Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences

A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early‐branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi‐sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well‐supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well‐supported eudicot clade, the early‐diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well‐supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal‐level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data.     

Colony-Site Selection Drives Management Priorities for Yelkouan Shearwater Populations

Abstract: We tested whether colony-site availability could allow for an increase in the unusually small breeding populations of yelkouan shearwater (Puffinus yelkouan) on the islands of the Port-Cros National Park (France) if feral cat eradication were undertaken. Comparisons between colony and noncolony sites indicated yelkouan shearwaters preferred deep-soiled and low-outcrop-covered coastal sites. A substrate cover, light avoidance, and sea proximity model suggested that 17.5% of unoccupied sites are suitable for colony establishment. The low proportion of suitable sites currently used by yelkouan shearwaters suggests that these colonies could be refuges and that feral cat eradication will probably lead to a breeding population increase.     

SYSTEMATIC NOTES (Part I)

Declines in populations of Palearctic migrants wintering in the Sahel of Africa have been linked to the impacts of climate change and habitat degradation in the region. Despite this, there is an almost complete lack of data on the density and distribution of Palearctic migrants wintering in the Sahel and whether they have the same habitat requirements as similar, resident Afrotropical species. We measured the density of five species of Palearctic warblers (Sylviidae) and 10 species of Afrotropical gleaning passerines (Sylviidae, Nectariniidae, Malaconotidae and Ploceidae) at 16 sites in the Sahel of northern Nigeria between October and April during two winters. Two species of Afrotropical gleaner (Hippolais pallida and Ploceus luteolus) showed seasonal variation in abundance, but this variation was unlikely to have decreased Afrotropical densities sufficiently to change the degree of competition experienced by Palearctic migrants. This observation, combined with a positive correlation between abundances of Afrotropical and Palearctic species, suggests that these two groups occur together and have similar spatial and temporal habitat requirements, and therefore possibly similar responses to habitat degradation. Sylvia communis appears to be the principal species utilising the region during spring migration, presumably for fattening prior to the trans-Saharan crossing, and is thus perhaps the most vulnerable species to habitat loss in the region.     

Effects of age,territoriality and breeding on survival of Bonelli’s Eagle Aquila fasciata

Survival typically contributes most to population trends in long‐lived birds and its accurate estimation is therefore vital for population management and conservation. We evaluated the effects of age, territoriality and reproduction on survival in Bonelli’s Eagle Aquila fasciata through multistate capture‐mark‐recapture analyses on a long‐term dataset. Monitoring was carried out in southeast France (1990–2008) and involved the surveying of territorial Eagles, the marking of fledged chicks, and the recording of resightings and recoveries of marked non‐territorial and territorial birds. Survival improved with age, but territoriality was not retained in the best model; yearly survival was estimated at 0.479 for fledglings (to 1 year of age), 0.570 for 1‐ and 2‐year‐olds, and 0.870 for 3‐year‐old and older individuals. The second best model supported a further increase in survival from 3‐year‐olds (0.821) to older individuals (0.880). In the third best supported model, territoriality enhanced survival, but only in 2‐year‐olds (0.632 vs. 0.562 for non‐territorial). We found no correlation between the previous breeding stage and future survival, consistent with the long lifespan of the study species. Nevertheless, 4‐year‐old and older successful breeders were more likely to breed the following year than failed adult breeders (0.869 vs. 0.582), suggesting that the cost of reproduction is small in comparison with the variation in quality among individuals or their territories.     

A NEW PCR METHOD OF CHARACTERIZING SEAFISH FRESHNESS

Objective criteria used to assess the fish freshness in the laboratory are currently inadequate. During contamination of muscle tissue, bacteria reduce trimethylamine oxide (TMAO) to trimethylamine (TMA) in the absence of oxygen. Based on this reaction, we envisaged a new approach and have developed and optimized a PCR method which targets the tor A gene sequence that encodes TMAO reductase. We applied this method to two fish species (Whiting (Merlangus merlangus) and Pouting (Gadus luscus)) during monitoring of spoilage, in parallel with assay of TVBN and enumeration of total aerobic flora. The PCR results tally with the chemical and microbiological findings. Used in quantitative PCR, this method could characterize fish freshness.     

Inactivation of thioredoxin f1 leads to decreased light activation of ADP‐glucose pyrophosphorylase and altered diurnal starch turnover in leaves of Arabidopsis plants

Chloroplast thioredoxin f (Trx f) is an important regulator of primary metabolic enzymes. However, genetic evidence for its physiological importance is largely lacking. To test the functional significance of Trx f in vivo, Arabidopsis mutants with insertions in the trx f1 gene were studied, showing a drastic decrease in Trx f leaf content. Knockout of Trx f1 led to strong attenuation in reductive light activation of ADP‐glucose pyrophosphorylase (AGPase), the key enzyme of starch synthesis, in leaves during the day and in isolated chloroplasts, while sucrose‐dependent redox activation of AGPase in darkened leaves was not affected. The decrease in light‐activation of AGPase in leaves was accompanied by a decrease in starch accumulation, an increase in sucrose levels and a decrease in starch‐to‐sucrose ratio. Analysis of metabolite levels at the end of day shows that inhibition of starch synthesis was unlikely due to shortage of substrates or changes in allosteric effectors. Metabolite profiling by gas chromatography–mass spectrometry pinpoints only a small number of metabolites affected, including sugars, organic acids and ethanolamine. Interestingly, metabolite data indicate carbon shortage in trx f1 mutant leaves at the end of night. Overall, results provide in planta evidence for the role played by Trx f in the light activation of AGPase and photosynthetic carbon partitioning in plants.     

Systematics of the Soft-plumaged Petrel Pterodroma mollis (Procellariidae): new insight from the study of vocalizations

The taxonomic status of the populations of the polytypic Soft-plumaged Petrel Pterodroma mollis is controversial. Previous taxonomic studies used morphological characters (measurements and colouration) and univariate statistics. In this study, I add the use of multivariate statistics on morphological (biometry and colouration) and behavioural characters (vocalizations) of the petrels. Vocalizations are especially relevant in nocturnal burrowing petrels (such as the Soft-plumaged Petrel) and act as behavioural isolating mechanisms. The analysis, based on 535 calls from seven of the 11 known breeding localities of the species, showed that physical parameters of the call did not overlap at all between breeding localities in the northern and southern hemispheres but did so within each hemisphere. Conversely, the morphological analysis, based on morphometries from ten localities, displayed wide and significant intra-hemisphere variation, whereas there was no consistent difference between northern and southern parts of the breeding range. Thus analysis of the two sets of characters gave contradictory results. Calls, owing to their role in species-specific recognition in these birds, should be given priority over other characters for species separation. I suggest that only two species should be recognized, Pterodroma mollis and Pterodroma feae, with three subspecies each. I also examined behavioural affinities between P. mollislfeae groups and other gadfly petrels and found that P. mollis/feae were closest to Pterodroma cahow, whilst Pterodroma hasitata on the one hand and Pterodroma phaeopygia and Pterodroma externa (which may comprise two species instead of one) on the other belong to other groups of gadfly petrels.