Seed survival and dispersal of an endemic Atlantic forest palm: the combined effects of defaunation and forest fragmentation

About 45 palm species occur in the Atlantic forest of Brazil, and most of them are affected by loss of seed dispersers resulting from forest fragmentation and hunting. Here we report the effects of habitat loss and defaunation on the seed dispersal system of an endemic palm, Astrocaryum aculeatissimum . We evaluated seed removal, insect and rodent seed predation, and scatter-hoarding in nine sites, ranging from 19 ha to 79 000 ha. We report the seedling, juvenile and adult palm densities in this range of sites. Endocarps remaining beneath the parent palm had a higher probability of being preyed upon by insects in small, mostly fragmented and more defaunated sites. The frequency of successful seed removal, scatter-hoarding and consumption by rodents increased in the larger, less defaunated sites. Successful removal and dispersal collapsed in small (< 1000 ha), highly defaunated sites and frequently resulted in low densities of both seedlings and juveniles. Our results indicate that a large fraction of Atlantic forest palms that rely on scatter-hoarding rodents may become regionally extinct due to forest fragmentation and defaunation. Current management practices including palm extraction and hunting pressure have a lasting effect on Atlantic forest palm regeneration by severely limiting successful recruitment of prereproductive individuals. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 141–149.     

Measurement of molecular diffusion in solution by multiphoton fluorescence photobleaching recovery

Multiphoton fluorescence photobleaching recovery (MP-FPR) is a technique for measuring the three-dimensional (3D) mobility of fluorescent molecules with 3D spatial resolution of a few microns. A brief, intense flash of mode-locked laser light pulses excites fluorescent molecules via multiphoton excitation in an ellipsoidal focal volume and photobleaches a fraction. Because multiphoton excitation of fluorophores is intrinsically confined to the high-intensity focal volume of the illuminating beam, the bleached region is restricted to a known, three-dimensionally defined volume. Fluorescence in this focal volume is measured with multiphoton excitation, using the attenuated laser beam to measure fluorescence recovery as fresh unbleached dye diffuses in. The time course of the fluorescence recovery signal after photobleaching can be analyzed to determine the diffusion coefficient of the fluorescent species. The mathematical formulas used to fit MP-FPR recovery curves and the techniques needed to properly utilize them to acquire the diffusion coefficients of fluorescently labeled molecules within cells are presented here. MP-FPR is demonstrated on calcein in RBL-2H3 cells, using an anomalous subdiffusion model, as well as in aqueous solutions of wild-type green fluorescent protein, yielding a diffusion coefficient of 8.7 x 10(-7) cm(2)s(-1) in excellent agreement with the results of other techniques.     

Zea systematics: ribosomal ITS evidence

Ribosomal internal transcribed spacer (ITS) sequences were used to evaluate the phylogenetics of Zea and Tripsacum. Maximum likelihood and polymorphism parsimony were used for phylogenetic reconstructions. Zea ITS nucleotide diversity was high compared to other plant species, but approximately equivalent to other maize loci. Coalescence of ITS alleles was rapid relative to other nuclear loci; however, there was still much diversity within populations. Zea and Tripsacum form a clade clearly differentiated from all other Poaceae. Four Zea ITS pseudogenes were identified by phylogenetic position and nucleotide composition. The phylogenetic position of Z. mays ssp. huehuetenangensis was clearly established as basal to the other Z. mays. The ITS phylogeny disfavored a Z. luxurians and Z. diploperennis clade, which conflicted with some previous studies. The introgression of Z. mays alleles into Z. perennis and Z. diploperennis was also established. The ITS data indicated a near contemporary divergence of domesticated maize and its two closest wild relatives.      

Higher temperature reduces the effects of litter quality on decomposition by aquatic fungi

1. We investigated the effects of riparian plant diversity (species number and identity) and temperature on microbially mediated leaf decomposition by assessing fungal biodiversity, fungal reproduction and leaf mass loss. 2. Leaves of five riparian plant species were first immersed in a stream to allow microbial colonisation and were then exposed, alone or in all possible combinations, at 16 or 24 °C in laboratory microcosms. 3. Fungal biodiversity was reduced by temperature but was not affected by litter diversity. Temperature altered fungal community composition with species of warmer climate, such as Lunulospora curvula, becoming dominant. 4. Fungal reproduction was affected by litter diversity, but not by temperature. Fungal reproduction in leaf mixtures did not differ or was lower than that expected from the weighted sum of fungal sporulation on individual leaf species. At the higher temperature, the negative effect of litter diversity on fungal reproduction decreased with the number of leaf species. 5. Leaf mass loss was affected by the identity of leaf mixtures (i.e. litter quality), but not by leaf species number. This was mainly explained by the negative correlation between leaf decomposition and initial lignin concentration of leaves. 6. At 24 °C, the negative effects of lignin on microbially mediated leaf decomposition diminished, suggesting that higher temperatures may weaken the effects of litter quality on plant litter decomposition in streams. 7. The reduction in the negative effects of lignin at the higher temperature resulted in an increased microbially mediated litter decomposition, which may favour invertebrate‐mediated litter decomposition leading to a depletion of litter stocks in streams.     

Mitochondrial DNA analysis of Rhipicephalus sanguineus s.l. from the western Iberian peninsula

Rhipicephalus sanguineus Latreille (1806) (Ixodida: Ixodidae) is considered to be the most widely distributed tick and to have a vast range of habitats and hosts, including livestock, pets and wildlife. In addition to morphological differences, recent investigations using approaches based on molecular genetic markers have revealed the existence of different R. sanguineus lineages in different geographic regions. In this study, 475 ticks collected from dogs in the western Iberian peninsula were studied both morphologically and genetically, using 12S and 16S rDNA and COI gene markers in order to clarify the controversy over the systematic status of R. sanguineus sensu lato in Western Europe, and to compare the present data with those sourced from studies conducted in other regions of the world. Despite the high morphometric variability, particularly on spiracles in both genders and in female genitalia, data obtained with different genetic molecular markers show very low variability, suggesting the existence of a unique species. In addition, the phylogenetic analysis showed genetic uniformity, supporting the existence of a well‐defined clade consisting of R. sanguineus s.l. specimens from Western Europe that are distinct from R. sanguineus s.l. from Africa. Furthermore, these data corroborate the existence of a polymorphic species in Western Europe, which requires to be consensually redescribed in view of its medical and veterinary importance in pathogen transmission.     

An eScience-Bayes strategy for analyzing omics data

Background  

The omics fields promise to revolutionize our understanding of biology and biomedicine. However, their potential is compromised by the challenge to analyze the huge datasets produced. Analysis of omics data is plagued by the curse of dimensionality, resulting in imprecise estimates of model parameters and performance. Moreover, the integration of omics data with other data sources is difficult to shoehorn into classical statistical models. This has resulted in ad hoc approaches to address specific problems.