Morphometrical analyses of Secale (Triticeae, Poaceae)

Some fifteen taxa ranked as species or subspecies have generally been recognized within Secale. However, most of these seem impossible to separate on morphology alone. Based on 14 morphological characters considered of diagnostic value and scored on 44 specimens representing most of the taxa a Principal Components Analysis (PCA) was carried out. Limited correlation was found between the characters and consequently the first three principal axes account for only about 60% of the total variation. The PCA shows only a weak separation of annual and perennial taxa. Further analyses mainly of spikelet characters support merging of most of the previously accepted taxa within each of these two groups. A total of three species with five infraspecific taxa are here proposed within the genus and a key is provided to the taxa.     

Phenetic studies in Nuphar Sm. (Nymphaeaceae):variation in sect. Nuphar

Previous taxonomic assessments of the hydrophytic genus Nuphar Sm. (Nymphaeaceae) have inadequately considered the range of morphological variation existing in the genus. A comprehensive statistical analysis of morphological features among the recognized taxa of Nuphar is presented here, first using 10 fruit characters to delimit the separation of two infrageneric groups of taxa, and secondly using 31 characters to quantify the morphological variation found within sect. Nuphar. Results from combined phenetic analyses provided empirical support for recognition of two infrageneric groups of species in the genus (largely by fruit, stigmatic disk margin, neck, and stigmatic disk size) and for separation of taxa within sect. Nuphar (by leaf size, and fruit disk and neck size). Statistical analyses demonstrate that extensive variation in ranges of character states exists among sect. Nuphar taxa. However, a suite of qualitative and quantitative characters can be used to recognize five species and three subspecies within this predominantly Old World assemblage.     

Revisiting the North American freshwater mussel genus Quadrula sensu lato (Bivalvia Unionidae): Phylogeny,taxonomy and species delineation

Freshwater mussels (Bivalvia, Unionidae) have suffered strong declines over the last century. High morphological plasticity of Unionidae causes disturbances in their systematics and taxonomy, hampering conservation efforts. Species that have historically been placed under the North American genus Quadrula have suffered from numerous taxonomic and species delineation problems since its inception. Four genera are presently recognized within Quadrula sensu lato, that is, Cyclonaias, Quadrula, Theliderma and Tritogonia, but their phylogenetic basis remains incompletely tested. In the present study, we reconstructed several two‐marker (mtDNA cytochrome c oxidase subunit I—COI and NADH dehydrogenase subunit 1—ND1) phylogenies with newly collected specimens and all previously available sequences covering most species within this group. We then delineated the species within the group using an integrative approach with the application of molecular statistical methods, morphometric (Fourier Shape) analyses and geographic distribution data. Four clades corresponding to these genera were consistently recovered in all phylogenies. To validate the generic status of these clades, molecular analyses were complemented with morphological, anatomical and ecological data compiled from the literature. Several revisions are here proposed to the current systematics and taxonomy of these genera, including the synonymization of Cyclonaias asperata under Cyclonaias kieneriana; the inclusion of Quadrula apiculata and Quadrula rumphiana under Quadrula quadrula; the placement of Quadrula nobilis under Tritogonia; and finally the separation of the Mobile River basin populations of Theliderma metanevra as a new species, that is, Theliderma johnsoni n. sp. The conservation implications of the proposed changes are then discussed.     

Mitochondrial DNA phylogeny of West African aplocheiloid killifishes (Cyprinodontiformes, Aplocheilidae)

