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Monophyletic Groups (monophyletic + groups)
Selected AbstractsMonophyletic groups within ,higher land birds', comparison of morphological and molecular dataJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2003G. Mayr Abstract The relationships within the ,higher land birds' and putatively related taxa are analysed in a study using 89 morphological characters and DNA sequences of three nuclear, protein-coding genes, c- myc, RAG-1, and myoglobin intron II. Separate analyses of the different data sets and a ,total evidence' analysis in which the data sets of the morphological and molecular analyses were combined are compared. All three analyses support the hitherto disputed sister group relationship between Pici (Ramphastidae, Indicatoridae and Picidae) and Galbulae (Galbulidae and Bucconidae). Previously unrecognized osteological synapomorphies of this clade are presented. All analyses further resulted in monophyly of the taxon [Aegothelidae + (Apodidae/Hemiprocnidae + Trochilidae)]. Analysis of the morphological data and of the combined data set also supported monophyly of the taxon [Strigiformes + (Falconidae + Accipitridae)]. The morphological data further support monophyly of the taxon (Upupidae + Bucerotidae). Other placements in the three analyses received either no or only weak bootstrap support. [source] Integrating DNA data and traditional taxonomy to streamline biodiversity assessment: an example from edaphic beetles in the Klamath ecoregion, California, USADIVERSITY AND DISTRIBUTIONS, Issue 5 2006Ryan M. Caesar ABSTRACT Conservation and land management decisions may be misguided by inaccurate or misinterpreted knowledge of biodiversity. Non-systematists often lack taxonomic expertise necessary for an accurate assessment of biodiversity. Additionally, there are far too few taxonomists to contribute significantly to the task of identifying species for specimens collected in biodiversity studies. While species level identification is desirable for making informed management decisions concerning biodiversity, little progress has been made to reduce this taxonomic deficiency. Involvement of non-systematists in the identification process could hasten species identification. Incorporation of DNA sequence data has been recognized as one way to enhance biodiversity assessment and species identification. DNA data are now technologically and economically feasible for most scientists to apply in biodiversity studies. However, its use is not widespread and means of its application has not been extensively addressed. This paper illustrates how such data can be used to hasten biodiversity assessment of species using a little-known group of edaphic beetles. Partial mitochondrial cytochrome oxidase I was sequenced for 171 individuals of feather-wing beetles (Coleoptera: Ptiliidae) from the Klamath ecoregion, which is part of a biodiversity hotspot, the California Floristic Province. A phylogram of these data was reconstructed via parsimony and the strict consensus of 28,000 equally parsimonious trees was well resolved except for peripheral nodes. Forty-two voucher specimens were selected for further identification from clades that were associated with many synonymous and non-synonymous nucleotide changes. A ptiliid taxonomic expert identified nine species that corresponded to monophyletic groups. These results allowed for a more accurate assessment of ptiliid species diversity in the Klamath ecoregion. In addition, we found that the number of amino acid changes or percentage nucleotide difference did not associate with species limits. This study demonstrates that the complementary use of taxonomic expertise and molecular data can improve both the speed and the accuracy of species-level biodiversity assessment. We believe this represents a means for non-systematists to collaborate directly with taxonomists in species identification and represents an improvement over methods that rely solely on parataxonomy or sequence data. [source] Diagnosis and detection of host-specific forms of Fusarium oxysporum,EPPO BULLETIN, Issue 3-4 2000R. P. Baayen Diagnosis and detection of host-specific forms of Fusarium oxysporum are traditionally based on the combination of diagnostic symptoms on the host with the presence of the fungus in the affected tissues. The classical approach is becoming increasingly problematic because more than one forma specialis may occur on a given host, along with non-pathogenic strains which are common soil and rhizosphere inhabitants. Neither formae speciales nor pathogenic races within formae speciales can be distinguished morphologically. Although united by joint pathogenicity to a given host, strains belonging to the same forma specialis need not be phylogenetically related. Development of diagnostics for host-specific groups in F. oxysporum requires monophyletic target groups. Recent studies on gene-genealogy and AFLP-based phylogenies show that the majority of formae speciales in F. oxysporum are polyphyletic (unnatural) and do not offer any prospects for the development of molecular diagnostics. In contrast, highly specific PCR primers have been developed for formae speciales (or races) that consist of a single clonal lineage, and for monophyletic groups of lineages within a forma specialis. Among others, specific PCR primers have thus been developed for F. oxysporum f. sp. basilici, specific races in F. oxysporum ff. spp. dianthi and gladioli, and for the EPPO A2 (EU II/A1) quarantine fungus F. oxysporum f. sp. albedinis which can reliably replace conventional isolation and pathogenicity testing procedures. [source] EMPIRICAL EVIDENCE FOR AN OPTIMAL BODY SIZE IN SNAKESEVOLUTION, Issue 2 2003Scott M. Boback Abstract The concept of optimal size has been invoked to explain patterns in body size of terrestrial mammals. However, the generality of this phenomenon has not been tested with similarly complete data from other taxonomic groups. In this study we describe three statistical patterns of body size in snakes, all of which indicate an optimal length of 1.0 m. First, a distribution of largest body lengths of 618 snake species had a