Cacao trees in tropical agroforestry landscapes of the Napu Valley in Central Sulawesi, Indonesia

All sample sites were situated at the northern tip of Napu Valley in Central Sulawesi, Indonesia. After an initial mapping of the study area, we selected 15 smallholder cacao plantations as sites for bird and bat exclosure experiments in March 2010. On each study site, we established 4 treatments for these exclosure experiments (bird exclosure - closed during daytime and open during night; bat exclosure - closed overnight and opened during daytime; full exclosure of both birds and bats - always closed and unmanipulated/open control treatments - always open). In each treatment, there were 2 cacao trees (total of 8 cacao trees per study site), surrounded by nylon filament (2x2 cm mesh size) that was opened and closed according to the activity period of day and night active flying vertebrates (05:00-06:00 am and 17:00-18:00 pm) on a daily basis. The mean tree height and diameter at breast height (dbh) result from two measures of all study trees at the beginning of the exclosure experiment (June 2010) and 6 months later (February 2011).

Epiphytic orchid diversity found on trees and shrubs in coffee cultivated Afromontane rainforest, SW Ethiopia

The moist evergreen Afromontane forest of SW Ethiopia has become extremely fragmented and most remnants are intensively managed for cultivation of coffee (Coffea arabica). We investigated the distributions of epiphytic orchids in shade trees and their understory in forests with contrasting management intensity to determine biodiversity losses associated with coffee cultivation and to determine the capacity of coffee shrubs to act as refugia for orchid species. We studied epiphytic orchids in managed forests and natural forests and recorded orchid diversity and abundance in different tree zones of 339 trees and in the understory. Coffee management was associated with a downward shift of orchid species as orchid species were occurring in significantly lower tree zones in managed forest. The number of shrubs in the understory of managed forest was not higher than in natural forests, yet orchid abundance was higher in the understory of managed forests. Local extinctions of epiphytic orchids and species losses in the outer tree zones (a contraction of habitat) in managed forests are most likely driven by losses of large, complex-structured climax trees, and changes in microclimate, respectively. Coffee shrubs and their shade trees in managed forests are shown here to be a suitable habitat for only a limited set of orchid species. As farmers continue to convert natural forest into managed forest for coffee cultivation, further losses of habitat quality and collateral declines in regional epiphytic orchid diversity can be expected. Therefore, the conservation of epiphytic orchid diversity, as well as other components of diversity of the coffee forests, must primarily rely on avoiding coffee management intensification in the remaining natural forest. Convincing farmers to keep forest-climax trees in their coffee forest and to tolerate orchids on their coffee shrubs may also contribute to a more favorable conservation status of orchids in Ethiopian coffee agroecosystems.

DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.