bluuebunny/crossref_metadata_2025_split huggingface dataset:
The phylogenetic relationships of the cyanobacterial lichens in the Lecanorales suborder Peltigerineae
Authors: Wiklund Elisabeth , Wedin Mats 
Published: July 2005

AbstractWe 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

AbstractWhile 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

AbstractThe 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

AbstractA 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

AbstractGiven 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractThe 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.
Phylogeny of frogs as inferred from primarily larval characters (Amphibia:Anura)★
Authors: Haas Alexander 
Published: July 2005

AbstractThis 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.
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

Abstract 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.
OS‐D‐like genes and their expression in aphids (Hemiptera: Aphididae)
Authors: Jacobs S. P. , Liggins A. P. , Zhou J.‐J. , Pickett J. A. , Jin X. , Field L. M. 
Published: July 2005

AbstractIt has been proposed that a family of small soluble binding proteins, variously named as chemosensory proteins, sensory appendage proteins, pherokines and OS‐D‐like proteins, are involved in insect chemoreception. These proteins are present in a wide range of insect species and have a characteristic four cysteine motif. We have cloned cDNAs and gene sequences encoding these proteins from a number of aphid species, the first report of such in the order Hemiptera and supporting the view that these genes predate the divergence of the Neoptera. In one aphid species, Megoura viciae, we have shown that the proteins are present primarily in adults with one protein being most abundant in antennae and legs. This supports the view that the proteins could be involved in chemoreception but our preliminary binding studies failed to detect binding to a range of compounds which are known to elicit an electrophysiological response by aphids.
Capillary feeding of specific dsRNA induces silencing of the isac gene in nymphal Ixodes scapularis ticks
Authors: Soares C. A. G. , Lima C. M. R. , Dolan M. C. , Piesman J. , Beard C. B. , Zeidner N. S. 
Published: July 2005

Abstract Ixodes scapularis transmits several pathogens including Borrelia burgdorferi. Bioactive compounds in tick saliva support tick feeding and influence pathogen transmission to the mammalian host. These studies utilized oral delivery of dsRNA to silence an anticomplement gene (isac) in I. scapularis nymphs. Silencing of isac significantly reduced fed‐tick weight compared to delivery of control lacZ dsRNA, and immunoblots specific for FlaB protein indicated a reduction in spirochete load in isac‐silenced infected nymphs. SDS‐PAGE demonstrated that isac gene silencing affected expression of a number of salivary and non‐salivary gland proteins in ticks. Finally, multiple isac cDNA homologues were cloned, and these may represent a new gene family coexpressed during tick feeding. This work presents a novel oral delivery approach for specific gene silencing in I. scapularis nymphs and characterizes the effect of isac on blood‐feeding in an attempt to block transmission of B. burgdorferi.
Population structure and colonization history of the olive fly, Bactrocera oleae (Diptera, Tephritidae)
Authors: NARDI FRANCESCO , CARAPELLI ANTONIO , DALLAI ROMANO , RODERICK GEORGE K. , FRATI FRANCESCO 
Published: July 2005

AbstractThe olive fly, Bactrocera oleae, is the major pest of olives in most commercial olive‐growing regions worldwide. The species is abundant in the Mediterranean basin and has been introduced recently into California and Mexico, creating problems for quarantine protection and international trade. Here, we use nuclear microsatellite markers and mitochondrial sequences to examine the history of olive fly range expansion and colonization. Sampled populations span the current distribution of the olive fly worldwide, including South and Central Africa, Pakistan, Mediterranean Europe and Middle East, California, and Mexico. The Pakistani populations appear to be genetically well differentiated from the remaining populations, though rooting the origins of the species is problematic. Genetic similarity and assignment tests cluster the remaining populations into two genetic groups — Africa and a group including the Mediterranean basin and the American region. That Africa, and not the Mediterranean, is the origin of flies infesting cultivated olive is supported by the significantly greater genetic diversity at microsatellite loci in Africa relative to the Mediterranean area. The results also indicate that the recent invasion of olive flies in the American region most likely originated from the Mediterranean area.