single mode at 1.0 m. Second, we found a positive relationship between the size of the largest member of an island snake assemblage and island area and a negative relationship between the size of the smallest member of an island snake assemblage and island area. Best-fit lines through these data cross at a point corresponding to 1.0 m in body length, the presumed optimal size for a one-species island. Third, mainland snake species smaller than 1.0 m become larger on islands whereas those larger than 1.0 m become smaller on islands. The observation that all three analyses converge on a common body size is concordant with patterns observed in mammals and partial analyses of four other disparate animal clades. Because snakes differ so strikingly from mammals (ectotherms, gape-limited predators, elongate body shape) the concordant patterns of these two groups provide strong evidence for the evolution of an optimal body size within independent monophyletic groups. However, snakes differ from other taxonomic groups that have been studied in exhibiting a body size distribution that is not obviously skewed in either direction. We suggest that idiosyncratic features of the natural history of ectotherms allow relatively unconstrained distributions of body size whereas physiological limitations of endotherms constrain distributions of body size to a right skew. [source] ARE PINNIPEDS FUNCTIONALLY DIFFERENT FROM FISSIPED CARNIVORES?EVOLUTION, Issue 3 2000THE IMPORTANCE OF PHYLOGENETIC COMPARATIVE ANALYSES Abstract., It is widely assumed that adaptations to an aquatic lifestyle are so profound as to produce only obvious differences between pinnipeds and the remaining, largely terrestrial carnivore species ("fissipeds"). Thus, comparative studies of the order Carnivora routinely examine these groups independently. This approach is invalid for two reasons. First, fissipeds are a paraphyletic assemblage, which raises the general issue of when it is appropriate to ignore monophyly as a criterion for inclusion in comparative studies. Second, the claim that most functional characters (beyond a few undoubted characteristic features) are different in pinnipeds and fissipeds has never been quantitatively examined, nor with phylogenetic comparative methods. We test for possible differences between these two groups in relation to 20 morphological, life-history, physiological, and ecological variables. Comparisons employed the method of independent contrasts based on a complete and dated species-level phylogeny of the extant Carnivora. Pinnipeds differ from fissipeds only through evolutionary grade shifts in a limited number of life-history traits: litter weight (vs. gestation length), birth weight, and age of eyes opening (both vs. size). Otherwise, pinnipeds display the same rate of evolution as phylogenetically equivalent fissiped taxa for all variables. Overall functional differences between pinnipeds and fissipeds appear to have been overstated and may be no greater than those among major fissiped groups. Recognition of this fact should lead to a more complete understanding of carnivore biology as a whole through more unified comparative tests. Comparative studies that do not include monophyletic groups for phylogenetically based comparative tests should be reconsidered. [source] Genetic population structure of the net-winged midge, Elporia barnardi (Diptera: Blephariceridae) in streams of the south-western Cape, South Africa: implications for dispersalFRESHWATER BIOLOGY, Issue 1 2003M. J. Wishart SUMMARY 1.,The net-winged midges (Diptera: Blephariceridae), with highly specific habitat requirements and specialised morphological adaptations, exhibit high habitat fidelity and a limited potential for dispersal. Given the longitudinal and hierarchical nature of lotic systems, along with the geological structure of catchment units, we hypothesise that populations of net-winged midge should exhibit a high degree of population sub-structuring. 2.,Sequence variation in the cytochrome c oxidase subunit I (COI) region of the mitochondrial DNA (mtDNA) was examined to determine patterns of genetic variation and infer historical and contemporary processes important in the genetic structuring of populations of Elporia barnardi. The DNA variation was examined at sites within streams, between streams in the same range, and between mountain ranges in the south-western Cape of South Africa. 3.,Twenty-five haplotypes, 641 bp in length, were identified from the 93 individuals sampled. A neighbour-joining tree revealed two highly divergent clades (,5%) corresponding to populations from the two mountain ranges. A number of monophyletic groups were identified within each clade, associated with individual catchment units. 4.,The distribution of genetic variation was examined using analysis of molecular variance (amova). This showed most of the variation to be distributed among the two ranges (,80%), with a small percentage (,15%) distributed among streams within each range. Similarly, variation among streams on Table Mountain was primarily distributed among catchment units (86%). A Mantel's test revealed a significant relationship between genetic differentiation and geographical distance, suggesting isolation by distance (P < 0.001). 5.,Levels of sequence divergence between the two major clades, representing the two mountain ranges, are comparable with those of some intra-generic species comparisons. Vicariant events, such as the isolation of the Peninsula mountain chain and Table Mountain, may have been important in the evolution of what is now a highly endemic fauna. 