bluuebunny/crossref_metadata_2025 huggingface dataset:
Taxic and Transformational Homology: Different Ways of Seeing
Authors: Carine Mark A. , Scotland Robert W.
Published: July 2005

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.
Strongest Evidence: Maximum Apparent Phylogenetic Signal as a New Cladistic Optimality Criterion
Authors: Salisbury Benjamin A.
Published: July 2005

A new method for phylogenetic inference, Strongest Evidence (SE), is described. In this method, a character's support for a phylogenetic hypothesis, its apparent phylogenetic signal, is greatest when the amount of implied homoplasy is most remarkably small given background knowledge alone. Because evolutionary rates are not assumed to be slow, background expectations for character length can be derived through modeling complete dissociation between branching pattern and character state assignments. As in unweighted parsimony, SE holds that fewer required evolutionary steps in a character indicates stronger support for a tree. However, in SE, the relationship between steps and support differs by unlabeled tree topology and character state distribution. Strongest evidence is contrasted in detail with both unweighted parsimony and Goloboff's method of implied weights. An iterative process is suggested for incrementally resolving a phylogenetic hypothesis while conducting cladistic analyses at increasingly local levels.
Phylogeny ofMelaleuca,Callistemon, and Related Genera of theBeaufortiaSuballiance (Myrtaceae) Based on 5S and ITS‐1 Spacer Regions of nrDNA
Authors: Ladiges P.Y. , McFadden G.I. , Middleton N. , Orlovich D.A. , Treloar N. , Udovicic F.
Published: July 2005

A phylogenetic analysis of genera within the informal suballianceBeaufortia(family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS‐1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three‐item parsimony analyses. Three‐item analysis gave more resolved trees than conventional parsimony analysis. TheBeaufortiasuballiance includes two major clades, with all Australian representatives ofCallistemon(shown to be monophyletic) and most Australian representatives ofMelaleucaforming one of these. The sister clade comprises a well‐defined group of endemic New Caledonian taxa (classified asCallistemonandMelaleuca), some Australian species ofMelaleuca, a clade including the Western Australia/Northern Territory generaBeaufortia, Lamarchea, andRegelia, and a clade including the south‐west Western Australian generaCalothamnus, Eremaea, Conothamnus, andPhymatocarpus. All molecular analyses sup port the monophyly ofConothamnusand ofRegelia, genera for which a number of species were included. Three‐item analysis of the combined data set supports the monophyly ofBeaufortia. The findings have implications for both taxonomy and biogeography.
Measuring Support for Phylogenies: The “Proportional Support Index”
Authors: Lee Michael S.Y.
Published: July 2005

The total support index (Bremer, 1994), a measure of cladogram support, is influenced both by character incongruence and by uninformative characters. A modified version of this index is therefore proposed—the proportional support index. This index measures the actual support for a cladogram relative to the maximum potential support as determined by the number of informative characters. This index is not distorted by uninformative characters and is thus a more accurate means to compare the strength of phylogenetic signals in different data sets.
Likelihood and Inconsistency
Authors: Farris James S.
Published: July 2005

Parsimony can be inconsistent, but not maximum likelihood—likelihood advocates often say. This difference and conclusions drawn from it have provided the main reasons advanced by likelihoodists against the use of parsimony. Recent statistical research, however, shows that maximum likelihood estimation of phylogenetic trees can become inconsistent in all but the simplest cases, so that under realistic conditions the consistency of maximum likelihood cannot be assured. If likelihoodists wish to dispose of parsimony, they will have to find another argument.
Taxic Homology = Overall Similarity
Authors: Kluge A.G. , Farris J.S.
Published: July 2005

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.
Phylogenetic Relationships of the Order Insectivora Based on Complete 12S rRNA Sequences from Mitochondria
Authors: Emerson Ginny L. , Kilpatrick C.W. , McNiff B.E. , Ottenwalder J. , Allard Marc W.
Published: July 2005

Despite numerous studies, there is no single accepted hypothesis of eutherian ordinal relationships. Among the least understood mammalian orders is the group Insectivora. Currently, molecular and morphological data are in conflict over the possible monophyly of the living members of Insectivora (lipotyphlans), and the relationships within the group remain largely unresolved. One of the primary criticisms concerning molecular analyses is the noticeable lack of data from a well‐sampled group of lipotyphlan insectivores. The mitochondrial 12S rRNA gene has been widely used to resolve interordinal and intraordinal relationships across a variety of mammalian taxa. This study compares 118 complete mammalian 12S rRNA sequences, representing all of the 18 eutherian orders and 3 metatherian orders, and includes as well taxa from each of the six families of lipotyphlan insectivores. Insectivoran lineages are thought to have diverged concurrently with the general radiation of mammalian orders. This study suggests that the 12S rRNA sequences lack the ability to resolve relationships extending into this period. This would explain the polyphyly, unusual affinities, and low support derived in this and other studies employing 12S rRNA sequences to diagnose relationships among eutherian orders. The results of these analyses suggest that even extensive taxon sampling is insufficient to provide well supported groups among eutherian orders. Additional genes and species sampling will be necessary to elucidate whether the Insectivora form a monophyletic group.
A Morphological Basis for Assessing the Phylogeny of the “Tenrecoidea” (Mammalia, Lipotyphla)
Authors: Asher Robert J.
Published: July 2005

