogenetic informativeness (PI) measure on our combined dataset as proposed by Townsend (2007) using the PhyDesign online tool developed by López-Giráldez and Townsend (2011). PhyDesign measures per-site estimates to project the utility of a particular gene for resolving phylogeny related questions across historical time. This method allows for a comparison of different genes and loci used for phylogenetics by providing an estimate of the cost effectiveness of character sampling for specific time units. The time units used herein are relative time periods. Schoch et al. (2009a) compared PI for the Ascomycota using a 6-gene phylogeny, but MCM7 was not evaluated in their study.

Taxon sampling
A total of 89 taxa were included in the study, which comprises 80 species belonging to 63 genera of lichenized and non-lichenized ascomycetes in the classes Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes (Table 1).

New taxa sequenced
We report 93 new sequences of which 65 are MCM7 and 28 are LSU (Table 1). Table  1 provides accession numbers for sequences used from GenBank in addition to those newly generated in this study. Most of the newly generated data for both MCM7 and LSU are from ascomycetes that occur as saprobes on wood in terrestrial (Miller and Huhndorf 2009) or freshwater habitats (Shearer and Raja 2010). Our study resulted in a > 80% sequencing success rate for MCM7, which is comparable to that found by Schmitt et al. (2009b). We obtained the best PCR amplification results for MCM7 with about 5 µl of total genomic DNA concentration per 25 µl of PCR reaction.
Both LSU and MCM7 alignments consisted of the same 89-taxon dataset. The original LSU dataset had a total of 1484 nucleotides. After aligning in MUSCLE and excluding nucleotides from the 5´ and 3´ ends due to missing data in most sequences, the LSU dataset consisted of 1141 nucleotides. The final LSU dataset after excluding 57 ambiguous characters and two short intron regions from Saccharomyces cerevisiae consisted of 1076 nucleotides. The LSU dataset had 551 constant characters, 123 variable characters, and 402 parsimony informative characters ( Table 2). The MCM7 dataset consisted of a total of 642 nucleotides (193 constant, 449 variable); there were no missing characters, ambiguous regions, or introns. The majority of informative characters were in third codon positions ( Table 2). The GC content of MCM7 was slightly higher than LSU, although nucleotide percentages were somewhat similar in both datasets (Table 2). Although MCM7 had fewer nucleotides analyzed, it had a higher percent (62%) of parsimony informative characters than LSU (37%) (   (Rodríguez et al. 1990) with unequal base frequencies, gamma distribution with among site variation and a proportion of sites are invariable. b Proportion of invariable sites c Variable sites gamma distribution parameter

Phylogenetic analyses
The estimated model parameter values obtained from AIC with modeltest are listed in Table 3. Application of separate models on the different codon positions for MCM7 did not affect the topology and posterior probabilities of clades (data not shown). Since PhyML and BI analyses produced trees with nearly identical topologies, only PhyML phylograms are shown (Figs 1-3).
Class-level relationships: The overall tree topologies of LSU and MCM7 genes were identical with the represented classes of fungi occurring as monophyletic (Figs 1 and 2). A total of 46 clades received strong support (≥ 70% BS and ≥ 95% BPP) with PhyBS, 52 for RAxBS, and 62 for BPP for LSU, whereas, 38, 39, and 46 clades were strongly supported for PhyBS, RAxBS, and BPP, respectively, for MCM7 (Table 2).    More major lineages within the Ascomycota were more strongly supported with LSU compared to MCM7 data. For LSU, nine nodes were strongly supported with PhyBS and ten with RAxBS, while twelve were strongly supported with BPP (Table 4). For MCM7, ten nodes were strongly supported with PhyBS and RAxBS, while only nine were strongly supported based on BPP (Table 4). The somewhat higher support for the LSU gene may be due to the greater sequence length for LSU when compared to MCM7 in the present study. Min and Hickey (2007) have shown that reducing sequence length can have a profound effect on the resolution of resulting phylogenetic trees. The net PI profile, which is based on sequence length, also shows the LSU gene has slightly higher phylogenetic informativeness at older nodes across relative older dates compared to MCM7 (Table 5, Fig. 6).
Genus and species level relationships: Within the Dothideomycetes, Eurotiomycetes, Geoglossomycetes, and Sordariomycetes, we selected more than one species/ strain within a genus to assess the performance of MCM7 (MS456) versus LSU. Our data shows that MCM7 can be used for assessing interspecific relationships of taxa within genera such as Camarops, Lasiosphaeria, (Sordariomycetes), Aspergillius (Eurotiomycetes), Geoglossum (Geoglossomycetes), and Aliquandostipite (Dothideomycetes). The above taxa sampled from their different classes within the Leotiomyceta each formed a monophyletic clade with high internal resolution and support based on MLBS and BPP values in each gene tree (see Figs 1 and 2, and Table 5). However, the combined gene tree showed even better resolution of relationships and clade support for the above genera (Fig. 3, Table 5). Removing the third codon position had a slight negative effect on clade support within genera (Fig. 5, Table 5).

