A/The Brief History of Three-Taxon Analysis

Recent claims by its advocates notwithstanding, three-taxon analysis (3ta) provides no method for recognizing reversals or for applying them as apomorphies. Accordingly, 3ta could be used as a phylogenetic method only under an assumption of irreversibility. Being a method for calculating trees from character data, 3ta is not connected to any particular rule (“interpretation”) for selecting resolutions of consensus trees considered as abstract diagrams. 3ta cannot be justified simply by invoking a general minimization principle such as Occam's Razor, since that would cover almost any method. Some more specific basis is needed, and consideration of proposed bases for 3ta shows that none is even remotely adequate.     

Taxic Homology = Overall Similarity

Modified three-taxon analysis (m3ta), a method in which three-taxon statements are produced from a nonadditive binary coding of the original data, has been proposed as a model-free way of assessing monophyly of groups, utilizing the taxic concept of homology. In fact the taxic concept amounts to a model, and, further, one that seems to conflict directly with evolution. M3ta is a type of grouping by all similarities and, like all such methods, would require a clock assumption if the tree were to be interpreted phylogenetically. Groupings based on this method, consequently, are phenetic, and they have little to do with monophyly. It has been proposed to define phylogenetic systematics in terms of grouping only by presences. While popular among advocates of 3ta, such definitions are completely inadequate, both because absences may be apomorphic and because phenetic methods can disagree with phylogenetic ones even when no absences are involved.     

Recycled

Both three-taxon analysis (3ta) and conventional parsimony analysis (CPA) fall within the cladistic framework. Attempts to exclude 3ta from the general cladistic framework so far seem to amount to declaring CPA as the only permissible analytic technique within cladistics. Critics of 3ta have failed to fully implement it in examples; as a result this criticism is faulty and does not support the claims made. Ultimately, the relative merit of 3ta will be resolved empirically, by comparison of classifications produced from it with classifications using other methods.     

IS FARRIS OPTIMIZATION PERFECT?: THREE-TAXON STATEMENTS AND MULTIPLE BRANCHING

Abstract — The three-taxon approach to phylogenetic analysis separates the universe of cladograms into a larger number of classes of solutions showing decreasing degrees of fit to data than does conventional Farris optimization. The three-taxon approach applies to character analysis Nelson and Platnick's interpretation 2 of multiple branching in cladograms.     

On the Three-Taxon Approach to Parsimony Analysis

The following three basic defects for which three-taxon analysis has been rejected as a method for biological systematics are reviewed: (1) character evolution is a priori assumed to be irreversible; (2) basic statements that are not logically independent are treated as if they are; (3) three-taxon statements that are considered as independent support for a given tree may be mutually exclusive on that tree. It is argued that these criticisms only relate to the particular way the three-taxon approach was originally implemented. Four-taxon analysis, an alternative implementation that circumvents these problems, is derived. Four-taxon analysis is identical to standard parsimony analysis except for an unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. This restriction follows directly from the basic tenet of the three-taxon approach, that character state distributions should be decomposed into basic statements that are, in themselves, still informative with respect to relationships. A reconsideration of what constitutes an elementary relevant statement in systematics leads to a reformulation of standard parsimony as two-taxon analysis and to a rejection of four-taxon analysis as a method for biological systematics.     

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.     

Taxic and Transformational Homology: Different Ways of Seeing

Hypotheses of taxic homology are hypotheses of taxa (groups). Hypotheses of transformational homology are hypotheses of transformations between character states within the context of an explicit model of character evolution. Taxic and transformational homology are discussed with respect to secondary loss and reversal in the context of three-taxon statement analysis and standard cladistic analysis. We argue that it is important to distinguish complement relation homologies from those that we term paired homologues. This distinction means that the implementation of three-taxon statement analysis needs modification if all data are to be considered potentially informative. Modified three-taxon statement analysis and standard cladistic analysis yield different results for the example of character reversal provided by Kluge (1994) for both complement relation data and paired homologues. We argue that these different results reflect the different approaches of standard cladistic analysis and modified t.t.s. analysis. In the standard cladistic approach, absence, as secondary loss, can provide evidence for a group. This is because the standard cladistic approach implements a transformational view of homology. In the t.t.s approach discussed in this paper, absence can only be interpreted as secondary loss by congruence with other data; absence alone can never provide evidence for a group. In this respect, the modified t.t.s. approach is compatible with a taxic view of homology.     

On the TTSC–FTSC Formulation of Standard Parsimony

Standard parsimony analysis has recently been described in a “three-taxon-like” way (the three-taxa statements for contiguous series–four-taxa statements for contiguous series, or TTSC–FTSC procedure) in order to clarify the differences between the standard approach and three-taxon analysis. It is shown that the alleged equivalence of standard parsimony analysis and the TTSC–FTSC procedure does not hold. Some minor defects of the procedure can be fixed within the TTSC–FTSC logic, but no solution is available for two basic problems: (1) the elementary three-taxon-like statements of the TTSC–FTSC procedure are highly artificial; and (2) the equivalence with standard parsimony depends on an incomplete correction for nonindependence between these statements. However, these findings do not invalidate the reported superiority of standard parsimony as a method for biological systematics.     

