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  • Articles  (44)
  • phylogeny  (44)
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  • 1995-1999  (44)
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  • 1998  (44)
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  • Articles  (44)
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  • Springer  (44)
  • MDPI Publishing
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  • 1995-1999  (44)
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  • 1
    Electronic Resource
    Electronic Resource
    Ein Archaeotrogon (Aves: Archaeotrogonidae) aus dem Mittel-Eozän der Grube Messel (Hessen, Deutschland)? (1998)
    Springer
    Journal of ornithology 139 (1998), S. 121-129 
    Details
    ISSN: 1439-0361
    Keywords: fossil birds ; Hassiavis laticauda n. gen. n. sp. ; Archaeotrogonidae Mourer-Chauviré 1980 ; feather preservation ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Description / Table of Contents: Zusammenfassung Ein Vogel aus dem Mittel-Eozän der Grube Messel (Hessen, Deutschland) wird als neue Gattung und Art der Archaeotrogonidae Mourer-Chauviré 1980 beschrieben (incertae sedis). Die Exemplare aus Messel wären die ersten artikulierten Skelette dieser Familie.Hassiavis laticauda n. gen. n. sp. unterscheidet sich vor allem im Bau des Coracoids von der GattungArchaeotrogon Milne-Edwards 1892. Besonders bemerkenswert ist die ausgezeichnete Erhaltung der Flügel- und Schwanzbefiederung einiger Exemplare. Einige Schwanzfedern des Holotypus zeigen eine Querbänderung, welche möglicherweise auf die ursprüngliche Pigmentierung dieser Federn zurückzuführen ist. Die phylogenetische Stellung der Archaeotrogonidae wird diskutiert. Zur Zeit sind keine Synapomorphien bekannt, welche diese Familie mit einer der bestehenden Ordnungen verbinden.
    Notes: Summary A bird from the Middle Eocene of the Grube Messel (Hessen, Deutschland) is described as a new genus and species of the Archaeotrogonidae Mourer-Chauviré 1980 (incertae sedis). The specimens from Messel would be the first articulated skeletons of this family.Hassiavis laticauda n. gen. n. sp. is distinguished from the genusArchaeotrogon Milne-Edwards 1892 in the morphology of the coracoid. The excellent preservation of the wing feathers and those of the tail in several of the specimens is exceptional. Some tail feathers of the holotype are barred, which might be traced back to the original pigmentation of these feathers. The phylogenetic position of the Archaeotrogonidae is discussed. At present no synapomorphies are known, which could set up a closer relationship between this family and one of the existing orders.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01651221
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  • 2
    Electronic Resource
    Electronic Resource
    Evolutionary distances and identification of Candida species in clinical isolates by Randomly Amplified Polymorphic DNA (RAPD) (1998)
    Springer
    Mycopathologia 142 (1998), S. 57-66 
    Details
    ISSN: 1573-0832
    Keywords: Candida ; identification ; PCR ; phylogeny ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Fast and reliable identification of different species of the genus Candida is important to define adequate therapeutic decisions, because the different species have highly variable susceptibilities to antifungal drugs; azoles and amphothericin B. Accurate statistical records on case history and epidemiological studies also depend on effective identification. To address this problem we established a RAPD method that enabled direct identification of five very common species of Candida. Initially, reference band patterns were established for C. albicans, C. tropicalis, C. parapsilosis, C. glabrata and C. krusei. One of the primers, M2, showed remarkably conserved intra-specific patterns of approximately 10 bands each, ranging in size from 2.0 to 0.1 kb. These patterns were significantly different and species-specific. Few bands were conserved between different species of Candida, which was assumed to be consistent with their phylogenetic relatedness. In addition, band patterns were constant and reproducible and DNA isolated from single colonies yielded sufficient DNA for identification. The reference band patterns were then used, in blind experiments, to identify species of Candida in 50 randomly chosen samples, including clinical isolates and ATCC strains. RAPD results were 100% consistent with results obtained by conventional diagnostic methods and were achieved in one day instead of several days taken by conventional methods. Because ideal identification methods should be consistent with phylogeny and taxonomy we tested whether RAPD could be used to calculate genetic distances. Comparison of RAPD phylogenetic trees with 18S rRNA trees showed significant differences in tree topologies which indicated that RAPD data could not accurately measure the relative distances between different species. Also, computer simulations of RAPD random patterns were used to test whether the observed degree of RAPD band pattern similarities could occur at random. These simulations suggested that the level of inter-specific band pattern similarities observed in our data could be obtained at random, while intra-specific pattern similarities could not. RAPD would be helpful to discriminate between isolates but not to quantitate the differences. We suggest that the inaccurate estimate of genetic distances from RAPD is a general limitation of the technique and not a specific problem of our identification method. Because of the repetitive character of the target sequences, genetic distances calculated from RAPD could be affected by paralogy, namely, recombination and duplication events not parallel with speciation events.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006998325716
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  • 3
    Electronic Resource
    Electronic Resource
    Mitochondrial DNA analysis of Sporothrix schenckii in North and South America (1998)
    Springer
    Mycopathologia 142 (1998), S. 115-118 
    Details
    ISSN: 1573-0832
    Keywords: epidemiology ; mitochondrial DNA ; phylogeny ; restriction fragment length polymorphism (RFLP) ; Sporothrix schenckii
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Mitochondrial DNA (mtDNA) types based on restriction fragment length polymorphism (RFLP) patterns with HaeIII were investigated in clinical isolates of Sporothrix schenckii in North and South America. In addition to 14 mtDNA types (Types 1–14) so far reported, six new mtDNA types, Types 15–20 were found in this study. Type 3 was divided into two subtypes, Subtype 3A and Subtype 3B based on RFLP with Msp1. Type 14 was also divided into three subtypes, Subtype 14A, Subtype 14B and Subtype 14C based on RFLP with Hha1. Nineteen isolates in the United States consisted of 1 isolate of Type 1, 12 of Type 2, 2 of Type 4, 3 of Type 14 (1 of Subtype 14B and 2 of Subtype 14C) and 1 of Type 15. Twenty nine isolates in Venezuela consisted of 13 of Type 3 (Subtype 3B), 6 of Type 4, 1 of Type 18, 3 of Type 19 and 6 of Type 20. Thirteen isolates in Argentina consisted of 2 of Type 3 (Subtype 3A), 4 of Type 4, 4 of Type 16 and 3 of Type 17. One isolate in Brazil was Type 3 (Subtype 3A). Based on the phylogeny of 20 mtDNA types (Types 1–20) constructed by estimating sequence divergences of mtDNA, mtDNA types were clustered into two groups: Group A (Types 1–3, Type 11 and Types 14–19) and Group B (Types 4–10, Types 12–13 and Type 20). These results suggest that S. schenckiiisolates in North and South America mainly belong to Group A.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006952702947
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  • 4
    Electronic Resource
    Electronic Resource
    Cleavase Fragment Length Polymorphism (CFLP): A Methodology to Further Exploit Polymorphisms from PCR Products of Plastid DNA (ptDNA) in Phaseolus (1998)
    Springer
    Plant molecular biology reporter 16 (1998), S. 271-282 
    Details
    ISSN: 1572-9818
    Keywords: CFLP ; Cleavase I ; Phaseolus ; phylogeny ; ptDNA intergenic regions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The CFLP methodology was applied for Cleavase I site detection within ptDNA intergenic regions (atpB-rbcL and rps14-psaB) at both interspecific and intraspecific levels in the genus Phaseolus. Optimal Cleavase I reaction temperature was 55 °C and the semi-dry electrophoretic transfer was more efficient than the original capillary one. Cleavase reactions yield a high number of fragments as compared to PCR-RFLP and allowed differentiation within and between landraces and wild forms of the Lima bean (Phaseolus lunatus L.) originating from Andean and Mesoamerican regions of Latin America. From sequencing data and using stemloop program (GCG, Madison), congruent numbers of hairpins/fragments were identified within the sequences, highlighting the robustness of the Cleavase I. Our results pointed out the ubiquity of short conserved motifs amongst a geographically localized group of species. In the vicinity of these motifs, synapomorphic-like substitutions were frequently observed. A phylogenetic tree based on these sequences is congruent with the CFLP pattern as well as with the widely accepted phylogeny of the genus. The usefulness of this new tool as alternative and/or complementary to PCR-RFLP technology on ptDNA is suggested and discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007500914695