A phylogenetic analysis of 35 mammalian taxa focusing on the lipotyphlan family Tenrecidae, based on 193 morphological character states across 71 characters, is undertaken to test several hypotheses of lipotyphlan relationships, including monophyly of the Lipotyphla, Tenrecidae, Malagasy Tenrecidae, and Caribbean Lipotyphla. Explicit tests of these hypotheses are central to understanding larger issues concerning Malagasy and Caribbean biogeography, in addition to mammalian phylogeny. Methodologically, several different parameters are created with which to determine the sensitivity of resulting clades to initial assumptions about a posteriori character weighting, missing data, and multistate character ordering. Clades produced by this data set that appear despite perturbations in these parameters and that are supported by other confidence‐assessment techniques contradict Malagasy tenrecid monophyly and the association of soricids with the Caribbean taxon Solenodon. Results regarding tenrecid and lipotyphlan monophyly are more ambiguous and depend on certain assumptions regarding treatment of character ordering, weighting, and missing data. An alternative phylogeny supporting an African mammal clade receives no support from the data set discussed herein.
Corroboration among Data Sets in Simultaneous Analysis: Hidden Support for Phylogenetic Relationships among Higher Level Artiodactyl Taxa
Authors: Gatesy John , O'Grady Patrick , Baker Richard H.
Published: July 2005

In the taxonomic congruence approach to systematics, data sets are analyzed separately, and corroboration among data sets is indicated by replicated components in topologies derived from the separate analyses. By contrast, in the total evidence and conditional combination approaches, characters from different data sets are mixed in combined phylogenetic analyses. In optimal topologies derived from such simultaneous analyses, support for a particular node may be attributed to one, some, or all of the individual data sets. Partitioned branch support (PBS) is one technique for describing the distribution of character support and conflict among data sets in simultaneous analysis. PBS is analogous to branch support (BS), but recognizes hidden support and conflicts that emerge with the combination of characters from different data sets. For both BS and PBS, support for a particular node is interpreted as the difference in cost between optimal and suboptimal topologies. A different measure, the clade stability index (CSI), assesses the robustness of a particular node through the successive removal of characters. Here, we introduce variations of the CSI, the data set removal index (DRI) and nodal data set influence (NDI), that indicate the stability of a particular node to the removal of entire data sets. Like PBS, the DRI and NDI summarize the influence of different data sets in simultaneous analysis. However, because these new methods and PBS use different perturbations to assess stability, DRI and NDI scores do not always predict PBS scores and vice versa. In this report, the DRI and NDI are compared to PBS and taxonomic congruence in a cladistic analysis of 17 data sets for Artiodactyla (Mammalia). Five indices of hidden support and conflict are defined and applied to the combined artiodactyl character set. These measures identify substantial hidden support for controversial relationships within Artiodactyla. Hidden character support is ignored in the taxonomic congruence approach to systematics, but the DRI, NDI, and PBS utilize this cryptic information in estimates of support among data sets for a given node.
Parsimony Analysis of Total Evidence from Extinct and Extant Taxa and the Cetacean‐Artiodactyl Question (Mammalia, Ungulata)
Authors: O'Leary Maureen A.
Published: July 2005

Many molecule‐based phylogenetic analyses find that the mammalian order Artiodactyla (even‐toed ungulates) is paraphyletic unless cetaceans (whales, dolphins, and porpoises) are nested within it, a hypothesis that runs contrary to traditional morphology‐based ideas. Here I present a total evidence analysis of this question based on 10 extant and 27 extinct taxa, using two character data partitions: (i) skeletal data and (ii) neontological data (soft morphology, retroposons, and DNA sequences [γ‐fibrinogen, β‐casein, and κ‐casein and mt cytochrome b]). A sensitivity analysis varying gap cost and transversion/transition ratio over nine parameters was implemented in the sequence alignment and in the parsimony analysis. The two data partitions are significantly incongruent, and the neontological data partition includes over six times as many characters as the osteological data partition. The osteological data partition, however, samples almost three times more taxa, taxa that cannot be sampled for neontological data because they are extinct. Osteological data resulted in artiodactyl monophyly, and neontological data resulted in artiodactyl paraphyly over all nine parameters. In the total evidence analysis the parameter most congruent with the overall character data is unresolved as to the sister taxon of Cetacea; however, the Adams consensus tree favors the neontological result. Extinction of almost 90% of the clade and particularly poor knowledge of stem taxa at the base of Artiodactyla make resolution of conflicting molecule‐ and morphology‐based phylogenetic signals particularly difficult.
The Phylogeny and Classification of Tapiromorph Perissodactyls (Mammalia)
Authors: Holbrook Luke T.
Published: July 2005

