bluuebunny/crossref_metadata_2025 huggingface dataset:
The Problem of Characters Susceptible to Parallel Evolution in Phylogenetic Reconstructions: Suggestion of a Practical Method and Its Application to Cave Animals
Authors: Marques Antonio Carlos , Gnaspini Pedro
Published: July 2005

We here propose a procedure to treat characters which are susceptible to parallel evolution (in this case, troglomorphisms) as a replacement for the two procedures used so far: to either completely consider or completely disregard these characters. These procedures may lead to one of two opposite errors, respectively, (1) to consider them as true synapomorphies when they are not or (2) to disregard them as true synapomorphies when they are. We suggest herein to recode the characters by splitting each troglomorphic character into as many as the number of taxa which show the given troglomorphic state. For each split character each taxon will have the derived state, while the others will be coded as missing data. We provide three real examples to test our procedure and conclude that it may give results different from those of the other two procedures. This means that our procedure does not repeat the two above “errors.” In addition, we believe that the procedure filters the possible biases, resulting in trees in which the troglomorphisms do have phylogenetic signals.
Larval Case Architecture and Implications of Host‐Plant Associations for North AmericanColeophora(Lepidoptera; Coleophoridae)1
Authors: Bucheli Sibyl , Landry Jean‐François , Wenzel John
Published: July 2005

The case‐bearing moths of North America are represented by a single genus,Coleophora, which contains approximately 144 described species. All are external seed or leaf miners that inhabit portable silk cases during most of the larval stage. Architectural and ecological characters from larval cases were used in cladistic analysis to investigate existing case groups for 32 North American species ofColeophora. Cladistic analysis confirmed monophyly of certain case groups, but not of others. Host‐plant preferences were also examined. The pattern of host plant use reflects more closely preference for certain plant tissues (seeds versus leaves) and growth forms (herbaceous versus woody) with exploitation of different plant taxa, rather than preference for certain plant taxa with exploitation of different plant tissues.
Phylogeny of the Eucoilinae (Hymenoptera: Cynipoidea: Figitidae)
Authors: Fontal‐Cazalla F.M. , Buffington M.L. , Nordlander G. , Liljeblad J. , Ros‐Farré P. , Nieves‐Aldrey J.L. , Pujade‐Villar J. , Ronquist F.
Published: July 2005

The Eucoilinae are a diverse and important group of parasitoids of Diptera, particularly in the tropics, but they are poorly known systematically and their generic classification is partly chaotic. Here, we present the first comprehensive cladistic analysis of higher eucoiline relationships. The analysis is based on 148 skeletal characters of adults documented in more than 1100 digital images available in an Internet‐accessible database. The characters were coded for 45 taxa representing 35 eucoiline genera, spanning the entire diversity of the group, and 7 outgroup genera. Relationships were partly difficult to resolve and parsimony analysis under implied weights performed considerably better than analysis under uniform weights. The results support the monophyly of the Eucoilinae and show that eucoilines are most closely related to the figitid subfamilies Emargininae and Pycnostigminae, but are ambiguous concerning the exact relationships among these three lineages. Of the 6 eucoiline genus groups recognized by Nordlander in 1982 (Entomol. Scand. 13, 269–292), only 2 are supported as monophyletic: the Trybliographa and Kleidotoma groups. The Gronotoma group is a paraphyletic assemblage of two different basal clades of eucoilines. The Rhoptromeris group is unnatural and only the 2 core genera, Rhoptromeris and Trichoplasta, form a monophyletic lineage. The data are ambiguous concerning the Ganaspis group, which appears to be paraphyletic, and the Chrestosema group, which may be a good clade. Based on the results we propose a modified system of informal genus groups in the Eucoilinae and discuss putative synapomorphies supporting each genus group. The proposed relationships imply that the first eucoilines were parasitoids of leaf‐mining agromyzids. The earliest split in the group was apparently between an Afrotropical and a Neotropical lineage, and much of the early radiation of the group occurred in these regions, particularly in the Neotropics.
A Posteriori and a Priori Methodologies for Testing Hypotheses of Causal Processes in Vicariance Biogeography
Authors: van Veller Marco G.P. , Kornet D.J. , Zandee M.
Published: July 2005