6.,The monophyletic nature of the catchment units suggests that dispersal is confined to the stream environment and that mountain ridges provide effective physical barriers to dispersal of E. barnardi. [source] Nuclear mitochondrial-like sequences in ants: evidence from Atta cephalotes (Formicidae: Attini)INSECT MOLECULAR BIOLOGY, Issue 6 2007J. Martins Jr Abstract Nuclear mitochondrial-like sequences (numts) are copies of mitochondrial DNA that have migrated to the genomic DNA. We present the first characterization of numts in ants, these numts being homologues to a mitochondrial DNA fragment containing loci the 3, portion of the cytochrome oxidase I gene, an intergenic spacer, the tRNA leucine gene and the 5, portion of the cytochrome oxidase II gene. All 67 specimens of Atta cephalotes (Hymenoptera: Formicidae: Attini) investigated had these homologues, which are within two monophyletic groups that we called numt1 and numt2. Numt1 and numt2 sequences are less variable than mitochondrial sequences and released from the severe purifying selection constraining the evolution of mitochondrial genes. Their formation probably involved bottlenecks related to two distinct transfer events of ancient and fast evolving mitochondrial DNA fragments to comparative slowly evolving nuclear DNA regions. [source] Ultrastructure of sperms in Acoela (Acoelomorpha) and its concordance with molecular systematicsINVERTEBRATE BIOLOGY, Issue 3 2004Anatoly Petrov Abstract. The sperms of the Acoela, a group of lower worms, are filiform cells with 2 flagella incorporated into the cell body. Their axonemes can variously have 9+2, 9+1, or 9+0 patterns of microtubules; and singlet microtubules in the cell body can be arranged in axial or cortical positions. An analysis of phylogenetic relationships of acoels based on molecular characters (18S rDNA sequence data) showed that these patterns of microtubules, where known, fell into discrete monophyletic groups. To test this hypothesis, we have expanded the database of sperm characters by examining the ultrastructure of a further 10 species representing 4 acoel families. As expected, the Convolutidae fell into 2 unrelated groups: "small-bodied convolutids"(Convoluta pulchra, Praeconvoluta tigrina, Pseudaphanostoma smithrii) having 9+2 axonemes and cortical microtubules, and "large-bodied convolutids" (including Wulguru cuspidata) having 9+0 axonemes and axial microtubules. Also, as expected, a member of the Mecynostomidae (Paedomecynostomum bruneum) has 9+1 axonemes and axial microtubules. Members of a family that appears intermediate by molecular characters, the Otocelididae, significantly have a variety of patterns: axonemes with both 9+2 and 9+0 patterns (Notocelis gullmarensis) or just 9+2 (the other species), and either axial (Philocelis brueggemanni), both axial and cortical (N. gullmarensis) microtubules, or microtubules that bend between axial and cortical positions along the length of the sperm (Otocelis sandara). Members of the Dakuidae (Daku woorimensis) also belong to this intermediate group, having 9+2 axonemes and axial microtubules, while in a fifth otocelidid (Stomatricha hochbergi), sperm characters are like those of the "large-bodied convolutids" (9+0 axonemes and axial microtubules). Characters of sperm morphology generally support the molecular hypothesis of relationships and confirm a suspected polyphyly of the families Convolutidae, Otocelididae, and Actinoposthiidae. [source] Role of Citrobacter amalonaticus and Citrobacter farmeri in dissimilatory perchlorate reductionJOURNAL OF BASIC MICROBIOLOGY, Issue 2 2004Nirmala Bardiya The article deals with the novel physiological function of dissimilatory perchlorate reduction by strains JB101 and JB109 isolated from a laboratory-enriched mixed consortium originating from a sewage treatment facility. The biochemical and physiological data of the strains showed good correspondence with members of the family Enterobacteriaceae. The partial 16S rDNA sequence of the strains JB101 and JB109 had similarity of 99.8% to Citrobacter amalonaticus and 98% to Citrobacter farmeri, respectively. The results inferred the possibility of Citrobacter spp. to form an important group of dissimilatory perchlorate reducers among the , subclass of Proteobacteria, since the majority of the perchlorate reducers belong to two monophyletic groups, Dechloromonas and Dechlorosoma in , subclass. The perchlorate-grown Citrobacter strains preferred perchlorate to nitrate as an electron acceptor unlike most of the reported dissimilatory perchlorate reducers. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Spatial analysis of taxonomic and genetic patterns and their potential for understanding evolutionary historiesJOURNAL OF BIOGEOGRAPHY, Issue 11 2004Sophia A. Bickford Abstract Aim, The aim of this research is to develop and investigate methods for the spatial analysis of diversity based on genetic and taxonomic units of difference. We use monophyletic groups of species to assess the potential for these diversity indices to elucidate the geographical components of macro-scaled evolutionary processes. Location, The range occupied by Pultenaea species in temperate and sub-tropical eastern Australia, extending from western South Australia (133° E,32° S) to Tasmania (146° E,43° S) to coastal central Queensland (148° E,20° S). Methods, We applied a series of both spatially explicit and spatially implicit analyses to explore the nature of diversity patterns in the genus Pultenaea, Fabaceae. We first analysed the eastern species as a whole and then the phylogenetic groups within them. We delineated patterns of endemism and biotic (taxon) regions that have been traditionally circumscribed in biogeographical studies of taxa. Centres of endemism were calculated using corrected weighted endemism at a range of spatial scales. Biotic regions were defined by comparing the similarity of species assemblages of grid cells using the Jaccard index and clustering similar cells using hierarchical clustering. On the basis that genetically coherent areas were likely to be more evolutionary informative than species patterns, genetic indices of similarity and difference were derived. A matrix of similarity distances between taxa was generated based on the number of shared informative characters of two sections of trnL-F and ndhF chloroplast nuclear regions. To identify genetically similar areas, we clustered cells using the mean genetic similarities of the species contained within each pair of cells. Measures of the mean genetic similarity of species in areas were delineated using a geographically local multi-scalar approach. Resultant patterns of genetic diversity are interpreted in relation to theories of the evolutionary relationships