Despite an excellent fossil record, the phylogeny of Perissodactyla is not well understood, in terms of both the relationships within Perissodactyla and the position of the Perissodactyla among the orders of mammals. This paper provides a phylogenetic analysis of one major perissodactyl lineage, the Tapiromorpha. This analysis combines a more comprehensive sampling of characters and taxa with rigorous tree‐searching methods to create a new hypothesis of tapiromorph relationships. The phylogeny of tapiromorph perissodactyls is analyzed using 45 characters of the skull, postcranial skeleton, and dentition scored for 29 taxa, including three nontapiromorph outgroups. Phylogenetic taxonomic definitions are constructed for suprageneric taxa. According to the results of this analysis, the Chalicotherioidea cannot be unequivocally assigned to the Tapiromorpha, nor can Homogalax or Cardiolophus. Isectolophus, Tapiroidea, and Rhinocerotoidea are unequivocal members of the Tapiromorpha. Heptodon is included in a monophyletic Tapiroidea. Amynodontid rhinocerotoids come out as the sister group to rhinocerotids, and indricotheres do not fall within the Hyracodontidae. The results of this study provide further arguments that tapiromorphs (and putative tapiromorphs) may be important for understanding the ancestral morphology of Perissodactyla.
Character Coding and Inapplicable Data
Authors: Strong Ellen E. , Lipscomb Diana
Published: July 2005

Inapplicable character states occur when character complexes are absent or reduced in some of the taxa. Several approaches have been proposed for representing such states in a character matrix so that the inapplicable condition has no effect on the placement of taxa and/or the applicable states are independent and not redundant. Here we examine each of these approaches and demonstrate that all have shortcomings. Coding inapplicables as “?” (reductive coding), although flawed, is currently the best way to analyze data sets that contain inapplicable character states.
Paralogy and the Centre of Origin Concept
Authors: Ebach Malte C.
Published: July 2005

Ancestral area methodology, applied to finding the centre of origin, conflicts with most cladistic biogeographic methods since it uses, not reduces, paralogy. A new term, area cladistics, is herein proposed as an efficient paralogy‐free (or reduced) method under the three‐item philosophy that currently exists with other methods under the broad term cladistic biogeography.
The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis
Authors: Nixon Kevin C.
Published: July 2005

The Parsimony Ratchet1 is presented as a new method for analysis of large data sets. The method can be easily implemented with existing phylogenetic software by generating batch command files. Such an approach has been implemented in the programs DADA (Nixon, 1998) and Winclada (Nixon, 1999). The Parsimony Ratchet has also been implemented in the most recent versions of NONA (Goloboff, 1998). These implementations of the ratchet use the following steps: (1) Generate a starting tree (e.g., a “Wagner” tree followed by some level of branch swapping or not). (2) Randomly select a subset of characters, each of which is given additional weight (e.g., add 1 to the weight of each selected character). (3) Perform branch swapping (e.g., “branch‐breaking” or TBR) on the current tree using the reweighted matrix, keeping only one (or few) tree. (4) Set all weights for the characters to the “original” weights (typically, equal weights). (5) Perform branch swapping (e.g., branch‐breaking or TBR) on the current tree (from step 3) holding one (or few) tree. (6) Return to step 2. Steps 2–6 are considered to be one iteration, and typically, 50–200 or more iterations are performed. The number of characters to be sampled for reweighting in step 2 is determined by the user; I have found that between 5 and 25% of the characters provide good results in most cases. The performance of the ratchet for large data sets is outstanding, and the results of analyses of the 500 taxon seed plant rbcL data set (Chase et al., 1993) are presented here. A separate analysis of a three‐gene data set for 567 taxa will be presented elsewhere (Soltis et al., in preparation) demonstrating the same extraordinary power. With the 500‐taxon data set, shortest trees are typically found within 22 h (four runs of 200 iterations) on a 200‐MHz Pentium Pro. These analyses indicate efficiency increases of 20×–80× over “traditional methods” such as varying taxon order randomly and holding few trees, followed by more complete analyses of the best trees found, and thousands of times faster than nonstrategic searches with PAUP. Because the ratchet samples many tree islands with fewer trees from each island, it provides much more accurate estimates of the “true” consensus than collecting many trees from few islands. With the ratchet, Goloboff's NONA, and existing computer hardware, data sets that were previously intractable or required months or years of analysis with PAUP* can now be adequately analyzed in a few hours or days.
Long‐Branch Abstractions
Authors: Siddall Mark E , Whiting Michael F
Published: July 2005

