bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher‐level bat phylogeny
Authors: Simmons Nancy B. , Geisler Jonathan H. 
Published: July 2005

AbstractNew information concerning strengths and weaknesses of different methods of coding taxonomic polymorphisms suggests that results of some previous studies may have been unintentionally biased by the methods employed. In this study, we demonstrate that a form of sensitivity analysis can be used to evaluate the effects of different methods of coding taxonomic polymorphisms on the outcome of phylogenetic analyses. Our earlier analysis of higher‐level relationships of bats (Mammalia: Chiroptera) employed superspecific taxa as terminals and scored taxonomic polymorphisms using ambiguity coding. Application of other methods of dealing with polymorphisms (excluding variable characters, inferring ancestral states, majority coding) to the same data yields phylogenetic results that differ somewhat from those originally reported based on ambiguity coding. Monophyly of some clades was supported in all analyses (e.g., Microchiroptera, Rhinopomatoidea, and Nataloidea), while other groups found to be monophyletic in the original study (e.g., neotropical Nataloidea) appeared unresolved or nonmonophyletic when other methods were used to code taxonomic polymorphisms. Several groupings that were apparently refuted in the initial study (e.g., Noctilionoidea including Mystacinidae) were supported in some analyses, reducing some of the apparent incongruence between the trees in our earlier analysis (which were based principally on morphology) and other trees based on molecular data. Perceived support for various groupings (branch support, bootstrap values) were in some cases significantly affected by the methods employed. These results indicate that sensitivity analysis provides a useful tool for evaluating effects of different methods of dealing with taxonomic polymorphism in superspecific terminal taxa. Variation in results obtained with different methods suggests that it is always preferable to sample at the species level when higher‐level taxa exhibit taxonomic polymorphism, thus avoiding methodological biases associated with different methods of dealing with taxonomic polymorphisms during data analysis.
Parsimony, likelihood, and simplicity
Authors: Goloboff Pablo A. 
Published: July 2005

AbstractThe latest charge against parsimony in phylogenetic inference is that it involves estimating too many parameters. The charge is derived from the fact that, when each character is allowed a branch length vector of its own (instead of the homogeneous branch lengths assumed in current likelihood models), the results for likelihood and parsimony are identical. Parsimony, however, can also be derived from simpler models, involving fewer parameters. Therefore, parsimony provides (as many authors had argued before) the simplest explanation of the data, or the most realistic, depending on one's views. If (as argued by likelihoodists) phylogenetic inference is to use the simplest model that provides sufficient explanation of the data, the starting point of phylogenetic analyses should be parsimony, not maximum likelihood. If the addition of new parameters (which increase the likelihood) to a parsimony estimation is seen as desirable, this may lead to a preference for results based on current likelihood models. If the addition of parameters is continued, however, the results will eventually come back to the same place where they had started, since allowing each character a branch length of its own also produces parsimony. Parsimony can be justified by very different types of models—either very complex or very simple. This suggests that parsimony does have a unique place among methods of phylogenetic estimation.
Cladistic analysis of languages: Indo‐European classification based on lexicostatistical data
Authors: Rexová Kateřina , Frynta Daniel , Zrzavý Jan 
Published: July 2005

AbstractThe phylogeny of the Indo‐European (IE) language family is reconstructed by application of the cladistic methodology to the lexicostatistical dataset collected by Dyen (about 200 meanings, 84 speech varieties, the Hittite language used as a functional outgroup). Three different methods of character coding provide trees that show: (a) the presence of four groups, viz., Balto‐Slavonic clade, Romano‐Germano‐Celtic clade, Armenian‐Greek group, and Indo‐Iranian group (the two last groups possibly paraphyletic); (b) the unstable position of the Albanian language; (c) the unstable pattern of the basalmost IE differentiation; but (d) the probable existence of the Balto‐Slavonic–Indo‐Iranian (“satem”) and the Romano‐Germano‐Celtic (+Albanian?) superclades. The results are compared with the phenetic approach to lexicostatistical data, the results of which are significantly less informative concerning the basal pattern. The results suggest a predominantly branching pattern of the basic vocabulary phylogeny and little borrowing of individual words. Different scenarios of IE differentiation based on archaeological and genetic information are discussed.
Taxon names as paradigms: the structure of nomenclatural revolutions
Authors: Härlin Mikael 
Published: July 2005

AbstractIn the present paper I argue that the two systems of phylogenetic nomenclature hitherto proposed represent, in a generalized sense, two different philosophies for how science develops and progresses. The phylogenetic system of definition initially proposed by de Queiroz and Gauthier [Syst. Zool. 39 (1990) 307], and later labeled PSD, is typically Popperian in the sense that science progresses toward truth by an accumulation of knowledge. Phylogenetic definitions of taxon names are assumed to adapt automatically to each new hypothesis of phylogeny, thereby reflecting better and better hypotheses. The phylogenetic system of reference proposed by Härlin [Zool. Scr. 27 (1998a) 381], on the other hand, is more Kuhnian, because it is built on the idea that successive hypotheses are incommensurable (and thus not cumulative) and that taxon names might be equalled with low‐level paradigms.
On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature
Authors: Härlin Mikael 
Published: July 2005

