bluuebunny/crossref_metadata_2025 huggingface dataset:
The Evolutionary Interplay of Social Behavior, Resource Use and Anti‐Predator Behavior in Zetoborinae+ Blaberinae+Gyninae+Diplopterinae Cockroaches: A Phylogenetic Analysis
Authors: Grandcolas Philippe
Published: July 2005

Theories of social evolution in cockroaches have mainly referred to hypotheses of evolutionary relationship between resource use and social system. The use of particular resources, such as scattered and enclosed habitat, was hypothesized to have favored evolution toward presociality or subsociality. A phylogenetic test of these hypotheses is carried out using the clade (Zetoborinae+ Blaberinae+Gyninae+Diplopterinae). Phylogenetic patterns of habitat use, social systems and anti‐predator behavior are inferred and compared to previous evolutionary hypotheses. There is much heterobathmy concerning these three attributes and five evolutionary paths are inferred which weakly corroborate the hypothesis of evolutionary relationship between resource use and social system. Anti‐predator behavior also appears to be possibly related evolutionarily to social systems.
Position and Delineation of Chrysopetalidae and Hesionidae (Annelida, Polychaeta, Phyllodocida)
Authors: Pleijel Fredrik , Dahlgren Thomas
Published: July 2005

Previous studies suggest that the polychaete taxa Hesionidae and Chrysopetalidae may not represent separate groups, that Pilargidae constitute a subgroup within Hesionidae, and that Hesionides and Microphthalmus are highly derived hesionids. Phylogenetic systematic analyses of Phyllodocida and the subgroup Nereidiformia are presented in order to clarify the position and delineation of these taxa. The phyllodocida analysis includes 18 families representing the majority of the taxa in the group, is rooted with Onuphidae, and is based on 42 absent/present coded morphological characters, obtained mainly from literature. All 69 resulting shortest trees include the clade (Chrysopetalidae, Nereididae, Hesionidae), but with either Syllidae, Nautiliniellidae, Pilargidae or (Aphroditiformia, Pisionidae) as sister. In‐ and outgroup taxon selection for the Nereidiformia study is dictated by the outcome of Phyllodocida analysis, with scores based on examined species of two chrysopetalids, four hesionids, one nereid, one pilargid, one pisionid, one syllid, plus the putative hesionids Hesionides arenaria and Microphthalmus sp. It is based on 46 absent/present coded morphological characters. Two equally parsimonious trees indicate that chrysopetalids and hesionids are well delineated, that pilargids and hesionids are non‐overlapping, and that Microphthalmus and Hesionides are not hesionids.
Three‐Dimensional Cost‐Matrix Optimization and Maximum Cospeciation
Authors: Ronquist Fredrik
Published: July 2005

In recent years, event‐based approaches have been gaining ground in coevolutionary and biogeographical inference. Unlike pattern‐based methods, event‐based protocols deal directly with evolutionary events, such as dispersals and host switches. Three protocols have been proposed to date: (1) a coevolutionary method based on optimization of a standard two‐dimensional cost matrix; (2) dispersal–vicariance analysis, based on optimization of a three‐dimensional cost matrix; and (3) the maximum cospeciation method, thus far not considered a cost matrix method. I describe here general three‐dimensional cost matrix optimization algorithms and how they can be applied to the maximum cospeciation problem. The new algorithms demonstrate that all existing event‐based protocols, as well as possible future methods based on more complicated process models, can be incorporated into the three‐dimensional cost matrix optimization framework.
Rooting with Multiple Outgroups: Consensus Versus Parsimony
Authors: Barriel Véronique , Tassy Pascal
Published: July 2005

Using outgroup(s) is the most frequent method to root trees. Rooting through unconstrained simultaneous analysis of several outgroups is a favoured option because it serves as a test of the supposed monophyly of the ingroup. When contradiction occurs among the characters of the outgroups, the branching pattern of basal nodes of the rooted tree is dependent on the order of the outgroups listed in the data matrix, that is, on the prime outgroup (even in the case of exhaustive search). Different equally parsimonious rooted trees (=cladograms) can be obtained by permutation of prime outgroups. An alternative to a common implicit practice (select one outgroup to orientate the tree) is that the accepted cladogram is the strict consensus of the different equally parsimonious rooted trees. The consensus tree is less parsimonious but is not hampered with extra assumption such as the choice of one outgroup (or more) among the initial number of outgroup terminals. It also does not show sister‐group relations that are ambiguously resolved or not resolved at all.
On the TTSC–FTSC Formulation of Standard Parsimony
Authors: De Laet Jan , Smets Erik
Published: July 2005