between species and species groups. Results, Centres of Pultenaea endemism were defined, those of clades 1 congruent with the spatially separated centres of clades 2 and 3. The taxonomic classification analysis defined cells with shared groups of species, which in some cases clustered when plotted in geographic space, defining biotic regions. In some instances the distribution of biotic regions was congruent with centres of endemism, however larger scale groupings were also apparent. In clade 1 one set of species was replaced by another along the extent of the range, with some connectivity between some geographically disjunct regions due to the presence of widespread species. In the combined analysis of clade 2 and 3 species the major biotic (taxonomic) groups with geographic coherence were defined by species in the respective clades, representing the geographic separation of these clades. However distinctive biotic regions within these main groupings of clades 2 and 3 were also apparent. Clustering cells using the mean genetic similarities of the species contained within each pair of cells indicated that some of the taxonomically defined biotic boundaries were the result of changes in composition of closely related species. This was most apparent in clades 1 and 2 where most cells were highly genetically similar. In clade 3 genetically distinct groups remained and were in part defined by sister taxa with disjunct distributions. Gradients in mean genetic similarity became more apparent from small to larger scales of analysis. At larger scales of analysis, regions of different levels of genetic diversity were delineated. Regions with highest diversity levels (lowest level of similarity) often represented regions where the ranges of phylogenetically distinctive species intergraded. Main conclusions, The combined analysis of diversity, phylogeny and geography has potential to reveal macro-scaled evolutionary patterns from which evolutionary processes may be inferred. The spatial genetic diversity indices developed in this study contribute new methods for identifying coherent evolutionary units in the landscape, which overcome some of the limitations of using taxonomic data, and from which the role of geography in evolutionary processes can be tested. We also conclude that a multiple-index approach to diversity pattern analysis is useful, especially where patterns may be the result of a long history of different environmental changes and related evolutionary events. The analysis contributes to the knowledge of large-scale diversity patterns of Pultenaea which has relevance for the assessment of the conservation status of the genus. [source] Cladistic and phylogenetic biogeography: the art and the science of discoveryJOURNAL OF BIOGEOGRAPHY, Issue 3 2003Marco G. P. Van Veller Abstract All methods used in historical biogeographical analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group, all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29, 427) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programmes, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon,area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographical context of speciation events. The recent contribution by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29, 427) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research programme, whereas phylogenetic biogeography is hypothetico-deductivist/falsificationist. Cladistic biogeography can become hypothetic-deductive by using a posteriori methods of analysis. [source] Differentiation of morphology, genetics and electric signals in a region of sympatry between sister species of African electric fish (Mormyridae)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2008S. LAVOUÉ Abstract Mormyrid fishes produce and sense weak electric organ discharges (EODs) for object detection and communication, and they have been increasingly recognized as useful model organisms for studying signal evolution and speciation. EOD waveform variation can provide important clues to sympatric species boundaries between otherwise similar or morphologically cryptic forms. Endemic to the watersheds of Gabon (Central Africa), Ivindomyrus marchei and Ivindomyrus opdenboschi are morphologically similar to one another. Using morphometric, electrophysiological and molecular characters [cytochrome b sequences and amplified fragment length polymorphism (AFLP) genotypes], we investigated to what extent these nominal mormyrid species have diverged into biological species. Our sampling covered the known distribution of each species with a focus on the Ivindo River, where the two taxa co-occur. An overall pattern of congruence among datasets suggests that I. opdenboschi and I. marchei are mostly distinct. Electric signal analysis showed that EODs of I. opdenboschi tend to have a smaller initial head-positive peak than those of I. marchei, and they often possess a small third waveform peak that is typically absent in EODs of I. marchei. Analysis of sympatric I. opdenboschi and I. marchei populations revealed slight, but significant, genetic partitioning between populations based on AFLP data (FST , 0.04). Taken separately, however, none of the characters we evaluated allowed us to discriminate two completely distinct or monophyletic groups. Lack of robust separation on the basis of any single character set may be a consequence of incomplete lineage sorting due to recent ancestry and/or introgressive hybridization. Incongruence between genetic datasets in one individual, which exhibited a mitochondrial haplotype characteristic of I. marchei but nevertheless fell within a genetic cluster of I. opdenboschi based on AFLP genotypes, suggests that a low level of recent hybridization may also be contributing to patterns of character variation in sympatry. Nevertheless, despite less than perfect separability based on any one dataset and inconclusive evidence for complete reproductive isolation between them in the Ivindo River, we find sufficient evidence to support the existence of two distinctive species, I. opdenboschi and I. marchei, even if not ,biological species' in the Mayrian sense. [source] Phylogeny