Antialgal ent-labdane diterpenes from Ruppia maritima

Seven ent-labdane diterpenes have been isolated from Ruppia maritima. The structures 15,16-epoxy-ent-labda-8(17),13(16),14-trien-19-al; 15,16-epoxy-ent-labda-8(17),13(16),14-trien-19-ol acetate; methyl 15,16-epoxy-12-oxo-ent-labda-8(17),13(16),14-trien-19-oate; 15,16-epoxy-ent-labd-8(17),13E-dien-15-ol and 13-oxo-15,16-bis-nor-ent-labd-8(17)-ene have been assigned to the five new compounds by spectroscopic means and chemical correlations. The phytotoxicity of the diterpenes has been assessed using the alga Selenastrum capricornutum as organism test.     

Waterbird impacts on widgeongrass Ruppia maritima in a Mediterranean wetland: comparing bird groups and seasonal effects

We studied the effect of waterbirds on the submerged macrophyte Ruppia maritima in eleven fish ponds within Doñana Natural Park (SW Spain). Separate exclosure designs allowed us to exclude flamingos or all waterbirds from 3×3 m plots within the ponds and compare them with control plots. Four experiments were conducted for three month periods at different points of the annual cycle with varying bird densities. Flamingos and wildfowl (ducks and coot) had significant negative additive effects on the presence of aboveground (leafs and shoots) or belowground (roots) parts of Ruppia at all times of the year. For plots where Ruppia was present, aboveground biomass was significantly higher in all-bird exclosures than in controls or flamingo exclosures. Presence and biomass of this annual plant varied significantly between seasons as did the density of seeds in sediments. Seasonal changes in seedbank densities were consistent with consumption by birds. There were no significant treatment×season interactions for Ruppia presence, aboveground biomass or seeds. This is the first exclosure study to compare the effects of waterbirds on submerged macrophytes at different times throughout the annual cycle, and the first to compare simultaneously the effects of different bird groups. Our findings refute previous suggestions that major effects of waterbirds are limited to temperate regions and to periods of early growth or when major concentrations of migratory wildfowl are formed in autumn. Flamingos are important in structuring shallow wetlands in the Mediterranean, and possibly many other regions.     

Structural characteristics of a diatom community epiphytic on Ruppia maritima

Epiphytic diatoms were collected from both the leaves and internodes of Ruppia maritima in a New Jersey salt marsh during the growing season of the host plant. Community diversity (H and the number of diatom taxa) values were initially high as Ruppia began its growth, but quickly dropped to sustained low levels as vegetative growth of the host ceased and new attachment sites were no longer available. A critical examination of all structural characteristics indicated that the leaves and internodes of Ruppia support a single, nearly homogeneous epiphytic diatom community. An analysis of variance indicated that differences between leaves and internodes were minimal, as did a comparison of the assemblages present on these two sites by a selected similarity index. A total of 57 taxa were encountered and the single dominant taxon was Navicula pavillardi, which accounted for one out of every three individuals counted. A comparison of the epiphytic diatom community with those inhabiting the sediments on the marsh proper revealed that the marsh sediments were the major source of individuals for Ruppia colonization.     

Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling

Background

Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study).

Methodology/Principal Findings

We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial.

Conclusions

We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.     

可溶性无机氮在川蔓藻组织中的累积规律

近20年来,由于稳定性同位素无放射性、无污染、不受环境条件限制、无衰变且实验时间不受限制等优点,使稳定性同位素示踪方法作为一种了解复杂生态过程的工具,得到了广泛的应用[1-7].     

Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists

Abstract:  As phylogenetic analyses become larger, one of the greatest methodological difficulties is representing speciose supraspecific clades in higher-level analyses (e.g. trilobites within studies of arthropod phylogeny). Several strategies have been proposed, including using representative single composite terminals or species-level exemplars, and various methods are currently used in the palaeontological literature. However, this is problematic, as simulation studies and empirical arguments in the systematics literature have clearly identified multiple exemplars as the optimal method. The continuing usage of suboptimal strategies in palaeontology may lessen the accuracy of phylogenies and hampers comparison between alternative studies. Here, I outline problems with suboptimal strategies, review arguments in support of multiple exemplars and provide guidelines for palaeontologists undertaking higher-level phylogenetic analyses.     

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. AVAILABILITY: icwww.epfl.ch/~stamatak     

Shoot demography and morphology of Zostera japonica and Ruppia maritima from British Columbia,Canada

Shoot dynamics and morphology were studied in co-occuring intertidal populations of Zostera japonica Aschers. and Graebn. and Ruppia maritima L. s.l. in southwestern British Columbia. Repeated mapping and examination of cohorts of shoots (ramets) in permanent plots on a gradient in elevation showed that the appearance and loss of shoots, age structure, survivorship and leaf and rhizome dimensions were all affected by position on the gradient. For both species, the area having the greatest exposure t o air had fewer shoots and a greater percentage of shoots flowering early in the season. The duration of vegetative growth in R. maritima was the same regardless of elevation, while plants of Z. japonica at high elevation initiated and ended flowering and entered a quiescent overwintering state earlier than plants at lower elevation.     