Classification or Phylogenetic Estimates?

[m]3ta is a method that seeks to implement a taxic view of homology. The method is consistent with Patterson's tests for discriminating homology from nonhomology. Contrary to the claims of Kluge and Farris, (1999, Cladistics 15, 205–212), m3ta is not a phenetic method—nor does it necessarily place the basal split in a tree between the phenetically most divergent taxa. [m]3ta does not seek to accurately recover phylogeny but rather it seeks to maximize the information content of taxic homology propositions. [m]3ta is a method of classification in which the unit of analysis is the relation of homology. [m]3ta differs from all phylogenetic methods because the units of analyses in phylogenetic methods, including sca, are transformation series.     

THREE-TAXON STATEMENTS: A MORE PRECISE USE OF PARSIMONY?

Abstract— Binary characters can be represented in data matrices by the three-taxon statements they imply. Transforming characters into three-taxon statements may increase the sensitivity of parsimony to differences in the fit of data to alternative cladograms. Extrapolation of the technique to multistate features allows semi-additive characters to be coded accurately. In many cases, analysis of the transformed data produces fewer equally parsimonious solutions than does analysis of the raw data. In other cases, additional equally parsimonious solutions, or even different solutions, may be produced; in those cases, the results appear to accommodate information from a larger number of characters than do the results from raw data.     

Phylogenetic inference: how much evolutionary history is knowable?

In order to reconstruct phylogenetic trees from extremely dissimilar sequences it is necessary to estimate accurately the extent of sequence divergence. In this paper a new method of sequence analysis, Markov triple analysis, is developed for determining the relative frequencies of nucleotide substitutions within the three branches of a three-taxon dendrogram. Assuming that nucleotide sites are independently and identically distributed and assuming a Markov model for nucleotide (or protein) evolution, it is shown that the unique Markov matrices can be reconstructed given only the joint probability distribution relating three taxa. (In the much simpler case involving only two taxa and two character states, Markov matrices can also be reconstructed, provided symmetry assumptions are placed on the elements of the matrices.) The method is illustrated using sequence data from the combined first and second codon positions derived from complete human, mouse, and cow mitochondrial sequences.      

Roles of the VMA3 gene product, subunit c of the vacuolar membrane H(+)-ATPase on vacuolar acidification and protein transport. A study with VMA3-disrupted mutants of Saccharomyces cerevisiae

VMA3, a structure gene of the vacuolar membrane H(+)-ATPase subunit c of Saccharomyces cerevisiae, has been cloned and characterized. The VMA3 gene encodes a hydrophobic polypeptide with 160 amino acids as reported previously by Nelson and Nelson (Nelson, H., and Nelson, N. (1989) FEBS Lett. 247, 147-153). Peptide sequence analysis indicated that the VMA3 gene product lacks N-terminal methionine and does not have a cleavable signal sequence. To investigate functional and structural roles of the subunit c for vacuolar acidification and protein transport to the vacuole, haploid mutants with the disrupted VMA3 gene were constructed. The vma3 mutants can grow in nutrient-enriched medium, but they have completely lost the vacuolar membrane H(+)-ATPase activity and the ability of vacuolar acidification in vivo. The subunit c was found to be indispensable for the assembly of subunits a and b of the H(+)-ATPase complex. The disruption of the VMA3 gene causes yeast cells with considerable lesions in vacuolar biogenesis and protein transport to the vacuole and inhibits endocytosis of lucifer yellow CH completely.     

Determination of Glucose by a Modification of Somogyi-Nelson Method

Nelson’s arsenomolybdate, the chromogenic reagent in Somogyi–Nelson method, was replaced by Folin–Ciocalteu phenol reagent. The major object was to remove the toxic arsenic compounds from the color reaction system. The color-producing ability of the phenol reagent was considerably lower than that of Nelson’s reagent. However, the modified method was favorably comparable to Somogyi–Nelson method in simplicity, reproducibility and stability of color development. The error in both the modified and Somogyi–Nelson method could be reduced to about one fourth by adding sodium benzoate (final concentration, about 0.5%) to the test solutions.     