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.
Cladistic Analysis of the Briza Complex (Poaceae, Poeae)
Authors: Bayón Néstor David
Published: July 2005

The Briza complex comprises 23 species from South America, Mesoamerica and Europe. They constitute a monophyletic group because of the tendency of the spikelets to be dorsiventrally compressed. A cladistic analysis of the complex was performed using 32 characters from morphology. The terminal taxa were the species of the genera Briza, Calotheca, Microbriza, Poidium and Rhomboelytrum. Dactylis and Arrhenatherum were chosen to root the cladograms. Results of the cladistic analysis of the complex provide support for the ideas of Nicora and Rugolo (1981, Darwiniana 23(1), 279–309): Briza, Calotheca, Microbriza, Poidium and Rhomboelytrum are supported as monophyletic groups. Within Briza, only the Chascolytrum group appears monophyletic, while the Briza and Uniolae groups are paraphyletic. Poidium ambiguum, sometimes placed in Poa, is considered here as Poidium.
Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes
Authors: Lipscomb Diana L , Farris James S , Källersjö Mari , Tehler Anders
Published: July 2005

Sequences of the small subunit (SSU) ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their phylogenetic signal ambiguous. Large ambiguous data sets may have many most‐parsimonious trees, and finding them all may be impossible using convential phylogenetic methods. To examine the reliability of the number and relationships of eukaryotic kingdoms proposed by previous analyses of the SSU, we calculated trees from aligned sequences from eukaryotes in the Ribosomal Database Project using parsimony jackknifing which uses a resampling procedure to rapidly search large data sets for the branches that are strongly supported and eliminates poorly supported groups. Two separate analyses were carried out: an analysis in which all bases were equally weighted, and one in which transversions only were used. The parsimony jackknife procedure was able to efficiently find trees in which most major groups of eukaryotes were supported and in which some evolutionary hypotheses proposed by previous workers were tested. The relationships of these major groups to each other were largely unresolved, indicating that the SSU data, as represented in this database, is insufficient for answering questions about these deep branches. Interestingly, the analysis of transitions differs from the results of the entire data set, primarily being less resolved. This indicates that transversional mutations are important contributors to the resolved structure of the tree.
Recycled
Authors: Siebert Darrell J , Williams David M
Published: July 2005

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.
Widespread Taxa and Component 2.0
Authors: Enghoff Henrik
Published: July 2005

Resolved area cladograms found by heuristic search with COMPONENT 2.0, with the option “map widespread associates” turned off, correspond to Assumption 1 only if the widespread taxon occupies a terminal position on the taxon‐area‐cladogram. If the widespread taxon occupies a basal position, the resolved area cladograms correspond to Assumption 2.
Problems Determining the Phylogenetic Position of Echiurans and Pogonophorans with Limited Data
Authors: Siddall Mark E , Fitzhugh Kirk , Coates Kathryn A
Published: July 2005

The phylogenetic position of Echiura and Pogonophora was recently reconsidered using 346 bp of elongation factor 1‐alpha (EF‐1α). On the basis of these results alone it was suggested that the relationships of Anne lida be reconsidered and that the systematics of the group changed accordingly. An examination of these data, however, reveals difficulties in the original analysis that relate to weighting and the relative inclusion or exclusion of available characters and of taxa. Wholesale revision of the systematics of Annelida or of groups therein awaits the availability of more comprehensive work.
Phylogeny of the Prolecithophora (Platyhelminthes) Inferred from 18S rDNA Sequences
Authors: Norén Michael , Jondelius Ulf
Published: July 2005

Complete nuclear 18S rDNA sequences from 14 species of the Prolecithophora were obtained and used, in combination with literature data, to generate the first parsimony‐based hypothesis of the phylogeny of the order Prolecithophora (Platyhelminthes). Bootstrap, parsimony jack‐knife, and Bremer support values were computed and compared. The monophyly of the Prolecithophora sensu stricto and the family Plagiostomidae is strongly supported. The taxa Separata, Combinata, and Plagiostomum are shown to be nonmonophyletic. Cylindrostomidae and Ulianinidae are transferred to Pseudostomidae. The Urastomidae is not part of the Prolecithophora.
Measuring Topological Congruence by Extending Character Techniques
Authors: Wheeler Ward
Published: July 2005

A measure of topological congruence which is an extension of the Mickevich–Farris character incongruence metric (i.e., ILD; Mickevich and Farris, 1981) is proposed. Group inclusion characters (1 = member of a clade; 0 = not a member) are constructed for each topology to be considered. The sets of characters derived from the topologies are then compared for character incongruence due to data set combination. Each homoplasy signifies a disagreement among topological statements. The value is normalized for potential maximum incongruence to adjust values for unresolved topologies. This measure is compared to other topological and character congruence techniques and explored in test data.
A Report on “One Day Symposium on Numerical Cladistics”
Authors: Horovitz Inés
Published: July 2005

