Molecular data illuminate cryptic nudibranch species: the evolution of the Scyllaeidae (Nudibranchia: Dendronotina) with a revision of Notobryon

Scyllaeidae represents a small clade of dendronotoid nudibranchs. Notobryon wardi Odhner, 1936, has been reported to occur in tropical oceans from the Indo‐Pacific and eastern Pacific to temperate South Africa. The systematics of Notobryon has not been reviewed using modern systematic tools. Here, specimens of Notobryon were examined from the eastern Pacific, the Indo‐Pacific, and from temperate South Africa. Additionally, representatives of Scyllaea and Crosslandia were studied. Scyllaeidae was found to be monophyletic. Notobryon was also found to be monophyletic and is the sister group to Crosslandia plus Scyllaea. The molecular data also clearly indicate that within Notobryon, at least three distinct species are present, two of which are here described. Genetic distance data indicate that eastern Pacific and South African exemplars are 10–23% divergent from Indo‐Pacific exemplars of Notobryon wardi. Scyllaea pelagica has been regarded as a single, circumtropical species. Our molecular studies clearly indicate that the Atlantic and Indo‐Pacific populations are distinct and we resurrect Scyllaea fulva Quoy & Gaimard, 1824 for the Indo‐Pacific species. Our morphological studies clearly corroborate our molecular findings and differences in morphology distinguish closely related species. Different species clearly have distinct penial morphology. These studies clearly reinforce the view that eastern Pacific, Indo‐Pacific, and temperate biotas consist largely of distinct faunas, with only a minor degree of faunal overlap. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 311–336.     

Comparative Analysis of Three Different Total Nucleic Acid Extraction Protocols for the Diagnosis of Geminiviruses in Squash (Cucurbita moschata)

Squash (Cucurbita moschata) is one of the most important crops in tropical countries. Geminiviruses are an important group of plant pathogens. In 2002 a new begomovirus was reported to naturally infect squash and some other crops in Costa Rica. Our objective was to compare, using molecular techniques, the extraction and further purification of DNA from squash by different extraction protocols and storage methods. A single infected sample was collected, half of the material was stored frozen at ?70°C, and the remainder was stored dehydrated in silica gel (SG). Total nucleic acids (TNAs) were extracted by three different protocols and were quantified by fluorometry, and the quality was analysed by electrophoresis in agarose gels, polymerase chain reaction (PCR) of the virus genome, dot blot and Southern blot hybridization. Even though the tissue stored in SG yielded a higher amount of TNAs, the genetic material exhibited lower integrity and this made it useful exclusively for the detection of geminiviral DNA by PCR amplification of short viral sequences and by hybridization with short viral probes. The Dellaporta method proved to be the most effective for the detection of geminiviral DNA in infected squash tissue. Although the cetyltrimethylammonium bromide method showed similar results, the procedure is more time‐consuming. Surprisingly, the citrate method showed either similar or worse results than the other methods.     

Possible Host Adaptation as an Evolution Factor of Cowpea aphid‐borne mosaic virus Deduced by Coat Protein Gene Analysis

Cowpea aphid‐borne mosaic virus (CABMV) causes major diseases in cowpea and passion flower plants in Brazil and also in other countries. CABMV has also been isolated from leguminous species including, Cassia hoffmannseggii, Canavalia rosea, Crotalaria juncea and Arachis hypogaea in Brazil. The virus seems to be adapted to two distinct families, the Passifloraceae and Fabaceae. Aiming to identify CABMV and elucidate a possible host adaptation of this virus species, isolates from cowpea, passion flower and C. hoffmannseggii collected in the states of Pernambuco and Rio Grande do Norte were analysed by sequencing the complete coat protein genes. A phylogenetic tree was constructed based on the obtained sequences and those available in public databases. Major Brazilian isolates from passion flower, independently of the geographical distances among them, were grouped in three different clusters. The possible host adaptation was also observed in fabaceous‐infecting CABMV Brazilian isolates. These host adaptations possibly occurred independently within Brazil, so all these clusters belong to a bigger Brazilian cluster. Nevertheless, African passion flower or cowpea‐infecting isolates formed totally different clusters. These results showed that host adaptation could be one factor for CABMV evolution, although geographical isolation is a stronger factor.     

PHENOTYPIC STOCHASTICITY PROTECTS LYTIC BACTERIOPHAGE POPULATIONS FROM EXTINCTION DURING THE BACTERIAL STATIONARY PHASE

It is generally thought that the adsorption rate of a bacteriophage correlates positively with fitness, but this view neglects that most phages rely only on exponentially growing bacteria for productive infections. Thus, phages must cope with the environmental stochasticity that is their hosts’ physiological state. If lysogeny is one alternative, it is unclear how strictly lytic phages can survive the host stationary phase. Three scenarios may explain their maintenance: (1) pseudolysogeny, (2) diversified, or (3) conservative bet hedging. To better understand how a strictly lytic phage survives the stationary phase of its host, and how phage adsorption rate impacts this survival, we challenged two strictly lytic phage λ, differing in their adsorption rates, with stationary phase Escherichia coli cells. Our results showed that, pseudolysogeny was not responsible for phage survival and that, contrary to our expectation, high adsorption rate was not more detrimental during stationary phase than low adsorption rate. Interestingly, this last observation was due to the presence of the “residual fraction” (phages exhibiting extremely low adsorption rates), protecting phage populations from extinction. Whether this cryptic phenotypic variation is an adaptation (diversified bet hedging) or merely reflecting unavoidable defects during protein synthesis remains an open question.     

