Development of a revised generic system for parmelioid lichens based on molecular phylogenetic studies using three molecular data sets (ITS and LSU nu rDNA and mt SSU rDNA)

Crespo, A., Blanco, O., Divakar, P. K. & Hawksworth, D. L.
Departamento de Biología Vegetal II. Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain

The genus rank in Parmelia segregates, called parmelioid lichens (Parmeliaceae, Lecanorales), is analysed and the taxonomic range is discussed based on phylogenetic basis. The topology of the trees, based on molecular characters, is faced by the concept of genera, based on traditional phenotypic characters. In most of cases traditional characters may support molecular hypothesis. But also some apparently discrepant molecular topologies have led to a reinterpretation of several classical characters. The phylogenetic analyses were developed on a Bayesian approach of a combined data set of two nuclear ribosomal sources (partial LSU and ITS sequences) and one mitochondrial gene (rSSU RNA). The topology of the tree showed several main monophyletic clades. In some of them we have already made a new generic arrangement.
(1) The clade of Chondropsis, Karoowia, Neofuscelia, Paraparmelia, Xanthomaculina and Xanthoparmelia. The synonymy of these genera under the conserved name Xanthoparmelia have been proposed also based on a common polysaccharide cell wall (Xanthoparmelia- type lichenan ) and affinities in ecology and biogeography.
(2) The clade of Rimelia, Canomaculina, Concamerella and Parmotrema. These genera were also proposed as synonymes (as Parmotrema sensu lato) because they form a monophyletic group and share a number of morphological characters.
(3) On the contrary Melanelia, as previously circumscribed, does not form a monophyletic group and two new genera (Melanohalea and Melanelixia) were proposed based on a reinterpretation of morphological features.


Linnaean nomenclature in a phylogenetic world

DePriest, P. T.
Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA

Almost 250 years ago, Linnaeus revolutionized taxonomy by introducing binomial nomenclature at a time when the world&Mac226;s flora and fauna could be known by a single, if exceptional, individual. His goals were pragmatic – the need to devise names and classification systems that his students could remember without reciting complex descriptions. Certainly, his sensational-sounding "sexual parts" classification for plants achieved this goal, but lasted only a few decades. His binomial nomenclature and hierarchical classification has lasted centuries, with periodic tweaks including additional hierarchical ranks, typification of names, and priority rules that are the basis of the International Code of Botanical Nomenclature (ICBN), and the parallel nomenclature codes for animals and bacteria. But will the Linnaean system last another decade? The recent phylogenetic revolution has caused systematists to ask if the ICBN can integrate phylogenetic information; if we need binomials at all. Alternative systems, the Phylocode and rank-free nomenclature, are proposed and championed. Criticisms of the Linnaean system and traditional nomenclature focus on concepts of circumscribing taxa, hierarchical ranks, and Linnaean binomials. On the basis of a recent review of the ICBN, it seems that with minor adaptation and explanations the systems can be fully responsive to incorporating phylogenetic information. The key is that the traditional nomenclature system is one of "naming" and, outside of requiring inclusion of its type, in no way limits how a taxonomist may circumscribe a taxon. Certainly, I propose that taxa are biologically meaningful when their circumscription produces a monophyletic group, but such circumscription is distinct from finding the accepted name. Whether you wish to prohibit all non-monophyletic groups or retain a favorite paraphyletic grade, Linnaean nomenclature can still provide the names you should remember.


From phylogeny to classification: What to do with paraphyletic grades, and is the phylocode a valid alternative?