Recent attention has been focused on the sensitivities of various tree reconstructing algorithms to sequence rate heterogeneity (long‐branch attraction). Phylogenetic conclusions from two recent empirical studies have been indicted as artifacts attributable to long‐branch attraction. Siddall et al.(1995) concluded that Myxozoa are cnidarians and sister group toPolypodium based on 18S rDNA and morphology. Haneltet al.(1996) argued that this result is due to long‐branch attraction. Whiting et al.(1997) concluded that the Strepsiptera are sister group to Diptera based on parsimony analysis of 18S rDNA, 28S rDNA, and morphology. Huelsenbeck (1997) argued that this result also is attributable to long‐branch attraction. We demonstrate that the analyses and arguments dismissing these results as the effects of long‐branch attraction are fundamentally flawed. The criteria employed by these authors were applied arbitrarily by them to the groups that they did not want, and yet using those same criteria, there is more reason to exclude other taxa besides Polypodium and there is more reason to disbelieve monophyly of Diptera than monophyly of Strepsiptera with Diptera. Moreover, it is asserted, long‐branch attraction cannot explain the presence of nematocysts in Myxozoa and halteres in Strepsiptera. For these reasons, and in light of the demonstration that long branches cannot attract each other in their mutual absence, we conclude that the monophyly of Myxozoa + Polypodium and Strepsiptera + Diptera is not due to long‐branch attraction. We suggest that maximum likelihood methods are extremely sensitive to taxon and character sampling and that these data sets are demonstrative of the long‐branch repulsion problem.
Data Decisiveness, Missing Entries, and the DD Index
Authors: De Laet Jan , Smets Erik
Published: July 2005

The decisiveness of a data set has been defined as the degree to which all possible dichotomous trees for that data set differ in length, and the DD statistic (the data decisiveness index) has been proposed to measure this degree. In this paper, we first discuss an exact nonre cursive formula for the length of indecisive datasets (DD = 0) that consist of informative binary characters in which no missing entries are allowed. Next, the concept of indecisive data sets is extended to data sets in which missing entries may be present. Last, indecisive data sets with missing entries are used as an aid to construct hypothetical data sets that single out some of the factors that influence the DD statistic. On the basis of these examples, it is concluded that the concept of data decisiveness is too elusive to be captured into a single and simple index such as DD.
Successive Weighting and Polymorphic Terminals—A Warning to PAUP Users
Authors: Rognes Knut
Published: July 2005

The naïve user of PAUP 3.1.1 (and earlier versions) is warned about a shortcoming in the program's successive weighting facility. With matrices containing multistate terminals, PAUP, under the “polymorphism” interpretation, will assign higher weight to characters with more within‐terminal steps, other things being equal, i.e. to characters with the largest amount of homoplasy. The shortcoming has been corrected in PAUP* version 4.0.
Homoplasy Increases Phylogenetic Structure
Authors: Kälersjö Mari , Albert Victor A. , Farris James S.
Published: July 2005

According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the largest nucleotide matrix treated to date—2538 rbc L sequences covering all major lineages of green plants—shows the opposite: although rapidly evolving and highly homoplastic, third positions contain most of the phylogenetic structure in the data. Frequency of change should thus be used with caution as a criterion for weighting or selecting characters.
Is Psammophily an Evolutionary Dead End? A Phylogenetic Test in the GenusWillemia(Collembola: Hypogastruridae)
Authors: D'Haese Cyrille
Published: July 2005

The law of the unspecialized states that specialized taxa have evolved from more generalized ancestors. Moreover, it is usually assumed that ecological specialization is irreversible and hence leads to extinction. This study aims to test these assumptions using a phylogenetic framework in a case study within the springtail genusWillemiaand its diverse life habits. This genus is represented mostly by loam‐dwelling species (generalized condition), but some species are psammophilous, living in sandy habitats (specialized condition). Fifty‐two morphological characters were examined in 34 of the 36 species of the genus and in three outgroups. The cladistic analysis yielded two most parsimonious trees (tree length 124 steps; consistency index 0.56; retention index 0.86). The evolution of psammophily versus loam‐confined life is compared to the cladogram: unexpectedly, psammophily is not an evolutionary innovation that occurred once in a monophyletic group; the evolutionary scenario that parsimoniously fits the phylogeny suggests that psammophily is ancestral to the genusWillemiaand reversed twice to loam‐confined life. These results demonstrate that habitat generalists can evolve from habitat specialists and therefore that habitat specializations are not necessarily an evolutionary dead end. Many other seemingly specialized characters may be shown to be equally malleable.
Methods in Vicariance Biogeography: Assessment of the Implementations of Assumptions 0, 1, and 2
Authors: van Veller Marco G. P. , Kornet D.J. , Zandee M.
Published: July 2005

