A comparison of phenetic and phylogenetic methods applied to the systematics of Oligochaeta

A comparative study of naidid subfamilies shows that a combination of ordination, Jaccard/Average Linkage cluster analysis and Wagner parsimony provides a useful basis for a rational phylogeny but that this does not differ markedly from the original proposed by Sperber nearly four decades ago. Hennig rules, modified by Wiley, permit a preliminary phylogeny and classification of the Annelida to be made by hand. An error in earlier versions suggested that the Dorydrilidae lacked prostate glands, and this is corrected.     

Theory and practice of botanical classification: Cladistics,phenetics and classical approaches—critical summary: Botanical systematics in 1987

Aristotelian principles still dominate botanical classification. Biological classification has undergone a major transformation during the period fromAdanson (1763) toDarwin (1859), from essentialism and the practice of downward classification, to empiricism and upward classification. The polythetic class was conceptualized during the 1950s. Interest in the species problem generated data from many different disciplines, the most recent being DNA systematics. These many disciplines have contributed to our understanding of evolutionary processes and to improved classifications. Many different phylogenetic models were developed and for different kinds of data. These models formed the basis of many algorithms to infer phylogenetic trees, some widely available in computer packages. This became possible with rapid growth of computer technology. These developments in turn catalyzed the formulation of divergent philosophical principles and approaches to classification. For instance, should methodological principles be divorced from knowledge about evolutionary processes? These approaches are discussed along with problems of reticulate evolution, intra-OTU-variation, homology, and other issues in the light of existing methodologies and their impact on classification. The next important direction in addition to development of new classificatory algorithms is the synthesis of various elements of different methodologies presently used in isolation.     

Phylogeny of flatfishes (Pleuronectiformes): comparisons and contradictions of molecular and morpho-anatomical data

Several species of flatfishes (Pleuronectiformes) have been studied by isoenzyme electrophoresis and DNA/DNA hybridization to establish the evolutionary relationships of this group of fishes. This molecular data-based phylogeny has been compared to previously described phylogenies based on morpho-anatomical criteria. A number of discrepancies are observed and discussed. The high degree of genetic divergence observed within the families of Pleuronectiformes indicates that their origin seems to be much older than suggested by their striking morphological similarity.     

A generalized taxon concept

A generalized taxon concept (GTC) is proposed with a method for revealing and ranking difficult taxa at any level in the taxonomic hierarchy. The method is based on cluster quality, denned jointly by die compactness of a cluster's contents and its isolation from its informational neighbours. The cluster contents are individuals in die case of species and at higher levels, taxa from the rank below. A standard, quality threshold value is obtained from clustering accepted taxa in the informational region. If the quality value of a problem cluster lies at or above the threshold it is accepted as a taxon and ranked with others at the current level. If it lies below, and is likely to be informationally useful, it may be accepted as a sub-taxon such as a subgenus or subfamily. Provision is made for coarsely scored data. The clustering is mainly based on homogeneity, where possible with a rapid, fuzzily cladistic de-weighting of symplesiomorphies by self-graded factors. The strengms of inter-item reactions such as breeding and DNA-DNA hybridization may also be used. The method is agglomerative so that it can rapidly reveal polythetic groups which may be riddled with exceptional property states caused by long exposure to natural selective forces. All this fits the evolutionary oudook of the GTC, which sees taxa as fuzzy clusters of populations and lineages sharing much of a genetic memory, moulded by a unique history of evolution and extinction. Practical problems of memods based on mis and other taxon concepts are briefly compared. The GTC's approach offers important refinements that could be valuable in helping to speed up urgent surveys of biodiversity, especially in the moist tropics.     

A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pleurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and Arpophyllinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phylogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pleurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pkurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and ArpophyUinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phytogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pkurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

Polygyrid relations: a phylogenetic analysis of 17 subfamilies of land snails (Mollusca: Gastropoda: Stylommatophora)