AbstractIn this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon name always refers to the same ancestor or ancestry is questionable.
A morphological analysis of marsupial mammal higher‐level phylogenetic relationships
Authors: Horovitz Inés , Sánchez‐Villagra Marcelo R 
Published: July 2005

AbstractPhylogenetic relationships among marsupial taxa have proven to be more complex than the simple grouping of species by continent. Recent marsupials are distributed across the New World, Australia, New Guinea, and certain neighboring islands. Morphological characteristics of various groups bridge different geographical areas. We investigated the origin of these characteristics by assembling a morphological data matrix consisting of a new suite of 149 postcranial characters and incorporated a series of previously published data on the craniodental (76 characters) and soft tissue (5 characters) anatomy. Twenty‐one marsupial terminal taxa representing all the major radiations of marsupials and 10 outgroups, most of which are exceptionally well‐preserved fossils such as Vincelestes, Ukhaatherium, and a few basal metatherian taxa, were investigated. A maximum parsimony analysis was conducted, resulting in one most parsimonious tree. Relationships among outgroups are congruent with current understanding of mammalian phylogeny. All currently accepted marsupial orders were recovered by the analysis. We confirmed previous results showing the South American “monito del monte”Dromiciops nested within the Australasian radiation. Within this australidelphian clade, Dromiciops was closely allied with the Diprotodontia. The South American paucituberculates appeared more closely related to the Australidelphia than to the American Didelphimorphia. The marsupial mole Notoryctes and the Peramelia were closely allied to each other and in turn were the sister group of the Dromiciops plus Diprotodontia clade. This pattern of relationships left Dasyuromorphia as the most basal offshoot of the Australidelphia. Whereas this tree topology recovers some signal that had been detected by previous studies, morphological and/or molecular, some novel hypotheses are also supported.
Morphology versus molecules: resolution of the positions of Nymphalis, Polygonia, and related genera (Lepidoptera: Nymphalidae)
Authors: Wahlberg Niklas , Nylin Sören 
Published: July 2005

AbstractThe debate on whether to combine different data sets for simultaneous analysis has continued to the present day unabated. We have studied the effects of combining one morphological data set with four molecular data sets (two mitochondrial gene sequences and two nuclear gene sequences) for a group of butterflies belonging to the tribe Nymphalini using partitioned Bremer support. We particularly focus our attention on a group of species belonging to the genera Aglais, Inachis, Roddia, Nymphalis, Kaniska, and Polygonia. We find that, despite significant incongruence between most data partitions, all data partitions contribute positively to the support of most nodes in the most parsimonious trees found for the combined data set. We also find that the morphological data set resolves one particular node (Kaniska basal to Polygonia) with good support, while the molecular data sets are ambiguous about the existence of this node. We suggest that partitioned Bremer support allows one to critically appraise the robustness of each node in a given tree and thereby identify nodes that may change with the addition of new data and nodes that are likely to remain unchanged with new data. We also suggest that morphological data are still crucial to our being able to understand the relationships of extant organisms, despite published views to the contrary. Based on our results we suggest that Inachis should be synonymized with Aglais, Roddia with Nymphalis, and Kaniska with Polygonia.
Molecular phylogeny of the Sphaerophorus globosus species complex
Authors: Högnabba Filip , Wedin Mats 
Published: July 2005

AbstractThe Sphaerophorus globosus complex (Lecanorales, lichenized Ascomycota) shows a large morphological variation, and three relatively distinct morphotypes can be distinguished in parts of the distribution area. Here, we utilize a multigene‐based maximum‐parsimony approach (nITS+
LSU rDNA, mtSSU rDNA, β‐tubulin, and actin) to investigate whether these morphotypes constitute distinct species. The results show that there are at least two well‐supported monophyletic groups that we interpret as phylogenetic species within the S. globosus complex. These species do not completely correspond to the predefined morphotypes. One group, an apparently undescribed species, contains noncoralloid specimens from the North American Pacific Northwest. The other group, S. globosus, consists of two well‐supported monophyletic groups: one contains coralloid epiphytic specimens from the North American Pacific Northwest that are morphologically indistinguishable from epiphytic specimens from Europe and are presently interpreted as belonging to the same species and the other is morphologically variable and contains terrestrial specimens from Europe, North America, and southernmost South America and coralloid epiphytic and epilithic specimens from Europe. The results suggest that the population in southernmost South America originated by long‐distance dispersal from arctic populations in the Northern Hemisphere.
A priori and a posteriori methods in comparative evolutionary studies of host–parasite associations
Authors: Dowling Ashley P.G , van Veller Marco G.P , Hoberg Eric P , Brooks Daniel R 
Published: July 2005