As we have argued previously, for the valid derivation of general area cladograms in vicariance biogeography, two requirements should be met. First, sets of area cladograms derived under assumptions 0, 1 and 2 should be inclusive (requirement I). Second, general area cladograms should be based on area cladograms, for different monophyletic groups, derived under the same assumption (requirement II). We now assess for their actual implementation of assumptions A0, A1, and A2 and for the extent to which they meet requirements I and II, the following methods (and correlated computer programs): Component Compatibility Analysis (CAFCA), Brooks Parsimony Analysis (PAUP), Component Analysis (Component 1.5), Reconciled Tree Analysis (Component 2.0), and Three Area Statement Analysis (TAS). For this purpose we use empirical (Heterandria, Xiphophorus, Cyttaria, Eriococcus/Madarococcus) and theoretical data sets. All programs appear to violate, to a different degree, requirement I (deriving inclusive sets of area cladograms under assumptions) when dealing with sympatric taxa under A1 or A2. Dealing with sympatric taxa a posteriori only prevents this violation. All programs examined appear to meet requirement II (deriving general area cladograms under a single assumption).
Phylogeny and Classification of the Superfamily Scorpionoidea Latreille 1802 (Chelicerata, Scorpiones): An Exemplar Approach
Authors: Prendini Lorenzo
Published: July 2005

S. A. Stockwell (1989, “Revision of the Phylogeny and Higher Classification of Scorpions (Chelicerata).” Univ. of California, Berkeley) proposed a cladogram and revised classification for the superfamily Scorpionoidea Latreille 1802 (comprising the families Bothriuridae, Diplocentridae, Heteroscorpionidae, Ischnuridae, and Scorpionidae), based on 47 morphological characters and 35 supraspecific terminal taxa, representing genera whose monophyly was implicitly assumed. Given the widespread practice of defining scorpion genera on the basis of plesiomorphic character states, the assumption of monophyly implicit in supraspecific terminal taxa reduces confidence in Stockwell's cladistic findings and, consequently, his revised suprageneric classification. A re‐investigation of scorpionoid phylogeny is presented here, based on 115 morphological characters (including the characters used by Stockwell) and 71 exemplar species. The criterion of “maximal morphological diversity” was employed for exemplar selection. This approach provides a stronger test of monophyly than random exemplar selection. Sixteen cladistic analyses were performed on the scorpionoid data matrix, which varied in the use of equal, successive, or implied weights and in the additive or nonadditive treatment of multistate characters. The preferred hypothesis, a single most parsimonious tree obtained by analysis with equal weights and 13 ordered multistate characters, yielded the scheme of relationships: (Bothriuridae ((Heteroscorpionidae Urodacinae) ((Hemiscorpiinae Ischnuridae) (Diplocentridae Scorpioninae)))). On the basis of these results, revisions are proposed to the existing suprageneric classification of the Scorpionoidea, including new diagnoses, new descriptions, and an illustrated key to the families and subfamilies. Familial status is provided for the scorpionid subfamilies Hemiscorpiinae and Urodacinae.
Phylogenetic Relationships of the Suborders of Coleoptera (Insecta)
Authors: Beutel Rolf G. , Haas Fabian
Published: July 2005

One hundred seven external and internal characters of larval and adult representatives of 28 genera of the coleopteran suborders were analyzed cladistically. Four groups of Neuropterida were introduced as outgroup. The analysis yielded 18 trees with a minimum of 194 steps (CI 0.691). All trees support the monophyly of all four suborders and a branching pattern (Archostemata + (Adephaga + (Myxophaga + Polyphaga))). The presence of elytra with meso‐ and metathoracic locking devices, the specific hind‐wing folding, the close connection of exposed sclerites, the absence of the mera, the absence of eight thoracic muscles, the reduced abdominal sternite I, and the invagination of terminal segments are autapomorphies of Coleoptera. The monophyly of Coleoptera excl. Archostemata is supported by further transformations of the thoracic sclerites such as absence of the mesothoracic discriminal line and katepisternal joint, by an internalized or absent metathoracic trochantin, by the presence of a bending zone in the hind‐wing, and by eight further muscle losses. Fusion of tibia and tarsus and presence of a single claw are larval synapomorphies of Myxophaga and Polyphaga. Adults are characterized by fusion of protrochantin and propleura and by the rigid connection of the meso‐ and metathoracic ventrites. The eucinetoid lineage of Polyphaga is characterized by the secondary absence of the bending zone of the alae. This results in a distinctly simplified wing folding mechanism. The monophyly of Cucujiformia (+ Bostrichoidea) is supported by the presence of cryptonephric Malpighian tubules. Transformations of fore‐and hind‐wings, reinforcement and simplification of the thoracic exoskeleton, and an efficient use of a distinctly reduced set of thoracic muscles play an important role in the early evolution of Coleoptera. Many different larval character transformations take place in the earlier Mesozoic within the suborders.
Arthropod Cladistics: Combined Analysis of Histone H3 and U2 snRNA Sequences and Morphology
Authors: Edgecombe Gregory D. , Wilson George D.F. , Colgan Donald J. , Gray Michael R. , Cassis Gerasimos
Published: July 2005