Methods used in vicariance biogeography fall into the categories of a posteriori methods (e.g., Component Compatibility Analysis and Brooks Parsimony Analysis) and a priori methods (e.g., Component Analysis, Reconciled Tree Analysis, and Three Area Statement Analysis). Each category corresponds to a particular methodology that arrives at general area cladograms by testing null hypotheses in a particular way. A posteriori methods assume the process of vicariance only (A0) as a common cause of the distribution of different monophyletic groups of taxa under the null hypothesis. Whenever a parsimony analysis of combined data from these monophyletic groups results in a general area cladogram with homoplasy, the null hypothesis is rejected and extinction and dispersal are invoked a posteriori as ad hoc process explanations. A priori methods assume not only vicariance (A0) but also combinations of vicariance with the processes of extinction (A1) and dispersal (A2) as possible causes of the distribution of the taxa of different monophyletic groups. Each assumed set of processes corresponds to a different null hypothesis. Under the assumption of independence and thus additivity of the processes involved, the sets of area cladograms obtained under A0, A1, and A2 from data of each monophyletic group must be inclusive (requirement I). Whenever no congruent area cladograms are found in the intersection of sets of area cladograms derived under the same assumption for different monophyletic groups (II), the corresponding null hypothesis is rejected.
Phylogeny of the Genus Cladonia s.lat. (Cladoniaceae, Ascomycetes) Inferred from Molecular, Morphological, and Chemical Data
Authors: Stenroos Soili , Hyvönen Jaakko , Myllys Leena , Thell Arne , Ahti Teuvo
Published: July 2005

Phylogenetic relationships within the genus Cladonia, including Cladina (Cladoniaceae, Lecanoromycetes), were reconstructed based upon simultaneous analyses of DNA sequences and morphological and chemical data. We used sequences from the internal transcribed spacer 1 (ITS1), the 5.8 rDNA gene, and the internal transcribed spacer 2 (ITS2) of the nuclear rDNA gene cluster, and partial sequences from the protein‐coding β‐tubulin gene. The analyses included 235 specimens of 168 taxa representing all currently recognized sections of Cladonia and Cladina and the outgroup genera Cladia, Pycnothelia, and Ramalea. Analyses were performed using optimization alignment with three different parameter values. The results of all analyses support the inclusion of Cladina in Cladonia. The current sectional division of Cladonia was not supported, and a new provisional classification for the genus is proposed.
A Morphological Test of the Monophyly of the Cardueline Finches (Aves: Fringillidae, Carduelinae)
Authors: Chu Philip C.
Published: July 2005

Monophyly of the cardueline finches (Aves: Fringillidae, Carduelinae), an assemblage of 119 species of seed‐eating songbirds, has not yet been rigorously tested. To test the hypothesis of cardueline monophyly I examined 37 taxa, among them 1 or 2 representatives from 16 of the 19 cardueline‐finch genera as well as 4 Hawaiian honeycreepers. Each taxon was scored for 225 morphological characters, 148 from the skeleton and 77 from the integument. Cladistic analysis of these data found the carduelines to be monophyletic, so long as the honeycreeper Telespiza cantans is considered to be cardueline; as for the other honeycreepers, they form a clade but do not group with either Telespiza or the carduelines. Both cardueline monophyly and the nonmonophyly of honeycreepers have comparatively strong support, with support for cardueline monophyly coming primarily from evolutionary modifications to the head skeleton.
RASA Attributes Highly Significant Structure to Randomized Data
Authors: Farris James S.
Published: July 2005

“Relative apparent synapomorphy analysis” (RASA), a method proposed as a statistical test of hierarchic structure in data, would better be called “relative apparent similarity analysis.” The method was supposed to work by finding the regression slope relating cladistic and phenetic measures of similarity, but in fact both the indices used are measures of phenetic similarity. The significance test tRASA originally proposed for RASA rejects far more often than it should under the null hypothesis. The source of this problem can be traced to the use of the RASA regression analogy, under which pairwise similarities calculated from a character matrix are treated as if they were independent random variables. That problem can be overcome by using a permutation test. Even with a permutation test, however, RASA can attribute highly significant hierarchic structure to randomized matrices, while often failing to recognize the structure of strongly structured matrices. RASA was able to detect structure in only 2 of 13 strongly structured data sets taken from the literature. The reason for this is that the regression slope criterion used in RASA has no reliable relationship to hierarchic structure. Some published simulations have purported to show that RASA recognizes structure effectively, but those conclusions are invalid because the original tRASA was used and because the calculations seem to have been performed incorrectly. New simulations using the same model show much lower effectiveness for RASA. The total support test is far more effective than RASA at recognizing hierarchic structure, and this is apparent in both simulations and real cases. Other simulations show that departure from a clock further decreases RASA's ability to recognize structure. This effect may help account for the very poor performance of RASA in real cases, which are seldom clocklike. The claim that RASA is a deductive procedure is unfounded and seems to have been used as part of a strategy for avoiding tests of the method. Because RASA is not a reliable indicator of hierarchic structure it should not be used to select characters or character codings.
A cladistic analysis of Scinax (Anura: Hylidae)
Authors: Faivovich Julián
Published: July 2005