and speciation of the eastern Asian cyprinid genus SarcocheilichthysJOURNAL OF FISH BIOLOGY, Issue 5 2008L. Zhang The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8·89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4·78 mya from the Chinese group. The northern,southern clades of S. nigripinnis began to diverge c. 2·12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0·34 mya. [source] Comparative sperm ultrastructure in NemerteaJOURNAL OF MORPHOLOGY, Issue 7 2010J. von Döhren Abstract Although the monophyly of Nemertea is strongly supported by unique morphological characters and results of molecular phylogenetic studies, their ingroup relationships are largely unresolved. To contribute solving this problem we studied sperm ultrastructure of 12 nemertean species that belong to different subtaxa representing the commonly recognized major monophyletic groups. The study yielded a set of 26 characters with an unexpected variation among species of the same genus (Tubulanus and Procephalothrix species), whereas other species varied in metric values or only one character state (Ramphogordius). In some species, the sperm nucleus has grooves (Zygonemertes virescens, Amphiporus imparispinosus) that may be twisted and give a spiral shape to the sperm head (Paranemertes peregrina, Emplectonema gracile). To make the characters from sperm ultrastructure accessible for further phylogenetic analyses, they were coded in a character matrix. Published data for eight species turned out to be sufficiently detailed to be included. Comparative evaluation of available information on the sperm ultrastructure suggests that subtaxa of Heteronemertea and Hoplonemertea are supported as monophyletic by sperm morphology. However, the data do not provide information on the existing contradictions regarding the internal relationships of "Palaeonemertea." Nevertheless, our study provides evidence that sperm ultrastructure yields numerous potentially informative characters that will be included in upcoming phylogenetic analyses. J. Morphol. 2010. © 2010 Wiley-Liss, Inc. [source] TAXONOMIC REEXAMINATION OF 17 SPECIES OF NITELLA SUBGENUS TIEFFALLENIA (CHARALES, CHAROPHYCEAE) BASED ON INTERNAL MORPHOLOGY OF THE OOSPORE WALL AND MULTIPLE DNA MARKER SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 1 2005Hidetoshi Sakayama In an attempt to reconstruct the natural taxonomic system for Nitella, 17 species of Nitella subgenus Tieffallenia were reexamined using SEM observations of the internal morphology of the oospore wall (IMOW) and phylogenetic analyses of 4553 base pairs from multiple DNA markers (atpB, rbcL, psaB, and ITS-5.8S rRNA genes). Our SEM observations identified three types of IMOW: homogeneous (HG), weakly spongy (W-SG), and strongly spongy (S-SG) types. Based on differences in the IMOW, species with reticulate or tuberculate oospore wall ornamentation in the external morphology of the oospore wall (EMOW) were subdivided into two distinct groups (characterized by the HG or S-SG types of IMOW, respectively), which were robustly separated from each other in our molecular phylogenetic analyses. In our molecular phylogeny, the subgenus Tieffallenia consisted of four robust monophyletic groups,three clades of the HG type and a spongy (S-SG and W-SG) type clade,that were characterized by differences in the IMOW and EMOW. In addition, our SEM observations and sequence data verified the distinct status of five species (N. japonica Allen, N. oligospira A. Braun, N. vieillardii stat. nov., N. imperialis stat. nov., and N. morongii Allen) that R. D. Wood had assigned as infraspecific taxa. Moreover, our SEM observations of the IMOW also suggested that N. megaspora (J. Groves) Sakayama originally identified by LM includes at least two distinct species, characterized by W-SG and S-SG types of IMOW, respectively. [source] SYSTEMATICS OF THE HILDENBRANDIALES (RHODOPHYTA): GENE SEQUENCE AND MORPHOMETRIC ANALYSES OF GLOBAL COLLECTIONS,JOURNAL OF PHYCOLOGY, Issue 2 2003Alison R. Sherwood Fifty-seven collections of marine and freshwater Hildenbrandia from North America, South America, Europe, and Africa were compared with 21 type and historically important specimens using multivariate morphometrics. Additionally, phylogenetic analyses of 48 specimens of Hildenbrandia and two specimens of Apophlaea were carried out based on sequences of the rbcL chloroplast gene and the nuclear 18S rRNA gene. Morphometric analyses based on vegetative cell and filament dimensions distinguished two groups of freshwater Hildenbrandia specimens, the first corresponding to those collections from North America and the Philippines and the second to those from Europe and the Canary Islands. The first group had smaller mean cell and filament dimensions (cells 4.0 × 4.4 ,m, filaments 46.5 ,m) and corresponded to H. angolensis, whereas the second group had larger mean dimensions (cells 5.8 × 6.6 ,m, filaments 55.3 ,m) and represented H. rivularis. Marine specimens were morphometrically distinguishable into two groups based on tetrasporangial division pattern as well as other thallus characters. However, measurements and character determinations of some type specimens differed greatly from the original descriptions, and thus further work to determine the stability of these characters is required. Phylogenetic reconstruction based on the 18S rRNA gene and rbcL gene sequence data generally demonstrated separation of the marine and freshwater forms of Hildenbrandia, with some marine taxa forming monophyletic groups (e.g. H. lecannellieri and H. occidentalis) and others forming paraphyletic groups (e.g. H. rubra). The two specimens of Apophlaea formed a monophyletic group within the paraphyletic genus Hildenbrandia. [source] THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCESJOURNAL OF PHYCOLOGY, Issue 2000S. Nemeth Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa, were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species. [source] Phylogenetic affinities of the Flabelligeridae (Annelida, Polychaeta)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2008S. I. Salazar-Vallejo Abstract Cirratuliformia includes