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  • 5
    Electronic Resource
    Electronic Resource
    Phylogenetic analysis and predicted secondary structures of the rDNA internal transcribed spacers of the powdery mildew fungi (Erysiphaceae) (1998)
    Springer
    Mycoscience 39 (1998), S. 441-453 
    Details
    ISSN: 1618-2545
    Keywords: Erysiphaceae ; internal transcribed spacer ; phylogeny ; powdery mildew ; secondary structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The nucleotide sequences of the internal transcribed spacer (ITS) regions of the ribosomal DNA including the 5.8S rRNA gene and the 5′ end of the 28S rRNA gene have been determined for 19 species in 10 genera of the powdery mildew fungi in order to analyze their phylogenetic relationship. These fungi were divided into two large groups based on the nucleotide length of the ITS regions, and this grouping was in line with that based on the morphological characters of the anamorphic stage rather than the teleomorphic stage. Although the variable ITS sequences were often ambiguously aligned, conserved sites were also found. Thus, a neighbor-joining tree was constructed using the nucleotide sequence data of the conserved sites of the ITS regions, the 5.8S rRNA gene, and the 5′ end of the 28S rRNA gene. The phylogenetic tree displayed the presence of four groups in the powdery mildews, which were distinguished by their morphology and/or host ranges. In the ITS2 region, the presence of a common secondary structure having four hairpin domains was suggested, in spite of the highly variable nucleotide sequences of this region. The predicted secondary structure was supported by the compensatory mutations as well as compensatory conserved sequences and high G+C content in the predicted stem regions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02460905
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  • 6
    Electronic Resource
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    Molecular phylogenetic study of the basidiomycetous anamorphic yeast genusTrichosporon and related taxa based on small subunit ribosomal DNA sequences (1998)
    Springer
    Mycoscience 39 (1998), S. 7-13 
    Details
    ISSN: 1618-2545
    Keywords: phylogeny ; SSU rDNA ; Trichosporon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Small subunit ribosomal DNA sequences of all species of the basidiomycetous anamorphic yeast genusTrichosporon were determined, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods. The sequence data showed that, with the exception ofT. pullulans, the genus is monophyletic, although its members have two different major ubiquinones, Q9 and Q10. The genus can be divided phylogenetically into three major clusters. Species with Q10 as the major ubiquinone constitute a single cluster, while those with Q9 form two clusters.Trichosporon pullulans was phylogenetically distinct from other taxa of the genus. It is located in a cluster containingCystofilobasidium capitatum, Mrakía frigida, Xanthophyllomyces dendrorhous and three species ofUdeniomyces. This result sugests thatT. pullulans does not belong to the genusTrichosporon.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02461572
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  • 7
    Electronic Resource
    Electronic Resource
    Morphometric and phylogenetic analysis of theDaviesia ulicifolia complex (Fabaceae, Mirbelieae) (1998)
    Springer
    Plant systematics and evolution 209 (1998), S. 93-122 
    Details
    ISSN: 1615-6110
    Keywords: Fabaceae ; Mirbelieae ; Daviesia ulicifolia ; Phenetics ; ordination ; phylogeny ; morphometric characters ; gap coding ; paraphyly ; species problem ; Flora of Australia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Daviesia ulicifolia is a widespread species that exhibits complex variation throughout its range. Using ordination and cluster analysis of morphometric characters we resolved ten terminal taxa for phylogenetic analysis. A data set including these and five closely related species was coded for a combination of morphometric and qualitative characters and analysed using parsimony. This revealed thatD. ulicifolia is paraphyletic by inclusion ofD. acicularis, D. arenaria andD. microcarpa. One terminal cluster is more similar to an outgroup species (D. arthropoda) than toD. ulicifolia and should be treated as a new species. Given recent theoretical and empirical studies showing paraphyly to be both expected and observed at species level, we propose that all existing species in this group continue to be recognised taxonomically. We suggest subdividingD. ulicifolia into several subspecies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00991527
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  • 8
    Electronic Resource
    Electronic Resource
    Genetic control of fruit polymorphism in the GenusFedia (Valerianaceae) in the light of dimorphic and trimorphic populations ofF. pallescens (1998)
    Springer
    Plant systematics and evolution 210 (1998), S. 199-210 
    Details
    ISSN: 1615-6110
    Keywords: Valerianaceae ; Valerianeae ; Fedia ; Fruit polymorphism ; seed dispersal ; supergene ; genetic control ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genusFedia consists of three species (F. cornucopiae, F. graciliflora andF. pallescens) of winter annual herbs, endemic to the western Mediterranean Basin. The deciduous terminal fruits of these taxa are polymorphic in the development of their pericarp and/or calyx, and each population is dimorphic or more rarely trimorphic. The three main fruit types are dispersed in several manners, and are specialized for either epizoochory or myrmecochory. On the basis of our experimental study of dimorphic and trimorphic populations ofF. pallescens subsp.pallescens, a genetic model is presented in order to explain the control of this intrapopulational polymorphism. It is postulated that two diallelic loci are tightly linked on the same chromosome in a functional supergene. One allele of each locus displays a dominance effect in the heterozygous state. Within the four possible homologous allelic segments, only two are present in the dimorphic populations, three in the trimorphic ones, and are otherwise associated in diverse combinations in the remaining taxa of the genus. Similar examples of fruit polymorphism are already documented in the tribeValerianeae, subtribeFediinae. The hypothesis is put forward that this fruit polymorphism is a synapomorphy for the subtribe.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00985668
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  • 9
    Electronic Resource
    Electronic Resource
    Phylogenetic relationships in thePrimulales inferred fromrbcL sequence data (1998)
    Springer
    Plant systematics and evolution 211 (1998), S. 93-102 
    Details
    ISSN: 1615-6110
    Keywords: Primulales ; Primulaceae ; Myrsinaceae ; Theophrastaceae ; DNA ; rbcL sequences ; phylogeny ; classification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cladistic analysis of phylogenetic relationships in thePrimulales has been conducted, based on nucleotide sequence data from the chloroplast DNA generbcL. The analysis included 16 taxa representing all three families in the order, and also six genera from other orders, viz.Magnolia (Magnoliaceae),Caltha (Ranunculaceae),Geranium (Geraniaceae),Nicotiana (Solanaceae),Diospyros (Ebenaceae), andManilkara (Sapotaceae). Previous cladistic analyses of morphological data have indicated that theTheophrastaceae are monophyletic, and that theMyrsinaceae are paraphyletic if including the genusMaesa. The results of the present work corroborate this conclusion, but also indicate that thePrimulaceae are paraphyletic.Maesa is part of an unresolved clade that also include theTheophrastaceae and thePrimulaceae, and theMyrsinaceae s. str. The latter is part of a monophyletic group also comprising thePrimulaceae-Lysimachiinae andCyclamen. It is concluded that dramatic changes in family circumscriptions are needed in order for taxonomy to reflect strictly monophyletic groups in thePrimulales.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00984914
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  • 10
    Electronic Resource
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    Evaluation of random amplified polymorphic DNA for species identification and phylogenetic analysis inStylosanthes (Fabaceae) (1998)
    Springer
    Plant systematics and evolution 211 (1998), S. 201-216 