The hylid frog genus Scinax ranges from southern Mexico to eastern Argentina. The 84 recognized species are currently arranged in five groups: the Scinax rubra, Scinax rostrata, Scinax catharinae, Scinax staufferi, and Scinax perpusilla species groups. Although a few species groups are distinctive, compelling evidence of monophyly is lacking for three groups, and their interrelationships remain virtually unknown. With the objective of testing the monophyly of the species groups and exploring their interrelationships, a cladistic analysis was performed, employing 86 characters from osteology, myology, adult and larval external morphology, reproductive biology, and karyotypes taken from 36 representative species of the five species groups plus eight outgroup taxa. The analysis of the resulting data matrix shows moderately well‐supported (as assessed through Bremer support and parsimony jackknifing) S. catharinae and S. rostrata species groups. The S. staufferi species group is polyphyletic, as currently composed, given that some of its species are nested within the S. catharinae species group. The only representative of the S. perpusilla species group is the sister species of the S. catharinae species group. Although weakly supported, the representatives of the S. rostrata and S. staufferi species groups are nested, separately, within the S. rubra species group. In order to have a taxonomy consistent with these results, it is proposed not to recognize the S. rubra group but to recognize a more inclusive rubra clade that includes all studied exemplars of the former S. rubra group, plus some of the S. staufferi group and all of the S. rostrata group. Similarly, a catharinae clade is recognized, within which all studied exemplars of the S. catharinae group (that now includes Scinax berthae and Scinax agilis) and the one studied representative of the S. perpusilla group are included.
The phylogeny of the Histeroidea (Coleoptera: Staphyliniformia)
Authors: Caterino Michael S. , Vogler Alfried P.
Published: July 2005

For its size (ca. 4000 species) the Histeridae is one of the most ecologically and morphologically diverse families of beetles. Its mostly predaceous members occupy a wide variety of habitats for which their morphologies may be highly modified. Previous attempts to resolve the phylogeny of the family based on morphological data have left many difficult issues unresolved. This study is the first to utilize either larval or molecular (18S rDNA) data in combination with adult morphology in an attempt to resolve these issues. We compare the performance of optimization alignment with a fixed positional homology approach, over a range of parameter space. Optimizing alignment parameters for combined analyses of 18S and morphology for both approaches resulted in very similar topologies. Contrary to previous hypotheses which held the cylindrical, subcortical forms of the family (e.g., Niponius, Trypanaeus, Trypeticus) to be the most primitive, our analyses find these to be highly specialized forms derived from within other more generalized taxa. Basal lineages within the family instead include Onthophilus, Anapleus, and Dendrophilus, all of which are ovoid, mainly generalist forms.
Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
Authors: Schulmeister Susanne , Wheeler Ward C. , Carpenter James M.
Published: July 2005

The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000–2700 bp for each taxon) from the nuclear genes 18S and 28S and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae +Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))).
Semi‐strict supertrees
Authors: Goloboff Pablo A , Pol Diego
Published: July 2005

A method to calculate semi‐strict supertrees is proposed. The semi‐strict supertrees are calculated by creating the matrix that represents all the groups in the source trees (as done in already existing techniques), and then finding the trees determined by the ultra‐clique. The ultra‐clique is defined as the set of characters where each possible subset is compatible with each possible subset from the entire matrix. Finding the ultra‐clique is computationally complex (since in most cases many of the characters have missing entries), but a heuristic method yields reliable results. When the trees have no conflict, or when there are only two trees, the method produces the exact result for any ordering of the input trees and any ordering of the groups within them; when there are more than two trees and they have conflict, a single ordering or sequence can create some spurious groups, but doing multiple sequences eliminates the spurious groups. The method uses only state set operations, and is thus easily implemented in computer programs. Unlike any existing type of supertree, semi‐strict supertrees display all the groups, and only those groups, that are implied by at least some combination of the input trees and contradicted by none. The idea that supertrees should take into account the number of occurences of a given group, so as to retain some groups even in the case of conflict, is discussed; it is argued that a conceptual equivalent of the majority rule consensus is not possible when the sets of taxa differ among trees. Also, when pruning taxa from a set of trees, the supertree can display groups that contradict the consensus for the entire trees, suggesting that supertrees for matrices with very dissimilar sets of taxa should be interpreted with caution. If (for any valid reason) the data cannot be combined in a single matrix, it is advisable that the taxon sets in the matrices be as similar as possible.
Cladistic coding of genomic maps
Authors: Gallut Cyril , Barriel Véronique
Published: July 2005

