A CRITICAL APPRAISAL OF MODERN GENERIC CONCEPTS IN LICHENOLOGY

After a brief historical survey, some current trends in the delimitation of lichen genera are discussed. A widespread tendency is that of elevating any supposedly monophyletic group of species to genus rank. As the term ‘ monophyletic ’ has no lower limit, this is likely to result in an explosive inflation of new genera, in a severe loss of the information carried by generic names and in a high degree of nomenclatural disorder. Five criteria are proposed for the acceptance or rejection of new generic segregates: (1) DNA testing for monophyly, (2) phylo-genetic analysis, (3) number of characters used, (4) number of species considered, (5) information content of the new splittings. Upon a critical analysis of several recent generic segregations, a more flexible approach to taxonomic ranks is recommended, and particularly, when most of the suggested criteria are not fulfilled, a more frequent use of the subgeneric rank, which does not imply name changes.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

Variation within teosinte. I. Numerical analysis of morphological data

Principal components analysis of 27 morphological characters for 18 accessions of teosinte and 3 accessions of maize separated teosinte into 6 phenetic groups which showed broad agreement with previous taxonomic groupings. Tests for regression suggested significant linear relationships with altitude; teosintes from higher elevations are generally more maize-like for a combination of characters. Introgression from maize may have blurred racial identities within teosinte, but variation among current teosinte accessions cannot be satisfactorily explained solely on the basis of known maize introgression. It appears instead that racial differentiation in teosinte was well established by the time of the domestication of maize. While current racial classification of teosinte is quite useful, it does not adequately reflect the amount of genetic variation, nor does it accurately portray many of the relationships within teosinte.     

STUDIES ON 08CINELLA FRIT LINN

As the result of studies on Oscinella frit during the years pro to 1928, it was considered that an attempt might be made to solve economic problem presented by this fly by hybridization of oats, i a resistant variety as one parent.
The technique adopted is described and the experimental data show that resistance to attack is an inheritable character (or complex characters), although difficult of precise measurement. Further, shown that agricultural quality and resistance to attack are not in patible.
Wet weather conditions during the flight of the fly have a marked effect in limiting the extent of damage to the crop.
It is suggested that varietal differences in extent of attack ma due to varietal differences in crude fibre production or depositio silica, both tending to increase the larval difficulties and there for resistance of the plant.
I have great pleasure in acknowledging the readiness with w Dr Hunter of the School of Agriculture, Cambridge, has given me benefit of his experience; also, the valuable criticism which Mr J. C. F. Fryer, of the Ministry of Agriculture Pathological Laboratory, Har-penden, has always placed freely at my disposal.     

Taxic Revisions

Parsimony analysis provides a straightforward way of assessing homology on a tree: a state shared by two terminals comprises homologous similarity if optimization attributes that state to all the stem species lying between those terminals. Three-taxon statements (3ts), although seemingly "exact" in that each either fits a tree or does not, do not provide a satisfactory assessment of homology, because that assessment can be internally contradictory and because 3ts systematically exclude homologous resemblance in reversed states. Modified 3ts analysis (m3ta), a method in which both plesiomorphic and apomorphic states of "paired homologue" (PH) characters (those other than presence/absence data) are regarded as "informative" (able to distinguish groups), can (obviously) group by symplesiomorphy and so form paraphyletic groups unless data are clocklike enough. Patterson's pattern analysis (ppa) has the same shortcoming, to which it adds the drawback that only characters fitting the tree perfectly are used, a restriction that can easily lead to discarding most of the structure in the data. Revised m3ta (rm3ta), a method in which plesiomorphic states are not taken as informative, can also form paraphyletic groups, because it cannot apply reversals as apomorphies. The idea that knowledge of phylogeny has been derived from classifications does not imply that nonevolutionary methods should be employed for classification, but instead means that systematic methods must be logically capable of phylogenetic interpretation. Neither m3ta nor rm3ta satisfies that requirement because of their contradictory assessments of homology.     

Why a right to life rules out infanticide: A final reply to Räsänen

Joona Räsänen has argued that pro‐life arguments against the permissibility of infanticide are not persuasive, and fail to show it to be immoral. We responded to Räsänen’s arguments, concluding that his critique of pro‐life arguments was misplaced. Räsänen has recently replied in ‘Why pro‐life arguments still are not convincing: A reply to my critics’, providing some additional arguments as to why he does not find pro‐life arguments against infanticide convincing. Here, we respond briefly to Räsänen’s critique of the substance view, and also to his most important claim: that possession of a right to life by an infant does not rule out the permissibility of infanticide. We demonstrate that this claim is unfounded, and conclude that Räsänen has not refuted pro‐life arguments against infanticide.     