Acrocirridae, Cirratulidae, Ctenodrilidae, Flabelligeridae, Flotidae and Sternaspidae. The phylogenetic affinities have not been settled due to a limited availability of type or non-type material and the relationship between acrocirrids and flabelligerids have been problematical. In our study, the type material of all type species for all flabelligerid, and most acrocirrid genera have been studied and the morphological features have been used in a phylogenetic analysis. The results indicate that Acrocirridae, Ctenodrilidae, Fauveliopsidae, Flabelligeridae and Flotidae are monophyletic and that Sternaspidae falls within Cirratulidae; however, the latter conclusion might be reversed through increased taxon-sampling. The flabelligerid genera Brada, Flabelligera, Pherusa and Stylarioides each consists of several monophyletic groups and may be split. Conversely, Bradiella includes Diversibranchius, and the pelagic Buskiella includes Flota. The generic affinities of Poeobius remain uncertain, collecting better materials may resolve this issue. [source] Molecular phylogeny and biogeography of Honey-buzzards (genera Pernis and Henicopernis)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2004A. Gamauf Abstract A partial sequence of the cytb gene (382 bp) was amplified and sequenced from 35 individuals (mainly museum specimens) of the genus Pernis representing all valid taxa (10) and two taxa (P. p. gurneyi, P. p. japonicus) with questionable validity as well as representatives of the Old World Perninae, namely Henicopernis and Aviceda, to assess their relationships to the genus Pernis. Furthermore, Gypaetus barbatus, Neophron percnopterus, and Buteo buteo were included as outgroup taxa. In the trees derived from the sequence data, Aviceda represents the sister group of the genus Pernis. The genus Henicopernis and the Old World vultures Gypaetus andNeophron appear rather distantly related to Pernis. Within the genus Pernis, two of the described species (Pernis apivorus, Pernis ptilorhyncus) form monophyletic groups, whereas the relationships of the two clades representing three subspecies of Pernis celebensis are still uncertain. Although this study is based on comparatively short DNA-sections, the trees deduced from these sequences can be considered as a first approach for inferring the phylogenetic relationships of the genus Pernis and related genera and for addressing questions concerning the evolutionary history, biogeography, and systematics of this group. Zusammenfassung Eine Teilsequenz des Cytochrom b Gens (382 bp) wurde von 35 Individuen (hauptsächlich Museumsmaterial) der Gattung Pernis amplifiziert und sequenziert. Inkludiert wurden alle validen Taxa (10) und zwei weitere (P.p. gurneyi, P. p. japonicus) mit zweifelhaftem taxonomischen Status. Weiters wurden die übrigen Vertreter der altweltlichen Perninae (Henicopernis, Aviceda) untersucht, um deren Verwandtschaft zum Genus Pernis festzustellen. Als Außengruppen-Taxa wurden Bartgeier Gypaetus barbatus, Schmutzgeier Neophron percnopterus und Mäusebussard Buteo buteo verwendet. In den aus den Sequenzen errechneten Bäumen stellt Aviceda die Schwestergruppe der Gattung Pernis dar. Die Gattungen, Henicopernis und die Altweltgeier Gypaetus und Neophron erscheinen mit der Gattung Pernis nur entfernt verwandt. Innerhalb der Gattung Pernis formen zwei der beschriebenen Arten (P. apivorus, P. ptilorhyncus) eine monophyletische Gruppe, die Verwandtschaftsverhältnisse der beiden anderen Clades, welche die drei Unterarten von P. celebensis repräsentieren, können jedoch auf der Basis dieser Sequenz nicht eindeutig geklärt werden. Obwohl diese Analyse auf relativ kurzen DNA-Abschnitten basiert, können die aus den Sequenzen abgeleiteten Stammbäume als erster Versuch angesehen werden, die Phylogenie der Wespenbussard-Gattung Pernis und verwandter Genera mittels molekularer Methoden und unter Berücksichtigung evolutionsbiologischer, biogeographischer und systematischer Aspekte darzustellen. [source] Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographical breaks congruent with fish community boundaries?MOLECULAR ECOLOGY, Issue 19 2009JARED B. LEE Abstract One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to determine if phylogeographical breaks in this species were congruent with previously defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we might find four clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographical regions. We generated DNA sequence data (mitochondrial cytochrome b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analysed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographical community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not predicted by community province boundaries. [source] Adaptive radiation in Lesser Antillean lizards: molecular phylogenetics and species recognition in the Lesser Antillean dwarf gecko complex, Sphaerodactylus fantasticusMOLECULAR ECOLOGY, Issue 6 2008R. S. THORPE Abstract The time associated with speciation varies dramatically among lower vertebrates. The nature and timing of divergence is investigated in the fantastic dwarf gecko Sphaerodactylus fantasticus complex, a nominal species that occurs on the central Lesser Antillean island of Guadeloupe and adjacent islands and islets. This is compared to the divergence in the sympatric anole clade from the Anolis bimaculatus group. A molecular phylogenetic analysis of numerous gecko populations from across these islands, based on three mitochondrial DNA genes, reveals several monophyletic groups occupying distinct geographical areas, these being Les Saintes, western Basse Terre plus Dominica, eastern Basse Terre, Grand Terre, and the northern and eastern islands (Montserrat, Marie Galante, Petite Terre, Desirade). Although part of the same nominal species, the molecular divergence within this species complex is extraordinarily high (27% patristic distance between the most divergent lineages) and is compatible with this group occupying the region long before the origin of the younger island arc. Tests show that several quantitative morphological traits are correlated with the phylogeny, but in general the lineages are not uniquely defined by these