The phylogenetic relationships of the shags and cormorants: can sequence data resolve a disagreement between behavior and morphology?

Taxonomic arrangements for the cormorants and shags (Phalacrocoracidae) had varied greatly until two quite similar arrangements, one based on behavior and the other on osteological characters, became the basis for current thought on the evolutionary relationships of these birds. The terms cormorant and shag, which had previously been haphazardly applied to members of the group, became the vernacular terms for the two major subdivisions within this family. The two taxonomies differ in places, however, with the behavioral taxonomy placing several species within the shags and the osteological taxonomy and phylogeny grouping those species (as the marine cormorants) and placing them within the cormorants. In an attempt to resolve the differences in the relationships hypothesized by behavior and morphology, we sequenced three mitochondrial genes (12S, ATPase 6, and ATPase 8). Initial equally weighted parsimony trees differed slightly from our two weighted parsimony trees, one of which was also our maximum-likelihood tree. Many of the branches within our trees were well supported, but some sections of the phylogeny proved difficult to resolve with confidence. Our sequence trees differ substantially from the morphological phylogeny and show that neither the shags nor the cormorants are monophyletic, but form an intermingled group. Some of the groups supported by both the behavioral and the morphological taxonomies (e.g., the cliff shags, Stictocarbo) appear to be polyphyletic. Conversely, the monophyly of the blue-eyed shags, a traditional group that the osteological analysis had found to be paraphyletic, was supported by the sequence data. Until more taxa are sampled and a fully robust phylogeny is obtained, a conservative approach accepting a single genus, Phalacrocorax, for the shags and cormorants is recommended.     

Phylogenetic position of the genus Bryhnia Kaurin (Brachytheciaceae,Bryophyta) inferred from chloroplast (rpl16, trnG,trnL–F) and nuclear (ITS) sequence data

Abstract

The systematic position of the genus Bryhnia Kaurin has been problematic and remains unsettled. A phylogenetic analysis of Bryhnia and closely related genera, based on the nuclear marker ITS1–5·8S–ITS2 and the plastid markers rpl16, trnG, and trnL–F, was carried out to clarify their relationships and systematic positions. The phylogenetic trees generated from Maximum parsimony and Bayesian analyses show that Bryhnia s.s., represented by B. novae-angliae (Sull. & Lesq.) Grout, B. hultenii E.B.Bartram, and B. scabrida (Lindb.) Kaurin, forms a maximally supported clade nested within Brachythecium Schimp. ‘Bryhnia scabrida’ sensu is Bryhnia brachycladula Cardot, and together they form a monophyletic group with Eurhynchiadelphus eustegia (Besch.) Ignatov & Huttunen and Myuroclada maximowiczii (G.G.Borshch.) Steere & W.B.Schofield. We propose the inclusion of the species currently recognized in Bryhnia in Brachythecium, with the transfer of Bryhnia brachycladula to the genus Myuroclada Besch. Bryhnia brachycladula is further treated as a synonym of the new combination, Myuroclada longiramea (Müll.Hal.) M.Li, Y.F.Wang, M.S.Ignatov & S.Huttunen.     

Molecular evidence for the hybridity ofIlex × wandoensis and the phylogenetic study of KoreanIlex based on ITS sequence data

In this study, internal transcribed spacer (ITS) regions within the nuclear ribosomal DNA of KoreanIlex were analyzed in order to investigate any molecular evidence thatI. × wandoensis could serve as a putative hybrid betweenI. cornuta andI. integra. We also sought to clearly identify taxonomic relationships and problems caused by consecutive external morphological characters among taxa in the genus. We sequenced 20 clones fromI. × wandoensis and found these individuals displayed intra-genomic polymorphisms within ITS regions. The analysis of the clones clearly demonstrated the presence of discrete sequences from bothI. cornuta andI. integra, thereby confirmingI. × wandoensis is a species that was formed by crossingI. cornuta andI. integra. Lastly, the subgenusIlex, which contains the evergreen species, failed to form a monophyletic group in a strict consensus tree that was prepared based upon ITS regions.I. crenata var.microphylla in the subgenus KoreaIlex, which has presented taxonomic problems previously, formed an independent clade within the consensus tree, thereby showing distinction fromI. crenata.) Genetic discontinuity ofI. macropoda andI. Macropoda for.pseudo-macropoda individuals couldn't be confirmed.     