African killifishes (Cyprinodontiformes, Aplocheilidae) historically associated with the genus Aphyosemion occur in two geographically distinct regions. One assemblage from far West Africa has been previously shown to be monophyletic and not closely related to the remaining eastern species of Aphyosemion (W. J. Murphy and G. E. Collier, 1997, Mol. Biol. Evol. 14, 790-799). This is supported by further analysis of mitochondrial DNA sequences from 19 species from 21 different localities, representing 19 of the putative 22 species of this western group. Phylogenetic analyses of these data corroborate the monophyly and sister-group relationship of two distinct groups of taxa: Callopanchax and Scriptaphyosemion. Many of the relationships within Scriptaphyosemion suggest that these taxa may have radiated within a short period of time relative to the rate of substitutions within these sequences. A third, and possibly paraphyletic group of species, Archiaphyosemion, is suggested to be the sister taxon to the first two groups. These three groups are elevated to generic rank and together represent the sister group to the genus Epiplatys. Biogeographic inference suggests that the ancestors of this group diversified westward through upland habitat and have only relatively recently entered the lowland habitats in which Scriptaphyosemion and Callopanchax have diversified, with the latter genus reacquiring a suite of traits collectively referred to as annualism.     

Integrative taxonomy approach for analysing evolutionary history of the tribe Euseiini Chant & McMurtry (Acari: Phytoseiidae)

Phylogenetic relationships within the mite Family Phytoseiidae are little known. The presently accepted classification is based on the opinion of specialists, but not on cladistics analysis. The present paper focuses on the tribe Euseiini, containing 271 species, three subtribes and 10 genera. It aims to determine phylogenetic relationships between these taxa and test their monophyly. Molecular analysis combining six markers has been carried out for taxa we succeeded in collecting. Morphological, biogeographic and ecological data have been analysed to determine how these factors can explain the evolutionary relationships emphasized on the phylogenetic tree. Those analyses have been carried out for the taxa available for the molecular study, but also for all species of the tribe. The tribe Euseiini and the two subtribes considered are monophyletic (at least considering the available taxa), supporting the present hypothesis on Phytoseiidae classification. However, the genus Iphiseius seems to not be valid and its unique species is included in the genus Euseius. Clades that were observed within the genus Euseius do not match with recent work on species groups within this genus. It seems that some morphological features such as an insemination apparatus shape and seta length on the dorsal shield constitute some elements explaining the clusters within the genus Euseius. Biogeographic and ecological data analysis led us to hypothesize a west Gondwanian origin of the tribe Euseiini (Africa and Neotropical areas) on Rosids plants (especially of the Orders Malpiphiales and Fabales: subclass Fabidae). Further analyses are still required to (i) take into account more taxa (especially rare ones and species from the Ethiopian part), (ii) to consider more accurate morphological features through more powerful microscopic apparatus, and (iii) to associate a phylogenetic and evolutionary scenario to life traits (pollen feeders).     

Three species of Isotoma (Collembola, Isotomidae) based on morphology, isozymes and ecology

Morphological markers and isozymes were used for identifying three presumed species of the Isotoma genus. Morphological traits separated three taxa of the genus. 10 isozymes determined by at least 11 loci were analysed from each taxon, and 2 loci were taxon-specific, supporting the hypothesis that the three taxa represented three species. The genetic variation found within the taxa measured as fraction of polymorphic loci at the 99% level was 0.82, 0.55 and 0.55 with the corresponding observed heterozygosity 0.15, 0.09 and 0.12. Two populations of the same taxon from Denmark and Norway, respectively, were very closely related. Additional ecological criteria, obtained from a literature survey, also revealed pronounced differences between the three taxa. Due to these facts three distinct species are proposed, namely I. anglicana Lubbock 1862, I. riparia Nicolet 1841 and I. viridis Bourlet 1839.     

Molecular systematics of Ceratostomella sensu lato and morphologically similar fungi