traits. The dwarf geckos show notably less nominal species-level adaptive radiation than that found in the sympatric southern clade of Anolis bimculatus, although both appear to have occupied the region for a broadly similar period of time. Nevertheless, the dwarf gecko populations on Les Saintes islets are the most morphologically distinct and are recognized as a full species (Sphaerodactylus phyzacinus), as are anoles on Les Saintes (Anolis terraealtae). [source] Dispersal and phylogeography of the agamid lizard Amphibolurus nobbi in fragmented and continuous habitatMOLECULAR ECOLOGY, Issue 6 2005D. A. DRISCOLL Abstract Approximately 90% of native vegetation has been cleared for agriculture in central New South Wales, Australia. Habitat loss has reduced and fragmented populations of the agamid lizard Amphibolurus nobbi. We compared genetic structure of populations of this species in an unmodified landscape with those from small nature reserves and linear remnants in farming areas. We ask: Is there evidence for reduced dispersal and population fragmentation among farm populations? Using 2008 bp mtDNA sequences and allozyme electrophoresis, we found that small populations in farming areas had as much genetic variation as populations in nature reserves. Application of nested clade analysis (NCA) indicated isolation-by-distance effects among populations from uncleared areas, but not among populations within farming locations. The genetic evidence therefore implied a high level of migration in the cleared landscapes. High dispersal after fragmentation may have resulted from either a burst of movement at the time of land clearing with dragons from many sources finding refuge in a few remnants, or from ongoing rapid dispersal through unsuitable habitat. A phylogeny based on mtDNA revealed that A. nobbi populations in the study area are deeply divided into two reciprocally monophyletic groups. Although we did not sample the entire species range, one of these evolutionarily significant units was only detected in remnant vegetation in the agricultural landscape. Therefore, a substantial subclade of this species may be vulnerable to extinction. Our findings emphasize that local populations of widespread species can harbour important intraspecific genetic diversity, supporting the case for maintaining widespread species throughout production landscapes. [source] Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizationsMOLECULAR ECOLOGY, Issue 4 2005JENNIFER L. TRUSTY Abstract A molecular phylogenetic study of Bystropogon L'Hèr. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution. [source] Phylogeny of Early Cretaceous spatangoids (Echinodermata: Echinoidea) and taxonomic implicationsPALAEONTOLOGY, Issue 2 2004Loïc Villier A phylogenetic analysis of 36 species provides a test for the taxonomy and the history of Early Cretaceous spatangoids. Most taxonomic units from genera to suborders are consistent with the proposed phylogenetic framework. We retain Hemiasterina, Micrasterina, Hemiasteridae, Schizasteridae, Hemiaster, Heteraster, Mecaster, and Periaster as original monophyletic groups. However, all of these clades originate without the classical apomorphies normally ascribed to them. We suggest a revision of their diagnoses and of the generic attributions of basal species. Some ill-defined, ,primitive', and paraphyletic taxa are recognised: Toxaster, Epiaster, Palhemiaster, and Toxasteridae. Even if they do not have phylogenetic meaning, they are retained here, pending a more complete revision. [source] Molecular phylogenetic analyses of the Japanese Ulva and Enteromorpha (Ulvales, Ulvophyceae), with special reference to the free-floating UlvaPHYCOLOGICAL RESEARCH, Issue 2 2003Satoshi Shimada SUMMARY In order to elucidate the species composition of free-floating Ulva that cause green tide in several bays in Japan, and to clarify the generic status of Ulva and Enteromorpha (Ulvales, Ulvophyceae), the nuclear encoded internal transcribed spacer (ITS) region including the 5.8S gene and the plastid encoded large subunit of ribulose-1, 5-bisphosphate carboxylase/ oxgenase (rbcL) gene sequences for 15 species were determined. Both ITS and rbcL analyses indicate that free-floating Ulva samples are divided into four different lineages that correspond to Ulva lactuca Linnaeus, U. pertusa Kjellman, U. armoricana Dion etal. and U. fasciata Delile. These four species are distinguished by cell morphology including the arrangement of cells, the shape and size of cells and the position of chloroplasts. Molecular data also indicated that Ulva and Enteromorpha are not separated as respective monophyletic groups within a large monophyletic clade and congeneric as shown by previous molecular studies using the ITS sequences alone. This strongly suggests that these genera are congeneric and Enteromorpha should be reduced to the synonym of Ulva. [source] Evolution of Filamentous Ascomycetes Inferred from LSU rDNA Sequence DataPLANT BIOLOGY, Issue 5 2000H. T. Lumbsch Abstract: The nuclear LSU rRNA gene was examined in order to evaluate the current phylogeny of ascomycetes, which is mainly based on nuclear SSU rRNA data. Partial LSU rRNA gene sequences of 19 ascomycetes were determined and aligned with the corresponding sequences of 13 other ascomycetes retrieved from Genbank, including all classes traditionally distinguished and most of the recently accepted classes. The classification based on SSU rDNA data and morphological characters is supported, while the traditional classification and classifications based on the ascus type are rejected. Ascomycetes with perithecia and cleistothecia form monophyletic groups, while the discomycetes are a paraphyletic assemblage. The Pezizales are basal to all other filamentous ascomycetes. The monophyly of Loculoascomycetes is uncertain. The results of the LSU rDNA analysis agree with those of the SSU rDNA and RPB2 gene analyses, suggesting that most classes circumscribed in the filamentous ascomycetes are monophyletic. The branching order and relationships among these classes, however, cannot be elucidated with any of these data sets. [source] Dicotyledonous wood anatomy and the APG