Biodiversity of Coral Reefs: What are We Losing and Why?

SYNOPSIS. Coral reefs are threatened by numerous anthropogenicimpacts, some of which have already had major effects worldwide.These unique tropical environments harbor a high diversity ofcorals, reef invertebrates, fish and other animals and plants.In most taxa, the species diversity of reef-associated organismsis poorly understood because many of the species have yet tobe collected and described. High coral mortality has been associatedwith natural events such as hurricanes, predator outbreaks andperiods of high temperature, but has also resulted from excessnutrients in sewage and from specific pollutants. Reef coralsand associated organisms are also threatened by the possibilityof global warming which will result in rising sea levels andperiods of increased temperature stress, and which may alsobring increased storm frequency and intensity. Although therecent extensive episodes of coral bleaching in the Caribbeanand eastern Pacific cannot be causally related to global warmingat this time, the close link between bleaching and temperaturesuggests that global warming will result in severe changes incoral assemblages. Major reef destruction has followed outbreaksof the predatory seastar Acanthaster planci in the Pacific.Although this is considered part of a natural disturbance cycle,there are indications that altered land use patterns and reductionof predators on this seastar by human activities may have increasedthe severity of outbreaks. Recreational and commercial use ofreefs has also increased, and has caused extensive damage, especiallynear areas of high population density. One of the most obviousand widespread losses to reef biota is the reduction in fishpopulations from intense overfishing in most reef areas of theworld. Coasts without adequately managed reefs have sufferedintense overfishing for both local and export purposes, to thepoint where the positive effects of fish on those reefs havebeen compromised. The combination of these destructive factorshas altered reefs in all localities, and many that were onceconsidered protected by distance and low population densityare now being exploited as well. On the positive side, improvedunderstanding of ecological processes on reefs combined withconcerted conservation efforts have managed to protect someextensive areas of reef for the future.     

Do Epigeal Termite Mounds Increase the Diversity of Plant Habitats in a Tropical Rain Forest in Peninsular Malaysia?

The extent to which environmental heterogeneity can account for tree species coexistence in diverse ecosystems, such as tropical rainforests, is hotly debated, although the importance of spatial variability in contributing to species co-existence is well recognized. Termites contribute to the micro-topographical and nutrient spatial heterogeneity of tropical forests. We therefore investigated whether epigeal termite mounds could contribute to the coexistence of plant species within a 50 ha plot at Pasoh Forest Reserve, Malaysia. Overall, stem density was significantly higher on mounds than in their immediate surroundings, but tree species diversity was significantly lower. Canonical correspondence analysis showed that location on or off mounds significantly influenced species distribution when stems were characterized by basal area. Like studies of termite mounds in other ecosystems, our results suggest that epigeal termite mounds provide a specific microhabitat for the enhanced growth and survival of certain species in these species-rich tropical forests. However, the extent to which epigeal termite mounds facilitate species coexistence warrants further investigation.     

Are We Losing the Best Parts of Our Protected Areas in Tropical Mountains?

Protected areas (PAs) on tropical mountains undergo greater forest destruction in their lower altitudes. We compared the extent of forested, nonforested, and fragmented areas between lowland (<1000 m asl) and montane zones of the Blue Mountains inside the Blue and John Crow Mountains National Park established in Jamaica in 1993. We found that in 2008, inside the montane zone, only 4 percent of forest was cleared, and forest fragmentation was minimal. In the lowland zone, however, the percentage of forest cleared was seven times as high, and the density of fragments was 11-fold higher. We established twenty-five 0.04 ha lowland plots; ordination of tree species composition in these plots reflected a rainfall gradient, showing that plots on the wetter northern side of the Blue Mountains were floristically different from those on the drier southern side. The conservation value of the remaining lowland forest is high because of its high endemism (18% of species in our plots) and beta diversity. In addition, IUCN Red List data show that about 71 percent of threatened tree species in the Blue Mountains grow in the lowland region, 92 percent of which are endemic. From these findings, we identify a ‘protected area hotspot zone’, which lies between the PA boundary and the core high-altitude zone, and which should be instituted in IUCN categories I and II PAs.     

Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life

Recent results from engineered and natural samples show that the starkly different lipids of archaea and bacteria can form stable hybrid membranes. But if the two types can mix, why don't they? That is, why do most bacteria and all eukaryotes have only typically bacterial lipids, and archaea archaeal lipids? It is suggested here that the reason may lie on the other main component of cellular membranes: membrane proteins, and their close adaptation to the lipids. Archaeal lipids in modern bacteria could suggest that the last universal common ancestor (LUCA) had both lipid types. However, this would imply a rather elaborate evolutionary scenario, while negating simpler alternatives. In light of widespread horizontal gene transfer across the prokaryotic domains, hybrid membranes reveal that the lipid divide did not just occur once at the divergence of archaea and bacteria from LUCA. Instead, it continues to occur actively to this day. Also see the video abstract here https://youtu.be/TdKjxoDAtsg .     

Why Is the Mechanical Efficiency of F1-ATPase So High?

The experimentally measured mechanical efficiency of the F₁-ATPase under viscous loading is nearly 100%, far higher than any other hydrolysis-driven molecular motor (Yasuda et al., 1998). Here we give a molecular explanation for this remarkable property.     

Survival of the Synesthesia Gene: Why Do People Hear Colors and Taste Words?

Synesthesia is a perceptual experience in which stimuli presented through one modality will spontaneously evoke sensations in an unrelated modality. The condition occurs from increased communication between sensory regions and is involuntary, automatic, and stable over time. While synesthesia can occur in response to drugs, sensory deprivation, or brain damage, research has largely focused on heritable variants comprising roughly 4% of the general population. Genetic research on synesthesia suggests the phenomenon is heterogeneous and polygenetic, yet it remains unclear whether synesthesia ever provided a selective advantage or is merely a byproduct of some other useful selected trait. Progress in uncovering the genetic basis of synesthesia will help us understand why synesthesia has been conserved in the population.     

Why Be Vigilant? The Case of the Alpha Animal

We compared patterns of vigilance behavior in a male- and a female-dominant species—white-faced capuchins and ring-tailed lemurs—and used the results to test four hypotheses to explain vigilance behavior in primates. Adult male white-faced capuchins spent significantly more time vigilant than females did, and much male vigilance appeared to be directed toward males from other social groups. This finding supports the protection of paternity hypothesis. No sex difference existed in vigilance behavior among the ring-tailed lemurs, and subjects of both sexes exhibited more vigilance toward predators/potential predators than toward extragroup conspecifics, which supports the predator detection hypothesis. A trade-off argument, suggesting that females tolerate males in a group in return for greater male vigilance, does not apply to ring-tailed lemurs in our study. In both the male-dominant capuchins and the female-dominant ring-tailed lemurs, the alpha subject in the majority of the study groups was significantly more vigilant than other group members were. In white-faced capuchins, the alpha male mates more often than subordinate males do; therefore, the greater degree of vigilance exhibited by the alpha male may correspond to the protection of his reproductive investment. In ring-tailed lemurs, there can be more than one matriline in a group. Thus, the greater amount of vigilance behavior exhibited by the alpha female may be related to protection of her matriline, which could ultimately lead to greater inclusive fitness. Alpha subjects in our study groups exhibited certain behaviors more frequently or exclusively. Accordingly, there may be a constellation of behaviors characteristic of alpha animals.     

Do new Access and Benefit Sharing procedures under the Convention on Biological Diversity threaten the future of biological control?

Under the Convention on Biological Diversity (CBD) countries have sovereign rights over their genetic resources. Agreements governing the access to these resources and the sharing of the benefits arising from their use need to be established between involved parties [i.e. Access and Benefit Sharing (ABS)]. This also applies to species collected for potential use in biological control. Recent applications of CBD principles have already made it difficult or impossible to collect and export natural enemies for biological control research in several countries. If such an approach is widely applied it would impede this very successful and environmentally safe pest management method based on the use of biological diversity. The CBD is required to agree a comprehensive Access and Benefit Sharing process in 2010, in preparation for which the IOBC (International Organization for Biological Control of Noxious Animals and Plants) Global Commission on Biological Control and Access and Benefit Sharing has prepared this position paper. Here, we first describe the practice of biological control in relation to the principles of ABS, illustrated extensively by case studies and successes obtained with biological control. Next, we emphasise the very limited monetary benefits generated in biological control when compared to other fields of ABS such as the collection of germplasm for development of human drugs, chemical pesticides or crop cultivars. Subsequently, we inform the biological control community of good ABS practice and challenges, and we hope to make clear to the community involved in ABS under the CBD the special situation with regard to biological control. Finally, based on the non-commercial academic research model, we make recommendations which would facilitate the practice of collection and exchange of biological control agents, propose a workable framework to assist policy makers and biological control practitioners, and urge biological control leaders in each country to get involved in the discussions with their national ABS contact point to take their needs into consideration.     