Combined analysis
Since no significant conflict occurred among well-supported clades in each tree topology, we concatenated the two gene regions. The combined LSU-MCM7 gene tree (Fig. 3) had a total of 801 parsimony informative characters (Table 2) and provided a more robust phylogenetic hypothesis of the Ascomycota (Fig. 3) than either individual tree topology. A total of 62 clades were strongly supported with PhyBS, 63 with RAxBS, and 61 with BPP ( Table 2). The combined tree also received higher nodal support for the major lineages included with 13 strongly supported lineages with PhyBS, twelve with RAxBS, and twelve with BPP (Table 4). The nodal support for the combined data set was higher for the total number of strongly supported clades as well as for the number of nodes strongly supported for the major lineages in comparison to the separate gene analyses (see Table 3, 4 and Figs 1-3). A number of nodes that were moderately (< 70 % BS and < 95% BPP) or poorly (< 50 % BS and < 70% BPP) supported in the separate gene analyses received strong support in the combined gene analyses (Table 4). Subclass lineages are given in italics Table 5. Genus level relationships among selected genera used in the present study. Support values and analyses are same as in Table 4.

Substitution saturation
There is no indication of substitution saturation in the first or second codon positions (Fig. 4). However, for the third codon position, it is evident that there is leveling off in the scatter plot when transition/transversion divergence are plotted against pairwise sequence divergence (Fig. 4). It is also clear that third codon position transitions reach a plateau. Saturation tests therefore indicate poor phylogenetic signal at the third codon position, and transitions appear to be saturated on a plot of substitution type against JC corrected genetic distances. The test of Xia et al. (2003) suggested that for the first and second codon positions of MCM7 sequences, the values for the index of substitution saturation I SS were 0.253 and 0.152, respectively, for 32 OTUs, and the critical I SS.C values were 0.659 and 0.658. This suggests that there were no significant levels of substitution saturation at the first and second positions (I SS < I SS.C , P < 0.0001). However, for the third codon position of MCM7, the observed I SS value of 0.807 is significantly greater than the I SS.C value of 0.658, suggesting that the third codon position has experienced substitution saturation (Xia et al. 2003). This statistical test therefore corroborates the scatter plot data and suggests that the third codon position is saturated and therefore might possess a poor phylogenetic signal. Therefore, we carried out an additional set of ML and BI analyses using a method called site stripping (Verbruggen and Theriot 2008), where we entirely removed the third codon position in order to assess the effects of saturated third codon position on the tree topology and statistical clade support. The PhyML tree resulting from an analysis of only first and second codon positions for MCM7 is presented in Fig. 5. The topology of this phylogenetic tree is not congruent with the LSU and MCM7 trees or the combined gene trees. One major difference was that the Xylariomycetidae clade nested within the Sordariomycetidae clade. In addition the nodal support for the major lineages was quite poor for the first and second codon position tree when compared to the separate LSU and MCM7 gene trees or the combined gene tree (Table 4). For example, Dothideomycetes and Eurotiomycetes did not receive support with PhyBS, RAxBS, or BPP (Table 4). However, the MCM7 gene tree with all codon positions included showed strong support for the Dothideomycetes and the Eurotiomycetes lineage was strongly supported with PhyBS (Table 4).

Phylogenetic Informativeness
We derived the profiles from rates of evolution of sites within genes using PhyDesign, an online platform for profiling PI (López-Giráldez and Townsend 2011, see also Townsend 2007), which provides a unique empirical metric for guiding marker selection and facilitates locus prioritization. The net PI correlates with the degree of nodal support, while the per site PI compares the relative power of gene performance without confounding effects of gene length (Townsend 2007, López-Giráldez andTownsend 2011). Net PI showed a higher pulse for MCM7 than LSU. However, LSU  Figure 5. Maximum Likelihood phylogeny of Leotiomyceta (Ascomycota) based on 1-2 codon position of MCM7 data set (428 bp) of 89 taxa using PhyML ((-ln)L score 7352). Support values, shading and classification as in Fig. 1. had a higher pulse of PI for older time units (beyond 0.4) (Fig. 6). Based on a per-site comparison, the MCM7 gene fragment (642 bp) produced a pulse of higher PI across relative time units compared to LSU (Fig. 6).