    Details
    ISSN: 1615-6110
    Keywords: Fabaceae ; Stylosanthes ; RAPDs ; phylogeny ; systematics ; taxon identification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Random amplified polymorphic DNA (RAPD) was assessed for its suitability as a tool to be used in the identification of taxa from the genusStylosanthes (Fabaceae, Papilionoideae, Aeschynomeneae). Five random primers were used to ‘fingerprint’ accessions from seven species in the genus, and generated RAPD profiles that were species-specific. Data were used to examine evolutionary relationships between taxa, employing both clustering and ordination techniques, and the results were compared with those from a previous cladistic analysis of chloroplast DNA (cpDNA) restriction fragments. Both multivariate approaches indicated relationships that were generally similar to those obtained by RFLP analysis of cpDNA. However, while cluster analysis grouped together all accessions within species, ordination placed certain accessions ofS. humilis, S. macrocephala andS. capitata into separate groups. Experiments to test the assumed homology of comigrating RAPDs estimated 85.7% homology for accessions within species, and 53.8% homology for accessions between species. The value of RAPD data in systematics is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00985359
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  • 11
    Electronic Resource
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    Phylogeny, diversity, and distribution inExostema (Rubiaceae): Implications of morphological and molecular analyses (1998)
    Springer
    Plant systematics and evolution 212 (1998), S. 215-246 
    Details
    ISSN: 1615-6110
    Keywords: Rubiaceae ; Exostema ; Morphology ; ITS sequences ; cladistics ; phylogeny ; diversity ; Caribbean biogeography
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The neotropical genusExostema comprises 25 species of trees and shrubs, ranging in distribution from Bolivia to Mexico and throughout the West Indies, with most species endemic to the Greater Antilles. Infrageneric relationships and species-level patterns of evolution were investigated in phylogenetic analyses using morphological, molecular, and combined data sets. All data sets resolved three main species groups which correspond to the three sections recognized byMcDowell (1996). However, the analyses of ITS sequence data placed the two South American species basal to the three main clades. Otherwise, the morphological and molecular data are highly compatible, and produce a more robust yet consistent phylogeny in the combined data analysis. Morphological evolution inExostema involves many specializations for xeric habitats, reflecting repeated ecological shifts from moist forest to exposed, seasonally dry environments during the diversification of the genus. Both moth and bee pollination syndromes are found inExostema, and shifts in pollination ecology appear pivotal to the differentiation of the three sections. Biogeographically,Exostema likely originated in South America and migrated via Central America to the Greater Antilles, where the morphological diversification and speciation are most extensive.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01089740
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  • 12
    Electronic Resource
    Electronic Resource
    Chloroplast DNA restriction site mapping and the phylogeny ofRanunculus (Ranunculaceae) (1998)
    Springer
    Plant systematics and evolution 213 (1998), S. 1-19 
    Details
    ISSN: 1615-6110
    Keywords: Ranunculaceae ; Ranunculus ; Chloroplast DNA ; phylogeny ; restriction site maps
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A chloroplast DNA restriction site map forRanunculus sceleratus (Ranunculaceae) was constructed using 14 restriction endonucleases. The total size of the chloroplast genome is 152.4kb. No inversions were detected relative to the tobacco chloroplast DNA. Cladistic analyses of chloroplast DNA restriction site polymorphism were employed in order to elucidate the phylogeny among 76 species of the genusRanunculus in a wide sense and one species ofTrautvetteria. A total of 341 informative restriction site changes were detected. Parsimony jackknifing, bootstrapping and decay analysis were undertaken in order to evaluate the amount of support for the monophyletic groups. The results suggest that the analysed species ofRanunculus are divisible into two main clades. Only few of the traditional sections and subgenera ofRanunculus are monophyletic. The genusTrautvetteria is nested within a clade comprising, e.g.Ranunculus cymbalaria, R. andersonii, R. lapponicus andR. ficaria. SubgenusBatrachium lies within a larger clade containing, e.g.R. sceleratus andR. hyperboreus. Contractions of the inverted repeat due to parallel deletions of 200–300 bp close to the JSB have occurred in many clades and the phylogenetic distribution of this size reduction was mapped among the species.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00988905
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  • 13
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    Family relationships of the enigmatic rosid generaBarbeya andDirachma from the Horn of Africa region (1998)
    Springer
    Plant systematics and evolution 213 (1998), S. 103-119 
    Details
    ISSN: 1615-6110
    Keywords: Barbeyaceae ; Dirachmaceae ; Elaeagnaceae ; Rhamnaceae ; Rosaceae ; Ulmaceae ; Urticales ; Barbeya ; Dirachma ; Actinorhizal symbiosis ; plastid DNA ; monotypic plant families ; phylogeny ; rbcL ; rosids ; trnL-F ; Africa ; Arabia ; Socotra ; Somalia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Barbeya is a monotypic genus in the Horn of Africa and adjacent parts of Arabia. It is usually treated as the familyBarbeyaceae and regarded as an aberrant member ofUrticales. Dirachma, with one species on Socotra and one in Somalia, is usually treated as the familyDirachmaceae, inGeraniales, but a position inMalvales has also been suggested. Analyses of molecular data, from bothrbcL andtrnL-F, indicate thatBarbeya andDirachma are closely related inter se as well as toRhamnaceae andElaeagnaceae. In an analysis based on morphologyBarbeya groups withElaeagnaceae, andDirachma withRhamnaceae andUlmaceae. In a combined molecular and morphological analysisBarbeya is the sister group ofElaeagnaceae andDirachma is the sister group of the wholeBarbeya-Elaeagnaceae-Rhamnaceae clade. However, the support for these arrangements is weak and, rather than mergingBarbeyaceae withDirachmaceae as suggested by the molecular analysis or withElaeagnaceae as suggested by the morphological and combined analyses, it seems best to retain bothBarbeyaceae andDirachmaceae in their present circumscriptions, but in both cases in completely new positions in the angiosperm system. The results are compatible with a new circumscription ofRhamnales comprisingRhamnaceae, Elaeagnaceae, Dirachmaceae andBarbeyaceae.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00988911
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  • 14
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    Taxonomy and Philosophy of Names (1998)
    Springer
    Biology and philosophy 13 (1998), S. 233-244 
    Details
    ISSN: 1572-8404
    Keywords: reference ; meaning ; individual ; class ; definition ; clade ; evolution ; phylogeny ; phylogenetic taxonomy ; systematics ; tree-thinking ; cladistics ; intention ; extension
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Philosophy
    Notes: Abstract Although naming biological clades is a major activity in taxonomy, little attention has been paid to what these names actually refer to. In philosophy, definite descriptions have long been considered equivalent to the meaning of names and biological taxonomy is a scientific application of these ideas. One problem with definite descriptions as the meanings of names is that the name will refer to whatever fits the description rather than the intended individual (clade). Recent proposals for explicit phylogenetic definitions of clade names suffer from similar problems and we argue that clade names cannot be defined since they lack intension. Furthermore we stress the importance of “tree-thinking” for phylogenetic reference to work properly.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006583910214
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  • 15
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    ‘Candidatus Phytoplasma australiense’ is the phytoplasma associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases (1998)
    Springer
    European journal of plant pathology 104 (1998), S. 619-623 
    Details
    ISSN: 1573-8469