Metagenomic Analysis of a Tropical Composting Operation at the S?o Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.     

Why are There Fewer Marsupials than Placentals? On the Relevance of Geography and Physiology to Evolutionary Patterns of Mammalian Diversity and Disparity

Placental mammals occupy a larger morphospace and are taxonomically more diverse than marsupials by an order of magnitude, as shown by quantitative and phylogenetic studies of several character complexes and clades. Many have suggested that life history acts as a constraint on the evolution of marsupial morphology. However, the frequent circumvention of constraints suggests that the pattern of morphospace occupation in marsupials is more a reflection of lack of ecological opportunity than one of biases in the production of variants during development. Features of marsupial physiology are a potential source of biases in the evolution of the group; these could be coupled with past macroevolutionary patterns that followed conditions imposed by global temperature changes. This is evident at the K/Pg boundary and at the Eocene/Oligocene boundary. The geographic pattern of taxonomic and morphological diversity in placental clades mirrors that of extant placentals as a whole versus marsupials: placentals of northern origin are more diverse those of southern one and include the clades that are outliers in taxonomic (rodents and bats) and ecomorphological (whales and bats) richness.     

Antarctic Marine Biodiversity – What Do We Know About the Distribution of Life in the Southern Ocean?

The remote and hostile Southern Ocean is home to a diverse and rich community of life that thrives in an environment dominated by glaciations and strong currents. Marine biological studies in the region date back to the nineteenth century, but despite this long history of research, relatively little is known about the complex interactions between the highly seasonal physical environment and the species that inhabit the Southern Ocean. Oceanographically, the Southern Ocean is a major driver of global ocean circulation and plays a vital role in interacting with the deep water circulation in each of the Pacific, Atlantic, and Indian oceans. The Census of Antarctic Marine Life and the Scientific Committee on Antarctic Research Marine Biodiversity Information Network (SCAR-MarBIN) have strived to coordinate and unify the available scientific expertise and biodiversity data to improve our understanding of Southern Ocean biodiversity. Taxonomic lists for all marine species have been compiled to form the Register of Antarctic Marine Species, which currently includes over 8,200 species. SCAR-MarBIN has brought together over 1 million distribution records for Southern Ocean species, forming a baseline against which future change can be judged. The sample locations and numbers of known species from different regions were mapped and the depth distributions of benthic samples plotted. Our knowledge of the biodiversity of the Southern Ocean is largely determined by the relative inaccessibility of the region. Benthic sampling is largely restricted to the shelf; little is known about the fauna of the deep sea. The location of scientific bases heavily influences the distribution pattern of sample and observation data, and the logistical supply routes are the focus of much of the at-sea and pelagic work. Taxa such as mollusks and echinoderms are well represented within existing datasets with high numbers of georeferenced records. Other taxa, including the species-rich nematodes, are represented by just a handful of digital records.     

Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia

Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the α subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified - the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean Mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the Mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.     

Morphotypes,varieties, or subspecies?: genetic diversity and differentiation of four Saintpaulia (Gesneriaceae) morphotypes from the East Usambara Mountains,Tanzania

Saintpaulia (H. Wendl.) is a forest-dependent, endangered plant genus endemic to Tanzania and Kenya. The taxonomy of Saintpaulia from the Usambara Mountains and adjacent lowlands in north-eastern Tanzania is problematic because of the morphological similarity of the species and the presence of considerable intraspecific variation. Conventional molecular phylogenetic methods have failed to reveal the genetic structure of this Saintpaulia complex. In this study, we assessed the genetic composition of 12 Saintpaulia populations, representing four different morphotypes, from the East Usambara Mountains using inter-simple sequence repeat (ISSR) markers. Relatively high genetic diversities were observed within populations (mean h  = 0.320), indicating their adaptive potential. Little genetic differentiation amongst populations (mean F _st  = 0.063) and the genetic divergence of the rosulate and trailing morphotypes support the hypothesis of ongoing divergent evolution within the East Usambara metapopulation(s) of Saintpaulia .  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 347–355.     

Invasion Success and Community Resistance in Single and Multiple Species Invasion Models: Do the Models Support the Conclusions?