Class-level relationships
The topologies of the major classes obtained using the LSU gene ( Fig. 1) as well as the MCM7 gene (Fig. 2) broadly agrees with previously published multi-gene phylogenies of Ascomycota (James et al. 2006, Lutzoni et al. 2004, Schoch et al. 2009a. We show that all classes in the present study are monophyletic, which corroborates earlier hypotheses by Eriksson and Winka (1997). Recently, Schoch et al. (2009b) proposed a new class, Geoglossomycetes, based on a multi-gene phylogeny.
Our results for the MCM7 gene are in agreement with Schoch et al.'s study as Geoglossomycetes is shown as a monophyletic group with strong MLBS and BPP support (Fig 2, Table 4), but, however, without strong support for its placement in relation to other classes of Leotiomyceta as noted previously (Schoch et al. 2009b). We did not recover support for the expanded subclass Pleosporomycetidae as found in a previous multi-gene study focused only on Dothideomycetes (Schoch et al. 2009c) and the influence of additional gene data and improved taxon sampling cannot be ruled out.
In spite of this, results of our study are also in agreement with those of Aguileta et al. (2008), who showed that MCM7 is a reliable marker for establishing phylogenetic relationships among fungi, and concur with Schmitt et al.'s (2009b) results regarding the phylogenetic utility of MCM7 for resolving relationships among the Ascomycota.

Genus and species-level relationships
We included more than one species or isolate of various genera such as Camarops, Lasiosphaeria (Sordariomycetes), Graddonia (Leotiomycetes), Aspergillus (Eurotiomycetes), and Aliquandostipite (Dothideomycetes) to test how MCM7 would perform in resolving relationships at the genus-level. Although several species of Jahnula were included in our study, we do not discuss results for this genus in more detail since independent data strongly suggest the genus may be polyphyletic within the order Jahnulales (Campbell et al. 2007, Suetrong et al. 2010. Currently, the ribosomal 18S small subunit and 28S large subunit are widely used genes for placing newly described genera of fungi within a class in the Ascomycota (see Begerow et al. 2010). Here we show MCM7 can be used along with LSU to resolve genus-level relationships. In general, we found slightly better resolution and support with likelihood BP and BPP for the aforementioned genera with MCM7 in comparison with LSU (Figs 1 and 2; Table 5). All clades within these genera were highly supported based on the combined gene analysis ( Fig. 3; Table 5). Our results are in agreement with those of Schmitt et al. (2009b), who showed the utility of MCM7 at the genus level for taxa such as Aspergillus, Lecanora, and Malcomiella. Peterson et al. (2010) also used MCM7 successfully with other protein coding genes such as RPB2 and TSR1 to resolve phylogenetic relationships of the genus Hamigera, an ascomycete fungus belonging to the Eurotiomycetes. The MCM7 gene was also recently used in species delimitation of a lichen forming fungus, Xanthoparmelia (Leavitt et al. 2011). The authors reported high parsimony informative variable characters in MCM7 compared to other protein coding (Beta-tubulin) as well as other ribosomal gene markers (ITS, LSU). More recently, Spribille et al. (2011) used MCM7 for phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius. Although MCM7 was reported as being highly variable and showed good phylogenetic signal, it showed a higher level of transition saturation at the third codon position (Spribille et al. 2011). The authors concluded that caution must be taken when using MCM7 to recover gene phylogenies. Although we did not find a significant difference in the nodal support between the MCM7 and LSU genes (Table 5), overall, based on our study and results of some recent studies, it seems likely that MCM7 shows good potential as a candidate gene for evaluating interspecific relationships among the Ascomycota.

Combine gene analyses
Combining datasets generally provides better resolution and nodal support for clades in phylogenetic analyses of the fungal kingdom (Lutzoni et al. 2004). Our combined LSU and MCM7 dataset showed enhanced phylogenetic resolution (Fig. 3) and increased nodal support for clades that were not strongly supported when analyzed separately (Table 4). Our data are in agreement with other Ascomycota studies that have shown that combining protein-coding data with nuclear ribosomal genes (either LSU or SSU) provides an increased number of supported nodes in phylogenetic analyses , Hansen et al. 2005, Miller and Huhndorf 2005, Tang et al. 2007). Hofstetter et al. (2007) concluded that for better resolution and support of clades in phylogenetic analyses of fungi more characters and proteincoding genes in particular are important. Our study also supports the prediction by Schmitt et al. (2009b) who suggested that MCM7 has a higher potential to resolve phylogenetic relationships between fungi when analyzed in combination with other commonly used genes such as LSU. In addition, our PI analyses using PhyDesign shows that MCM7 was a more phylogenetically informative gene than LSU. Schoch et al. (2009a) also found that protein-coding genes had better PI profiles than those of rDNA genes.