A recent symposium on numerical cladistics held at the American Museum of Natural History in New York City, addressed novel methods for searching tree space, applications of randomizations in cladistic analysis, and data management. One of the major concerns in systematics is that of finding the global optimum in tree length. The space to search is complex because it includes many local optima. It is a difficult task to escape local optima without a great loss in efficiency. The ideal is to search among suboptimal topologies and still obtain an answer in a reasonable amount of time. Nixon presented a new family of methods called “parsimony ratchet,” which are successful at escaping local optima. Moilanen presented a new program which may have similar advantages. Two presentations, one by Goloboff and Farris and another by Farris, Goloboff, Källersjö, and Oxelman, introduced modifications to parsimony jackknifing that improved its accuracy when compared to normal heuristic searches. Wheeler discussed the advantages of new methods of analyzing DNA and protein sequence data, which eliminate multiple alignment; the most recent one packs nucleotides into strings which constitute the new characters. Siddall discussed different applications of randomization in cladistics and their logical consistency, finding some more acceptable than others. Nixon and Carpenter presented a new program for managing data. This symposium will probably be a landmark judging from the originality and practicality of the points presented.
Are Third Positions Really That Bad? A Test Using Vertebrate Cytochrome b
Authors: Björklund Mats
Published: July 2005

In the analysis of coding DNA sequences for phylogenetic purposes 3rd positions are commonly downweighted, or excluded, and 2nd positions are likewise given high weight. The basis of this is a belief that the larger numbers of 3rd position substitutions imply a larger amount of misleading information than the slowly evolving 2nd positions. This paper tests this assertion by splitting 10 vertebrate data sets into three parts consisting of 1st, 2nd, and 3rd positions only. The relative performance of these data sets was tested by a number of suggested methods for assessing the phylogenetic content in a data set. Contrary to the prediction, the relative performance was 3rd > 1st > 2nd. This implies that a downweighting of 3rd positions in favour of 2nd positions is not supported by the analyses of their phylogenetic content. There are several reasons to believe that the overall amount of change is a poor predictor of the level of homoplasy and these are discussed. The overall conclusion is that unless there is solid evidence that 3rd positions really are misleading, they should not be treated so by default.
Molecular Phylogeny and Biogeography of the Native Rodents of Madagascar (Muridae: Nesomyinae): A Test of the Single‐Origin Hypothesis
Authors: Jansa Sharon A. , Goodman Steven M. , Tucker Priscilla K.
Published: July 2005

Complete nucleotide sequences from the mitochondrial cytochrome b gene (1143 bp) were used to investigate the phylogenetic relationships among the native rodents of Madagascar. Specifically, this study examines whether the nine genera of nesomyines form a monophyletic group relative to other Old World murids. All nine of the nesomyine genera, including multiple individuals from 15 of the 21 described species, were included in the analysis, and their monophyly was assessed relative to the murid subfamilies Mystromyinae, Petromyscinae, Dendromurinae, Cricetomyinae, Murinae, Rhizomyinae, and Calomyscinae. Phylogenetic analysis of the resulting 95 taxa and 540 characters resulted in 502 equally parsimonious cladograms. The strict consensus tree weakly refutes the monophyly of Nesomyinae and suggests that the Malagasy rodents form a clade with dendromurines (as represented by Steatomys) and the African rhizomyine Tachyoryctes. The cladogram strongly refutes the association of the South African genus Mystromys with the Malagasy genera and suggests that Petromyscus and Mystromys form a monophyletic group. We provide the first explicitly phylogenetic scenario for the biogeographic history of nesomyine rodents. Our phylogenetic hypothesis indicates: (1) rodents invaded Madagascar only once, (2) they came from Asia not from Africa as is commonly assumed, and (3) there was a secondary invasion of rodents from Madagascar into Africa.
Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur
Authors: Yoder Anne D. , Irwin Jodi A.
Published: July 2005

DNA sequences from three mitochondrial genes and one nuclear gene were analyzed to determine the phylogeny of the Malagasy primate family Lemuridae. Whether analyzed separately or in combination, the data consistently indicate that Eulemur species comprise a clade that is sister to a Lemur catta plus Hapalemur clade. The genus Varecia is basal to both. Resolution of cladogenic events within Eulemur was found to be extremely problematic with a total of six alternative arrangements offered by various data sets and weighting regimes. We attempt to determine the best arrangement of Eulemur taxa through a variety of character and taxon sampling strategies. Because our study includes all but one Eulemur species, increased taxon sampling is probably not an option for enhancing phylogenetic accuracy. We find, however, that the combined genetic data set is more robust to changes in taxon sample than are any of the individual data sets, suggesting that increased character sampling stabilizes phylogenetic resolution. Nonetheless, due to the difficult nature of the problem, we may have to accept certain aspects of Eulemur interrelationships as uncertain.
A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems
Authors: Lee Dong‐Chan , Bryant Harold N.
Published: July 2005