Elton's concept of community-level resistance to invasion has derived significant theoretical support from community assembly models in which species invade (colonize) singly at low densities. Several theoretical models have provided support to this concept and are frequently cited as providing evidence that invasion resistance occurs in nature. The underlying assumptions of these models however, are derived from island or island-like systems in which species invade infrequently at low abundances. We suggest that these island-like models cannot be generalized to systems in which species arrive in greater frequencies and densities. To investigate the effects of altering the basic assumptions of these original models, we utilized assembly algorithms similar to those used in previous studies, but allowed either two species to invade per time step or single species invasions at relatively high inoculation densities. In these models, invasion resistance only occurred when the invasion process was restricted to single species invading at low densities (as in previous models). When two species were allowed to invade per time step, invasion resistant states did not occur in any of 20 simulated communities, even after 10,000 invasion events. Relaxation of the assumption of invasion at low density also resulted in a lack of invasion resistance. These results may explain why the strict concept of complete invasion resistance appears only to operate in island and island-like systems.     

Local and Landscape Factors Driving the Structure of Tropical Anuran Communities: Do Ephemeral Ponds have a Nested Pattern?

The sets of species in animal and plant communities often comprise nested subsets of the species in broader communities. Although most mechanisms causing nested patterns are known and have been demonstrated for different environments and taxa, how amphibian communities are structured in ephemeral ponds in tropical disturbed landscapes remains unknown. We investigated if pond size, duration, presence of trees (local factors), and the proportion of forest cover surrounding ponds (landscape factor) affect anuran species richness and composition, and if pond assemblages showed a nested pattern. We sampled 11 ephemeral ponds in a pasture matrix near a large Atlantic Forest remnant in Brazil and measured local and landscape variables inside two buffer zones around each pond (100 and 500 m). We marked 1514 individuals from 23 anuran species, and found that richness in ponds ranged from 3–14 species. Both local and landscape factors explained frog species richness in the sampled ponds, and seemed to affect community composition. Frog communities occurred in a non‐nested pattern, contrary to our expectations: species found in poor subsets were not found in larger, more complex ponds. Local and landscape characteristics create a variety of environments in ephemeral ponds, even in impoverished ones; these characteristics restrict pond occupancy for some species, and result in a non‐nested pattern.     

Why respiratory biology? The meaning and significance of respiration and its integrative study

Traditionally the process of respiration is divided into threephases: (1) cellular respiration, (2) transport of respiratorygases and (3) ventilation of the gas exchange organs (breathing).Thereby organisms assimilate chemical energy from the environment,and within their cells transfer it from molecule to moleculein a stepwise fashion. Although studied separately, these phasesrepresent a continuum and cellular respiration in all life formshas much in common. Ironically, these respiratory foci havebeen artificially delineated by their own practitioners, whotend to publish in their own journals, and attend their ownconferences. The goal of modern respiratory biology should beto understand biological connectivity and complexity by viewingan organism as a series of interconnecting systems from moleculeto ecosystem. The future of science in general, and biologyin particular, lies in disciplinary networking: combining theresults of traditional disciplines to better understand thewhole. Because of its universality, Respiratory Biology canbest provide this bridge and improve interdisciplinary studiesin biology generally. To this end, the First International Congressof Respiratory Biology was held from August 14 to 16, 2006,at Bonn, Germany. As evident from the success of this inauguralmeeting, these are exciting times for Respiratory Biology. Theexplosion of "X-omics" and systems biology, the powerful geneticapproaches to disease treatment, and the long-standing and newlyemerging questions in evolutionary biology and ecology; allportend a continuing role of respiratory biology as a key integrativediscipline.     

Why Do Unrelated Insertion Sequences Occur Together in the Genome of Escherichia Coli?

Natural isolates of Escherichia coli are polymorphic for the presence or absence of insertion sequences. Among the ECOR reference collection of 71 natural isolates studied for the number of copies of the insertion sequences IS1, IS2, IS3, IS4, IS5 and IS30, the number of strains containing no copies of the insertion sequences were 11, 28, 23, 43, 46 and 36, respectively. Significant correlations occur in the ECOR strains in the presence or absence of unrelated insertion sequences in the chromosome and plasmid complements. Strains containing any insertion sequence are more likely to contain additional, unrelated insertion sequences than would be expected by chance. We suggest that the positive correlations result from horizontal transfer mediated by plasmids. A branching-process model for the plasmid-mediated transmission of insertion sequences among hosts yields such a correlation, even in the absence of interactions affecting transposition or fitness. The predictions of the model are quantitatively in agreement with the observed correlations among insertion sequences.