Linnaeus' sexual system and flowering plant phylogeny

Carl Linnaeus brought order to the knowledge of plants and animals by arranging all known species in encyclopaedic works. He proposed a system of plants, the sexual system, based on the number and arrangement of male and female organs. His artificial sexual system has since long been replaced by 'natural' or phylogenetic systems but there has never been a comprehensive comparison of the sexual system with modern plant classification. The currently most often used classification of flowering plants is the APG-system. It is based on comprehensive phylogenies of flowering plants, reconstructed by analyses of DNA data. The APG-system covers all flowering plants which are classified in 453 families and these are classified in 45 orders. Most of the species were not known at time of Linnaeus. Families and orders in the APG-system are arranged in larger informal groups representing major branches in the flowering plant phylogenetic tree. Three such groups are the monocots, the rosids, and the asterids.
I have examined all genera published in Species plantarum (1753) and classified them according to order and major groups in the APG-system. All classes except one, number 15 Tetradynamia, comprises groups of unrelated plants. Not surprisingly, the sexual system does not display what we know today about plant relationships. As is evident from this analysis, there is little correspondence between the sexual system and the APG-system. This does not mean that the sexual system has been useless or misleading. When it was introduced, it formed the basis for much intensified research and increased knowledge of plants.     

L'analyse et la synthèse en systématique végétale

Analysis and synthesis have been widely used in systematics since, at least, the XIXth Century. Even now, the four major authors (Cronquist, Dahlgren, Takhtajan, Thorne) of angiosperm systems use “synthetic” to qualify their classifications. This word — synthetic or synthesis — has many different meanings that can create ambiguity. Among these meanings, is there one that can be justifiably used to define biological classifications? Although much more than the following applications can be found in the botanical literature, this paper will mainly deal with six meanings which are still in use in contemporary systematics. A synthetic classification has been understood as a classification built upward, from the lower to the higher categories. If we define synthesis as the operation that starts with elements and proceeds to a whole, then upward classification could be viewed as a synthesis in which the concept of hierarchy plays a primordial role, a role that is not initially a part of synthesis. Moreover, synthesis cannot replace all classificatory processes, and other criteria of taxa must be used in addition to synthesis Historically, synthesis has replaced analysis; the latter being employed by Linnaeus in his sexual system. Indeed, Linnaeus used a divisive method in producing his classification; and since division was seen as synonymous to analysis and recognized as a method that led to artificial taxa, leading French taxonomists Adanson, Lamarck and A.-L. de Jussieu among others, rejected analysis and viewed their classifications as synthetic, i.e., based on the natural method. Therefore, a system of value took place: natural was better than artificial, synthesis better than analysis. Reinforcing the importance of synthesis was the belief in a concept widely accepted at the end of the XVIIIth Century: that of continuity. Linking groups and forming a continuum was a procedure eminently synthetic. Such a procedure, known as “chaining”, produced series or sequences of taxa. Analysis was used solely to express the idea of dichotomous or analytical keys, a Lamarckian innovation that enabled taxonomists to identify plants. But whether classifications are built from lower to higher categories (a synthesis of taxa) or from higher to lower categories (an analysis of taxa), another simultaneous, concomitant movement is implied: with the latter, a synthesis of characters, with the former, an analysis of characters. Therefore, a synthetic classification is nevertheless an analytical classification.Basing groups on resemblance instead of difference, results in yet another application of synthesis. This application is probably due to the analogy with “composition”. Already, a separation between resemblance and difference among characters is an analysis. More important, still, is that at a certain rank some characters are used to join whereas, at another rank, they separate. Thus, depending on ranks and taxa, characters are applied in a synthetic or analytical procedure. Here also, other criteria are needed to support group delimitation.In connection with the upward (synthetic) movement in classifying taxa, the use of a great number of characters was also considered to be synthesis. This has been a recurring theme in taxonomy over the last two centuries and was sometimes seen as the Gilmourian approach to classification. When would we be justified to talk about synthesis? After how many characters? In fact, it is not the number of characters that matters but how characters are handled. The use of many characters has been closely linked to the idea of natural groups and its joining with synthesis seems to derive from the association of “natural” and “synthetic”.Synthetic classifications equally imply the common idea that they must represent a résumé of information stemming from all biological fields or disciplines. If classifications portray evolution, as many systematists suggest, then it cannot be just a résumé. And one must first decide what classifications are about: a controversial subject among different schools of thought in taxonomy. This explains another meaning attached to synthesis. Biological classifications have been said to be a synthesis or résumé of two types of information: that of similarity and that of phylogeny. Anagenesis is sometimes viewed as incremental to classification and makes up for a third type of information. Even though taxonomists would (for once!) agree that a classification should be based on phenetic, cladogenetic and anagenetic data, such a classification cannot qualify as a synthesis since it is not a composition and does not meet the definition given above (an operation that starts with elements and goes on to a whole). It is impossible to represent these three types of data together in one classification scheme; they express three, sometimes irreducible, points of view. For such a classification, the word “eclectic” is preferable and closer to reality.The use of synthesis as one term of the dialectical movement has made hesitant steps in taxonomy. Indeed, the two opposed theses that evolve into the synthesis are hardly met in classification and the “dialectical” synthesis promulgated by a few taxonomists can be referred back to synthesis as a résumé.Is classification synthetic because it appears to be based on inductive procedures, as it is sometimes implied by different authors who link deduction and analysis (stemming from downward classification)? In logic, synthesis is sometimes (and questionably so) associated with deduction. Moreover, synthesis cannot follow from induction which deals, for example, with the universality of characters. In that sense, there is no composition and so no synthesis. Thus, although induction has been part of classification, it is not a synthetic method.Apart from the ambiguity originating from the multiple meanings of the word “synthesis” in the context of taxonomy, synthetic classifications do not fully express all the complexity and procedures that lead to it. Actually, a classification is as much a synthesis as an analysis. Both methods are complementary, and should not be opposed as is sometimes the case. This opposition was implicit in the debate between Linneans and Jussieans, surrounding the development of the natural method. If one wants to use “synthetic”, then one should be explicit about its meaning. Taxonomists should also be aware of the incompleteness of synthesis in constructing a classification and should be careful not to create a system of value based upon philosophical ground. They should always prefer a complementary mode of thinking when feasible, instead of an “either-or” approach.     