    Keywords: 16S rRNA gene ; 16S/23S spacer region ; phylogeny ; sequence analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Sequence comparisons and phylogenetic analysis of the 16S rRNA genes and the 16S/23S spacer regions of the phytoplasmas associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases revealed minimal nucleotide differences between them resulting in the formation of a monophyletic group. Therefore, along with Australian grapevine yellows, the phytoplasmas associated with Phormium yellow leaf and papaya dieback should also be considered as ‘Candidatus Phytoplasma australiense’.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008693904427
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  • 16
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    Levels of Homoplasy in the Evolution of the Mammalian Skeleton (1998)
    Springer
    Journal of mammalian evolution 5 (1998), S. 113-126 
    Details
    ISSN: 1573-7055
    Keywords: homoplasy ; Mammalia ; phylogeny ; skeleton
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract It is commonly believed that there are differences in the evolutionary lability of the crania, dentition, and postcrania of mammals, the latter two being more prone to homoplasy because of strong selective pressures for feeding and locomotion, respectively. Further, because of the fragmentary nature of fossils, phylogenetic analyses of extinct taxa often must utilize characters based on only one of these systems. In this paper the levels of homoplasy (as measured by the consistency index; CI) were compared in characters based on these three anatomical systems in therian mammals. No statistically significant differences were found in the overall CIs of 41 data sets based on dental, cranial, or postcranial characters. Differences in homoplasy within data sets with two or three kinds of data were not statistically significant. These findings suggest that dental, cranial, and postcranial characters can be equally prone to homoplasy and none should be automatically dismissed, disregarded, or systematically weighted in phylogenetic analyses. The level of homoplasy in characters derived from a given region of the skeleton may differ depending on the taxonomic level of the taxa considered. Dental, cranial, and postcranial characters may not constitute “natural” classes, yet examination of the phylogenetic signal of these subsets of data previous to a simultaneous analysis can shed light on significant aspects of the evolutionary process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1020549505177
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  • 17
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    Molecular Systematics of the Subfamily Caprinae (Artiodactyla, Bovidae) as Determined from Cytochrome b Sequences (1998)
    Springer
    Journal of mammalian evolution 5 (1998), S. 217-236 
    Details
    ISSN: 1573-7055
    Keywords: phylogeny ; parsimony ; Bovidae ; Caprinae ; cytochrome b ; a priori weighting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have sequenced the complete mitochondrial DNA cytochrome b gene from 18 species of the subfamily Caprinae and two outgroup taxa. Additional sequences retrieved from the literature were used to constitute a data set of 32 cytochrome b sequences comprising all genera usually included within the Caprinae. Phylogenetic relationships were assessed by PAUP using three new weighting schemes based on homoplasy analyses. Each type of substitution considered at each of the three codon positions was weighted according to its homoplasy level, as measured by the consistency index (CI), the slope of saturation (S), or their product (CIS). These differentially weighted parsimony analyses indicate that (1) the subfamily Caprinae is monophyletic, but only with the exclusion of Saiga from the group; (2) there is no support for monophyly of the four tribes currently recognized (Caprini, Rupicaprini, Ovibovini, and Saigini), suggesting relationships different from those traditionally accepted; (3) the caprine group consists of three major clades corresponding to (a) Budorcas and Ovis, (b) Capricornis, Ovibos, and Naemorhedus, and (c) Capra, Hemitragus, and Pseudois; and (4) the basal branching pattern is very weakly supported by bootstrap or branch support values except for the sister-group relationship of Pantholops with all other caprines, and the phylogenetic positions of Ammotragus, Oreamnos, and Rupicapra remain unclear.
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    URL: http://dx.doi.org/10.1023/A:1020560412929
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    Phylogenetic relationships ofSphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences (1998)
    Springer
    Plant systematics and evolution 209 (1998), S. 75-83 
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    ISSN: 1615-6110
    Keywords: Fungi ; Ascomycetes ; Caliciales ; Lecanorales ; Sphaerophoraceae ; Stereocaulaceae ; Lichens ; molecular evolution ; phylogeny ; small subunit ; ribosomal DNA ; 18S rDNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract SSU rDNA was sequenced from the lichenized fungiBunodophoron scrobiculatum andLeifidium tenerum (Sphaerophoraceae), andStereocaulon ramulosum andPilophorus acicularis (Stereocaulaceae) and analysed by maximum parsimony with 44 homologous ascomycete sequences in a cladistic study. A small insertion (c. 60 nt.) was found in the sequence ofLeifidium tenerum. Sphaerophoraceae constitutes a strongly supported monophyletic group which groups together withLecanora dispersa and theStereocaulaceae. Together withPorpidia crustulata, this larger group is a sistergroup to thePeltigerineae. This analysis thus supports theLecanorales as monophyletic, includingSphaerophoraceae and thePeltigerineae, but does not provide strong support for this monophyly. The analysis also suggests that the prototunicate ascus in theSphaerophoraceae is a reversion to the plesiomorphic state. Based on morphological, anatomical and chemical reasons,Sphaerophoraceae is proposed to belong to one of the groups presently included in the paraphyletic suborderCladoniineae within theLecanorales.
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    URL: http://dx.doi.org/10.1007/BF00991525
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    The potential of AFLPs in biosystematics: A first application inSolanum taxonomy(Solanaceae) (1998)
    Springer
    Plant systematics and evolution 210 (1998), S. 87-103 
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    ISSN: 1615-6110
    Keywords: Solanaceae ; Solanum ; AFLP markers ; DNA fingerprinting ; phylogeny ; polyploids ; potato ; tomato
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Using the AFLP technique highly informative DNA fingerprints were generated from 19 taxa ofSolanum sect.Petota (potatoes) and three taxa ofSolanum sect.Lycopersicum (tomatoes). Both phenetic and cladistic analyses were conducted from the individual genotypic level to the species level. An AFLP fingerprint, using a combination of suitable AFLP primers, generated 12 to 71 scorable fragments per genotype which was sufficient for taxonomic interpretation. The classifications based on the molecular markers were generally in agreement with current taxonomic opinions. Unexpectedly,S. microdontum was associated with ser.Megistacroloba rather than with ser.Tuberosa, andS. demissum (ser.Demissa) and species of ser.Acaulia appeared closely affiliated. AFLP is an efficient and reliable technique to generate biosystematic data and therefore a promising tool for evolutionary studies.
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    URL: http://dx.doi.org/10.1007/BF00984729
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    Collapse ofIsertieae, re-establishment ofMussaendeae, and a new genus ofSabiceeae (Rubiaceae); phylogenetic relationships based onrbcL data (1998)
    Springer
    Plant systematics and evolution 211 (1998), S. 71-92 
    Details
    ISSN: 1615-6110
    Keywords: Gentianales ; Rubiaceae ; Isertieae ; Mussaendeae ; Sabiceeae ; Tamridaea ; Chloroplast DNA ; rbcL ; phylogeny ; Socotra
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The circumscription of theIsertieae has been under debate for a long time and recently a phylogeny based on morphological data has been presented (Andersson 1996), contradicting the classification ofRobbrecht (1988, 1993). Our investigation of molecular data neither supports the phylogeny ofAndersson nor the classification ofRobbrecht, but instead indicates totally new relationships ofIsertieae, Mussaendeae, andSabiceeae. TheIsertieae are a bigeneric tribe of subfam.Cinchonoideae, whileMussaendeae andSabiceeae are two separate tribes of subfam.Ixoroideae. We have also referred a species from Socotra (Yemen) with disputed position to the tribeSabiceeae and we place it in a new genus,Tamridaea, with the single speciesT. capsulifera comb. nov. NewrbcL sequences of 20 taxa are presented and analysed, fromGentianaceae:Gentianella; fromLoganiaceae:Spigelia; and fromRubiaceae:Amphidasya, Aoranthe, Chomelia, Coussarea, Gonzalagunia, Heinsia, Hippotis, Isertia (three taxa),Mussaenda, Pseudomussaenda, Pseudosabicea, Rondeletia, Sabicea, Schradera, Tamridaea, andVirectaria.