A new method of genomic maps analysis is described. The purpose of the method is to reconstruct phylogenetic relationships from the genomic organization of taxa. Our approach is based on gene order coding. This coding allows the description of genome topology without a prior hypothesis about evolutionary events and phylogenetic relationships. Different characters are used for each gene: (1) presence/absence, (2) orientation, and (3) relative position. The relative position of a particular gene inside the genome is the pair of genes surrounding it. The relative position character represents all the positions of a gene in the sampled genomes. It is coded as a multistate character. Our coding method has a priori variable cost implications on operators such as inversion, transposition, and gene loss/gain, which we discuss. The overall approach best fits the “duplication, random loss” evolutionary model. The coding method allows the reconstitution of a possible hypothetical common ancestor genome at each node of the tree. This reconstitution is based on the character states’ optimization; it comes down to choosing, among all possible optimizations, the optimization compatible with a complete genome topology at each internal node. The multistate coding of gene relative position, which is an undeniable advantage of this method, permits this reconstitution.
Basal subtribes of the Nymphidiini (Lepidoptera: Riodinidae): phylogeny and myrmecophily
Authors: Hall Jason P.W. , Harvey Donald J.
Published: July 2005

Three cladistic analyses, based predominantly on adult morphology, are presented for myrmecophilous riodinid butterflies in the tribe Nymphidiini. The first is a species‐level analysis of all 22 species recognized here in Aricoris (=Audre auctt.) using 27 characters. The second is a species‐level analysis of all 24 species recognized here in Synargis using 53 characters. The third is a generic‐level analysis of all six genera (Aricoris, Ariconiasn. gen., Lemonias, Thisbe, Juditha, and Synargis) recognized here as belonging in the basal clades of the Nymphidiini (=Lemoniadina auctt.) using 17 characters, with members of the Theopeina and Nymphidiina included with the ingroup to assess the monophyly of subtribes. Almost all characters are illustrated. The first analysis indicates that Aricoris consists of five monophyletic species groups, with the relationship ((constantius gr.colchis gr.)+(chilensis gr.(aurinia gr.+epulus gr.))), and contains the type species of Eiseleia and Audre, which are synonymized with Aricoris (n. syns.). The second analysis indicates that Synargis consists of four monophyletic species groups, with the relationship (phliasus gr.(regulus gr.+(pittheus gr.+abaris gr.))), and contains the type species of Ematurgina and Thysanota, which are synonymized with Synargis (n. syns.). The third analysis indicates that the Lemoniadina, or basal clades of the Nymphidiini, are paraphyletic with respect to the Theopeina and Nymphidiina, with the generic relationship ((Aricoris+Ariconias)+(((Lemonias+Thisbe)+(Juditha+Synargis))+(Theopeina+Nymphidiina))). We therefore restrict the Lemoniadina to include Lemonias, Thisbe, Juditha, and Synargis and provide the name Aricorina n. subtribe for Aricoris and Ariconias. All nymphidiine subtribes are characterized and a synonymic checklist for the Aricorina and Lemoniadina is presented. A “supertree” composed of the species‐level phylogenies derived here for Aricoris and Synargis, and those derived elsewhere for Ariconias, Lemonias, Thisbe, and Juditha, is used to map the distribution of larval host plant and attending ant taxa and the occurrence of aphytophagy. Observed patterns are discussed.
Distinguishing “or” from “and” and the case for historical identification
Authors: Kluge Arnold G
Published: July 2005

The adequacy of a probabilistic interpretation must be judged according to the nature of the event, or thing, being inferred. For example, conditional (frequency) probability is not admissible in the inference of phylogeny, because basic statements of common ancestry do not fulfill the requirements of the relations specified by the probability calculus. The probabilities of the situation peculiar to the time and place of origin of species are unique. Moreover, according to evolutionary theory, an event of species diversification is necessarily unique, because species are parts of a replicator continuum—species arise from ancestral species. Also, these probabilities cannot be ascertained, because the relevant situation cannot be repeated—it is unique. Finally, the applicability of conditional (frequency) probability is denied, because events of common ancestry have already occurred—there is nothing to predict. However, hypotheses of species relationships can be identified objectively according to the degree to which they have survived simultaneous testing with critical evidence, not with generally confirming evidence. The most parsimonious hypothesis of species relationships represents the least disconfirmed, best supported, proposition among the alternatives being compared. That hypothesis does not, however, deserve any special epistemological status beyond serving as the focus of the next round of testing.
Extending phylogenetic studies of coevolution: secondary Brooks parsimony analysis, parasites, and the Great Apes
Authors: Brooks Daniel R , McLennan Deborah A
Published: July 2005