Evolution of Iris subgenus Xiphium based on chromosome numbers, FISH of nrDNA (5S, 45S) and trnL–trnF sequence analysis

The subgenus Xiphium is one of the six infrageneric divisions of the genus Iris. Chromosome numbers of six of the seven Xiphium species are known. Here the aim was to infer genetic and phylogenetic relationships based on chromosome numbers, chromosome markers and plastid sequences. Chromosomal locations of 5S and 45S rDNA loci were determined in 19 populations of the 7 species by fluorescence in situ hybridization (FISH). Additionally, the trnL–trnF plastid spacer was sequenced and a phylogenetic analysis performed. Based on chromosome markers, subgenus Xiphium species were classified into four groups that differed in the number and locations of both types of nrDNA: (1) I. tingitana (2n = 28), I. filifolia (2n = 30, 34) and I. xiphium (2n = 34), (2) I. juncea (2n = 32) and I. boissieri (2n = 36), (3) I. serotina (2n = 34) and (4) I. latifolia (2n = 42). Although the trnL–trnF phylogeny was not fully resolved, the sequence analysis showed a well-supported subgroup of I. filifolia, I. tingitana and I. xiphium, as well as I. juncea. FISH physical maps of the Iris subgenus Xiphium taxa are species dependent. I. filifolia, I. tingitana and I. xiphium are very closely related species and share cytogenetic characteristics. Disploidy appears to have been central in the evolution of this subgenus, given a series of chromosome numbers (2n = 28, 30, 32, 34, 36, 42) and our phylogenetic results. Clear differences were found among European and African populations of I. filifolia. A different taxonomic treatment of I. filifolia is supported for populations on both sides of the Strait of Gibraltar.     

Dermatoglyphic and anthropometric relationships within the I?upiat (Eskimo) hand

On the basis of earlier findings with Easter Islanders suggesting a positive correlation between dermatoglyphic variables and hand anthropometric measurements, the present study was designed to determine if such a relationship could be generalized to another population, namely, I?upiat (Eskimo). Since some dermatoglyphic and anthropometric variables were available for both sides of the body, the extension of this study to explore the question of asymmetry was also possible. The I?upiat sample numbered 142 male and 176 female adult inhabitants of five Alaskan North Slope communities. The major findings of this study included, for males, significant negative correlations between left arm length and digital ridge counts and positive relationships between the palmar variable of axial index and hand length on both hands. For females, the hand breadth/length index was negatively related to most of the digital variables. Very little definitive information regarding the relationship of the asymmetry variables between the two types of measures was ascertained.     

Morphology of Luolishania longicruris (Lower Cambrian,Chengjiang Lagerstätte,SW China) and the phylogenetic relationships within lobopodians

New material of the lobopodian Luolishania longicruris has been recovered from the Lower Cambrian Chengjiang Lagerstätte, southwest China. The specimens throw new light on several morphological features of the species, including the paired antenniform outgrowths, eyes, head shield, setae and other cuticular projections, as well as the differentiated sclerites, appendages, claws, and lobopod interspaces. L. longicruris shows well developed tagmosis: a distinct head and a trunk divided into two sections. The new data allow a revised comparison with other lobopodians. Miraluolishania haikouensis Liu et al., 2004 is considered to be a junior synonym of L. longicruris Hou and Chen, 1989. Evidence from gut filling and specialized morphological characters indicates that L. longicruris may have had a filter feeding lifestyle. A new cladistic analysis suggests that fossil lobopodians are paraphyletic or even polyphyletic and L. longicruris may be an important representative of the stem lineage leading to arthropods.     

Caffeoylquinic acid derivatives from the roots of Arctium lappa L. (burdock) and their structure–activity relationships (SARs) of free radical scavenging activities

Eight caffeoylquinic acid (CQA) derivatives have been identified from the roots of Arctium lappa L. (burdock), including three new derivatives (1–3) together with five known derivatives (4–8). Their chemical structures were determined by 1D and 2D NMR as well as HR-TOF-MS data. The free radical scavenging activities of each compound were determined experimentally and found to be significant, especially the tri-CQA (8) and di-CQAs (6–7). Besides, our data showed that the number of caffeoyl groups in the caffeoyl derivatives played a crucial role for these physiological functions.     