沉水植物川蔓藻的生态学特征及其对环境变化的响应

川蔓藻是近海生态系统中重要的初级生产者, 了解它的生态学特征对于河口海岸带的生态修复具有重要意义。本文结合我们在天津滨海湿地生态修复工程中对于川蔓藻的研究成果, 从以下几个方面探讨了川蔓藻的生态学特征及其与环境的关系: 川蔓藻对极端环境因子的适应; 川蔓藻在资源分配上的繁殖策略; 川蔓藻的矿质营养代谢以及对栖息地生物地球化学循环的影响; 川蔓藻种群衰退的原因; 川蔓藻在环境修复中的应用。其中着重讨论了川蔓藻对环境变化的响应, 并结合我们的研究工作展望了它在环境工程与近岸水体修复中的应用潜力。     

沉水植物川蔓藻的生态学特征及其对环境变化的响应

川蔓藻是近海生态系统中重要的初级生产者,了解它的生态学特征对于河口海岸带的生态修复具有重要意义。本文结合我们在天津滨海湿地生态修复工程中对于川蔓藻的研究成果,从以下几个方面探讨了川蔓藻的生态学特征及其与环境的关系：川蔓藻对极端环境因子的适应;川蔓藻在资源分配上的繁殖策略;川蔓藻的矿质营养代谢以及对栖息地生物地球化学循环的影响;川蔓藻种群衰退的原因;川蔓藻在环境修复中的应用。其中着重讨论了川蔓藻对环境变化的响应,并结合我们的研究工作展望了它在环境工程与近岸水体修复中的应用潜力。     

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.     

Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers

Nuclear introns are increasingly used as phylogenetic markers. Here, we present a multidisciplinary approach towards optimal locus selection and amplification using Asian pitvipers as an example of a non‐model taxon, and raise the profile of length variant heterozygotes (LVHs) in intron loci. Taxon‐specific primers were identified using a bioinformatic approach, and also designed from existing exon primed, intron crossing (EPIC) primer amplifications. Eleven further universal EPIC primer pairs were assayed using a range of PCR optimization strategies. Taxon‐specific primers yielded the most consistent amplifications, but assaying a large number of universal EPIC primers yielded another appropriate locus for phylogenetic purposes. Modified Taq DNA polymerases such as JumpStart?Taq either significantly improved the specificity and yield of EPIC PCR amplifications (of low copy number nuclear targets), or resulted in amplifications that were not significantly worse than those derived from a generic Taq DNA polymerase. Finally, LVHs were detected in all loci that were sequenced suggesting that they are relatively common in introns. This study provides an efficient and cost effective template for the successful identification of intron markers for molecular systematics which is universally applicable to other non‐model taxon groups. © The Willi Hennig Society 2005.     

Stochastic models for phylogenetic trees on higher-order taxa

Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of higher-order taxa. A coherent model for trees on (say) genera should involve both a species-level model and a model for the classification scheme by which species are assigned to genera. We present a general framework for such models, and describe three alternate classification schemes. Combining with the species-level model of Aldous and Popovic (Adv Appl Probab 37:1094–1115, 2005), one gets models for higher-order trees, and we initiate analytic study of such models. In particular we derive formulas for the lifetime of genera, for the distribution of number of species per genus, and for the offspring structure of the tree on genera. David Aldous’s research was supported by NSF Grant DMS-0704159.     

Comprehensive phylogenetic reconstruction of amoebozoa based on concatenated analyses of SSU-rDNA and actin genes

Evolutionary relationships within Amoebozoa have been the subject of controversy for two reasons: 1) paucity of morphological characters in traditional surveys and 2) haphazard taxonomic sampling in modern molecular reconstructions. These along with other factors have prevented the erection of a definitive system that resolves confidently both higher and lower-level relationships. Additionally, the recent recognition that many protosteloid amoebae are in fact scattered throughout the Amoebozoa suggests that phylogenetic reconstructions have been excluding an extensive and integral group of organisms. Here we provide a comprehensive phylogenetic reconstruction based on 139 taxa using molecular information from both SSU-rDNA and actin genes. We provide molecular data for 13 of those taxa, 12 of which had not been previously characterized. We explored the dataset extensively by generating 18 alternative reconstructions that assess the effect of missing data, long-branched taxa, unstable taxa, fast evolving sites and inclusion of environmental sequences. We compared reconstructions with each other as well as against previously published phylogenies. Our analyses show that many of the morphologically established lower-level relationships (defined here as relationships roughly equivalent to Order level or below) are congruent with molecular data. However, the data are insufficient to corroborate or reject the large majority of proposed higher-level relationships (above the Order-level), with the exception of Tubulinea, Archamoebae and Myxogastrea, which are consistently recovered. Moreover, contrary to previous expectations, the inclusion of available environmental sequences does not significantly improve the Amoebozoa reconstruction. This is probably because key amoebozoan taxa are not easily amplified by environmental sequencing methodology due to high rates of molecular evolution and regular occurrence of large indels and introns. Finally, in an effort to facilitate future sampling of key amoebozoan taxa, we provide a novel methodology for genome amplification and cDNA extraction from single or a few cells, a method that is culture-independent and allows both photodocumentation and extraction of multiple genes from natural samples.     

Glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima: molecular characterization and phylogenetic implications

The hyperthermophilic bacterium Thermotoga maritima, which grows at up to 90°C, contains an L-glutamate dehydrogenase (GDH). Activity of this enzyme could be detected in T. maritima crude extracts, and appeared to be associated with a 47-kDa protein which cross-reacted with antibodies against purified GDH from the hyperthermophilic archaeon Pyrococcus woesei. The single-copy T. maritima gdh gene was cloned by complementation in a glutamate auxotrophic Escherichia coli strain. The nucleotide sequence of the gdh gene predicts a 416-residue protein with a calculated molecular weight of 45852. The gdh gene was inserted in an expression vector and expressed in E. coli as an active enzyme. The T. maritima GDH was purified to homogeneity. The NH₂-terminal sequence of the purified enzyme was PEKSLYEMAVEQ, which is identical to positions 2–13 of the peptide sequence derived from the gdh gene. The purified native enzyme has a size of 265 kDa and a subunit size of 47 kDa, indicating that GDH is a homohexamer. Maximum activity of the enzyme was measured at 75°C and the pH optima are 8.3 and 8.8 for the anabolic and catabolic reaction, respectively. The enzyme was found to be very stable at 80°C, but appeared to lose activity quickly at higher temperatures. The T. maritima GDH shows the highest rate of activity with NADH (V _max of 172U/mg protein), but also utilizes NADPH (V _max of 12U/mg protein). Sequence comparisons showed that the T. maritima GDH is a member of the family II of hexameric GDHs which includes all the GDHs isolated so far from hyperthermophiles. Remarkably, phylogenetic analysis positions all these hyperthermophilic GDHs in the middle of the GDH family II tree, with the bacterial T. maritima GDH located between that of halophilic and thermophilic euryarchaeota. Received: 15 July 1996 / Accepted: 12 October 1996     

Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences

A biogeographic study of Saxifraga section Saxifraga was performed based on phylogenetic analyses of ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. ITS sequences from 21 species and 31 populations were examined to identify colonization patterns for the two species of Saxifraga occurring in Macaronesia and for S. globulifera in the west Mediterranean basin. Phylogenetic analysis of the sequence data yield a single most parsimonious tree with many of the major clades well supported by bootstrap and decay values. The ITS tree provided resolution at specific and populational levels that points to two biogeographic patterns within the genus. In contrast to the molecular evidence provided by other authors for a Mediterranean origin of several Macaronesian genera of angiosperms, our results indicate that the Madeiran archipelago was colonized a single time by a species of Saxifraga originating from the Eurosiberian region. On the other hand, the molecular evidence also suggests that populations of S. globulifera from North Africa have been isolated for a long time from populations occurring in the Iberian Peninsula, and that the endemic S. reuteriana has evolved from the Iberian populations of S. globulifera. The Mediterranean Sea has probably been an effective isolating barrier for some plant groups that occur in Europe and North Africa.     

Molecular phylogenetic analyses indicate that the Ixodes ricinus complex is a paraphyletic group

The Ixodes ricinus species complex is a group of ticks distributed in almost all geographic regions of the world. Lyme borreliosis spirochetes are primarily transmitted by tick species within this complex. It has been hypothesized that the Lyme vector ticks around the world are closely related and represent a monophyletic group. This implies that vector competence in ixodid ticks for Lyme agents might have evolved only once. To test this hypothesis, we used a molecular phylogenetic approach. Two fragments of mitochondrial 16S ribosomal deoxyribonucleic acid were sequenced from 11 species in the I. ricinus complex and from 16 other species of Ixodes. Phylogenetic analysis using Bayesian methodology indicated that the I. ricinus complex is not a monophyletic group unless 3 additional Ixodes species are included in it. The known major vectors of Lyme disease agents in different areas of the world are not sister taxa. This suggests that acquisition of the ability to transmit borreliosis agents in species of Ixodes may have multiple origins.