Dowling recently compared the empirical properties of Brooks parsimony analysis (BPA) and the leading method for studying phylogenetic aspects of coevolution, reconciled tree analysis (using the computer program TreeMap), based on a series of simulations. Like the majority of authors who have compared BPA with other methods, however, Dowling considered only the form of BPA proposed in 1981 and did not take into account various modifications of the method proposed from 1986 to 2002. This leaves some doubt as to the robustness of his assessments of both the superiority of BPA and its shortcomings. We provide a précis of the principles of contemporary BPA, including ways to implement it algorithmically, using either Wagner algorithm‐based or Hennigian argumentation‐based approaches, followed by an empirical example. Our study supports Dowling's fundamental conclusions about the superiority of primary BPA relative to TreeMap. However, his conclusions about the shortcomings of BPA due to inclusive ORing (i.e., the production of ghost taxa) are incorrect, as secondary BPA eliminates inclusive ORing from the method. Secondary BPA provides a more complete account of the evolutionary associations between the parasite groups and their hosts than does primary BPA, without sacrificing any indirectly generated information about host phylogeny. Secondary BPA of two groups of nematodes inhabiting Great Apes shows that TreeMap analysis underestimated the amount of cospeciation in the evolution of the nematode genus Enterobius.
Countering concerted homoplasy
Authors: Harris Simon R , Wilkinson Mark , Marques Antonio C
Published: July 2005

Concerted homoplasy is a concern in phylogenetics because of its potential to generate strong but misleading evidence of relationships. Marques and Gnaspini (Cladistics 17, 371–381, 2001) proposed a method of recoding characters suspected of concerted homoplasy that avoids problems associated with their wholesale exclusion or inclusion. Here we show that the proposed method is analytically equivalent to excluding the recoded characters.
The problem of characters susceptible to parallel evolution in phylogenetic analysis: a reply to Marquès and Gnaspini (2001) with emphasis on cave life phenotypic evolution
Authors: Desutter‐Grandcolas Laure , D’Haese Cyrille , Robillard Tony
Published: July 2005

Marquès and Gnaspini [Cladistics 17 (2001) 371–381] analyzed the problem of the phylogenetic treatment of characters submitted to parallel evolution. Their proposal aimed at preserving the potential phylogenetic significance of supposedly homoplastic characters and considering them for phylogeny reconstruction. As an example, they used the troglobiomorphic features of animals restricted to caves; according to their preliminary hypothesis of homoplasy, troglobitic animals would exhibit a particular phenotype, referred to as troglobiomorphic, which they would acquire under similar selective pressures from the subterranean environment. We examined Marquès and Gnaspini's approach not from the point of view of its technical flaws, but from the point of view of the authors’ basic assertions on the treatment of troglobiomorphic characters and more generally the inclusion/exclusion/transformation of characters prior to phylogenetic analysis. In the present paper, we argue that this approach is invalidated by the repeated use of ad hoc hypotheses, which are supported neither by an existing phylogenetic pattern nor by available data. We consequently contest the adequateness of this approach with a cladistic analysis of historical questions.
The phylogenetic relationships of the cyanobacterial lichens in the Lecanorales suborder Peltigerineae
Authors: Wiklund Elisabeth , Wedin Mats
Published: July 2005

We present major cladistic analyses of the Lecanoromycetes (Ascomycota, Fungi) focusing on the Lecanorales suborder Peltigerineae, a group including the majority of the cyanobacterial lichens. DNA sequence datasets from the mtSSU and nLSU rDNA were produced and analyzed with maximum parsimony and parsimony jackknifing. The results suggest that the Lecanorales is monophyletic. The Peltigerineae (including Placynthiaceae, Peltigeraceae, Lobariaceae, Nephromataceae, Collemataceae, Coccocarpiaceae, Pannariaceae, and Massalongia) is likewise a monophyletic group. The Lobariaceae, and Lobaria in the traditional sense, are strongly supported as monophyletic, in contrast to results of other investigations based on nITS rDNA data. Pseudocyphellaria may be paraphyletic. Placynthiaceae is the sister group to the Collemataceae and Collema may be nested within Leptogium. Pannariaceae in the traditional sense is not a monophyletic group. Finally, the Lecanorineae is nonmonophyletic in all analyses, and the Cladoniineae and Teloschistineae are nested within the Lecanorineae in the combined analysis.
The problem with “the Paleoptera Problem:” sense and sensitivity
Authors: Ogden T.Heath , Whiting Michael F
Published: July 2005

While the monophyly of winged insects (Pterygota) is well supported, phylogenetic relationships among the most basal extant pterygote lineages are problematic. Ephemeroptera (mayflies) and Odonata (dragonflies) represent the two most basal extant lineages of winged insects, and determining their relationship with regard to Neoptera (remaining winged insects) is a critical step toward understanding insect diversification. A recent molecular analysis concluded that Paleoptera (Odonata Ephemeroptera) is monophyletic. However, we demonstrate that this result is supported only under a narrow range of alignment parameters. We have further tested the monophyly of Paleoptera using additional sequence data from 18SrDNA, 28S rDNA, and Histone 3 for a broader selection of taxa and a wider range of analytical methodologies. Our results suggest that the current suite of molecular data ambiguously resolve the three basal winged insect lineages and do not provide independent confirmation of Odonata + Neoptera as supported via morphological data.
Iterative pass optimization of sequence data
Authors: Wheeler Ward C
Published: July 2005