The systematic position and phylogenetic relationships of Ceratostomella sensu lato and phenotypically similar fungi using comparative morphological and culture studies and phylogenetic analyses of the nuclear large- and small-subunit ribosomal DNA were explored. In the light of inferred phylogenies and morphological data the genus Ceratostomella is redescribed, the generic concept is emended and four species are accepted (viz. C. cuspidata, C. pyrenaica, C. rhynchophora and C. rostrata). A new genus Xylomelasma is introduced and delimited from Ceratostomella, with two new species described (viz. X. novaezelandiae and X. sordida). In culture species of both Ceratostomella and Xylomelasma produced sterile mycelium. The genus Lentomitella with a phaeoisaria-like anamorph formed in vitro is reinstated to encompass taxa formerly attributed to the broadly perceived Ceratostomella with three accepted species (viz. L. cirrhosa, L. crinigera and L. tomentosa). Lentomitella and Ceratostomella are clearly distinguishable by the morphology of asci, ascospores and centrum. Lentomitella is compared to phenotypically similar Ceratosphaeria, which formed a harpophora-like anamorph in vitro. In the present phylogenies Ceratostomella, Ceratosphaeria, Lentomitella and Xylomelasma are shown as clearly separate genera belonging to three different groups of perithecial ascomycetes. Ceratostomella, Lentomitella and Xylomelasma reside within a large unsupported clade consisting of members the Ophiostomatales, the freshwater Annulatascaceae and a group of nonstromatic, terrestrial taxa. Ceratosphaeria is well supported within the Magnaporthaceae. The systematic value of morphological characters of ascospores, paraphyses, asci, centrum and conidiogenesis in segregating taxa from Ceratostomella sensu lato and their relatives is discussed.     

Plumage based classification of the bowerbird genus Sericulus evaluated using a multi-gene, multi-genome analysis

Past classifications of taxa within the bowerbird genus Sericulus (family: Ptilonorhynchidae) conflict since the discovery of hybrids identified though male plumage characteristics. We use molecular data to help define species within this genus, and by estimating a phylogeny, test for lability in the evolution of male plumage patterns. Because this genus includes the most brightly colored bowerbird species, and is hypothesized to be the basal genus of the avenue building bowerbird clade, the organization of the four taxa within this genus is especially important in understanding how bowerbird plumage coloration evolved. Analyses of two mitochondrial and six nuclear gene regions confirm the basal placement of Sericulus in the avenue building bowerbirds and Sericulus monophyly, and suggests the Australian S. chrysocephalus is the basal Sericulus species. Our analysis additionally supports the existence of three New Guinea Sericulus species, contrary to some previous plumage based classifications, as they are genetically equidistant from each other. Molecular and geographic data of New Guinea are consistent suggesting a series of speciation events starting approximately 3.7-4.3MYA leading to four extant Sericulus species. The absence of resolution within the New Guinea species precludes any statements of trait lability, but does suggest that traits under high selection pressures may not accurately indicate species level distinctions within this genus.     

PHYLOGENY OF CARTERIA (CHLOROPHYCEAE) INFERRED FROM MOLECULAR AND ORGANISMAL DATA1

Comparative ultrastructural data have shown that at least two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small- and large-subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1) testing hypotheses that distinct groups of species exist within the genus and 2) assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C. lunzensis, C. crucifera, and C. olivieri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox, and Eudorina). Two other Carteria taxa, C. radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretations of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphological, ultra-structural, life history, and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus.     

Is the mega-diverse genus Ocyptamus (Diptera, Syrphidae) monophyletic? Evidence from molecular characters including the secondary structure of 28S rRNA

Phylogenetic relationships between two New World Syrphinae taxa (Diptera, Syrphidae), i.e. the highly diverse genus Ocyptamus and the large genus Toxomerus, were analysed based on molecular characters. The monophyly of both taxa was tested and the taxonomic status of included subgenera and species groups was examined. Toxomerus constitutes the monogeneric tribe Toxomerini with more than 140 described species, while Ocyptamus (tribe Syrphini) is a very diverse genus (over 300 spp.) with multiple recognised subgenera and species groups. Sequence data from three gene regions were used: the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The secondary structure of two expansion segments (D2, D3) of the ribosomal 28S RNA gene is presented for the family Syrphidae and used for the first time in a multiple sequence alignment. Molecular data were analysed using parsimony, maximum likelihood and Bayesian inference. Toxomerus was always recovered as monophyletic within Ocyptamus, and relationships to other New World taxa such as Salpingogaster (Eosalpingogaster) were well-supported. Only the subgenera and species groups of Ocyptamus were consistently recovered as monophyletic lineages, thus the apparent non-monophyly of Ocyptamus demands reclassification of this clade.     