A phylogenetic study of the palm family (Palmae) based on chloroplast DNA sequences from thetrnL —trnF region

Phylogenies of the palm family based on DNA sequences from thetrnL —trnF region of the chloroplast genome are presented. Although the region is highly conserved in palms and relatively few sites in the aligned data matrix are parsimony informative, a variety of relationships among members of the family are revealed by the analyses, some of which are congruent with the current classification of the palms, and others which are not. However, consensus trees contain high levels of ambiguosity, partly due to the inadequate numbers of informative characters in the dataset. Additional data are required before well resolved palm phylogenies can be generated.     

TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations

Seven hundred fifty-two to one thousand ninety-seven base pairs of the trnL intron and trnL–trnF intergenic spacer of the chloroplast DNA of 55 Juncaceae taxa (Juncus, Luzula, Rostkovia, and Oxychloë) was sequenced. Seventeen structural mutations (13 indels marked A to M, 3 parts of the trnF pseudogene, and insertion o within a pseudogene) within the chloroplast trnL–trnF region were examined as possible indicators for phylogenetic relationships in Juncaceae. Juncus trifidus (section Steirochloa) was clearly separated from the other taxa by two large (>80 bp) indels. The Southern Hemisphere clade was strongly supported by a unique insertion (334 bp) in the trnL intron. The monophyly of Luzula was supported by three small (<10 bp) indels in the trnL-F spacer. They were found in all 22 examined members that represent the taxonomic and geographical diversity of the genus Luzula. A tandemly duplicated tRNA pseudogene was found in the Juncus subgenus Juncus species and is supported by four small unique indels too. The acceptor stem and D-domain-encoding regions are separated by a unique 8-bp insertion. The T-domain and acceptor stem-encoding regions were not found in the pseudogene repeats. Only the Juncus sections Ozophyllum and Iridifolii contain the 5 acceptor stem, D-domain, and anticodon domain of the tRNAF encoding DNA. The structural mutations in the trnL intron and the trnL–trnF intergenic spacer are useful for phylogenetic reconstruction in the Juncaceae.     

Purification and characterization of NAD(P)H quinone reductase from the latex of Hevea brasiliensis Müll.-Arg. (Euphorbiaceae)

NAD(P)H quinone reductase [NAD(P)H-QR] present in the latex of Hevea brasiliensis Müll.-Arg. (Euphorbiaceae) was purified to homogeniety from the B-serum fraction obtained by freeze-thawing of the bottom fraction of ultracentrifuged fresh latex. The purification protocol involved acetone fractionation, heat treatment, ion exchange chromatography and affinity chromatography. The M(r) determined by SDS-PAGE for the protein subunit was 21 kDa, and the molecular mass of the native enzyme estimated by gel filtration was 83 kDa, indicating that the native enzyme is a homotetramer. The enzyme showed pH stability over a range of 6 to at least 10 (with an optimum at pH 8) and thermal stability up to 80 degrees C. High NAD(P)H-QR activity (70%) was still retained after 10 h of preincubation at 80 degrees C. A comparable substrate specificity for this enzyme was observed among menadione, p-benzoquinone, juglone, and plumbagin, with only duroquinone generating a lower activity. Positive correlations between latex NAD(P)H-QR activity and rubber yield per tapping [fresh latex (r=0.89, P<0.01), dry rubber (r=0.81, P<0.01)] together with flow time (r=0.85, P<0.01) indicated that enzyme activity could possibly be used as a marker to predict the yield potential of selected clones.     

