Diversity of extinct and living actinistian fishes (Sarcopterygii)

Synopsis A total of 121 actinistian species belonging to 47 genera and 17 undetermined actinistians is reported from the literature. There are 69 valid species with fair assessment of their phylogenetic position; 21 valid species with poor assessment of their phylogenetic position; 31 actinistian incertae sedis; and 18 taxa that had been identified incorrectly as actinistians or are nomen nuda. The fossil record of the actinistians covers a history of approximately 380 million years. The greatest diversity occurred during the Scythian (Early Triassic).     

Evolution of myosin filament arrangements in vertebrate skeletal muscle

A survey of skeletal muscles throughout craniates shows basic kinds of myosin filament arrangement, simple-lattice and superlattice, within the A-band of each sarcomere. Distribution of simple- and superlattice arrangements across a phylogeny of craniates suggests that the superlattice arrangement is primitive and that Amia and teleosts are derived in showing simple-lattice arrangements. Two taxa examined (Scyliorhinus and Acipenser) show both lattice types within the same organism implying that there is not a simple evolutionary transformation of one to the other fiber arrangement. We discuss the possible functional significance of the different lattice types. We believe that the crossbridges may have greater competition for actin binding sites in simple-lattice muscles compared to the superlattice types. © 1996 Wiley-Liss, Inc.     

Taxonomy and fossils: a critical appraisal

Many compendia at the species, genus and family levels document the fossil record, but these are not standardized, nor usually critical in content, and few are available on the World Wide Web. The sampling of the available record is good for organisms with fossilizable parts, but preservational constraints on the entire morphology, life history and geographical distribution lead to difficulties in recognizing and naming species. We recommend abandoning some of the palaeontological species concepts such as chronospecies and stratospecies, and we advocate species recognition based on unique combinations of characters. The compilation of species lists is extremely time consuming, and given the inherent problems we suggest that compilation of generic lists is a more achievable goal because genera are recognized by definitive morphological characters. In calculating taxon duration, care must be taken to distinguish between mono-, para- and polyphyletic groups, the first being the only reliable unit for use in calculating diversity curves. We support the inclusion of fossils into classifications based on Recent organisms, but we recognize some of the problems this may pose for standard Linnaean classifications. Web-based taxonomy is the way forward, having the advantages of speed and currency of information dissemination, universal access with links to primary literature and increasingly sophisticated imagery. These advantages over conventional outlets will only be realized with careful Web design and a commitment to maintenance.     

Systematic review with meta-analysis of the epidemiological evidence relating smoking to COPD, chronic bronchitis and emphysema

Background

Smoking is a known cause of the outcomes COPD, chronic bronchitis (CB) and emphysema, but no previous systematic review exists. We summarize evidence for various smoking indices.

Methods

Based on MEDLINE searches and other sources we obtained papers published to 2006 describing epidemiological studies relating incidence or prevalence of these outcomes to smoking. Studies in children or adolescents, or in populations at high respiratory disease risk or with co-existing diseases were excluded. Study-specific data were extracted on design, exposures and outcomes considered, and confounder adjustment. For each outcome RRs/ORs and 95% CIs were extracted for ever, current and ex smoking and various dose response indices, and meta-analyses and meta-regressions conducted to determine how relationships were modified by various study and RR characteristics.

Results

Of 218 studies identified, 133 provide data for COPD, 101 for CB and 28 for emphysema. RR estimates are markedly heterogeneous. Based on random-effects meta-analyses of most-adjusted RR/ORs, estimates are elevated for ever smoking (COPD 2.89, CI 2.63-3.17, n = 129 RRs; CB 2.69, 2.50-2.90, n = 114; emphysema 4.51, 3.38-6.02, n = 28), current smoking (COPD 3.51, 3.08-3.99; CB 3.41, 3.13-3.72; emphysema 4.87, 2.83-8.41) and ex smoking (COPD 2.35, 2.11-2.63; CB 1.63, 1.50-1.78; emphysema 3.52, 2.51-4.94). For COPD, RRs are higher for males, for studies conducted in North America, for cigarette smoking rather than any product smoking, and where the unexposed base is never smoking any product, and are markedly lower when asthma is included in the COPD definition. Variations by sex, continent, smoking product and unexposed group are in the same direction for CB, but less clearly demonstrated. For all outcomes RRs are higher when based on mortality, and for COPD are markedly lower when based on lung function. For all outcomes, risk increases with amount smoked and pack-years. Limited data show risk decreases with increasing starting age for COPD and CB and with increasing quitting duration for COPD. No clear relationship is seen with duration of smoking.

Conclusions

The results confirm and quantify the causal relationships with smoking.     

RAD51 and Breast Cancer Susceptibility: No Evidence for Rare Variant Association in the Breast Cancer Family Registry Study

Background

Although inherited breast cancer has been associated with germline mutations in genes that are functionally involved in the DNA homologous recombination repair (HRR) pathway, including BRCA1, BRCA2, TP53, ATM, BRIP1, CHEK2 and PALB2, about 70% of breast cancer heritability remains unexplained. Because of their critical functions in maintaining genome integrity and already well-established associations with breast cancer susceptibility, it is likely that additional genes involved in the HRR pathway harbor sequence variants associated with increased risk of breast cancer. RAD51 plays a central biological function in DNA repair and despite the fact that rare, likely dysfunctional variants in three of its five paralogs, RAD51C, RAD51D, and XRCC2, have been associated with breast and/or ovarian cancer risk, no population-based case-control mutation screening data are available for the RAD51 gene. We thus postulated that RAD51 could harbor rare germline mutations that confer increased risk of breast cancer.