Molecular phylogenies in the genus Mus: Comparative analysis of electrophoretic, scnDNA hybridization, and mtDNA RFLP data

In this paper, we present data on murid rodents obtained by three major techniques used in biochemical systematics today: protein electrophoresis, scnDNA hybridization and mtDNA RFLP. The data have been analysed by both phenetic and cladistic methods and results of the three techniques were compared with one another. Four clear major levels of divergence (or nodes) can be recognized by all methods. Node 1 groups four subspecies of M. musculus ( domesticus, bactrianus, castaneus and musculus ). Node 2 groups four species: M. musculus, M. spretus, M. spicilegus and M. spretoides . Node 3 groups the stem of node 2 and three strictly Oriental species ( M. caroli, M. cervicolor and M. cookii ) Node 4 groups the previous lineages with Oriental Pyromys and Coelomys and the Ethiopian Nannomys . However, the relationships within each level cannot be resolved without ambiguity. We argue that this is not due to the resolutive power of our methods, but to a biological reality, that is successive adaptive radiations marked by quasi-simultaneous speciation events linked with geographical colonization. Our estimation of divergence time between different taxa showed that the genus Mus is very young. The youngest 'bona fide' species are 1.1 Myr old, or even less than 0.3 Myr if one takes into consideration the two sibling species M. spicilegus and M. spretoides . It appears that mtDNA evolves three to six times faster than scnDNA. The zoogeographical history of the genus can be reconstructed as a séries of adaptative radiations leading to the present day distribution of the Palaearctic, Oriental, and Ethiopian groups of taxa.     

Molecular phylogeny of Anthyllis spp

For the genus Anthyllis (Fam. Fabaceae, tribe Loteae), with few exceptions, little information is available on the genetic variation among and within species. This genus contains 20 species distributed throughout Europe, Africa, and the Mediterranean basin. The most widespread species is A. vulneraria, and over 30 intraspecies taxa have been identified based on plant morphology. To study the molecular phylogeny of the genus, the sequences of the internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA of 10 Anthyllis species, including 11 subspecies of A. vulneraria and three subspecies of A. montana, were obtained and analysed together with sequences of five other species of the genus obtained from GenBank. Our results suggest that the genus Anthyllis is not monophyletic and is divided in two main clades: the Anthyllis sensu strictu and the "tetraphylla clade". The former includes most of the Anthyllis species, and the latter includes three annual species more closely related to Lotus. All the taxa were also analysed according to seven chloroplast microsatellites, and these data closely confirm the results obtained with the ITS phylogeny.     

Cytogenetic and cladistic studies in Anacyclus (Compositae: Anthemideae)

The details of a cytogenetic study on 8 taxa of the mediterranean genus Anacyclus are presented. The results include information of the gross morphology, pollen fertilities and meiotic pairing behaviour of F₁ hybrids supplemented by data on the karyotype morphology and DNA contents of parenthal plants. The results indicate that evolution in the genus has been accompanied by chromosomal repatterning. There are three distinctive groups within the experimental taxa, a pair of closely related perennials and two groups of annuals. There is considerable genome homology within each group but major differences between them. The groups are discussed in terms of their systematic relationships with other members of the genus in an effort to provide an explicit evolutionary model for the origin of different taxa. The understanding of the relationships of the annual taxa is complicated by sympatry and the occurrence of natural hybrids.     

Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA

The phylogenetic relationships among rhacophorid frogs are under dispute. We use partial sequences of three mitochondrial (12S rRNA, 16S rRNA, and cytochrome b) and three nuclear protein-coding (Rag-1, rhodopsin exon 1, and tyrosinase exon 1) genes from 57 ingroup taxa and eight outgroup taxa to propose a hypothesis for phylogenetic relationships within Rhacophoridae. Our results support recognition of the genus Feihyla, and Chiromantis is the sister taxon to the clade formed by Feihyla, Polypedates and Rhacophorus. We place Aquixalus odontotarsus within Kurixalus, and the remaining species of Aquixalus and Philautus jinxiuensis into the genus Gracixalus. We give Philautus (Kirtixalus) the rank of genus and place Philautus menglaensis within it. The division of species groups among Chinese Rhacophorus needs revision, and a cryptic species is revealed within Rhacophorus nigropunctatus. Rhacophorus pingbianensis is considered a synonym of Rhacophorus omeimontis. The validity of Rhacophorus hui is confirmed by present molecular evidence.     