The problem of determining the minimum‐cost hypothetical ancestral sequences for a given cladogram is known to be NP‐complete. This “tree alignment” problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment‐based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure—the iterative improvement method—to create alignments at internal nodes by solving a series of median problems. The combination of a three‐sequence direct optimization with iterative improvement and a branch‐length‐based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed.
Implied alignment: a synapomorphy‐based multiple‐sequence alignment method and its use in cladogram search
Authors: Wheeler Ward C
Published: July 2005

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple‐alignment step, thereby creating topology‐specific, dynamic homology statements. Hence, no multiple‐alignment is required to generate cladograms. Unlike general and globally optimal multiple‐alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These “lines of correspondence” link ancestor–descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion–deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed.
From basepairs to birdsongs: phylogenetic data in the age of genomics
Authors: Freudenstein John V , Pickett Kurt M , Simmons Mark P , Wenzel John W
Published: July 2005

Given the quantity of molecular data now available, including complete genomes for some organisms, one can ask whether there is a need for any data beyond complete genomic sequences for phylogenetic analysis. One reason to look beyond the genome is that not all character information is encoded in organismal genomes. We propose a hierarchy of characters that ranges from biologically transmitted but nongenomically encoded characters, such as bird songs, to characters that are genomically encoded. All of these characters can retain historical information and are potentially useful for phylogenetic analysis. In addition, a number of phenotypic levels that are expressions of the genome can be identified. The question whether it is worth including any of these levels if all of the underlying sequence data have been collected arises, since issues of redundancy occur. Utilization of phenotypic levels that are ultimately based on sequences may facilitate reconstructing homologies that are not evident from sequence data alone. We propose the use of simultaneous analysis of sequence data and as many levels of phenotypic characters as possible to take advantage of homology information that may be more easily recovered from the latter. A method that eliminates redundancy to the degree that it can be detected is proposed.
Search‐based optimization
Authors: Wheeler Ward C
Published: July 2005

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP‐complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non‐additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed‐state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed‐state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost‐efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP‐complete phylogenetic optimization problems such as genomic break‐point analysis.
The repugnant and the mature in phylogenetic inference: atemporal similarity and historical identity
Authors: Kluge Arnold G
Published: July 2005

The significance of “being similar” in the inference of species relationships is refuted once again (see also Hennig, 1966, Phylogenetic Systematics, Univ. of Illinois Press, Urbana, IL). Without merit is Rieppel and Kearney's (Biol. J. Linn. Soc., 2002, 75, 59–82) claim that submitting the relational property of topological similarity, their preferred definition of character, to falsifying tests of similarity benefits that kind of inference. Such a priori uses of similarity, in character analysis, are consistent with observational theory, where a character is defined intensionally in terms of immutable properties. However, the induced hypotheses that follow from this theory, not the deductive test that Rieppel and Kearney wanted, remain controversial, because their predictability is a consequence of circular reasoning, and their projectabality fails empirically from incongruent observation reports. Further, a category mistake is made when the abstract, similarity‐defined, group of organisms is reified, as a part of history. In addition, Rieppel and Kearney failed to provide a special theory for similarity, which renders similarity scientifically repugnant (Quine, 1969, Ontological Relativity and Other Essays, Columbia Univ. Press, New York). A return to Hennig's (1966) evolutionary concept of evidence, as transformation series, is urged, and from which a testable character hypothesis can be formulated. There is no one operation for determining character states in this system—it can be anything that leads to the testable hypothesis of synapomorphy, as an historical identity relation. Character compatibility and conjunction, but not similarity, provide a priori tests in phylogenetic character analysis. In turn, the phylogenetic system of inference leads to explanations of homology, as historical identities, which exemplifies the goal of achieving a mature state of historical knowledge (not of Quine, 1969). Such maturity obtains from attempts to falsify hypotheses of species relationships with severely tested evidence, not from induction of “the” observation statement that Rieppel and Kearney sought to justify their true belief in a hypothesis of relationships.
Cladogenesis and reticulation in the Hawaiian endemic mints (Lamiaceae)
Authors: Lindqvist Charlotte , Motley Timothy J , Jeffrey John J , Albert Victor A
Published: July 2005