Morphological, developmental, ultrastructural, and gene order characters are catalogued for the same set of arthropod terminals as we have scored in a recent study of histone H3 and U2 snRNA sequences (D. J. Colgan et al., 1998, Aust. J. Zool. 46, 419–437). We examine the implications of separate and simultaneous analyses of sequence and non‐sequence data for arthropod relationships. The most parsimonious trees based on 211 non‐sequence characters (273 apomorphic states) support traditional higher taxa as clades, including Mandibulata, Crustacea, Atelocerata, Myriapoda, and Hexapoda. Combined analysis of morphology with histone H3 and U2 sequences with equal character weights differs from the morphological results alone in supporting Progoneata + Hexapoda (= Labiophora) in favor of a monophyletic Myriapoda, resolves the entognathous hexapods as a grade, and supports pycnogonids as sister group to Euchelicerata (rather than as basal euarthropods). Monophyly of Chelicerata (including pycnogonids), Mandibulata, Crustacea, Progoneata, Chilopoda, and Hexapoda is maintained under a range of transition/transversion and third codon weights, whereas Atelocerata and Myriapoda/Labiophora do not withstand all sensitivity analyses.
A Review of Arthropod Phylogeny: New Data Based on Ribosomal DNA Sequences and Direct Character Optimization
Authors: Giribet Gonzalo , Ribera Carles
Published: July 2005

Ribosomal gene sequence data are used to explore phylogenetic relationships among higher arthropod groups. Sequences of 139 taxa (23 outgroup and 116 ingroup taxa) representing all extant arthropod “classes” except Remipedia and Cephalocarida are analyzed using direct character optimization exploring six parameter sets. Parameter choice appears to be crucial to phylogenetic inference. The high level of sequence heterogeneity in the 18S rRNA gene (sequence length from 1350 to 2700 bp) makes placement of certain taxa with “unusual” sequences difficult and underscores the necessity of combining ribosomal gene data with other sources of information. Monophyly of Pycnogonida, Chelicerata, Chilopoda, Chilognatha, Malacostraca, Branchiopoda (excluding Daphnia), and Ectognatha are among the higher groups that are supported in most of the analyses. The positions of the Pauropoda, Symphyla, Protura, Collembola, Diplura, Onychophora, Tardigrada, and Daphnia are unstable throughout the parameter space examined.
Phylogeny and Speciation of Felids
Authors: Mattern Michelle Y. , McLennan Deborah A.
Published: July 2005

The phylogeny of the Felidae is reconstructed using a total evidence approach combining sequences from 12S rRNA, 16S rRNA, NADH‐5, and cytochrome b genes with morphological and karyological characters. The 1504‐character data set generated two equally parsimonious trees (CI = 0.413, 1795 steps) of which a strict consensus revealed one polytomy in the placement of the bay cat group. The tree supports several traditional groupings such as the genera Panthera and Lynx and the ocelot group of small South American felids, and it provides additional resolution of relationships within and among the major felid lineages. Combining phylogenetic, distributional, and ecological data indicates that vicariant speciation has played a relatively minor role in the diversification of the felids (approximately 26% of events), while sympatric speciation has been more important than expected on theoretical grounds (approximately 51.8% of events), although postspeciation dispersal may have blurred the boundaries between sympatric, parapatric, and peripheral isolate modes. An examination of ecological changes on the felid tree shows repeated patterns of resource partitioning in time (activity patterns), space (preferred habitat type), and food (as measured by body size) among closely related species. The rapid diversification of the cats thus appears to have been associated more with ecological than with geological separation.
Pattern of Phylogenetic Relationships among Members of the Tribe Melitaeini (Lepidoptera: Nymphalidae) Inferred from Mitochondrial DNA Sequences
Authors: Wahlberg Niklas , Zimmermann Marie
Published: July 2005