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    URL: http://dx.doi.org/10.1007/BF00984913
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    Allozyme divergence among four species ofPodaechmea s. l. and the status ofUrsulaea (Bromeliaceae, Bromelioideae) (1998)
    Springer
    Plant systematics and evolution 213 (1998), S. 207-215 
    Details
    ISSN: 1615-6110
    Keywords: Bromeliaceae ; Aechmea ; Podaechmea ; Systematics ; phylogeny ; allozymes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genetic relationships ofAechmea mexicana, A. lueddemanniana, A. macvaughii andA. tuitensis were investigated using starch gel electrophoresis. Eight enzyme systems encoded by ten putative gene loci were resolved in seventeen populations.Nei's (1978) genetic distances were obtained from allelic frequencies and used with UPGMA algorithm. Results indicate that some populations belonging to different species display genetic similarities closer to each other than to some conspecific populations. Our results do not support the proposed genusUrsulaea (Read & Baensch 1994), sinceA. tuitensis was closer toA. lueddemanniana andA. mexicana than toA. macvaughii.
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    Rhizobium strains that nodulate Trifolium semipilosum Fres. are phylogenetically distinct (1998)
    Springer
    Plant and soil 207 (1998), S. 147-154 
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    ISSN: 1573-5036
    Keywords: inoculation ; rDNA ; phylogeny ; Rhizobium ; Trifolium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The genetic relationships of Rhizobium isolated from temperate and tropical perennial Trifolium species were investigated using PCR-based nucleotide sequence analysis of 16S and 23S rDNA regions. Comparative analysis of partial 23S rDNA sequences clustered Rhizobium isolates effective with T. semipilosum, T. repens, T. pratense, T. hybridum and T. fragiferum into two distinct groups. These groups were consistent with the pattern of symbiotic effectiveness observed in cross-inoculation experiments. Our data suggested that strains from T. semipilosum were more closely related phylogenetically to R. etli, indicating that these strains do not belong in the R. leguminosarum bv trifolii group. Further differentiation of Rhizobium strains effective on T. semipilosum was reflected in the broader metabolic profile observed using the BIOLOG MicroPlate TM system to evaluate carbon utilization.
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    rRNA based identification and detection systems for rhizobia and other bacteria (1998)
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    Plant and soil 204 (1998), S. 1-19 
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    ISSN: 1573-5036
    Keywords: hybridization ; in situ identification ; phylogeny ; probe design ; rhizobia ; rRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylogeny; they also provide useful target sites for identification and detection with nucleic acid probes. Based on the currently available 16S rRNA sequence data, bacteria of the rhizobial phenotype (plant nodulation, nitrogen fixation) are members of three moderately related phylogenetic sub-groups of the α-subclass of the Proteobacteria: i.e. the rhizobia group, the bradyrhizobia group, and the azorhizobia group. All rhizobia, azo-, brady-, meso- and sinorhizobia are closely related to and in some cases phylogenetically intermixed with, non-symbiotic and/or non-nitrogen-fixing bacteria. Especially in the case of Bradyrhizobium japonicum strains, the 16S rRNA sequence data indicate substantial heterogeneity. Specific probe design and evaluation are discussed. A multiprobe concept for resolving specificity problems with group specific probes is presented. In situ identification with group specific probes of rhizobia in cultures as well as rhizobia and cyanobacteria within plant material is shown.
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    Rough periwinkle polymorphism on the east coast of Yorkshire: comparison of RAPD-DNA data with morphotype (1998)
    Springer
    Hydrobiologia 378 (1998), S. 71-78 
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    ISSN: 1573-5117
    Keywords: RAPD ; Littorina saxatilis ; L. neglecta ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A genetic analysis of ‘morphotypes’ of Littorina saxatilis from two locations on the north-east coast of England (Filey and Ravenscar), using randomly amplified DNA polymorphisms (RAPD) generated with a single primer, revealed quite different patterns of variation. Thin shelled, wide-apertured (H-form) animals from Ravenscar tended to cluster separately from thick shelled (M) forms, indicating genetic differentiation of these morphs. Animals of similar morphology (H and M) from Filey (about 30 km distant) did not display such an obvious pattern, and although there was still evidence of differentiation from discriminant analysis of RAPD data, levels of correct classification were reduced at Filey. This suggests that the utility of a single RAPD primer for separation of such forms varies over a relatively small distance. L. arcana from Ravenscar, included as an outgroup, were generally well differentiated from L. saxatilis and were noted to exhibit less variation, a phenomenon that has been noted previously in some allozyme and RAPD analyses. A similar RAPD analysis undertaken on small, barnacle dwelling, brooding forms from Peak Steel, Ravenscar revealed that animals appeared to have as great a tendency to cluster together on a microgeographic scale (by collection patch) as by ‘species’ ( L. neglecta or L. saxatilis b) although predominance of certain species in individual patches largely explains this. Discriminant analysis of RAPD presence/absence data did correctly place over 90% of barnacle dwelling animals to their respective species, and we consider this as evidence of separate gene pools. RAPD is taken to be a useful tool for screening genetic variation in this complex of animals on a local scale when either a pre-selected informative primer is utilised or a battery of primers is used, but its efficacy may be reduced when a single primer is employed for screening animals from different shores.
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    Phylogenetic relationships of phylum Rotifera with emphasis on the families of Bdelloidea (1998)
    Springer
    Hydrobiologia 287-388 (1998), S. 101-107 
    Details
    ISSN: 1573-5117
    Keywords: Acanthocephala ; aschelminthes ; cladistics ; evolution ; Gnathostomulida ; phylogeny ; pseudocoelomates ; Rotifera
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We investigated phylogenetic relationships of phylum Rotifera using cladistic analysis to uncover all most-parsimonious trees from a data set comprising 60 morphological characters of nine taxa: one Acanthocephala, six Rotifera, and two outgroups (Turbellaria, Gnathostomulida). Analysis of our matrix yielded a single most-parsimonious tree. From our analysis we conclude the following: (1) Class Digononta is paraphyletic; (2) it is still premature to reject rotiferan monophyly; (3) the classification hierarchy that best conforms to this morphologically based, cladistic analysis is similar to several traditional schemes. In spite of these results, it is significant that this analysis yielded a tree that is incongruent with those trees developed from molecular data or by using the principles of evolutionary taxonomy.
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    Phylogenetic relationships of phylum Rotifera with emphasis on the families of Bdelloidea (1998)
    Springer
    Hydrobiologia 387-388 (1998), S. 101-107 
    Details
    ISSN: 1573-5117
    Keywords: Acanthocephala ; aschelminthes ; cladistics ; evolution ; Gnathostomulida ; phylogeny ; pseudocoelomates ; Rotifera
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We investigated phylogenetic relationships of phylum Rotifera using cladistic analysis to uncover all most-parsimonious trees from a data set comprising 60 morphological characters of nine taxa: one Acanthocephala, six Rotifera, and two outgroups (Turbellaria, Gnathostomulida). Analysis of our matrix yielded a single most-parsimonious tree. From our analysis we conclude the following: (1) Class Digononta is paraphyletic; (2) it is still premature to reject rotiferan monophyly; (3) the classification hierarchy that best conforms to this morphologically based, cladistic analysis is similar to several traditional schemes. In spite of these results, it is significant that this analysis yielded a tree that is incongruent with those trees developed from molecular data or by using the principles of evolutionary taxonomy.