Character coding entails assumptions that may be problematic within the context of parsimony analysis using current computer algorithms. The example discussed here involves a character‐variable (e.g., tail color) that is inapplicable in some taxa in the analysis because the part (e.g., tail) with which it is associated is lacking in those taxa. The part and character‐variable can be coded as separate characters, or they can be fused into a single character. If the part and character‐variable are coded as separate characters there is transformational independence between the part and the character‐variable, but the logical dependence inherent to the hierarchical relationship between the part and its character‐variable is only partly accounted for. Fusing the part and character‐variable into one multistate character fully accounts for the logical dependence, but it is equivocal regarding the transformational independence. Separate coding is consistent with the primary homology statement that the part is homologous in all taxa possessing it, whereas fused coding is equivocal regarding this hypothesis of primary homology. As a result fused coding involves a loss of phylogenetic information. Use of a stepmatrix or other mechanisms associated with fused coding that preserve this phylogenetic information involves weighting schemes or ordered characters that have other assumptions that may also be difficult to justify.
Fixed Character States and the Optimization of Molecular Sequence Data
Authors: Wheeler Ward
Published: July 2005

A method is proposed to optimize molecular sequence data that does not employ multiple sequence alignment. This method treats entire homologous contiguous stretches of sequence data as individual characters. This sequence is treated as the homologous unit employed in phylogeny reconstruction. The sets of specific sequences exhibited by the terminal taxa constitute the character states. The number of states is then less than or equal to the number of unique sequences (or homologous fragments) exhibited by the data. A matrix of transformation costs is created to relate the states to one another. The cells of this matrix are defined as the minimum transformation cost between each pair of states based on insertion–deletion and base substitution costs. The diagnosis of a topology then follows existing dynamic programming techniques, with the number of states greatly expanded. Since the possible sequences reconstructed at nodes are limited to those exhibited by the terminals, cladograms constructed in this way may be longer than those of other methods in that they require a greater number of weighted evolutionary events. Example data, the effects of missing data, restricted ancestors, and putative long‐branch attraction are discussed.
Two Requirements for Obtaining Valid Common Patterns under Different Assumptions in Vicariance Biogeography
Authors: van Veller Marco G.P. , Zandee M. , Kornet D.J.
Published: July 2005

In vicariance biogeography, widespread or sympatric taxa can be dealt with under assumptions 0, 1, and 2. Data from cladogenetic relationships among taxa of a monophyletic group and their distribution over areas are assumed, in the order 0 → 1 → 2, to represent decreasing information about vicariance events. A less strict assumption carries a larger solution set, i.e., the number of possible area cladograms increases with the decrease in strictness of the assumption applied. We formulate two requirements for obtaining valid general area cladograms from data of several monophyletic groups of taxa. First, the assumptions, and with them the sets of area cladograms derived under these assumptions, should be inclusive. Second, sets of single group area cladograms should be compared for different monophyletic groups under a single assumption. When these two requirements are met, area cladograms become consistent with respect to the processes (vicariance, extinction, and dispersal) that are a priori assumed. The explanatory power increases for any particular monophyletic group of taxa when the set of valid general area cladograms contains a subset of area cladograms derived under a more strict assumption. We discuss examples from literature of how violation of these two requirements affects the results.
Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima
Authors: Goloboff Pablo A.
Published: July 2005

New methods for parsimony analysis of large data sets are presented. The new methods are sectorial searches, tree‐drifting, and tree‐fusing. For Chase et al.'s 500‐taxon data set these methods (on a 266‐MHz Pentium II) find a shortest tree in less than 10 min (i.e., over 15,000 times faster than PAUP and 1000 times faster than PAUP*). Making a complete parsimony analysis requires hitting minimum length several times independently, but not necessarily all “islands” for Chase et al.'s data set, this can be done in 4 to 6 h. The new methods also perform well in other cases analyzed (which range from 170 to 854 taxa).
Frigatebirds, Tropicbirds, and Ciconiida: Excesses of Confidence Probability
Authors: Farris James S. , Källersjö Mari , Crowe Timothy M. , Lipscomb Diana , Johansson Ulf
Published: July 2005