The complete nucleotide sequence of the mitochondrial DNA of the agnathan Lampetra fluviatilis: bearings on the phylogeny of cyclostomes

There are two competing theories about the interrelationships of craniates: the cyclostome theory assumes that lampreys and hagfishes are a clade, the cyclostomes, whose sister group is the jawed vertebrates (gnathostomes); the vertebrate theory assumes that lampreys and gnathostomes are a clade, the vertebrates, whose sister group is hagfishes. The vertebrate theory is best supported by a number of unique anatomical and physiological characters. Molecular sequence data from 18S and 28S rRNA genes rather support the cyclostome theory, but mtDNA sequence of Myxine glutinosa rather supports the vertebrate theory. Additional molecular data are thus needed to elucidate this three-taxon problem. We determined the complete nucleotide sequence of the mtDNA of the lamprey Lampetra fluviatilis. The mtDNA of L. fluviatilis possesses the same genomic organization as Petromyzon marinus, which validates this gene order as a synapomorphy of lampreys. The mtDNA sequence of L. fluviatilis was used in combination with relevant mtDNA sequences for an approach to the hagfish/lamprey relationships using the maximum-parsimony, neighbor-joining, and maximum-likelihood methods. Although trees compatible with our present knowledge of the phylogeny of craniates can be reconstructed by using the three methods, the data collected do not support the vertebrate or the cyclostome hypothesis. The present data set does not allow the resolution of this three-taxon problem, and new kinds of data, such as nuclear DNA sequences, need to be collected.     

Breeding cycle of the Cape petrel Daption capense at Nelson Island, Antarctica

Timing and duration of the breeding cycle of the Cape petrel Daption capense were studied during two breeding seasons (1990/1991 and 1991/1992) at Nelson Island, South Shetland Islands, Antarctica. In 1991/1992 the copulatory period extended over 53 days, with median date and a peak about 28 and 19 days respectively, before the median date of laying. Laying began 85 days after arrival, with mean (= median) date on 2 December (SD = 2.5 days). The distributions of laying, hatching and fledging dates showed a similar degree of synchrony and did not differ between years. Incubation and chick period were equally long (46 days), the former being less variable (coefficient of variation = 2.8% and 4.6%, respectively). Mean completed nesting cycle (92 days) was about 2 days shorter at Nelson Island than elsewhere and tended to shorten as the breeding season progressed. Its mean length represented 86% of the whole nesting period (107 days), which in turn represented 56% of the period of continuous colony attendance. Timing and duration of nesting stages did not differ between colonies or sets of nests subjected to various levels of disturbance. Received: 8 July 1996 / Accepted: 11 November 1996     

Review of monophyly of the Kyphosidae (sensu Nelson, 1994), inferred from the mitochondrial ND2 gene

 Girella, Kyphosus, Scorpis, and some other perciform fishes have been regarded as being related to each other. Nelson (1994) recognized them as the subfamilies under the Kyphosidae, but he did not show any synapomorphic characters uniting them. Johnson and Fritzsche (1989) suggested that the perciform group characterized by RLA pattern 10, namely, Girellidae, Kyphosidae (not of Nelson, 1994), Scorpididae, Microcanthidae, Kuhliidae, Arripidae, Oplegnathidae, Terapontidae, and families of the Stromateoidei, form a monophyletic group. We estimated the phylogenetic relationships of fishes of the group to review monophyly of the Kyphosidae (sensu Nelson, 1994) by partially sequencing the mitochondrially encoded NADH dehydrogenase subunit 2 gene. Labracoglossa-Scorpis, Oplegnathus, Kyphosus, Kuhlia, Microcanthus, and Girella constituted a single clade with relatively high reliability values for both the neighbor-joining (NJ) and maximum-likelihood (ML) trees, but the monophyly of Kyphosidae (sensu Nelson, 1994) was not supported. The group characterized by RLA pattern 10 formed a monophyletic group both in the NJ and ML trees here; however, additional basal perciform taxa need to be analyzed to resolve it more clearly. Received: June 27, 2001 / Revised: September 29, 2001 / Accepted: October 28, 2001     

系统聚类分析在镰刀菌鉴定中的应用

根据Nelson,Toussoun&Marasas(1983)的分类系统,选取在PDA和CLA培养基上的50个编码性状,利用系统聚类分析的平均连锁法,初步建立了30种镰刀菌属(Fusarium)真菌为基础的计算机鉴定系统。用这个系统对玉米穗粒腐病上的三个未知菌株(Fusarium sp.1,F.sp.2,F.sp.3)进行鉴定的结果表明,F.sp.1为F.graminearum,F.sp.2为F.moniliforme,F     

A Family Level Analysis of Tardigrade Phylogeny

In the present study a character data set suitable for cladistic analysis at the family level was developed. A data matrix consisting of 50 morphological characters from 15 families of tardigrades was analyzed by maximum parsimony. Kinorhynchs, loriciferans, and gastrotrichs were used as outgroups. The results agree with the currently accepted hypothesis that Eutardigrada and Heterotardigrada are distinct monophyletic groups. Among the eutardigrades, Eohypsibiidae was found to be a sister group to Macrobiotidae+Hypsibiidae, while Milnesiidae was the basal eutardigrade family. The basal heterotardigrade family was found to be Oreellidae. Echiniscoideans grouped with some traditional Arthrotardigrada (Renaudarctidae, Coronarctidae+Batillipedidae) suggesting that the arthrotardigrades are not monophyletic. The 18S rRNA gene sequence of Batillipes mirus Richters, 1909 and Calohypsibius schusteri Nelson & McGlothlin, 1996 were obtained and their addition to a previously published dataset supports the monophyly of Heterotardigrada and of Parachela versus Apochela within the Eutardigrada.