MCM7 codon saturation
In this study the third codon position in MCM7 appears to be saturated based on scatter plots of substitution saturation curves (Fig. 4), which agrees with results of empirical tests by Xia et al. (2003). Spribille et al. (2011) also showed a higher level of transition-saturation at the third codon position for MCM7 gene in their phylogenetic analyses. Substitution saturation appears to be a common problem among protein-coding genes routinely used for inferring phylogenetic relationships among fungi (Liu et al. 1999, Hansen et al. 2005, Miller and Huhndorf 2005, Sung et al. 2007). There are currently two schools of thought regarding the inclusion or exclusion of third codon positions from saturated protein-coding genes and their method of utilization for phylogenetic analyses. One group is of the opinion that third codon positions should be excluded in ML analysis because these fast evolving, saturated characters can decease the signal/noise ratio, thus providing misleading interpretations of evolutionary relationships (Blouin et al. 1998, Swofford et al. 1996, Xia et al. 2003. Conversely, the other group suggests the inclusion of the third codon position since the presence of more phylogenetically informative characters helps with potentially decreasing stochastic errors and increases branch-support values (Edwards et al. 1991, Källersjö et al. 1998, Müller et al. 2006, Simmons et al. 2006. Björklund (1999), however, suggests that unless one finds evidence that third codon positions are significantly misleading they should not be eliminated from analyses a priori. Based on our analyses of the MCM7 dataset with and without third codon positions (Fig. 2, all codon positions included, and Fig. 5, third codon positions excluded), we found that exclusion of third codon positions did not have a major effect on the monophyly of the classes, except that the subclass Xylariomycetidae was nested within the Sordariomycetidae when third codon positions were excluded (Fig. 5). However, exclusion of third codon positions led to a loss of nodal support (MLBS and BPP) for several clades both at the class and genus level (Table 4, 5). These results are in agreement with those found by Edwards et al. (1991), who found that removal of third codon positions in mitochondrial genes in a group of birds resulted in "biological unreasonable" groupings as well as loss of BS for one of the branches in their phylogenetic tree. Hackett (1996) also found that removal of saturated third codon positions from mitochondrial genes in another bird study resulted in a loss of phylogenetically informative transversions. Therefore, for our 89-taxon MCM7 gene phylogeny it seems appropriate to include the third codon positions in order to retain appropriate tree topology as well as MLBS and BPP nodal support. We concur with the conclusions of Simmons et al. (2006) that despite indications of saturation, third codon positions must be included in phylogenetic analyses since they contain a large number of phylogenetically informative characters.

Conclusions
We have presented evidence for the phylogenetic utility of MCM7 among the Ascomycota. Results of the PI profiles show that MCM7 was more informative than LSU. Here we show that this locus can also be used successfully for determining phylogenetic relationships of non-lichenized ascomycetes and provides good resolution and support at half the cost compared to LSU because we used only two primers to sequence the MCM7 gene as opposed to four primers used routinely for LSU. In addition, no introns were present in the MCM7 gene for the taxa sequenced in our study. MCM7 seems to qualitatively contribute to better resolution of higher as well as lower taxonomic level clades. We also show that combined LSU and MCM7 gene phylogeny had superior resolving power for both class and genus level relationships since all major classes received high BS in both PhyML and RAxML bootstrap analyses as well as high BPP values. We report that although the third codon position of MCM7 is saturated, it may be better to analyze the dataset with all codon positions included. Exclusion of third codon positions compromised the overall topology of the tree and, in some clades, resulted in poor nodal support with MLBS and BPP, perhaps due to exclusion of a significant number of phylogenetically informative characters. Lutzoni et al. (2004) suggested "there is a great need for housekeeping protein-coding genes to be sequenced and combined with other loci to assemble the fungal tree of life". The results from this study suggest that MCM7 will make an important contribution toward such an effort.

Future Directions
MCM7 shows good potential to be a candidate gene for fungal phylogeny reconstruction, especially for the Ascomycota. However, future studies comparing MCM7 with RPB1, RPB2, and EF1 alpha are warranted for the Ascomycota to better understand which single copy protein coding locus is easiest to PCR amplify and sequence, while at the same time also provides the greatest amount of phylogenetic informativeness.