Genetic Variation and Relationships Within Taxus and Between the Genus and Pseudotaxus in China

In the present paper, genetic diversity of 12 populations of four Taxus taxa and one species of monotypic genus Pseudotaxus in China were studied by horizontal starch gel electrophoresis. Seven enzymes encoded by nine loci were assessed. Genetic diversity within 5 taxa were relatively high with the proportion of polymorphic loci ( P ) ranging from 44.4 % to 77.8 %, average number of alleles per locus (A) from 1.6 to 2.1; mean expected and observed heterozygosity ( He, Ho) per locus from 0. 065 to 0.152 and 0. 068 to 0.111, respectively. Combined with the analysis of other characters, the results from allozyme analysis suggest that there be very close relationships between the three species and one variety in Taxus, with high genetic identities (I) between them(from 0. 727 to 0. 995) except those between T. yunnanensis and other taxa in Taxus (0. 727～ 0. 804). Consequently, we propose that these taxa in Taxus be treated as different geographical races within a single species. Also the taxonomic position of Pseudotaxus as a distinct genus is supported by ourallozyme data.     

Phylogenetic analysis of the repleta species group of the genus Drosophila using multiple sources of characters

The species in the repleta group of the genus Drosophila have been placed into five subgroups-the mulleri, hydei, mercatorum, repleta, and fasciola subgroups. Each subgroup has been further subdivided into complexes and clusters. Extensive morphological and cytological analyses of the members of this species group have formed the foundation for the proposed relationships among the members of the repleta species group. Fifty-four taxa, including 46 taxa belonging to the repleta species group, were sequenced for fragments of four genes-16S ribosomal DNA (16S), cytochrome oxidase II (COII), and nitrogen dehydrogenase 1 (ND1) of the mitochondrial genome and a region of the hunchback (hb) nuclear gene. We also generated a partial data set of elongation factor 1-alpha (Ef1alpha) sequences for a subset of taxa. Our analysis used both DNA characters and chromosomal inversion data. The phylogenetic hypothesis we obtained supports many of the traditionally accepted clades within the mulleri subgroup, but the monophyly of taxonomic groups outside of this subgroup appears not to be supported. Phylogenetic analysis revealed one well-supported, highly resolved clade that consists of closely related members of the mulleri and buzzatii complexes. The remaining taxa, a wide assortment of taxonomic groups, ranging from members of other species groups to members of several subgroups and members of three species complexes from the mulleri subgroup are found in poorly supported arrangements at the base of the tree.     

A molecular phylogeny of East African Amytta (Orthoptera: Tettigoniidae,Meconematinae) with data on their cytogenetics

This is the first study to address the molecular phylogeny of East African Meconematinae. We used DNA sequence data from the three genes cytochrome oxidase subunit I (COI ), 16S rRNA and histone H3 to reconstruct the relationships within the genus Amytta using Bayesian Inference and maximum likelihood. We included 45 individuals representing 19 Meconematinae taxa from Africa, Europe and Australia, and three outgroup species to explore taxonomic limits at different levels. Members of the genus Amytta belong to three related lineages within Meconematinae. Species of Amytta were found to be monophyletic with Meconema and Phlugidia as sister groups. The molecular results are in accordance with previous morphological and ecological studies. Chromosome numbers and the type of sex determination systems found in Amytta agrees with the three lineages also found in the phylogenetic tree. We conclude that the radiation of Amytta species is geological young. Biogeographical patterns caused by climatic fluctuations of the past seen also in other nonrelated Orthoptera taxa such as the coptacrine genus Parepistaurus are the drivers of biodiversity in the area.