Photosynthetic response of Tempranillo grapevine to climate change scenarios

Photosynthesis in C₃ plants is CO₂ limited and therefore any increase in Rubisco carboxylation substrate may increase net CO₂ fixation, unless plants experience acclimation or other limitations. These aspects are largely unexplored in grapevine. Photosynthesis analysis was used to assess the stomatal, mesophyll, photochemical and biochemical contributions to the decreasing photosynthesis observed in Tempranillo grapevines (Vitis vinifera) from veraison to ripeness, modulated by CO₂, temperature and water availability. Photosynthesis and photosystem II photochemistry decreased from veraison to ripeness. The elevated CO₂ and temperature increased photosynthesis, but transiently, in both well irrigated (WI) and water‐stressed plants. Photosynthetic rates were maxima 1 week after the start of elevated CO₂ and temperature treatments, but differences with treatments of ambient conditions disappeared with time. There were not marked changes in leaf water status, leaf chlorophyll or leaf protein that could limit photosynthesis at ripeness. Leaf total soluble sugars remained at ripeness as high as 2 weeks after the start of treatments. On the other hand, and as expected, CO₂ diffusional limitations impaired photosynthesis in grapevine plants grown under water scarcity, stomatal and mesophyll conductances to CO₂ decreased and in turn low chloroplastic CO₂ concentrations limited photosynthetic CO₂ fixation. In summary, photochemistry and photosynthesis from veraison to ripeness in Tempranillo grapevine were dominated by a developmental‐related decreasing trend that was only transiently influenced by elevated CO₂ concentrations.     

The Impact of Cyclone Fanele on a Tropical Dry Forest in Madagascar

Cyclones, which change tree communities and alter forest structure, are thought to have had a significant selective pressure on the flora and fauna of Madagascar. Very little information, however, is available on the actual impact of cyclones on Malagasy ecosystems. On 21 January 2009, Cyclone Fanele made landfall on the western coast of Madagascar with sustained winds of 185 km/h. We examined the immediate effects of the cyclone on tropical dry forest structure in the Kirindy Mitea National Park. In July and August 2009, we measured the height, diameter at breast height (dbh), and damage for 1361 trees in nine 25 × 25 m plots. We found that: (1) over 95 percent of trees experienced some sort of damage, including 8.8 percent mortality; (2) understory and emergent trees experienced significantly higher mortality than canopy trees; and (3) stem density was reduced 9.2±4.5 percent and biomass was reduced 13.4±8.1 percent after the cyclone. Dbh was the best predictor of trunk damage and mortality. This extensive alteration of forest structure will have a substantial short‐ and long‐term impact on the biotic communities of western Madagascar.     

Cytological evidence supports the taxonomic status of the Sino‐Himalayan species Cimicifuga frigida (Ranunculaceae)

Although Cimicifuga foetida L. (Ranunculaceae) has been shown to be a distinct species distributed only in northern Asia (Siberia, Mongolia), the Sino‐Himalayan species C. frigida Royle remains to be much confused with the Chinese endemic C. mairei H. Lév. The independent species status of C. frigida is recognized by some authors, but refuted by others. A cytogeographical study has shown that the ploidy level is well correlated with the geographical distribution of C. frigida and C. mairei. Cimicifuga frigida is a tetraploid (2n = 32) occurring in the Sino‐Himalayan region, whereas C. mairei is a diploid (2n = 16) occurring in central and southwestern China. There is only minor overlap in their geographical distributions in northwestern Yunnan, China. The ploidy level is also well correlated with the morphological characters, in particular the shape of the staminodes, which has previously been used as the only reliable morphological character to distinguish between C. frigida and C. mairei. The cytogeographical pattern, therefore, lends strong support for the recognition of the independent species status of C. frigida. This species is the only polyploid species currently known in the genus.     

Ethanol from sugarcane in Brazil: a ‘midway’ strategy for increasing ethanol production while maximizing environmental benefits

This article reviews the history and current state of ethanol production from sugarcane in Brazil and presents a strategy for improving ecosystem services and production. We propose that it is possible to produce ethanol from sugarcane while maintaining or even recovering some of Brazil's unique neotropical biodiversity and ecosystem climate services. This approach to the future of sustainable and responsible ethanol production is termed the ‘midway’ strategy. The ‘midway’ strategy involves producing the necessary biotechnology to increase productivity while synergistically protecting and regenerating rainforest. Three main areas of scientific and technological advance that are key to realizing the ‘midway’ strategy are: (i) improving the quality of scientific data on sugarcane biology as pertains to its use as a bioenergy crop; (ii) developing technologies for the use of bagasse for cellulosic ethanol; and (iii) developing policies to improve the ecosystem services associated with sugarcane landscapes. This article discusses these three issues in the general context of biofuels production and highlights examples of scientific achievements that are already leading towards the ‘midway’ strategy.