system of angiosperm classificationBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1-2 2000PIETER BAAS FLS The recently proposed classification by the Angiosperm Phylogeny Group (APG) of angiosperms based on monophyletic groups as recognized mainly by molccular analysis is used here to discuss wood anatomical diversity patterns at the ordinal level. The APG orders are compared with the most recent ,classical' orders as listed in the second edition of 7 h e Plant Book for ,improved' or ,deteriorated' wood anatomical coherence. Although homoplasy in wood anatomical characters, largely due to ecoloqical adaptations, limits the value of wood anatomy at higher levels of classification, many families and orders tend to have characteristic combinations of microscopic wood features. Out of the 29 APG dicot orders, seven (Aquifoliales, Cucurbitales, Gentianales, Geraniales, Myrtales, Sapindales, Saxifragales) show an increase in wood anatomical homogeneity relative to their ,classical' predecessors; four APG dicot orders (Apiales, Ericales, Fabales, and Rosales) show a drcrrase, although within the orders several suprafamilial subclades are homogeneous. For the remaining 18 orders. wood anatomical diversity remains about the same as in previous classfications or the APG ordinal composition is almost identical to the ,classical' composition. The results support the value of both molecular markers and wood anatomical characters in phylogenetic classification. Because the ,classical' ordinal classifications have been partly inspired by wood anatomical information, one might have expected a ?greater wood anatomical coherence in them than in the largely molecularly delimited APG orders if wood anatomy did not provide significant phylogenetic sisgnals at higher taxonomic levels. The reverse appears to be the case. Among the wood anatomical characters included in the comparison, vestured intervessel pits, large and simple ray parenchyma pits, and sometimes also wide and tall rays appear to characterize orders. Some orders tend to be characterized by a combination of ,primitive' features in the Baileyan sense: scalariform perforations, fibres with distinctly bordered pits, apotracheal parenchyma, and heterocellular rays. This raises the question as to whethcr in thcsc cladcs this entire combination of characteristics should not he viewrd as synapomorphic rather than symplesiomorphic. [source] The phylogeny of the Pantropical genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae)CLADISTICS, Issue 1 2010Lena Brüstle The phylogeny of the genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae) is clarified with a cladistic analysis based on five molecular markers and morphology. Sixteen species from Africa, America, Asia, and Australia are included in the analysis. Two separate Asian clades are recovered, one of them being the sister group to a clade with the American and African species. With the exception of the continental south-east Asian species, all Gondwanan regions have monophyletic faunas. According to the present data, the continental south-east Asian fauna comprises two monophyletic groups, one of which is the sister group to African and American species. Vicariance seems to be the logical explanation for the distribution of these lignicolous beetles. © The Willi Hennig Society 2009. [source] Phylogeny of the Thylacosterninae (Coleoptera, Elateridae)CLADISTICS, Issue 2 2009Varpu Vahtera The phylogeny of the Elateridae subfamily Thylacosterninae was studied using morphological characters and mitochondrial 16S rDNA sequences. Five monophyletic groups were recovered: the Asian Cussolenis, the American Pterotarsus, Balgus and Thylacosternus, and the African "Cussolenis", which is described here as Lumumbaia new genus Muona & Vahtera (type-species Cussolenis attenuatus Fleutiaux, 1925). The following new combinations are made: Lumumbaia africanus (Fleutiaux, 1897) [Soleniscus], Lumumbaia praeustus (Fleutiaux, 1926) [Cussolenis], Lumumbaia nigripes (Fleutiaux, 1926) [Cussolenis], Lumumbaia robustus (Fleutiaux, 1925) [Cussolenis], Lumumbaia attenuatus (Fleutiaux, 1925) [Cussolenis] and Lumumbaia notabilis (Fleutiaux, 1926) [Cussolenis]. A key to the genera of the subfamily is provided. The data were efficient in recovering generic limits within the group. At species level the mitochondrial 16S rDNA data seemed to work unpredictably, either agreeing or not with traditional species-level limits based on male genitalia and body structure. The evolution of bioluminescence is optimized as a feature originating in the ancestors of clicking elateroids. © The Willi Hennig Society 2009. [source] Phylogenetic analysis of bovine pestiviruses: testing the evolution of clinical symptomsCLADISTICS, Issue 5 2004L. R. Jones This study presents a phylogenetic analysis of 115 bovine pestiviruses. A sequence data set from the 5, untranslated genomic region was analyzed with maximum parsimony, bootstrapping and parsimony jackknifing. We tested for the proposed classifications of the group and analyzed the evolution of the symptoms associated with Pestivirus infections in bovines. Based on the historical framework provided by our phylogenetic trees, we also characterized the extent and importance of contamination caused in biologicals by the virus. Our phylogenetic analyses showed that the previously defined genotypes are monophyletic, except for genotype 1a. Based on our cladograms, we propose the existence of more than 12 monophyletic groups within the species BVDV 1. The mapping of clinical symptoms suggests that the emergence of some genotypes could have been driven by a change in the pathogenic process. Enteric Problems appear to be ancestral, while Reproductive and Respiratory Problems arise with the emergence of genotypes 1b, 1d and the herein-proposed genotype Arg 1. The distribution of contaminant strains on the cladograms shows that pestiviral contamination is a common process, and also suggests that a contaminated product might be a vehicle for virus dispersion. Implications for virus evolution, virus taxonomy, veterinary medicine and biotechnology are discussed. [source] | ||||||||||||||||||||||||||||||||||