We report a cladistic analysis of 77 butterfly species of the tribe Melitaeini (Lepidoptera: Nymphalidae) based on mitochondrial DNA gene sequences. We sequenced ca. 536 bp from the 16S ribosomal DNA (rDNA) and a 1422‐bp sequence from the cytochrome oxidase I gene. Alignments are critical to statements of homology, especially when aligning rDNA sequences. We aligned the 16S sequences using conventional methods and direct optimization. We found that direct optimization of the sequences produced the best alignments and our preferred phylogenetic hypothesis. Our results suggest that many of the previously proposed genera are paraphyletic and we conclude that there are four monophyletic groups of species in our cladogram: theEuphydryasgroup, thePhyciodesgroup, theChlosynegroup, and theMelitaeagroup. The following genera are found to be paraphyletic:Castilia, Chlosyne, Didymaeformia, Eresia, Melitaea, andThessalia. In addition, recognition of the monophyletic generaCinclidia, Mellicta, andTelenassawould render other genera paraphyletic. Our phylogenetic hypothesis indicates that the melitaeines originated in the Nearctic and have colonized the Neotropics three times and the Palaearctic twice.
Classification or Phylogenetic Estimates?
Authors: Scotland Robert W. , Carine Mark A.
Published: July 2005

[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.
When Are Random Data Not Random, or Is the PTP Test Useful?
Authors: Peres‐Neto Pedro R. , Marques Fernando
Published: July 2005

Recently, empirical evidence was presented that the permutation tail probability (PTP) test has extremely low discriminatory power when assessing character covariance in phylogenetic data based on bootstrap measures of confidence. Here we are concerned with the problem of using one statistical approach, especially when applied to empirical data, to judge the performance of another. Applying an appropriate statistical approach, we statistically demonstrated that the PTP test is extremely weak in detecting the absence of character covariation. In addition, we show that PTP is highly dependent on the number of terminals and the proportion of character states in phylogenetic matrices. In conclusion, we advocate the use of simulation studies when testing the performance of statistical tools applied to phylogenetic data.
Simulated Evolutionary Optimization and Local Search: Introduction and Application to Tree Search
Authors: Moilanen Atte
Published: July 2005

Tree search and its more complicated variant, tree search and simultaneous multiple DNA sequence alignment, are difficult NP‐complete optimization problems, which require the application of advanced computational techniques, if large data sets are to be solved within reasonable computation times. Traditionally tree search has been attacked with a search strategy that is best described as multistart hill‐climbing; local search by branch swapping has been performed on several different starting trees. Recently a different tree search strategy was tested in the Parsigal parsimony program, which used a combination of evolutionary optimization and local search. Evolutionary optimization algorithms use principles adopted from biological evolution to solve technical optimization tasks. Evolutionary optimization is a stochastic global search method, which means that the method is able to escape local optima, and is in principle able to produce any solution in the search space (although this may take a long time). Local search techniques, such as branch swapping, employ a completely different search strategy; they exploit local information maximally in order to achieve quick improvement in the value of the objective function. However, local search algorithms lack the ability to escape from local optima, which is a fundamental requirement for any search algorithm that aims to be able to discover the global optimum of a multimodal optimization problem. Hence it seems that an optimization strategy combining the good properties of both evolutionary algorithms and local search would be ideal. In this study, aspects of global optimization and local search are discussed, and the method of simulated evolutionary optimization is reviewed in detail. The application of simulated evolutionary optimization to tree search in Parsigal is then reviewed briefly.
Beyond NEXUS: Universal Cladistic Data Objects
Authors: Nixon Kevin C. , Carpenter James M. , Borgardt Sandra J.
Published: July 2005

The subject of data management in cladistics is discussed. Proprietary, nonrelational data “formats” are no solution to the problems of data storage and transfer among programs; rather, commercially available standards for query language should be implemented in a system of data objects.
Nothofagus Biogeography Revisited with Special Emphasis on the Enigmatic Distribution of Subgenus Brassospora in New Caledonia
Authors: Swenson Ulf , Backlund Anders , McLoughlin Stephen , Hill Robert S.
Published: July 2005