Lücking, R.
The Field Museum, Chicago, USA

The major hurdle of modern systematics is the translation of phylogenies into classifications. The nature of both approaches is intrinsically different: while phylogeny studies continuous relationships between taxa, classification separates discrete groups. Several problems arise from this.
1) Strict cladistic practice accepts only monophyletic groups, but it is not inherent in a cladogram which monophyletic groups are to be recognized as taxa and at which taxonomic level. 2) Monophyletic groups are based on radiations that produced major clades before within-clade diversification, and hence might not be recoverable using molecular markers. 3) The essential difference between monophyletic and paraphyletic groups is that in the latter, clade divergence occurred after within-clade diversification. 4) Most phylogenies show monophyletic clades nested within paraphyletic residuals. 5) The Linnean system is inappropriate to produce a modern classification that follows strict cladistic principles. Recognition of nested clades as taxa is not possible, unless the residual paraphyletic grades are also recognized as taxa. To achieve complete monophyly, systematists are forced to either lump or split across clearly recognizable taxa, and introduce major taxonomic changes based on formal grounds, especially at genus, level due to the nature of the Linnean binominal. The phylocode is to be considered as an alternative but does not solve the lumping/splitting problem, nor does it address the problem of Linnean binominals. We suggest the following solutions: 1) Taxa can be defined at different taxonomic levels by reflecting the amount of independent character variation. 2) Because the lack of evidence to proof otherwise, paraphyletic groups can be accepted as natural. 3) However, if only monophyletic clades are accepted as taxa, we present a solution that allows to retain Linnean binominals without unnecessary lumping or splitting.


Integrating molecular and morphological data in the systematics of fungi

Parmasto, E.
Department of Mycology, Estonian Agricultural University, Tartu, Estonia

The use of molecular characters in addition to morphological ones, and the use of cladistic methods has remarkably changed our knowledge on the phylogeny of fungi. A single classification, common for all users, which is based on all available data ought to be coined. Classifications using molecular characters (sequencing data a.o.) are in several cases congruent with the present system (of mainly genera). In other cases, due to the widespread parallelism in changes of morphological character states, the new phylogeny hypotheses are different from the classification in current use. In these cases, the main conclusion drawn from the contradiction of molecular and morphological data is that we have to re-evaluate the usefulness of the characters we used. But there are also cases when cladistic analyses based on molecular and morphological characters are giving extremely different topologies of phylogenetic trees. One of the examples is the system of Hymenochaetales (Basidiomycota, Hymenomycetes): if the tree based on rDNA LSU sequence data is accepted, there are almost no synapomorphic morphological characters supporting the branching pattern.
Molecular data taken from the GenBank used for a phylogenetic analysis are in many cases erroneous, mainly due to misidentifications. When only one or some representative species are used to characterize presumably monophyletic genera, the topology of the resulting tree depends on the selection of the species. The number of species included in a study is usually relatively small, causing sampling errors; when additional taxa and species of closely related genera are included, the resulting tree topology is changing. Many studies have been published where no attempts have been made to use combined datasets or to compare molecular data based trees with the morphology-based ones. Studies where changes of morphological characters are mapped on trees obtained using sequence data are surprisingly rare.
Shortly: phylogenetic studies of fungi based on molecular characters are extremely fruitful, but we are only halfway in compiling more or less stable classifications. Until that, the modern trend of using rankless taxonomy and denoting clades arbitrarily is causing some chaos. The so-called Linnean hierarchy is nothing more – and nothing less – than a way of showing the phylogenetic relations between species or species groups in an easily understandable way. A system of organisms is a way of communication between all biologists, not only among taxonomists themselves.


Optional lichenization – an overlooked fungal evolutionary strategy, and alternatives for dealing with this in classification and naming

Wedin, M., Döring, H. & Gilenstam, G.
Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden

Lichenization is one of the most important fungal lifestyles, often claimed to be a major force in fungal evolution. Lichen fungi are assumed to be obligate symbionts, but here we show examples of epiphytic species having the option to undergo their whole sexual lifecycle either as lichens or as saprotrophs. This switch between nutritional modes allows the exploitation of different niches during the forest succession. We suggest that this environmental plasticity may be common in some taxonomic groups, and propose that it may be a general strategy in fungi adapted to unpredictable successional forest habitats. The two different lifestyles obviously result in morphologically very different fungi, with different ecological roles in the ecosystem. We acknowledge that some may feel a need to give these ecological expressions of the same fungal species different names; in effect, this is similar to the well-known green algal-cyanobacterial photobiont switch situation in many lichens. We will end by reviewing the pros and cons of various formal and informal nomenclatural solutions to this kind of infraspecific variation.

top