Because it is based on a significance test that takes the shape of the tree as given, the Rzhetsky/Nei Confidence Probability (CP) can attribute high “confidence” to groups with little or even literally no support. CP further overestimates confidence in that it takes no account of reliability of alignment, and it shows instability in that drastic changes in results can be produced by small changes in data. Instability can arise when alignment is uncertain, since different alignment strategies can lead to slightly different matrices. Parsimony jackknifing offers a more reliable and stable way of assessing support. To take ambiguities of alignment into account with parsimony jackknifing, we suggest “consensus” and “average” methods of summarizing jackknife results from several alignments. Reanalyzing 12S and 16S rRNA data on pelecaniform birds, we find that CP has overestimated support for the Ciconiida, for placing frigatebirds with condors, and for placing tropicbirds with cormorants.
Searching for Most Parsimonious Trees with Simulated Evolutionary Optimization
Authors: Moilanen Atte
Published: July 2005

This study describes novel algorithms for searching for most parsimonious trees. These algorithms are implemented as a parsimony computer program, PARSIGAL, which performs well even with difficult data sets. For high level search, PARSIGAL uses an evolutionary optimization algorithm, which feeds good tree candidates to a branch‐swapping local search procedure. This study also describes an extremely fast method of recomputing state sets for binary characters (additive or nonadditive characters with two states), based on packing 32 characters into a single memory word and recomputing the tree simultaneously for all 32 characters using fast bitwise logical operations. The operational principles of PARSIGAL are quite different from those previously published for other parsimony computer programs. Hence it is conceivable that PARSIGAL may be able to locate islands of trees that are different from those that are easily located with existing parsimony computer programs.
Noise
Authors: Wenzel John W. , Siddall Mark E.
Published: July 2005

The proliferation of DNA sequence data has generated a concern about the effects of “noise” on phylogeny reconstruction. This concern has led to various recommendations for weighting schemes and for separating data types prior to analysis. A new technique is explored to examine directly how noise influences the stability of parsimony reconstruction. By appending purely random characters onto a matrix of pure signal, or by replacing characters in a matrix of signal by random states, one can measure the degree to which a matrix is robust against noise. Reconstructions were sensitive to tree topology and clade size when noise was added, but were less so when character states were replaced with noise. When a signal matrix is complemented with a noise matrix of equal size, parsimony will trace the original signal about half the time when there is only one synapomorphy per node, and about 90% of the time when there are three synapomorphies per node. Similar results obtain when 20% of a matrix is replaced by noise. Successive weighting does not improve performance. Adding noise to only some taxa is more damaging, but replacing characters in only some taxa is less so. The bootstrap and g1 (tree skewness) statistics are shown to be uninterpretable measures of noise or departures from randomness. Empirical data sets illustrate that commonly recommended schemes of differential weighting (e.g. downweighting third positions) are not well supported from the point of view of reducing the influence of noise nor are more noisy data sets likely to degrade signal found in less noisy data sets.
Within‐Terminal Steps and Fit Calculation—A Warning to Pee‐Wee Users
Authors: Rognes Knut
Published: July 2005

Because Pee‐Wee (version 2.5.1 and earlier versions) treats all within‐terminal steps (internal steps) as homoplasies, if the command “ccode = (space).;” is in effect, it reports incorrect, and consistently too low, fit values for characters having states that occur only within polymorphic terminals (WPTO states). For matrices with WPTO states, this property of Pee‐Wee may bias tree search in favour of characters having fewer WPTO states, other things being equal. Contrary to the intended purpose of the Goloboff criterion, Pee‐Wee may even, in certain cases involving WPTO states, assign higher weight (fit) to characters with more homoplasy and therefore resolve character conflict in favour of less reliable characters.
Comments on Allard and Carpenter (1996), or the “Aquatic Ape” Hypothesis Revisited
Authors: Page Roderic D.M. , Charleston Michael A.
Published: July 2005

The results of Allard and Carpenter's (Cladistics 12, 183–198, 1996) paper on weighting and congruence among mammalian mitochondrial genes are an artefact of errors in their data matrix; their “blue whale” ATPASE8 sequence is human, the actual blue whale sequence is assigned to the grey seal, and the “horse” sequence is that of the harbor seal. When these errors are corrected there is no evidence that the mitochondrial genes are incongruent.
Congruence among Mammalian Mitochondrial Genes
Authors: Allard Marc W. , Farris J.S. , Carpenter James M.
Published: July 2005