The Hawaiian endemic mints, which comprise 58 species of dry‐fruited Haplostachys and fleshy‐fruited Phyllostegia and Stenogyne, represent a major island radiation that likely originated from polyploid hybrid ancestors in the temperate North American Stachys lineage. In contrast with considerable morphological and ecological diversity among taxa, sequence variation in the nrDNA 5S non‐transcribed spacer was found to be remarkably low, which when analyzed using standard parsimony resulted in a lack of phylogenetic resolution among accessions of insect‐pollinated Phyllostegia and bird‐pollinated Stenogyne. However, many within‐individual nucleotide polymorphisms were observed, and under the assumption that they could contain phylogenetic information, these ambiguities were recoded as new character states. Substantially more phylogenetic structure was obtained with these data, including the resolution of most Stenogyne species into a monophyletic group with an apparent recent origin on O’ahu (3.0 My) or the Maui Nui island complex (2.2 My). Subsequent diversification appears to have involved multiple inter‐island dispersal events. Intergeneric placements for a few morphotypes, seemingly misplaced within either Phyllostegia or Stenogyne, may indicate reticulation as one polymorphism‐generating force. For a finer scale exploration of hybridization, preliminary AFLP fragment data were examined among putative hybrids of Stenogyne microphylla and S. rugosa from Mauna Kea, Hawai’i, that had been identified based on morphology. Cladistic analysis (corroborated by multivariate correspondence analysis) showed the morphologically intermediate individuals to group in a strongly supported monophyletic clade with S. microphylla. Therefore, reticulation could be both historic and active in Stenogyne, and perhaps a force of general importance in the evolution of the Hawaiian mints. The relatively greater extent of lineage‐sorted polymorphisms in Stenogyne may indicate selective differentiation from other fleshy‐fruited taxa, perhaps through the agency of highly specialized bird pollinators that restricted gene flow with other Hawaiian mint morphotypes.
A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes
Authors: Giannini Norberto P , Simmons Nancy B
Published: July 2005

The phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) has been investigated using several different molecular datasets. These studies differed widely in taxonomic and locus sampling, and their results tended to lack resolution of internal nodes and were themselves largely incongruent. To address this, we assembled a data set of 5 loci (up to 3.5 kbp from 12S rDNA, 16S rDNA, tDNA‐valine, cytochrome b, and the nuclear gene c‐mos) for 43 species of megachiropterans and 6 microchiropteran outgroups. We analyzed these data with direct optimization under equal costs for substitutions and indels. We used POY in a parallel setting, and searches consisted of replicated swapping + refinements (ratcheting, tree fusing, and iterative pass optimization). Our results indicate that Megachiroptera and all recognized genera (including Pteropus) are monophyletic, and that Melonycteris is the sister group of the clade containing all the other genera. Clades previously proposed using molecular data, as well as many new and traditional groups, were well‐supported, and various sources suggest that the degree of conflict with morphological data may be considerably less marked than previously supposed. Analysis of individual loci suffer 70% loss in the number of compatible groups recovered across all analyses with respect to combined analyses. Our results indicate that, within Megachiroptera, nectarivory and cave‐dwelling originated several times, but echolocation (used for obstacle detection) evolved only once. Megachiropterans likely originated in SE Asia‐Melanesia, and colonized Africa at least four times.
Probabilities for completely pectinate and symmetric cladograms
Authors: Stone J.R.
Published: July 2005

Formulas for nonalgorithmically calculating probabilities for completely pectinate and symmetric cladograms are presented.
Phylogeny of frogs as inferred from primarily larval characters (Amphibia:Anura)★
Authors: Haas Alexander
Published: July 2005

This paper presents larval evidence and evaluates its contribution to the discussion of frog phylogeny;136 larval characters,6 reproductive biology characters, and 14 adult morphology characters were scored for 81 frog and 4 caudate species.More than 90% of the data matrix entries represent original data derived from personal direct examination of specimens.Some larval characters are described for the rest time and many others have not been assessed for specic taxa or in a broad phylogenetic context before.Ho‐ moplasy appears common in this and other amphibian morphological data sets.The data supported and conrmed various well‐ known clades, among others the Anura, Bufonidae, Ceratophryinae, Discoglossidae, Dendrobatidae, Hyperoliidae, Microhylidae, South American microhylids, Phyllomedusinae, Pseudinae, Pipoidea, Pipidae, and Scoptanura.The Ascaphidae was sister group to all other anurans and the Pipoidea was placed more basally than in some previous analyses.The Eurasian pelobatids formed a clade, whereas Spea and Pelodytes did not group robustly with them.Pelobatoid frogs emerged as a paraphyletic “transitional” assemblage including Heleophryne. The resolution of basal neobatrachian splits remained labile, although some subclades within the Neobatrachia were robustly supported. The “Hylidae” was paraphyletic, and hyline species were paraphyletic with respect to the Pseudinae.Hemisus clearly was in a clade with the Hyperoliidae and is proposed to be included in that family.Scaphiophryne was conrmed as basal taxon within the Microhylidae.Compared to the larval stages of the most recent common ancestor of anurans, members of the Scoptanura (microhylids except scaphiophrynines)have accumulated the highest number of apomorphic character states in anuran evolution.
The use of fyke nets as a quantitative capture technique for freshwater eels (Anguilla spp.) in rivers
Authors: JELLYMAN D. J. , GRAYNOTH E.
Published: July 2005

