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Background The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. Results In this study, we analysed the transcriptome of four tropical tree species ( Carapa guianensis , Eperua falcata , Symphonia globulifera and Virola michelii ) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera ) and 23390 (for Eperua falcata ) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera ) and 9076 (for Virola surinamensis ) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 ( S. globulifera ) and 1.05 ( V. surinamensi s) mismatches/100 bp in variation-containing contigs. Conclusion The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.

Tension wood of Laetia procera (Poepp.) Eichl. (Flacourtiaceae), a neo-tropical forest species, shows a peculiar secondary wall structure, with an alternance of thick and thin layers, while opposite wood of this species has a typical secondary wall structure (S1 + S2 + S3). Samples for the study of microstructural properties were collected upon the estimation of growth stresses in the living tree, in order to analyze the correlation of the former with the latter. Investigation using optical microscopy, scanning electron microscopy and UV microspectrophotometry allowed the description of the anatomy, ultra-structure and chemistry of this peculiar polylaminate secondary wall. In the thick layers, cellulose microfibril angle is very low (i.e., microfibril orientation is close to fibre axis) and cellulose microfibrils are well organized and parallel to each other. In the thin layers, microfibrils (only observable in the inner layer) are less organized and are oriented with a large angle relative to the axis of the cell. Thick layers are lightly lignified although thin layers show a higher content of lignin, close to that of opposite wood secondary wall. The more the wood was under tensile stress, the less the secondary wall was lignified, and lower the syringyl on guaiacyl lignin units' ratio was. The innermost layer of the secondary wall looks like a typical S3 layer with large microfibril angle and lignin occurrence. The interest of this kind of structure for the understanding of stress generation is discussed.

Our objective was to asses site parameters, species diversity, phytomass structure and element stores of a Terrafirme forest prior to subsequent studies on nutrient fluxes during forest conversion. The soil was classified as a Xanthic Ferralsol, with a low effective cation exchange capacity (ECEC), low nutrient status and a deeply weathered solum. On 0.75 ha, including all trees with a DBH >7 cm, we identified 222 tree species belonging to 58 families. The above-ground phytomass was estimated using logarithmic regression analysis on two plots of 0.25 ha each. Despite differences in forest structure and species composition, no major differences were found in terms of total phytomass or overall element stores. The mean living above-ground phytomass (LAGP) was 257 Mg$\\text{ha}^{-1}$, and mean quantity of litter 14 Mg$\\text{ha}^{-1}$, while dead wood contributed between 10 to 17% of total above-ground phytomass ($32-56\\text{Mg}\\ \\text{ha}^{-1}$). Element store in LAGP was medium to high compared to other studies on tropical forest systems, while LAGP itself was comparatively low. Comparing 26 humid tropical forest stands recorded in literature, no correlation was found between LAGP and the amount of N and base cations stored in LAGP. However, a correlation between LAGP and P storage in LAGP ($R^{2}=0.76$) indicates the important role P may play in phytomass accumulation on zonal tropical soils. More then 60% of C, 20% of total N, 10% of total P and 66-88% of total K, Ca and Mg of the system (including the first meter of soil) were concentrated in the above-ground phytomass, including deadwood and litter. Consequently, phytomass destruction in form of forest conversion will lead to major element losses from the system.

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This chapter contains sections titled: Extinctions over time Extinction debt Are birds the most endangered taxa? Case studies of recent bird extinctions Drivers of extinctions Extinction vulnerability Ecosystem resonance of bird extinctions Extinction resistence

Background Tropical rainforests (TRFs) harbour almost half of the world’s vascular plant species diversity while covering only about 6–7% of land. However, why species richness varies amongst the Earth’s major TRF regions remains poorly understood. Here we investigate the evolutionary processes shaping continental species richness disparities of the pantropical, epiphytic and mostly TRF-dwelling orchid mega-genus Bulbophyllum ( c. 1948 spp. in total) using diversification analyses based on a time-calibrated molecular phylogeny (including c. 45–50% spp. each from Madagascar, Africa, Neotropics, and 8.4% from the Asia-Pacific region), coupled with ecological niche modelling (ENM) of geographic distributions under present and past (Last Glacial Maximum; LGM) conditions. Results Our results suggest an early-to-late Miocene scenario of ‘out-of-Asia-Pacific’ origin and progressive, dispersal-mediated diversification in Madagascar, Africa and the Neotropics, respectively. Species richness disparities amongst these four TRF lineages are best explained by a time-for-speciation (i.e. clade age) effect rather than differences in net diversification or diversity-dependent diversification due to present or past spatial-bioclimatic limits. For each well-sampled lineage (Madagascar, Africa, Neotropics), we inferred high rates of speciation and extinction over time (i.e. high species turnover), yet with the origin of most extant species falling into the Quaternary. In contrast to predictions of classical ‘glacial refuge’ theories, all four lineages experienced dramatic range expansions during the LGM. Conclusions As the Madagascan, African and Neotropical lineages display constant-rate evolution since their origin (early-to-mid-Miocene), Quaternary environmental change might be a less important cause of their high species turnover than intrinsic features generally conferring rapid population turnover in tropical orchids (e.g., epiphytism, specialization on pollinators and mycorrhizal fungi, wind dispersal). Nonetheless, climate-induced range fluctuations during the Quaternary could still have played an influential role in the origination and extinction of Bulbophyllum species in those three, if not in all four TRF regions.