Methodology/Principal Findings

We screened the coding exons and proximal splice junction regions of the gene for germline sequence variation in 1,330 early-onset breast cancer cases and 1,123 controls from the Breast Cancer Family Registry, using the same population-based sampling and analytical strategy that we developed for assessment of rare sequence variants in ATM and CHEK2. In total, 12 distinct very rare or private variants were characterized in RAD51, with 10 cases (0.75%) and 9 controls (0.80%) carrying such a variant. Variants were either likely neutral missense substitutions (3), silent substitutions (4) or non-coding substitutions (5) that were predicted to have little effect on efficiency of the splicing machinery.

Conclusion

Altogether, our data suggest that RAD51 tolerates so little dysfunctional sequence variation that rare variants in the gene contribute little, if anything, to breast cancer susceptibility.     

Multi-scale phylogenetic structure in coastal dune plant communities across the globe

Aims Studies integrating phylogenetic history and large-scale community assembly are few, and many questions remain unanswered. Here, we use a global coastal dune plant data set to uncover the important factors in community assembly across scales from the local filtering processes to the global long-term diversification and dispersal dynamics. Coastal dune plant communities occur worldwide under a wide range of climatic and geologic conditions as well as in all biogeographic regions. However, global patterns in the phylogenetic composition of coastal dune plant communities have not previously been studied.Methods The data set comprised vegetation data from 18463 plots in New Zealand, South Africa, South America, North America and Europe. The phylogenetic tree comprised 2241 plant species from 149 families. We calculated phylogenetic clustering (Net Relatedness Index, NRI, and Nearest Taxon Index, NTI) of regional dune floras to estimate the amount of in situ diversification relative to the global dune species pool and evaluated the relative importance of land and climate barriers for these diversification patterns by geographic analyses of phylogenetic similarity. We then tested whether dune plant communities exhibit similar patterns of phylogenetic structure within regions. Finally, we calculated NRI for local communities relative to the regional species pool and tested for an association with functional traits (plant height and seed mass) thought to vary along sea–inland gradients.Important findings Regional species pools were phylogenetically clustered relative to the global pool, indicating regional diversification. NTI showed stronger clustering than NRI pointing to the importance of especially recent diversifications within regions. The species pools grouped phylogenetically into two clusters on either side of the tropics suggesting greater dispersal rates within hemispheres than between hemispheres. Local NRI plot values confirmed that most communities were also phylogenetically clustered within regions. NRI values decreased with increasing plant height and seed mass, indicating greater phylogenetic clustering in communities with short maximum height and good dispersers prone to wind and tidal disturbance as well as salt spray, consistent with environmental filtering along sea–inland gradients. Height and seed mass both showed significant phylogenetic signal, and NRI tended to correlate negatively with both at the plot level. Low NRI plots tended to represent coastal scrub and forest, whereas high NRI plots tended to represent herb-dominated vegetation. We conclude that regional diversification processes play a role in dune plant community assembly, with convergence in local phylogenetic community structure and local variation in community structure probably reflecting consistent coastal-inland gradients. Our study contributes to a better understanding of the globally distributed dynamic coastal ecosystems and the structuring factors working on dune plant communities across spatial scales and regions.     

The relative importance of disturbance and environmental stress at local and regional scales in French coastal sand dunes

Questions: 1. Is there a primary role of disturbance at local scale and of environmental stress at regional scale? 2. Does disturbance increase or decrease environmental stress at local scale? Location: The Atlantic coastal dune system of the Aquitaine Region (France). Methods: Species biomass and 16 environmental variables were sampled in 128 quadrats along a local beach‐inland gradient and a regional North‐South gradient. Environmental data were analysed with ANOVAs and vegetation‐environment relationships with Canonical Correspondence Analysis. Results: At the local scale community composition was primarily driven by disturbance due to sand burial, whereas water and nutrient stress better explained regional differences. However, random biogeographical events are very likely to also affect community composition at the largest scale. The main interaction between environmental stress and disturbance was the mitigation of nutrient stress induced by disturbance at a local scale. This was due to a positive direct effect of sand burial and a positive indirect effect of wind (decrease in VPD by ocean spray). Although wind had also a significant effect on soil conductivity and pH, there was no evidence that these factors had any role in community composition. Conclusions: Our results support the hypothesis that disturbance had a primary role at local scale and environmental stress at regional scale but further research is needed to separate the effect of stress from that of dispersal at regional scale. We also demonstrated that environmental stress in primary succession may not always decline with decreasing disturbance.     

A fossil clupeomorph fish from the Albian of the Northwest Territories of Canada, with notes on cladistic relationships of clupeomorphs

A primitive clupeomorph, Erichalcis arcta gen. et sp. nov. is described from the Albian of Northwest Territories, Canada. Erichalcis is uniquely specialized among clupeomorphs in the presence of enlarged lateral line scales and in the structure of the caudal skeleton. Erichalcis is classified as Clupeiformes incertae sedis. The two recognized suborders, Clupeoidei and Denticipitoidei are examined with respect to primitive and derived character states. It is concluded that the clupeoids and denticipitoids are divergently specialized in details of the union between the supraorbital and infraorbital sensory canals and the recessus lateralis. It is further suggested that the reduction in size and the posterior shift of the dermosphenotic in clupeoids is correlated with an upper division of the levator arcus palatini muscle and an antero-dorsal process on the hyomandibular. Cladistic relationships of some Cretaceous clupeomorphs are proposed and it is suggested that Diplomystus brevissimus Cope not be included in the Clupeoidei.