AbstractBrooks parsimony analysis (BPA) and reconciliation methods in studies of host–parasite associations differ fundamentally, despite using the same null hypothesis. Reconciliation methods may eliminate or modify input data to maximize fit of single parasite clades to a null hypothesis of cospeciation, by invoking different a priori assumptions, including a known host phylogeny. By examining the degree of phylogenetic congruence among multiple parasite clades, using hosts as analogs of taxa but not presuming a host phylogeny or any degree of cospeciation a priori, BPA modifies the null hypothesis of cospeciation if necessary to maintain the integrity of the input data. Two exemplars illustrate critical empirical differences between reconciliation methods and BPA: (1) reconciliation methods rather than BPA may select the incorrect general host cladogram for a set of data from different clades of parasites, (2) BPA rather than reconciliation methods provides the most parsimonious interpretation of all available data, and (3) secondary BPA, proposed in 1990, when applied to data sets in which host‐switching produces hosts with reticulate histories, provides the most parsimonious and biologically realistic interpretations of general host cladograms. The extent to which these general host cladograms, based on cospeciation among different parasite clades inhabiting the same hosts, correspond to host phylogeny can be tested, a posteriori, by comparison with a host phylogeny generated from nonparasite data. These observations lead to the conclusion that BPA and reconciliation methods are designed to implement different research programs based on different epistemologies. BPA is an a posteriori method that is designed to assess the host context of parasite speciation events, whereas reconciliation methods are a priori methods that are designed to fit parasite phylogenies to a host phylogeny. Host‐switching events are essential for explaining complex histories of host–parasite associations. BPA assumes coevolutionary complexity (historical contingency), relying on parsimony as an a posteriori explanatory tool to summarize complex results, whereas reconciliation methods, which embody formalized assumptions of maximum cospeciation, are based on a priori conceptual parsimony. Modifications of basic reconciliation methods, embodied in TreeMap 1.0 and TreeMap 2.02, represent the addition of weighting schemes in which the researcher specifies allowed departures from cospeciation a priori, with the result that TreeMap results more closely agree with BPA results than do reconciled tree analysis results.
The evolution of the laterophysic connection with a revised phylogeny and taxonomy of butterflyfishes (Teleostei: Chaetodontidae)
Authors: Smith Wm.Leo , Webb Jacqueline F , Blum Stanley D 
Published: July 2005

AbstractThe higher‐level relationships of butterflyfishes were examined using 37 morphological characters. This analysis combines characters derived from a histological study describing variation in the morphology of the laterophysic connection (an association between the swim bladder and the lateral‐line canals) with previously described morphological characters. The phylogenetic analysis resulted in four equally parsimonious trees that only differed in the placement of two of the 11 chaetodontid genera (Amphichaetodon and Forcipiger). We compare our analysis with previous hypotheses, present a new taxonomy consistent with the proposed cladistic relationships, and diagnose Chaetodon with five unreversed synapomorphies, including the evolution of characters composing the laterophysic connection. A new character‐based diagnosis of Chaetodon is provided and species are allocated accordingly; Chaetodon now includes the former Parachaetodon ocellatus and excludes the former subgenera Prognathodes and Roa. The evolution of the laterophysic connection is examined by optimizing character‐state transformations on the new hypothesis of relationships.
Phylogenetics of Sigmodontinae (Rodentia, Muroidea, Cricetidae), with special reference to the akodont group, and with additional comments on historical biogeography
Authors: D’Elıacute;a Guillermo 
Published: July 2005

AbstractThis is the first cladistic analysis of sigmodontine rodents (Cricetidae, Sigmodontinae) based on nuclear and mitochondrial DNA sequences. Two most parsimonious cladograms (7410 steps in length; CI=0.199; RI=0.523) were discovered. Sigmodontinae appears well supported. Sigmodon is sister to the remaining living sigmodontines. It is shown that Euneomys is not a phyllotine and that the Reithrodon group is not monophyletic. Results corroborate that the abrothricines form a natural group that is not part of the akodont radiation. The akodontine tribe is well supported, and is composed of five main clades, whose limits and relationships are thoroughly discussed. For instance, the scapteromyines do not form a natural group and they fall within the akodontine clade. Additionally, I present some taxonomic judgments and comments on the historical biogeography of sigmodontines in the light of the newly discovered relationships. For example, five akodontine divisions are suggested: the Akodon, the Bibimys, the Blarinomys, the Oxymycterus, and the Scapteromys Divisions. It is shown that traditional hypotheses of sigmodontine historical biogeography are falsified by the recovered topology.
Improvements to resampling measures of group support
Authors: Goloboff Pablo A , Farris James S , Källersjö Mari , Oxelman Bengt , Ramıacute;rez Martıacute;n J , Szumik Claudia A 
Published: July 2005