The classification of ferns

Intensive morphological studies have been devoted to the more primitive ferns, which represent a small minority of living species, but too little is yet known about the vast majority of other ferns, with the result that recent attempts at a natural classification show considerable differences of treatment.
The problem is complicated by convergent evolution in the characters of almost all parts of a fern plant. Not only similar soral form, but also similar frond form, types of venation, scales, etc. have been developed on different evolutionary lines.
To illustrate the nature of the problem an attempt has been made to state the probable characters of a primitive leptosporangiate fern, and the kinds of ways in which existing ferns have developed from this condition. Evolutionary change in different parts of the plant has proceeded in different ways and to different degrees in the many genera of existing ferns. Primitive characters of one kind or another are shown by a great number of ferns, along with highly advanced characters of other kinds.
Recent schemes of classification are briefly compared, and a summary is given of the author's own scheme, with notes on evolutionary trends in the various groups as he sees them.
Much more information is needed on which to establish a really satisfactory scheme. The present one is put forward in the hope that others will take up the work. With modern facilities for travel, it is to be hoped that more botanists will come to the tropics and see ferns and other too-little-known plants in their native habitats. Morphological study needs to be undertaken with an understanding of the living plant and of its environment.     

Toward resolving family-level relationships in rust fungi (Uredinales)

Rust fungi (Basidiomycota, Uredinales) consist of more than 7000 species of obligate plant pathogens that possess some of the most complex life cycles in the Eumycota. Traditionally, a limited number of synapomorphic characters and incomplete life-cycle and host-specificity data have hampered phylogenetic inference within the Uredinales. The application of modern molecular characters to rust systematics has been limited, and current contradictions, especially in the deeper nodes, have not yet been resolved. In this study, two nuclear rDNA genes (18S and 28S) were examined across the breadth of the Uredinales to resolve some systematic conflicts and provide a framework for further studies of the group. Three suborders of rusts are recovered. Of the 13 rust families most widely accepted, 8 are supported in full or in part (Coleosporiaceae, Melampsoraceae, Mikronegeriaceae, Phakopsoraceae p.p., Phragmidiaceae, Pileolariaceae, Pucciniaceae, Raveneliaceae), 3 are redundant (Cronartiaceae, Pucciniastraceae, Pucciniosiraceae), and the status of 2 (Chaconiaceae, Uropyxidaceae) could not be resolved. The Mikronegeriaceae and Caeoma torreyae are the most basal rusts sampled. It is concluded that morphology alone is a poor predictor of rust relationships at most levels. Host selection, on the other hand, has played a significant role in rust evolution. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.     