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    A higher-plant type ζ-carotene desaturase in the cyanobacterium Synechocystis PCC6803 (1998)
    Springer
    Plant molecular biology 36 (1998), S. 725-732 
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    ISSN: 1573-5028
    Keywords: ζ-Carotene desaturase gene ; J852 ; lycopene ; neurosporene ; phylogeny ; Synechocystis PCC6803
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The genomic DNA sequence of Synechocystis was analysed for putative ζ-carotene desaturase genes. Two promising candidates slr0940 and slr0033 were found with similarities to the structurally different ζ-carotene desaturase genes from higher plants and Anabaena, respectively. Only the expression product of the analogue to the plant gene, slr0940, was able to mediate the 2-step desaturation of ζ-carotene via neurosporene to lycopene after complementation of this pathway in Escherichia coli. When enzyme reactions were carried out with this protein, activity was obtained with either ζ-carotene or neuroporene as substrates. The in vitro reaction was inhibited by the pyrimidine derivative J852 which is effective as experimental herbicide in plants. The occurrence of two different types of ζ-carotene desaturases among cyanobacteria and the phylogenetic consequences on chloroplast evolution are discussed.
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    Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria (1998)
    Springer
    Genetica 102-103 (1998), S. 383-391 
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    ISSN: 1573-6857
    Keywords: directional mutational pressure ; genomic GC content ; amino acid composition ; hydrophobicity ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The relationship between change in genomic GC content and protein evolution in bacteria was studied by simple correlational analysis (at the genus level) and by Felsenstein's (1985) independent contrast test. We first used the dnaA gene in bacteria as an example to show (1) that the amino acid composition of a protein can be dramatically affected by mutational pressure (the genomic GC content), (2) that surprisingly, deleting relatively closely-related genera may increase rather than decrease the correlation between genomic GC content and amino acid composition, and (3) that most unexpectedly, as the genomic GC content increases, both strongly hydrophobic and strongly hydrophilic amino acids tend to change to ambivalent amino acids, suggesting that the majority of these amino acid substitutions are not caused by positive Darwinian selection. These patterns were then also shown to hold for the 14 other genes studied, indicating their generality for the evolution of bacterial proteins. As directional mutation pressure can affect the amino acid composition of proteins, it may mislead phylogenetic inference, even if protein instead of DNA sequences are used.
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    URL: http://dx.doi.org/10.1023/A:1017028102013
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    Evolution of the Monotremes: Phylogenetic Relationship to Marsupials and Eutherians, and Estimation of Divergence Dates Based on α-Lactalbumin Amino Acid Sequences (1998)
    Springer
    Journal of mammalian evolution 5 (1998), S. 95-105 
    Details
    ISSN: 1573-7055
    Keywords: monotremes ; echidna ; platypus ; phylogeny ; α-lactalbumin ; lysozyme
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The amino acid sequences of the α-lactalbumins of the echidna, Tachyglossus aculeatus, and the platypus, Ornithorhynchus anatinus, were compared with each other and with those of 13 eutherian and 3 marsupial species. Phylogenetic parsimony analyses, in which selected mammalian lysozymes were used as outgroups, yielded trees whose consensus indicated that the two monotremes are sister taxa to marsupials and eutherians and that the latter two clades are each other's closest relatives. The data do not support the notion of a Marsupionta (monotreme–marsupial) clade. Pairwise comparison between the α-lactalbumins yielded maximum-likelihood distances from which divergence dates were estimated on the basis of three calibration points. The distance data support the view that the echidna and platypus lineages diverged from their last common ancestor at least 50 to 57 Ma (million years ago) and that monotremes diverged from marsupials and eutherian mammals about 163 to 186 Ma.
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    The Phylogeny of the Myrmecophagidae (Mammalia, Xenarthra, Vermilingua) and the Relationship of Eurotamandua to the Vermilingua (1998)
    Springer
    Journal of mammalian evolution 5 (1998), S. 237-265 
    Details
    ISSN: 1573-7055
    Keywords: Xenarthra ; anteaters ; Eurotamandua ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A cladistic investigation of the phylogenetic relationships among the three extant anteater genera and the three undoubted extinct myrmecophagid genera is performed based upon osteological characteristics of the skull and postcranial skeleton. One hundred seven discrete morphological characters are analyzed using the computer program PAUP. Characters are polarized via comparison to the successive xenarthran outgroups Tardigrada (represented by the living sloth Bradypus) and Cingulata (represented by the recent armadillos Dasypus and Euphractus). The analysis results in a single most-parsimonious tree (TL = 190, CI = 0.699, RI = 0.713). The tree corroborates the monophyly of the subfamilies Cyclopinae and Myrmecophaginae, the former including the extant Cyclopes and the Pliocene genus Palaeomyrmidon. Within the Myrmecophaginae the Miocene genus Protamandua is the sister taxon to a clade including the remaining three genera. The recent Tamandua is in turn the sister taxon to the extant Myrmecophaga plus the Pliocene genus Neotamandua. Contrary to the suggestions of recent authors, weak support is provided for the taxonomic distinctiveness of the latter genus from the recent Myrmecophaga. The monophyly of the Myrmecophagidae is supported by 15 unequivocal synapomorphies. The monophyly of the Cyclopinae and Myrmecophaginae is supported by 3 and 13 unambiguous synapomorphies, respectively. The enigmatic Eocene genus Eurotamandua, from the Messel fauna of Germany, is coded for the 107 morphological characters above and included in two subsequent PAUP analyses. The palaeanodont Metacheiromys is also added to these two analyses as a nonxenarthran outgroup to test for the possibility that Eurotamandua lies outside the Xenarthra. In the first analysis, Eurotamandua is constrained a priori to membership in the Vermilingua. The single most-parsimonious tree (TL = 224, CI = 0.618) that results places Eurotamandua as the sister group to the remaining anteater genera, contra Storch and Habersetzer's (1991) assignment of Eurotamandua to the vermilinguan subfamily Myrmecophaginae. Eurotamandua shares six unequivocal synapomorphies with other anteaters, including the absence of teeth and the presence of a lateral tuberosity on the fifth metatarsal. The remaining vermilinguans are united by 11 unequivocal synapomorphies, plus an additional 10 ambiguous synapomorphies. In the second analysis, the position of Eurotamandua is unconstrained. The resulting single most-parsimonious tree (TL = 219, CI = 0.632) places Eurotamandua outside Vermilingua as the sister group to the Pilosa (Vermilingua plus Bradypus). The monophyly of this node is supported by four unambiguous synapomorphies in the unconstrained analysis. Further manipulation of this second analysis shows that placement of Eurotamandua as the sister group to the Xenarthra or to the Palaeanodonta adds three steps to the shortest tree but is more parsimonious than its placement as a sister group to the Vermilingua is the previous analysis. The addition of pangolins to the analysis does little to alter the major phylogenetic conclusions of the study. The allocation of Eurotamandua to the Xenarthra, but as a sister group to the Pilosa, is a novel arrangement which leaves open the biogeographic question of how a xenarthran reached Western Europe during the Eocene.
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    Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences (1998)
    Springer
    Antonie van Leeuwenhoek 73 (1998), S. 331-371 
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    ISSN: 1572-9699
    Keywords: Ascomycetous yeasts ; phylogeny ; ribosomal DNA ; systematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.