AbstractSeveral aspects of current resampling methods to assess group support are reviewed. When the characters have different prior weights or some state transformation costs are different, the frequencies under either bootstrapping or jackknifing can be distorted, producing either under‐ or overestimations of the actual group support. This is avoided by symmetric resampling, where the probability p of increasing the weight of a character equals the probability of decreasing it. Problems with interpreting absolute group frequencies as a measure of the support are discussed; group support does not necessarily vary with the frequency itself, since in some cases groups with positive support may have much lower frequencies than groups with no support at all. Three possible solutions for this problem are suggested. The first is measuring the support as the difference in frequency between the group and its most frequent contradictory group. The second is calculating frequencies for values of p below the threshold under which the frequency ranks the groups in the right order of support (this threshold may vary from data set to data set). The third is estimating the support by using the slope of the frequency as a function of different (low) values of p; when p is low, groups with actual support have negative slopes (closer to 0 when the support is higher), and groups with no support have positive slopes (larger when evidence for and against the group is more abundant).
From Haeckel to Hennig: the early development of phylogenetics in German‐speaking Europe
Authors: Willmann Rainer 
Published: July 2005

AbstractAn outline of the development of phylogenetic thinking and methodology in German literature published between 1862 and 1942 is presented. Central European biologists and palaeontologists of the first post‐Darwinian generation of biologists holding evolutionary views were directly stimulated by Darwin. Members of the second generation, mostly born after 1850, were largely influenced also by colleagues of the first post‐Darwinian generation, mainly by Haeckel. Among them were O. Abel, V. Franz, R. Hertwig, A. Naef, L. Plate, and R. v. Wettstein. Opinions on the relationship between systematics and phylogeny differed considerably. Many authors admitted that phylogeny must be mirrored in systematics but at the same time shared Haeckel's views on classification, which permitted paraphyletic groupings. Particularly Abel and Naef took systematics several steps further, and many important elements of phylogenetic systematics were developed several decades before Hennig. Naef presented a definition of a phylogenetic group that exactly matches Hennig's definition of monophyly. He also formulated a species concept that was implicitly based on reproductive isolation. This was an important presupposition for viewing speciation as the splitting of a stem species into daughter species. However, many authors of the first half of the 20th century repeated old, but established views on phylogenetics, while others overlooked or misunderstood earlier progressive views thus causing slow development of phylogenetic systematics in Central Europe. Its development almost stopped between 1925 and 1950, because of a widespread shift towards typology and extreme idealistic morphology. During that time very few persons such as W. Zimmermann and W. Hennig assembled elements of phylogenetic systematics and combined them with their own thoughts to create a sound theory and methodology.
Sources of character conflict in a clade of water striders (Heteroptera: Gerridae)
Authors: Damgaard Jakob , Cognato Anthony I 
Published: July 2005

AbstractIncongruence among trees reconstructed with different data may stem from historical (gene tree‐species tree conflict) or process (character change biases) phenomena. Regardless of the source, incongruent data, as determined with “global” measures of homoplasy, have often been excluded from parsimony analysis of the combined data. Recent studies suggest that these homoplasy measures do not predict the contribution of each character to overall tree structure. Branch support measures identify, on a character to node basis, sources of support and conflict resulting from a simultaneous analysis of the data. We implement these branch support measures to identify sources of character conflict in a clade of water striders consisting of Gerris Fabricius, Aquarius Schellenberg, and Limnoporus Stål species. Separate analyses of morphology, mitochondrial cytochrome oxidase I (COI), large mitochondrial ribosomal subunit (16SrRNA), and elongation factor‐1α (EF‐1α) data resulted in cladograms that varied in resolution and topological concordance. Simultaneous analysis of the data resulted in two trees that were unresolved for one node in a strict consensus. The topology agreed with current classification except for the placements of Aquarius chilensis and the Aquarius remigis species group closer to Gerris than to congeneric species. Branch support measures indicated that support derived from each data set varied among nodes, but COI had an overall negative effect on branch support. However, Spearman rank correlation of partitioned branch support values indicated no negative associations of branch support between any data sets and a positive association between EF‐1α and 16SrRNA. Thus incongruence among data sets was not drastic and the gene‐tree versus species tree phenomenon was not implicated. Biases in character change were a more likely reason for incongruence, although saturation curves and incongruence length difference for COI indicated little potential for homoplasy. However, a posteriori inspection of COI nucleotide change with reference to the simultaneous analysis tree revealed AT and codon biases. These biases were not associated with branch support measures. Therefore, it is difficult to predict incongruence or identify its cause. Exclusion of data is ill advised because every character is potentially parsimony informative.