Cytotoxic constituents from the leaves of Jerusalem artichoke (Helianthus tuberosus L.) and their structure–activity relationships

Bioassay-directed phytochemical study of the Jerusalem artichoke (Helianthus tuberosus L.) leaves led to the isolation of a new sesquiterpene lactone of 3-Hydroxy-8β-tigloyloxy-1,10-dehydroariglovin (1), ten known sesquiterpene lactones (2–11) and two known flavones (12–13). Their chemical structures were elucidated on the basis of NMR (1D and 2D) and mass spectroscopic analysis. The cytotoxic activities of those compounds were subsequently tested against the MCF-7, A549 and HeLa cancer cells lines. The results indicated that sesquiterpene lactones 1–11 exhibited consistent cytotoxicity against all three cancer cell lines, while flavones 12 and 13 showed selective inhibitory activity against HeLa cell lines. Among them, compound 3 exhibited significant growth inhibitory activity against all three cell lines. The IC₅₀ values of compound 3 against MCF-7, A549 and HeLa were 1.97 ± 0.04, 7.79 ± 0.44, 9.87 ± 0.20 μg/ml, respectively. In addition, some structure–activity relationships of these sesquiterpene lactones for cytotoxicity were explored and summarized in this study.     

Studies on copper and cobalt tolerance in three closely related taxa within the genusSilene L. (Caryophyllaceae) from Zaïre

Summary Experiments were carried out on the tolerance to and uptake of copper and cobalt by three members of a phylogenetic series of taxa within the genusSilene from Zaïre which were reputed to represent a progression of increasing adaptation to metalliferous soils. Plants studied were the widespread and presumably non-tolerantSilene burchelli var.angustifolia (B), a more tolerant variant of this taxon (E) designated an ecotype, and the metallophyteS. cobalticola (C). Studies on the effects of both metals, singly and in combination, on seed germination, seedling and plant performance and yield, and metal uptake from soil cultures, confirmed in general the sequence B<E<C in relation to tolerance of both copper and cobalt. The experimental evidence also supports the ecotypic status of E and points to E and C being relatively more tolerant to copper than to cobalt.     

Solution structure of Fe(II)–azide–bleomycin derived from NMR data: transition from Fe(II)–bleomycin to Fe(II)–azide–bleomycin as derived from NMR data and structural calculations

The coordination cage of the metal center in Fe(II)-bleomycin has been proposed to consist of the secondary amines in β-aminoalanine, the pyrimidinylpropionamide and imidazole rings, and the amide nitrogen in β-hydroxyhistidine as equatorial ligands, and the primary amine in β-aminoalanine and either the carbamoyl group in mannose or a solvent molecule occupying the axial sites. With the aim of supporting or not supporting coordination of a water molecule to the metal center in Fe(II)-bleomycin, the solution structure of Fe(II)-azide-bleomycin has been derived from NMR data. The structural changes that occur in Fe(II)-bleomycin upon azide binding have been monitored by comparing the experimental results with those obtained from the calculated structures for both bleomycin adducts. The results of this investigation strongly support a model of Fe(II)-bleomycin with six endogenous ligands as the most likely structure held in solution by this metallobleomycin in the absence of DNA.     

Length–weight relationships for some plecoptera and ephemeroptera from a carbonate stream in central Apennine (Italy)

The relationship between dry weight and body length for larvae of Plecoptera (Leuctra spp., Isoperla grammatica, Nemoura cinerea) and Ephemeroptera (Baetis spp., Habrophlebia fusca, Paraleptophlebia submarginata, Ecdyonurus helveticus, Rhithrogena semicolorata), collected from a carbonate stream in the Apennine (central Italy), is reported. The power equation f(x) = Ax ^B has been applied to fit the curves of dry weight vs. body size (length) in the ranges 0.03–13.00 mg and 2–14 mm, respectively; a total of 674 larvae were examined. The power model was in very good agreement with experimental data. Moreover, the error between measured and estimated weight was in the 4–20% range. The data on Isoperla grammatica, Leuctra spp., Rhithrogena semicolorata and Baetis spp. were compared to those in a previous study in a different geographical setting (south-western Germany’s Black Forest) obtaining similar results but with lower errors. We used and compared two methods: the weighted least-square method (WLS) and an analysis of covariance (ANCOVA). The values of the A and B coefficients obtained with the two methods were very similar (<6% discrepancy for either A or B). We found the best fits for all the examined Plecoptera (species, genus, and order level), while the results for Ephemeroptera were varied, with loose fits at the order level and also for Leptophlebiidae collectively considered. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: R. Bailey     

Nucleotide and derived amino acid sequence of the cyanogenic β-glucosidase (linamarase) from white clover (Trifolium repens L.)