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    Morphological evidence for the evolutionary origin of Astigmata (Acari: Acariformes) (1998)
    Springer
    Experimental and applied acarology 22 (1998), S. 559-594 
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    ISSN: 1572-9702
    Keywords: Astigmata ; Oribatida ; Malaconothroidea ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A century ago, Antonio Berlese first discussed the close phylogenetic relationship between the large mite groups Oribatida and Astigmata. Since then, information having phylogenetic value has greatly increased and the paradigms within which we interpret it have changed. Herein I refine the general hypothesis that Astigmata originated within oribatid mites and suggest Malaconothridae as a possible sister group. Among the 14 apomorphies used to support the origin of Astigmata within oribatid mites are possession of lateral opisthosomal glands, regression of hysterosomal setal pair f1, paired prelarval denticles, partially internalized chelicerae with incomplete adaxial walls, an atelobasic rutellum, pretarsal condylophores that articulate posteriorly with the tarsus, a dorsally fused palp tibia and tarsus and transdehiscent ecdysis. A further 13 apomorphies support the origin of Astigmata at some level within Malaconothroidea. These include absence of an oblique labiogenal articulation, presence of a distal rutellar lamella, shortening of the palp tarsus, larval regression of hysterosomal seta f2, loss of the bothridial seta in all instars, and several losses and modifications of leg setae. The hypothesis brings to light evolutionary questions that were previously obscured by incorrect or inappropriate classifications. The nomenclatural problems that arise from it are best solved by considering Astigmata as a subgroup within Oribatida.
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    Host plant associations in the spider mite Tetranychus urticae (Acari: Tetranychidae): insights from molecular phylogeography (1998)
    Springer
    Experimental and applied acarology 22 (1998), S. 201-214 
    Details
    ISSN: 1572-9702
    Keywords: Mitochondrial COI ; ribosomal ITS2 ; host race formation ; phylogeny ; Tetranychidae ; geographic structure.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This article integrates studies on the genetic variation of T. urticae populations and the interspecific variation of several tetranychid species. It aims at obtaining insights into the roles of the historical, geographical and ecological factors in the partitioning of variation of species. Two types of molecular markers were used to determine whether the patterns of genetic variation in mites inhabiting different host plants can shed light on the existence of host plant associations. The ribosomal sequences of the second internal transcribed spacer (ITS2), which evolves through concerted evolution, are good indicators of long-term isolation between populations and reveal exceptional homogeneity in a worldwide sampling of T. urticae. The mitochondrial cytochrome oxidase I (COI) sequences do not disclose old divergences related to host plant in this mite but rather suggest recent geographic colonization patterns of the species. Allozyme variation on a fine scale gives some evidence of host associations in the case of citrus trees. However, if any divergence of mites related to this host plant exists, it probably prevails in local populations only and it should not be old enough to be revealed by a phylogenetic analysis of mitochondrial COI sequences. The phyletic constraint in the evolution of feeding specificity in the family Tetra-nychidae is investigated based on a phylogenetic analysis of mitochondrial sequences. The results provide some support for the hypothesis that an evolutionary trend towards polyphagy has occurred in the family. Overall, it seems that the major characteristic of T. urticae is its high colonization potential. Polyphagy has enhanced its successful spread and may have led to connectivity between populations worldwide. © Rapid Science Ltd. 1998
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    The evolutionary relationships of rotifers and acanthocephalans (1998)
    Springer
    Hydrobiologia 287-388 (1998), S. 83-91 
    Details
    ISSN: 1573-5117
    Keywords: phylogeny ; acanthocephala ; rotifera ; bilateria ; evolution ; 18S rRNA gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Advances in morphological and molecular studies of metazoan evolution have led to a better understanding of the relationships among Rotifera (Monogononta, Bdelloidea, Seisonidea) and Acanthocephala, and their relationships to other bilateral animals. The most accepted morphological analysis places Acanthocephala as a sister group to Rotifera, although other studies have placed Acanthocephala as a sister taxon to Bdellodea or Seisonidea. Molecular analyses using nuclear 18S rRNA and mitochondrial 16S rRNA genes support Acanthocephala as a sister taxon to Bdelloidea, although no molecular data is available for Seisonidea. Combining molecular and morphological analyses of Bilateria leads to a tree with Platyhelminthes, Rotifera, Acanthocephala and Gnathostomulida (and probably Gastrotricha) as a sister group to the annelid-mollusc lineage of the Spiralia (Lophotrochozoa).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1017060902909
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    Notentera ivanovi Joffe et al., 1997: a contribution to the question of phylogenetic relationships between ‘turbellarians’ and the parasitic Plathelminthes (Neodermata) (1998)
    Springer
    Hydrobiologia 383 (1998), S. 245-250 
    Details
    ISSN: 1573-5117
    Keywords: parasite ; morphology ; phylogeny ; Plathelminthes ; Neodermata
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Notentera ivanovi is a parasitic platyhelminth found in the gut of a polychaete, Nephthys ciliata. N. ivanovi has no mouth, pharynx, or intestine; the dorsal epidermis of adult animals forms a thick pad which is very similar to gut epithelia even at the light microscopic level. Structure of ciliary rootlets and dermal glands with peculiar striated secretion bodies point to close relationships with the Fecampiidae, though other important characters imply placing the genus Notentera in a separate family. In mature sperm of N. ivanovi, the axonemes are fully incorporated; they are directed from proximal to distal, as in the Neodermata. We argue that new family, Notenteridae, should be included in the taxon Fecampiida. We also suggest that all Plathelminthes with neodermatan type of spermiogenesis (Fecampiidae, Urastomidae, and Neodermata) form a monophyletic branch within the Plathelminthes Neoophora.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003486232038
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  • 36
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    A new species of giant planarian from Lake Baikal, with some remarks on character states in the Dendrocoelidae (Platyhelminthes, Tricladida, Paludicola) (1998)
    Springer
    Hydrobiologia 383 (1998), S. 69-75 
    Details
    ISSN: 1573-5117
    Keywords: Platyhelminthes ; Tricladida ; Dendrocoelidae ; Bdellocephala ; Baikal ; taxonomy ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract On the basis of newly collected material the subspecies Bdellocephala angarensis bathyalis Timoshkin & Porfirjeva, 1989 is raised to full species status, B. bathyalis Timoshkin & Porfirjeva, 1989. Specimens of this species have been collected in Lake Baikal from depths ranging between 610 and 1060 m. The species is characterized by a light, uniform brown pigmentation, absence of eyes, distinct atrial folds, and large size. It is suggested that two features may be useful in elucidating the phylogenetic relationships between dendrocoelid genera: pharynx musculature, and presence of an extra layer of circular muscle in the ventral subepidermal body musculature.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003480604296
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  • 37
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    A phylogeny of the Platyhelminthes: towards a total-evidence solution (1998)
    Springer
    Hydrobiologia 383 (1998), S. 155-160 
    Details
    ISSN: 1573-5117
    Keywords: Platyhelminthes ; total-evidence ; phylogeny ; ultrastructure ; rRNA ; cladistics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We advocate a total-evidence approach for the reconstruction of working phylogenies for the Turbellaria and the phylum Platyhelminthes. Few morphology-based character matrices are available in the systematic literature concerning flatworms, and molecular-based phylogenies are rapidly providing the only means by which we can estimate phylogenies cladistically. Character matrices based on gross morphology and ultrastructure are required and should be internally consistent, i.e. character coding should follow a set of a priori guidelines and character duplication and contradiction is avoided. In order to test our molecular phylogenies we need complementary data sets from morphology. To understand morphological homology we need phylogenetic evidence from independent (e.g. molecular) data. Fully complementary morphological and molecular data sets enable us to validate phylogenetic hypotheses and the combination of these sets in phylogenetic reconstruction utilises all statements of homology. Working phylogenies which include all phylogenetic information not only shed light on individual character evolution, but form a strong basis for comparative studies investigating the origin and evolutionary radiation of the taxonomic group under scrutiny.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003436821134
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  • 38
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    Selected characters of the copulatory organs in the land planarian family Bipaliidae and their taxonomic significance (Tricladida: Terricola) (1998)
    Springer
    Hydrobiologia 383 (1998), S. 77-82 
    Details
    ISSN: 1573-5117
    Keywords: Terricola ; land planarian ; Bipalium ; copulatory organs ; numerical taxonomy ; phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Preliminary analysis was made of 76 species in the monotypic family Bipaliidae, for which the copulatory apparatus has been described. Four characters from the copulatory organs were selected: profile of the female organ (three character states), approachment of the ovovitelline ducts to the female organ (two states), shape of the penial papilla (two states), and shape of the male antrum wall (three states). Data were scored for five preliminary ingroup taxa, viz., the restricted genus Placocephalus, and four other a priori defined subgroups within the family, viz., the genus Bipalium sensu stricto and three other informal taxonomic groupings. An artificial outgroup taxon was constructed on the basis of character states generalized from the Geoplanidae subfamilies Caenoplaninae, Pelmatoplaninae and Rhynchodemidae subfamily Microplaninae. Analysis of the data matrix resulted in a single most parsimonious tree with the following topology: (outgroup (Placocephalus (Bipalium, group A (group B1, group B2)))).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003417712473
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  • 39
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    On the phylogeny of families and genera within the Temnocephalida (1998)
    Springer
    Hydrobiologia 383 (1998), S. 263-268 
    Details
    ISSN: 1573-5117
    Keywords: Epidermis ; musculature ; phylogeny ; plathelminthes ; sucker ; systematics ; tentacles ; Temnocephalida
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Temnocephalida includes species demonstrating many intermediate steps presenting the transition from commensalism to parasitism. Dramatic morphological changes also occurred within this group but the number of supraspecific taxa is small, making the Temnocephalida an excellent model for evolutionary studies. Having summarised original and relevant published morphological data, we suggest a cladogram (phylogenetic tree) which nearly fully resolves the order of branching of families and main genera within the Temnocephalida. We also introduce a new family, the Diceratocephalidae nov. fam.