The family of polygyrid land snails in North America is significant for its sympatric shell convergences, diversity of mating systems and complex zoogeography; its monophyly and its relation to other families has long been questionable. Cladistic analysis has been performed on one representative each of 17 subfamilies, including all three polygyrid subfamilies and one or more subfamilies each from all ten of the families that have been proposed as the polygyrid sister groups. Eighteen anatomical synapomorphies are used, of which eight are newly discovered, four are differently assessed from previous studies, and six are traditional. The resulting strict consensus tree of alternative maximum-parsimony cladograms is: (Acavidae (Ammonitellidae Corillidae ((Discidae Oreohelicidae) (Helminthoglyptidae Bradybaenidae Polygyridae (Thysanophoridae (Camaenidae Sagdidae)))))).
According to this working hypothesis, the Polygyridae are monophyletic, and their sister group remains unresolved, although the Acavidae, Ammonitellidae, Corillidae, Discidae and Oreohelicidae can be ruled out. Of the five classifications of stylommatophoran families that have been proposed in the past 12 years, the consensus tree is closest to that of Nordsieck. For future morphological work, three regions are recommended as potentially rich in unused phylogenetic information: the fertilization pouch-seminal receptacle complex, the ureter at the pneumostome and the ventral-chain ganglia. Simultaneous dissection, wkh side-by-side comparisons, is recommended over other methods for detecting homologies in land snails. Molecular characters should be exploited, because of the scarcity and the frequent homoplasy of morphological characters.     

A unifying theory for methods of systematic analysis

A unifying theory for systematic analysis states that a number of methods should be used jointly to cope with various kinds of data; also that groups should be as consistent as possible, be made with least information loss, and where needed, be polythetic. A test of relationship, homogeneity, can use various kinds of data. It can take account of the internal variation of aggregate items such as genera. It can give due emphasis to smaller clusters that have likely important contexts of external items. It helps in analysing trends, cores and hazes in dendrograms. A proposed detector for formal groups can be based on measures of isolation, identifiability and inclusiveness. Non-mathematical, inter-item reaction tests such as hybridization and serology can also be used in grouping. All relationship data are used polythetically to reveal natural groups. This leads to a unified informational concept for taxa. This is more useful than the biological species concept that is restricted to inter-breeding data. All the methods appear to be analogues of the powerful human grouping instinct. The resulting compatibility is important as precise methods are needed mainly when the data are too complex for the mind to use reliably. Cladograms can be made by self-graded deweighting of homogeneity and agglomerative clustering. Unlike classical cladistics this can reveal any polythetic group. Finding the derived states for making cladograms is often much too hypothetical for a fully cladistic approach to be properly precise. Instead, where the evidence is weak, a milder strength of graded deweighting is used for the cladistic properties, which help to show relationships along with the others. Axiomatic failures of other classes of grouping methods are discussed. Unavoidable remnants of instinctive processing lower the precision of all the methods. The Uniter computer program, based on the theory, is tested with finely graded values of artificially ‘evolved’ items and with coarsely coded cladistic data. The results show that with natural data, the program should act as a fairly sensitive probe of past evolutionary branching. Another test shows how specimens from species complexes can be grouped and how distinctions between groups are analysed.     

Cladistic and phenetic analysis of relationships in Vicia subgenus Vicia (Fabaceae) by morphology and isozymes

 Variation of 80 multistate morphological characters and isozymes encoded by 13 loci among 23 vetch species of the type subgenus of the genus Vicia in comparison with V. dumetorum, V. pisiformis and V. sylvatica of the subgenus Cracca is described and analyzed with cladistic parsimony and phenetic neighbour-joining methods by using two different ways of coding. Morphological analyses showed the subgenus Vicia monophyletic and revealed subgroups in a general agreement with traditionally recognized sections, except showing V. faba nested within section Narbonensis and ambiguity in the position of V. lathyroides and V. bithynica. Parsimony analysis of orthozymes as presence/absence characters revealed in the subgenus two basic monophyletic clades: 1) V. faba and three species of the section Peregrinae, V. michauxii, V. aintabensis and V. peregrina, in one subclade linked with species of the Narbonensis and Hyperchusa sections together with V. pisiformis of subgenus Cracca in a second subclade; 2) species belonging to sections Vicia, Sepium, Pseudolathyrus and Lathyroides together with V. sylvatica of the subgenus Cracca. Neighbour-joining analysis of orthozymes revealed the same two basic groups, differing only in the relative position of some species in subclusters. Both isozyme analyses showed paraphyly of the subgenera Vicia and Cracca. Parsimony analysis of orthozymes as character states of isozymes yielded a largely unresolved strict consensus cladogram of 209 most parsimonious trees, and reweighting of characters failed to produce a stable tree. Phylogenetic congruence and discordance among morphological and isozyme analyses, coding ways, homoplasy and weighting of characters are discussed. Received November 20, 2001 Accepted January 31, 2002