The nucleotide sequence and derived amino acid sequence of two different -glucosidase cDNA clones were determined. One clone (TRE104) was identified as the cyanogenic -glucosidase by homology with the N-terminal and internal peptide amino acid sequence of the purified enzyme. The biological function of the other -glycosidase (TRE361) is not known. Co-segregation of genomic restriction fragments uniquely identified by each cDNA clone shows that these two genes are linked in the white clover genome. Both TRE104 and TRE361 fragments co-segregate with cyanogenic -glucosidase activity. Extensive homology was found between the white clover -glucosidase sequences and a group of prokaryote and mammalian -glycosidases. This group of sequences has no homology with a separate set of -glucosidase genes isolated from fungi and the thermophilic bacterium Clostridium thermocellum.     

Cloning and nucleotide sequence of the α-galactosidase cDNA from Cyamopsis tetragonoloba (guar)

Polyadenylated mRNA was purified from the aleurone cells of Cyamopsis tetragonoloba (guar) seeds germinated for 18 h and used for the construction of a cDNA library. Clones with the -galactosidase encoding gene were identified using oligo-nucleotide mixed probes based on the NH₂ terminal amino acid sequence and on the sequence of an internal peptide. The nucleotide sequence of the cDNA clone showed that the enzyme is synthesized as a precursor with a 47 amino acid NH₂ terminal extension. This pre-sequence most likely functions to target the protein outside the aleurone cells into the endosperm. Based upon structural features, it is proposed to divide the precursor into a pre-(signal sequence) part and a glycosylated pro-part comparable with those of the yeast mat A/ factor and killer factor. A comparison of the derived amino acid sequence of this -galactosidase from plant origin revealed significant stretches of homology with respect to the amino acid sequences of the enzymes from Saccharomyces cerevisiae and from human origin but only to a minor extent compared with the -galactosidase from Escherichia coli.     

Isozyme variation and species relationships in peanut and its wild relatives (Arachis L. — Leguminosae)

Summary Arachis hypogaea (peanut or groundnut) is an AABB allotetraploid whose precise ancestry is not yet clear. Its closest diploid relatives are the annual and perennial wild species included with it in the section Arachis. Variation in these species for 11 different enzymes was studied by starch-gel electrophoresis. Differences attributed to at least 13 genetic loci were found among eight enzymes, while three enzymes appeared uniform throughout the section. Values for Nei's genetic distance were calculated for all pairs of species and were used to estimate relationships. All diploid species, apart from two whose validity had previously been questioned, could be distinguished by their overall zymotypes, but few contained unique alleles. When species were grouped by their mean genetic distances, they formed two clusters, which agreed reasonably well with the division of the section into annual versus perennial species. The single B-genome species was an outlier within the annual group. A. hypogaea showed fixed heterozygosity at four loci (in ssp. hypogaea) or six loci (in ssp. fastigiata), which agrees with previous conclusions that the peanut is an allotetraploid. None of the diploids included in this survey could be conclusively identified as donors of either the A or the B genome to the tetraploids. The two subspecies of A. hypogaea differed consistently in two of the thirteen putative loci studied. This may call into question the simple hypothesis that A. hypogaea originated from just two diploid species.     

Are spurred cyathia a key innovation? Molecular systematics and trait evolution in the slipper spurges (Pedilanthus clade: Euphorbia, Euphorbiaceae)

The study of traits that play a key role in promoting diversification is central to evolutionary biology. Floral nectar spurs are among the few plant traits that correlate with an enhanced rate of diversification, supporting the claim that they are key innovations. Slight changes in spur morphology could confer some degree of premating isolation, explaining why clades with spurs tend to include more species than their spurless close relatives. We explored whether the cyathial nectar spur of the Pedilanthus clade (Euphorbia) may also function as a key innovation. We estimated the phylogeny of the Pedilanthus clade using one plastid (matK) and three nuclear regions (ITS and two G3pdh loci) and used our results and a Yule model of diversification to test the hypothesis that the cyathial spur correlates with an increased diversification rate. We found a lack of statistical support for the key innovation hypothesis unless specific assumptions regarding the phylogeny apply. However, the young age (hence small size) of the group may limit our ability to detect a significant increase in diversification rate. Additionally, our results confirm previous species designations, indicate higher homoplasy in cyathial than in vegetative features, and suggest a possible Central American origin of the group.