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    URL: http://dx.doi.org/10.1023/A:1003438321560
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  • 40
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    Flatworm phylogeny from partial 18S rDNA sequences (1998)
    Springer
    Hydrobiologia 383 (1998), S. 147-154 
    Details
    ISSN: 1573-5117
    Keywords: Platyhelminthes ; Acoelomorpha ; phylogeny ; 18S rDNA ; cladistic ; decay index ; jack-knife
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Partial 18S rDNA sequences from 29 flatworms and 2 outgroup taxa were used in a cladistic analysis of the Platyhelminthes. Support for the clades in the resulting single most parsimonious tree was estimated through bootstrap analysis, jack-knife analysis and decay indices. The Acoelomorpha (Acoela and Nemertodermatida) were absent from the most parsimonious tree. The Acoela and the Fecampiidae form a strongly supported clade, the sister group of which may be the Tricladida. There is some support for monophyly of the rhabdocoel taxon Dalyellioida, previously regarded as paraphyletic. The sister group of the Neodermata remains unresolved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003487410231
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  • 41
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    The Philodinavidae (Rotifera Bdelloidea): a special family (1998)
    Springer
    Hydrobiologia 385 (1998), S. 77-85 
    Details
    ISSN: 1573-5117
    Keywords: Bdelloidea ; Philodinavidae ; rotatory apparatus ; phylogeny ; SEM ; systematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Here we focus on the fine morphology and present observations on the biology of representatives of family Philodinavidae. Philodinavus paradoxus and Henoceros falcatus were collected and cultured under laboratory conditions. Rotifers of both species are tiny, about 200 μm long, have protrudable trophi and creep with leech-like movements. A very specific feature of these rotifers is their corona; a V-shaped lower lip contours the mouth opening, bilaterally bordered by two arched cuticular structures (‘cheeks’). The presence of the cheeks is a feature shared by the third genus, Abrochtha. On the basis of the morphology and biology of the three genera, we advance the hypothesis that Philodinavus is a primitive bdelloid, and that it can have originated Henoceros and Abrochtha, from which the other bdelloids could have stemmed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003458611180
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  • 42
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    The Philodinavidae (Rotifera Bdelloidea): a special family (1998)
    Springer
    Hydrobiologia 385 (1998), S. 77-85 
    Details
    ISSN: 1573-5117
    Keywords: Bdelloidea ; Philodinavidae ; rotatory apparatus ; phylogeny ; SEM ; systematics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Here we focus on the fine morphology and present observations on the biology of representatives of family Philodinavidae. Philodinavus paradoxus and Henoceros falcatus were collected and cultured under laboratory conditions. Rotifers of both species are tiny, about 200 μm long, have protrudable trophi and creep with leech-like movements. A very specific feature of these rotifers is their corona; a V-shaped lower lip contours the mouth opening, bilaterally bordered by two arched cuticular structures (‘cheeks’). The presence of the cheeks is a feature shared by the third genus, Abrochtha. On the basis of the morphology and biology of the three genera, we advance the hypothesis that Philodinavus is a primitive bdelloid, and that it can have originated Henoceros and Abrochtha, from which the other bdelloids could have stemmed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1003458611180
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  • 43
    Electronic Resource
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    The evolutionary relationships of rotifers and acanthocephalans (1998)
    Springer
    Hydrobiologia 387-388 (1998), S. 83-91 
    Details
    ISSN: 1573-5117
    Keywords: phylogeny ; acanthocephala ; rotifera ; bilateria ; evolution ; 18S rRNA gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Advances in morphological and molecular studies of metazoan evolution have led to a better understanding of the relationships among Rotifera (Monogononta, Bdelloidea, Seisonidea) and Acanthocephala, and their relationships to other bilateral animals. The most accepted morphological analysis places Acanthocephala as a sister group to Rotifera, although other studies have placed Acanthocephala as a sister taxon to Bdellodea or Seisonidea. Molecular analyses using nuclear 18S rRNA and mitochondrial 16S rRNA genes support Acanthocephala as a sister taxon to Bdelloidea, although no molecular data is available for Seisonidea. Combining molecular and morphological analyses of Bilateria leads to a tree with Platyhelminthes, Rotifera, Acanthocephala and Gnathostomulida (and probably Gastrotricha) as a sister group to the annelid-mollusc lineage of the Spiralia (Lophotrochozoa).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1017060902909
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  • 44
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    Alternative Cyanide-sensitive Oxidase Interacting with Photosynthesis in Synechocystis PCC6803. Ancestor of the Terminal Oxidase of Chlororespiration? (1998)
    Springer
    Photosynthetica 35 (1998), S. 223-231 
    Details
    ISSN: 1573-9058
    Keywords: absorbance ; azide ; cyanobacteria ; cytochromes ; flash irradiation ; KCN ; NaN3 ; phylogeny ; respiration ; salicyl hydroxamic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Influence of respiration on photosynthesis in Synechocystis PCC6803 was studied by measuring the redox transients of cytochrome f (cyt f) upon excitation of the cells with repetitive single turnover flashes. Upon the addition of KCN the flash-induced oxidation of cyt f was increased and the rereduction of cyt f+ was accelerated. Dependence of these effects on the concentration of KCN clearly demonstrated the existence of two cyanide-sensitive oxidases interacting with photosynthesis: cyt aa3, which was sensitive to low concentrations of cyanide, and an alternative oxidase, which could be suppressed by using ≥1 mM KCN. The interaction between the photosynthetic and the respiratory electron transport chains was regulated mainly by the activity of the alternative cyanide-sensitive oxidase. The oxidative pathway involving the alternative cyanide-sensitive oxidase was insensitive to salicyl hydroxamic acid and azide. The close resemblance of the inhibition pattern reported here and that described for chlororespiration in algae and higher plants strongly suggest that an oxidase of the same type as the alternative cyanide-sensitive oxidase of cyanobacteria functions as a terminal oxidase in chloroplasts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006958706540
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