It is widely expected that habitat destruction in the tropics will cause a mass extinction in coming years, but the potential magnitude of the loss is unclear. Existing literature has focused on estimating global extinction rates indirectly or on quantifying effects only at local and regional scales. This paper directly predicts global losses in 11 groups of organisms that would ensue from disturbance of all remaining tropical forest habitats. The results are based on applying a highly accurate method of estimating species richness to 875 ecological samples. About 41% of the tree and animal species in this dataset are absent from disturbed habitats, even though most samples do still represent forests of some kind. The individual figures are 30% for trees and 8–65% for 10 animal groups. Local communities are more robust to disturbance because losses are partially balanced out by gains resulting from homogenization.

Understanding tropical forest dynamics and planning for their sustainable management require efficient, yet accurate, predictions of the joint dynamics of hundreds of tree species. With increasing information on tropical tree life histories, our predictive understanding is no longer limited by species data but by the ability of existing models to make use of it. Using a demographic forest model, we show that the basal area and compositional changes during forest succession in a neotropical forest can be accurately predicted by representing tropical tree diversity (hundreds of species) with only five functional groups spanning two essential trade-offs—the growth-survival and stature-recruitment trade-offs. This data-driven modeling framework substantially improves our ability to predict consequences of anthropogenic impacts on tropical forests.

One of the primary anthropogenic activities driving the shrinking of tropical forests is urban development, which often results in the formation of fragmented forest areas surrounded by diverse human-modified landscapes. Isolation and fragmentation of natural habitats have been linked to a variety of detrimental effects on ecosystems and biodiversity. Currently, there is limited information on how urban forest fragmentation affects avian communities in tropical regions. Our study investigated the impacts of habitat fragmentation on bird community assemblages in four forest patches and in one continuous forest within rapidly developing Greater Kuala Lumpur, Malaysia. Using point count sampling method, we recorded 4,144 bird encounters spanning 196 resident and migratory species, nearly 60% of which are experiencing global population decline. Our findings show that continuous forests can support greater avian diversity than fragmented forests. We also found that bird community assemblages differed significantly amongst forest types, with continuous forest having the most distinct bird community and highest species evenness. Our study further identified the value of retaining urban forests as habitats and biological corridors for resident birds and as stopover sites for migratory birds, including rare, threatened, or endangered species (RTE). Maintaining existing urban forest areas is therefore crucial for the conservation of bird species, both at a local and global level. This can be further enhanced by incorporating these forests into Important Bird and Biodiversity Area (IBA) networks in the region.

Compared with non-limestone forests, limestone forests tend to show lower pteridophyte diversity, yet they are known to harbor a unique set of species due to their substrate conditions and naturally fragmented habitat areas. Pteridophyte assemblage composition, however, has not been quantitatively investigated in Xishuangbanna, southwestern China, known as one of the most species-rich areas of China. Using a fully standardized sampling protocol, we tested the following hypotheses: (1) pteridophyte species composition is different between limestone forests (LF) and non-limestone forests (NLF); and the differences are attributable to (2) lower species richness in LF; (3) greater spatial and temporal turnovers (beta diversity) in LF; and (4) higher proportion of pteridophyte species restricted to LF. We found significant differences in pteridophyte assemblage compositions between LF and NLF. Average species richness per transect (alpha diversity) was lower in LF than in NLF, but we found no difference in overall species richness (gamma diversity) between LF and NLF at the scale of this study, because species turnover among samples (beta diversity) was higher in LF than in NLF. A total of 23 species were restricted to LF and 32 species restricted to NLF; however, geographic distribution of LF species was limited to certain habitat patches within this habitat. Our results suggest that LF pteridophyte biodiversity cannot be protected by conserving a limited number of habitat patches, because loss of one LF habitat patch may result in local extinction of species or extinction of endemic species that are yet to be discovered.