Mitochondrial protein coding genes were combined into a single matrix that included the 13 protein coding genes for 22 mammals, resulting in 11,448 characters each, or more than a quarter of a million base pairs of mitochondrial sequence. This matrix was examined for three separate a priori weighting strategies, including equal weighting, transversion weighting, and codon weighting. The incongruence length difference test obtained a significant value for equally weighted data and for one of our differentially weighted analyses. Thus, in one case, transversion only, weighting did effect previously incongruent data matrices, making them congruent. The tree produced for the various weighting strategies was identical in all of the treatments. These results support the conclusion that a priori weighting schemes should not be used to remove incongruence (presumably one does not want to introduce incongruence), but instead a simultaneous analysis strategy which includes treating all of the data equally weighted should be considered.
A Fundamental Problem with Amino‐Acid‐Sequence Characters for Phylogenetic Analyses
Authors: Simmons Mark P.
Published: July 2005

Protein‐coding genes may be analyzed in phylogenetic analyses using nucleotide‐sequence characters and/or amino‐acid‐sequence characters. Although amino‐acid‐sequence characters “correct” for saturation (parallelism), amino‐acid‐sequence characters are subject to convergence and ignore phylogenetically informative variation. When all nucleotide‐sequence characters have a consistency index of 1, characters coded using the amino acid sequence may have a consistency index of less than 1. The reason for this is that most amino acids are specified by more than one codon. If two different codons that both code for the same amino acid are derived independent of one another in divergent lineages, nucleotide‐sequence characters may not be homoplasious when amino‐acid‐sequence characters may be homoplasious. Not only may amino‐acid‐sequence characters support groupings that are not supported by nucleotide‐sequence characters, they may support contradictory groupings. Because this convergence is a problem of character delimitation, it affects the results of all tree‐construction methods (maximum likelihood, neighbor joining, parsimony, etc.). In effect, coding amino‐acid‐sequence characters instead of nucleotide‐sequence charactersputativelycorrects for saturation anddefinitelycauses a convergence problem. An empirical example from theMhclocus is given.
A Cladistic Analysis of the New World Species of Lotus L. (Fabaceae, Loteae)
Authors: Arambarri Ana M.
Published: July 2005

The genus Lotus L. is a monophyletic group diagnosed by the possession of a standard claw with thickened infolded margin, stamens diadelphous, and the style hardened from the base. It comprises approximately 200 species distributed throughout the world. A cladistic analysis of the New World species was performed using 39 morphological and anatomical characters (29 from seed morphology and anatomy, 1 from plant habit, 1 from leaf morphology, 6 from flower morphology, and 2 from fruit morphology). Dorycnium, Edentolotus, Krokeria, and Pedrosia, of the Old World, and 28 species of the New World were considered terminal taxa. Tetragonolobus Scop. was chosen to root the cladograms and Dorycnium Mill. to reroot them. With Tetragonolobus the analysis yielded 15 equally parsimonious trees, each with a length of 74 steps, a consistency index of 0.62, and a retention index of 0.89. The 15 initial trees and the strict consensus tree defined 12 monophyletic groups. All terminal taxa form a monophyletic group diagnosed by the presence of a radicular lobe discernible to conspicuous (character 10); rim aril thick (character 13); stipules absent (character 31); and style simple and nondilated (character 36). The New World species form a monophyletic group on the basis of the seed relationship of length to width in hilar view 1.5:1 to 2:1 (character 5); micropyle linear‐deltoid to bifurcate (character 19); and keel erostrate (character 33). Identical monophyletic groups were obtained when Dorycnium was used as root. These results are discussed in the context of data on cytology and morphology.
On the Other “Phylogenetic Systematics”
Authors: Nixon Kevin C. , Carpenter James M.
Published: July 2005

De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor “widely held belief” systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new “Phylogenetic Systematics”—instead we have been presented with a vague and sketchy manifesto based upon the assertion that “clades are individuals” and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for “node pointing,” yet even their own examples show that the opposite is true, and their node pointing system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the node pointing system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.
Systematics and Biogeography of Hard Ticks, a Total Evidence Approach
Authors: Klompen J.S.H. , Black William C. , Keirans James E. , Norris Douglas E.
Published: July 2005

Systematic relationships among the basal Ixodidae are examined using one morphological and three molecular data sets, 18S and 28S nuclear and 16S mitochondrial rDNA. Although different combinations of partitions are incompatible in a partition homogeneity test, combining them produces similar or better support for most major lineages through both additive and complementary effects. The different data sets are not complete for all taxa, but inclusion or exclusion of taxa with missing data for one or more data sets (8 of 29 ingroup taxa) does not influence overall tree topology and only weakly affects support levels. The only notable effect was based on gap treatment in the 28S data set. Gap treatment completely changes the arrangement and support levels for one basal node. The combined analyses show strong support for the Metastriata, a lineage including most endemic Australian Ixodes, and a lineage including the remaining Ixodes, but not for the Prostriata (=Ixodes s.l.). The distribution pattern of endemic Australian taxa (nearly all included in three exclusively Australian basal lineages) suggests that these lineages, and by extension the Ixodidae, originated after the isolation of Australia in the late Cretaceous, much more recently than previously indicated.
Evolution Is Not a Necessary Assumption of Cladistics
Authors: Brower Andrew V.Z.
Published: July 2005