Dispersals versus vicariance events and the presence of subgenus Brassospora in New Caledonia are two riddles of Nothofagus biogeography, a genus also distributed in New Guinea, New Zealand, South America, Southeast Australia, and Tasmania. Within a cladistic framework using the software COMPONENT 2.0, we demonstrate that most parsimonious area cladograms (areagrams) sensu cladistic biogeography need not always be the most plausible explanation nor reflect alternative geological hypotheses. The most parsimonious Nothofagus history sensu historical biogeography is reconstructed where a minimum of dispersed taxa is hypothesized and vicariance events are identified. A fully resolved well‐established Nothofagus phylogeny was reconciled with three geological hypotheses (geograms) of East Gondwana break‐up: (a) the conventional view, (b) an Australian—New Caledonian relationship, and (c) a biotic interchange between New Guinea and New Caledonia. Fossils determined to subgenus were optimized to the predicted lineages in the reconciled tree. Due to extensive extinctions, a maximum of three vicariance events are inferred, all being basal in the subgenera, an indication of subgeneric diversification prior to the break‐up of Gondwana. Two taxa, N. gunnii and N. menziesii, are hypothesized as being long‐distance dispersed. The most parsimonious solution suggests a close relationship between New Guinea and New Caledonia, supporting a Brassospora colonization route, but this hypothesis fails to predict numerous extinct lineages observed in the fossil record and thus must be rejected. The traditional break‐up sequence of Gondwana is not the most parsimonious solution, indicating one incongruent node, but causes no overall incongruence with the fossil record. Considering all parameters, the occurrence of Brassospora in New Caledonia is most parsimoniously explained as a single colonization event from New Zealand where the subgenus subsequently went extinct in the Pliocene.
The Phylogeny of Cockroach Families: Is the Current Molecular Hypothesis Robust?
Authors: Grandcolas Philippe , D'Haese Cyrille
Published: July 2005

A recent molecular phylogenetic analysis of cockroaches (Kambhampati, 1996, Syst. Entomol. 21, 89–98) contradicted with phylogenetic studies that were based on morphology. The DNA data set of that study (431–443 bp from 12S rRNA gene) has been reanalyzed by using: (1) the published alignment, (2) the alignment actually used by the author, (3) another alignment based on a cladistic procedure, and (4) a larger number of terminal taxa and different outgroups. The original tree was not retrieved using the analysis parameters of this author and the resulting trees appeared to be highly unstable, depending on changes in alignment and in outgroup or on an increase in the taxon sample size. It is concluded that this DNA data set alone cannot be used currently to draw a robust phylogenetic hypothesis. This data set should be expanded or combined in a more general phylogenetic analysis using all other available data sets. Therefore, the results from other recent analyses, both morphological and molecular, which placed the well‐known subsocial woodroach Cryptocercus in the family Polyphagidae, currently remain the best corroborated phylogenetic hypothesis.
The Phylogeny of the Lophopidae and the Impact of Sexual Selection and Coevolutionary Sexual Conflict
Authors: Soulier‐Perkins Adeline
Published: July 2005

A cladistic analysis of Lophopidae was performed, using 73 observed morphological characters and 41 taxa. This analysis involved 36 genera belonging to the Lophopidae family and 5 outgroups. For a better understanding of the selected characters some illustrations are provided. The most parsimonious cladograms obtained show that the Lophopidae cannot be considered as a monophyletic lineage unless two genera are withdrawn from this family: Hesticus Walker, 1862, and Silvanana Metcalf, 1947. The systematic position of these two genera remains uncertain. They cannot yet be included in another family of Fulgoromorpha. A cladistic analysis of each of the 19 remaining Fulgoromorphan families must be performed first. A new family could be created for these two genera, but not before we are sure that these two genera are in no way members of an existing family. The outgroup problem is discussed. The monophyletic lineage represented by the Lophopidae can be divided into four natural groups: Carriona+, Makota+, Sarebasa+, and Bisma+. When a cladistic analysis is completed using a data matrix without characters linked to females, the cladogram obtained presents a disrupted basal resolution. Female characters appear to bring a phylogenetic signal important basally in the evolution of the Lophopidae but also apically, directly between the relationships of some genera. A similar analysis, using a matrix without characters linked to males, provides a phylogeny disrupted between the groups that form the Lophopidae and in the basal resolution in these groups. The respective impacts of the genitalic characters are discussed in relation to sexual selection conflict.
Taxic Revisions
Authors: Farris James S. , Kluge Arnold G. , De Laet Jan E.
Published: July 2005

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.
Palm‐Pitviper (Bothriechis) Phylogeny, mtDNA, and Consilience
Authors: Taggart Travis W. , Crother Brian I. , White Mary E.
Published: July 2005

The phylogeny of the neotropical palm‐pitviper genus Bothriechis has been previously inferred from morphology and allozymes. These nuclear‐based data sets were found to be congruent and also consilient with the geologic history of the region. We present mtDNA sequence data as an additional data set in the inference of Bothriechis phylogeny and analyze it separately and combined with previous data. The mtDNA phylogeny is incongruent with the nuclear data sets. Based on a number of factors, we hypothesize that the incongruence is due to both mtDNA introgression and lineage sorting. We argue that mtDNA represents extrinsic data and as such should be used as a consilient data set.