Genetic therapy, person-regarding reasons and the determination of identity -- a reply to Robert Elliot

I have outlined two ways of defending the claim that there are so-called person-regarding reasons for practising gene therapy on human conceptuses. One is metaphysical and concerns our nature and identity. The upshot of it is that, in cases of most interest, this therapy does not affect our identity, by bringing into existence anyone of our kind who would not otherwise have existed. The other defence is value theoretical and claims that even if genetic therapy were to affect the identity of beings our kind, there could still be person-regarding reasons for performing it, since we can be benefited and harmed by being caused to exist or not to exist. Robert Elliot has attacked both of these lines, and my present objective is to show how his criticisms can be deflected.     

Comparative stem anatomy of Mirabilis (Nyctaginaceae)

Mirabilis, a primarily American genus of 50?C60 species almost restricted to the New World, is the most diverse within Nyctaginaceae. It not only has the greatest number of species, but also many life forms, with annual herbaceous, suffrutescent and shrubby species and with prostrate, decumbent to erect stems that are sometimes clambering. Stem anatomy has been studied only for M. jalapa, and its characteristics extrapolated to the entire genus. In this study we evaluated the taxonomic significance of stem anatomical characters from 24 species of Mirabilis, as well as their potential relation to habit evolution. Qualitative and quantitative characters of transverse and longitudinal sections were evaluated using light and scanning electron microscopy. Stem anatomy varies in several features. The phloem is arranged in short tangential spreading bands or in large tangential bands forming semi-complete rings; the conjunctive tissue is fibrous, with thin-walled sclereids and fibres, or parenchymatous; the vessels are solitary or grouped in radial multiples or clusters; the xylem fibres are very thin-walled or thin- to thick-walled with simple to minutely bordered pits; most species are raylessness; the pith has parenchyma or thin-walled sclereids or brachysclereids. The distribution of anatomical characters in Mirabilis does not correspond with the current infrageneric classification. We suggest that some stem anatomical characters are correlated with habit and that the vascular cylinder and pith characters are related to an increase in mechanical strength. This study provides new information and novel characters about the stem anatomy not only of Mirabilis, but of the family.     

Is the Neotropical flora ready for the PhyloCode?

Nomenclatural systems are structured around classification, and together they enable increasingly informed communication about biological diversity. Challengers of Linnaean classification and nomenclature have proposed the PhyloCode, a new set of rules that would govern the way systematists classify and name the diversity of life. Monographs and floras are two fundamental vehicles for communicating information about plant diversity. These works provide a comprehensive foundation of botanical research upon which other scientific studies are based. Information conveyed by monographs and floras is utilized directly or indirectly both within and outside the scientific arena by a wide range of consumers, such as educators, agronomists, ecologists, conservationists, amateur naturalists, and even lawmakers, to name a few. Both classification and nomenclature are essential to the process of synthesis that leads to monographic and floristic treatments and the communication that they facilitate. Conversion to a new system would have far-reaching consequences for the flow of information from systematics to other scientific disciplines, and to society. The purposes of this article are to address the proposed conversion from the perspective of monographic and floristic research focused on Neotropical plant diversity and to point out some difficulties in applying the PhyloCode to the Neotropical flora. Although we welcome improvements in the current nomenclatural system, we conclude that the PhyloCode is not prepared to replace the Linnaean system as a new way to communicate information about Neotropical plant diversity.     