Although the point has already been emphasized by various authors that the assumption of descent with modification is not required to justify cladistics, recent debate suggests that there is still confusion surrounding the necessary and sufficient background knowledge underlying the method. Three general axioms necessary to justify cladistics—the discoverability of characters, hierarchy, and parsimony—are reviewed. Although the assumption of evolution is sufficient to justify cladistics, it is also sufficient to justify competing approaches like maximum likelihood, which suggests that the philosophical support for the cladistic approach is strengthened by purging reference to descent with modification altogether.
Phylogenetic Species, Nested Hierarchies, and Character Fixation
Authors: Goldstein Paul Z. , DeSalle Rob
Published: July 2005

Cladistic mechanics and ramifications of various species concepts rooted in phylogenetic theory are explored. Published discussions of the phylogenetic species concept (PSC) have been hampered by persistent misconceptions surrounding its ontology and applicability, and by confusion of various incompatible versions of species concepts claiming to follow from Hennig's (1966),Phylogenetic Systematics,Univ. of Illinois Press, Urbana work. Especially problematic are topology‐ or tree‐based versions of species diagnosis, which render diagnoses dependent on relationships depicted as hierarchically structured regardless of any lack of underlying hierarchy. Because the applicability of concepts such as monophyly, paraphyly, and polyphyly rests ultimately on the underlying hierarchical distribution of characters, representations of tokogenetic or reticulating systems as nested hierarchies are necessarily inaccurate. And since hierarchical representations—even if accurate—of nonrecombining genetic elements need not coincide with the organisms that bear them, tree‐based diagnoses are further hampered, except potentially as retrospective tools. The relationship between tree‐based species delineations and the criterion of character fixation is explored. Fixation of characters by which one identifies phylogenetic species is further distinguished from the fixation of character state differences, and the implications of that distinction are explored with reference to the interpretation of speciation events. It is demonstrated that character fixation in alternative species need not coincide with the achievement of reciprocal monophyly. While the PSC retains shortcomings, some of the more frequently criticized aspects of the PSC are functions of sampling that are no more problematic than for any basic systematic endeavor.
Corroboration versus “Strongest Evidence”
Authors: Farris James. S.
Published: July 2005

Background knowledge comprises accepted (well‐corroborated) theories and results. Such theories are taken to be true for the purpose of interpreting evidence when assessing the corroboration of a hypothesis currently in question. Accordingly, background knowledge does not properly include rejected theories, false assumptions, or null models. In particular, regarding a model of random character distribution as “background knowledge” would rule out corroboration of phylogenetic hypotheses, since it would make character data irrelevant to inferring phylogeny. The presence of homoplasy is not grounds for treating characters as if they were randomly distributed, since characters can show strong phylogenetic structure even when they show homoplasy. This means that clique (compatibility) analysis is unjustified, since that method depends crucially on the assumption that characters showing any homoplasy at all are unrelated to phylogeny. Although likelihood does not measure corroboration, corroboration is closely connected to likelihood: for given evidence and background, the most likely trees are also best corroborated. Most parsimonious trees are best corroborated; the apparent clash between parsimony and likelihood is an artifact of the use of unrealistic models in most “maximum likelihood” methods.
Diagnostic Efficiency of Three‐Taxon Analysis
Authors: Farris James S.
Published: July 2005

Matrices of three‐taxon statements (3ts) represent a transformation of original data in that they are calculated from normal data matrices. Normal matrices cannot be considered transformational (or 3ts matrices original) in that sense, because the 3ts transformation cannot be reversed. That the 3ts transformation cannot be reversed also means that the transformation discards information. Use of 3ts greatly reduces the efficiency with which data can be represented through the diagnoses of a classification. This happens because, unlike normal characters, 3ts provide no direct way of identifying a feature as the same in several different organisms. The ensemble retention index R does not have the same interpretation in three‐taxon analysis (3ta) as it does with normal data matrices. In normal analyses R measures diagnostic efficiency, whereas 3ta always has minimal efficiency. Although usually interpreted phylogenetically, parsimony analysis can be applied descriptively without assuming any evolutionary process. This means that objecting to evolution as theoretical, unknown, or nonexistent would provide no grounds for rejecting parsimony in favor of 3ta, even if one did believe the objection.
Homology and the Optimization of DNA Sequence Data
Authors: Wheeler Ward
Published: July 2005