Abstract  Fyke netting is a convenient and effective technique for capturing freshwater eels, and catch‐per‐unit‐effort is usually assumed to be an index of eel abundance. The present study investigated the potential of depletion fishing using baited fyke nets to obtain population estimates of longfin eels Anguilla dieffenbachii Gray, in a river in the South Island of New Zealand. The probability of capture (capture efficiency) of a single night's fishing increased with increasing size of eel, and ranged from 0.2 to 0.9 for eels <400 mm, to 0.7–0.9 for eels ≥500 mm. The capture efficiency of baited vs unbaited nets was assessed in a small stream that was electric fished after netting trials were completed. Baited nets proved to be an effective method of assessing abundance of longfin eels (>400 mm) but not shortfins (A. australis Richardson); capture efficiency of the population of longfins (the sum of fyke caught and electric fished eels) was 0.4 for a single night's fyke netting, increasing to 0.8 over four nights. Comparable efficiencies for shortfins were <0.1 and 0.3 respectively. Unbaited nets were markedly less efficient for both species.
Policy needs to improve marine capture fisheries management and to define a role for marine protected areas in Indonesia
Authors: MOUS P. J. , PET J. S. , ARIFIN Z. , DJOHANI R. , ERDMANN M. V. , HALIM A. , KNIGHT M. , PET‐SOEDE L. , WIADNYA G.
Published: July 2005

Abstract  Management of Indonesia's marine capture fisheries faces a huge dilemma: evidence suggests that most, if not all, of Indonesia's capture fisheries are fully or overexploited, but the fishery sector is still expected to contribute to the increase of Indonesia's gross national product (GNP) through an increase in total catches. Furthermore, the current practice of using catch‐effort data and Maximum Sustainable Yield (MSY) models to inform Indonesia's fisheries policies is flawed, putting sustainability and long‐term profitability of Indonesia's fisheries at risk. It is argued that the following shift in capture fisheries management policy must be achieved to ensure the survival of Indonesia's fish stocks and fisheries:

1 a shift in fisheries policy from development‐oriented management towards management for sustainability;

2 acceptance by fisheries managers that ‘untapped resources’ may not exist or cannot be exploited profitably;

3 acceptance by fisheries managers that any transfer of fishing effort between fishing grounds may contribute to collapse of local fisheries;

4 a shift in fisheries management from MSY models to eco‐system based management, wherein Marine Protected Areas should play an important role.
Molecular differentiation between chromosomally defined incipient species of Anopheles funestus
Authors: Michel A. P. , Guelbeogo W. M. , Grushko O. , Schemerhorn B. J. , Kern M. , Willard M. B. , Sagnon N’F. , Costantini C. , Besansky N. J.
Published: July 2005

Anopheles funestus Giles is one of the most important vectors of malaria in sub‐Saharan Africa. The population structure of this mosquito in Burkina Faso, West Africa based on chromosomal inversion data led to the description of two chromosomal forms, Kiribina and Folonzo. Because both forms co‐occur in the same locales yet differ significantly, both in the frequency of inverted arrangements on chromosome arms 3R and 2R and in vectorial capacity, they were hypothesized to be emerging species with at least partial barriers to gene flow. This hypothesis would be strengthened by molecular evidence of differentiation between Kiribina and Folonzo at loci outside chromosomal inversions. We surveyed molecular variation in sympatric populations of the two forms using sequences from the mitochondrial ND5 gene and genotypes at sixteen microsatellite loci distributed across the genome. Both classes of marker revealed slight but significant differentiation between the two forms (mtDNA FST = 0.023, P < 0.001; microsatellite FST = 0.004, P < 0.001; Rst = 0.009, P = 0.002). Locus‐by‐locus analysis of the microsatellite data showed that significant differentiation was not genome‐wide, but could be attributed to five loci on chromosome 3R (FST = 0.010, P < 0.001; Rst = 0.016, P = 0.002). Importantly, three of these loci are outside of, and in linkage equilibrium with, chromosomal inversions, suggesting that differentiation between chromosomal forms extends beyond the inversions themselves. The slight overall degree of differentiation indicated by both marker classes is likely an underestimate because of recent population expansion inferred for both Folonzo and Kiribina. The molecular evidence from this study is consistent with the hypothesis of incipient speciation between Kiribina and Folonzo.