Rethinking the phylogeny of scleractinian corals: a review of morphological and molecular data

Scleractinian corals, which include the architects of coral reefs, are found throughout the world's oceans and have left a rich fossil record over their 240 million year history. Their classification has been marked by confusion but recently developed molecular and morphological tools are now leading to a better understanding of the evolutionary history of this important group. Although morphological characters have been the basis of traditional classification in the group, they are relatively few in number. In addition, our current understanding of skeletal growth and homology is limited, and homoplasy is rampant, limiting the usefulness of morphological phylogenetics. Molecular phylogenetic hypotheses for the order, which have been primarily focused on reef-building corals, differ significantly from traditional classification. They suggest that the group is represented by two major lineages and do not support the monophyly of traditional suborders and most traditional families. It appears that once a substantial number of azooxanthellate taxa are included in molecular phylogenetic analyses, basal relationships within the group will be clearly defined. Understanding of relationships at lower taxonomic levels will be best clarified by combined analyses of morphological and molecular characters. Molecular phylogenies are being used to inform our understanding of the evolution of morphological characters in the Scleractinia. Better understanding of the evolution of these characters will help to integrate the systematics of fossil and extant taxa. We demonstrate how the combined use of morphological and molecular tools holds great promise for ending confusion in scleractinian systematics.     

Variation of stone sculpin <Emphasis Type="Italic">Paracottus knerii</Emphasis> (Cottidae,Scorpaeniformes) of Baikal and waters of Baikal region

Sixteen samples of the stone sculpin Paracottus knerii from Baikal Lake, Angara River, and seven water bodies of the Baikal and Angara basins are studied. Variation of the morphometric and meristic characters is considered. It is found that the variation of a number of characters is biotopically conditioned and directed at fish adaptation to deepwater and dwelling in the conditions of rapid current. There are also the characters whose variation does not show any regularity, and it is a consequence of the discontinuity of range of the species. It is shown that the individual pairs of populations have differences in a number of characters, and these differences conform to the subspecies (CD > 1.28) and species levels (presence of hiatus). However all such pairs are connected by “ring overlaps,” thus, it is not possible to consider them as independent taxa.     

On quality of evidence in phylogeny reconstruction: a reply to Zrzavý's defence of the 'Ecdysozoa' hypothesis

Zrzavý’s arguments against the critical analyses of data supporting the Ecdysozoa hypothesis (Wägele et al., J. Zool. Syst. Evol. Res. 37, 211–223, 1999) are discussed. Zrzavý does not understand that the same basic principle of a priori weighting can be applied to sequence data as well as to morphological characters. Quality of evidence is the same as probability of homology, which is estimated from the number of discernible identical details. In sequences it is the number of identical nucleotides. Spectral analyses, dismissed by Zrzavý, visualize patterns of putative homologies present in alignments and also the number of positions supporting splits by chance alone. In cases in which old phylogenetic signals for a given monophylum are eroded in a gene, plesiomorphies and chance patterns will have strong influence on tree topologies and spectra. If plesiomorphies are a cause of errors, the addition of taxa that shorten internal branches is a remedy, although, in many cases such taxa may be extinct. The place of a priori estimations of data quality in a sequence of steps necessary for a phylogenetic analysis is shown. Morphological complexity is used as a proxy for a complex genetic basis and is used as a major criterion to compare characters of the Ecdysozoa and the Articulata. The details associated with the character ‘complex cuticle’ are discussed. Neither moulting nor the known components of the cuticle are novelties occurring only in Ecdysozoa. A published total evidence analysis is used to show that the number of coded characters does not necessarily reflect the quality of the data set. Zrzavý’s misunderstanding of the role of evolutionary scenarios is clarified and the importance of the use of additional biological data for plausibility arguments is explained. Plausibility arguments in favour of the Articulata hypothesis rely on facts found in functional morphology and in the fossil record. Zrzavý’s critique follows the actual mainstream but does not uncover logical mistakes or erroneous data analyses in the work of 86 . It is concluded that the Articulata hypothesis is a well‐founded alternative to the Ecdysozoa; it is based on much better morphological evidence and supported by plausibility arguments that currently do not exist for the Ecdysozoa.     

A phylogenetic analysis of the land plants

Phylogenetic systematics (cladistics) is a theory of phylogeny reconstruction and classification widely used in zoology. Taxa are grouped hierarchically by the sharing of derived (advanced) characters. The information is expressed in a cladogram, a best estimate of a phylogeny. Plant systematists generally use a phenetic system, grouping taxa on overall similarity which results in many groups being formed, at least in part, on the basis of shared primitive characters.
The methods of phylogenetic systematics are used to create a preliminary cladogram of land plants. The current classification of land plants is criticized for its inclusion of many groups which are not monophyletic.
Objections to the use of phylogenetic systematics in botany, apparent convergences within major groups and frequent hybridization, are shown to be invalid. It is concluded that cladistic analysis presents the best estimate of die natural hierarchy of organisms, and should be adopted by plant systematists in their assessment of plant interrelationships.