Three methods of nucleotide character analysis are discussed. Their implications for molecular sequence homology and phylogenetic analysis are compared. The criterion of inter‐data set congruence, both character based and topological, are applied to two data sets to elucidate and potentially discriminate among these parsimony‐based ideas.
Methods for Quick Consensus Estimation
Authors: Goloboff Pablo A. , Farris James S.
Published: July 2005

A method that allows estimating consensus trees without exhaustive searches is described. The method consists of comparing the results of different independent superficial searches. The results of the searches are then summarized through a majority rule, consensed with the strict consensus tree of the best trees found overall. This assumes that to the extent that a group is recovered by most searches, it is more likely to be actually supported by the data. The effect of different parameters on the accuracy and reliability of the results is discussed. Increasing the cutoff frequency decreases the number of spurious groups, although it also decreases the number of correct nodes recovered. Collapsing trees during swapping reduces the number of spurious groups without significantly decreasing the number of correct nodes recovered. A way to collapse branches considering suboptimal trees is described, which can be extended as a measure of relative support for groups; the relative support is based on the Bremer support, but takes into account relative amounts of favorable and contradictory evidence. More exhaustive searches increase the number of correct nodes recovered, but leave unaffected (or increase) the number of spurious groups. Within some limits, the number of replications does not strongly affect the accuracy of the results, so that using relatively small numbers of replications normally suffices to produce a reliable estimation.
Exploring the Behavior of POY, a Program for Direct Optimization of Molecular Data
Authors: Giribet Gonzalo
Published: July 2005

The performance of the computer program for phyloge netic analysis, POY, and its two implemented methods, “optimization alignment” and “fixed‐states optimization,” are explored for four data sets. Four gap costs are analyzed for every partition; some of the partitions (the 18S rRNA) are treated as a single fragment or in increasing fragments of 3, 10, and 30. Comparisons within and among methods are undertaken according to gap cost, number of fragments in which the sequences are divided, tree length, character congruence, topological congruence, primary homology statements, and computation time.
Efficiency of Parallel Direct Optimization
Authors: Janies Daniel A. , Wheeler Ward C.
Published: July 2005

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40‐taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed‐up for 16 slave processors on the large cluster. However, there is no appreciable speed‐up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size.
Phylogeny of the Trilobite SubgenusAcanthopyge (Lobopyge)
Authors: Ebach Malte C. , Ahyong Shane T.
Published: July 2005

Cladistic analysis of the trilobite subgenusAcanthopyge (Lobopyge)has not been previously attempted, apart from an inferred phylogeny of the Lichida by Thomas and Holloway (1988,Philos. Trans. R. Soc. London B Biol. Sci.321, 179–262). Results of two separate analyses with variable taxonomic sampling show a possible cosmopolitan affinity for Australian Devonian species ofA. (Lobopyge)and corroborate the placement ofA. (Lobopyge) rohriinA. (Lobopyge).Benelopygeis a junior subjective synonym ofA. (Lobopyge).
Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis1
Authors: Grandcolas Philippe , Deleporte Pierre , Desutter‐Grandcolas Laure , Daugeron Christophe
Published: July 2005

As many data as possible must be included in any scientific analysis, provided that they follow the logical principles on which this analysis is based. Phylogenetic analysis is based on the basic principle of evolution, i.e., descent with modification. Consequently, ecological characters or any other nontraditional characters must be included in phylogenetic analyses, provided that they can plausibly be postulated heritable. The claim of Zrzavý (1997, Oikos 80, 186–192) or Luckow and Bruneau (1997, Cladistics 13, 145–151) that any character of interest should be included in the analysis is thus inaccurate. Many characters, broadly defined or extrinsic (such as distribution areas), cannot be considered as actually heritable. It is argued that we should better care for the precise definition and properties of characters of interest than decide a priori to include them in any case in the analysis. The symmetrical claim of de Queiroz (1996, Am. Nat. 148, 700–708) that some characters of interest should better be excluded from analyses to reconstruct their history is similarly inaccurate. If they match the logical principles of phylogenetic analysis, there is no acceptable reason to exclude them. The different statistical testing strategies of Zrzavý (1997) and de Queiroz (1996) aimed at justifying inclusion versus exclusion of characters are ill‐conceived, leading respectively to Type II and Type I errors. It is argued that phylogenetic analyses should not be constrained by testing strategies that are downstream of the logical principles of phylogenetics. Excluding characters and mapping them on an independent phylogeny produces a particular and suboptimal kind of secondary homology, the use of which can be justified only for preliminary studies dealing with broadly defined characters.