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The Late Miocene (11.6–5.3 Ma) is a crucial period in the history of the Asian monsoon. Significant changes in the Asian climate regime have been documented for this period, which saw the formation of the modern Asian monsoon system. However, the spatiotemporal structure of these changes is still ambiguous, and the associated mechanisms are debated. Here, we present a simulation of the average state of the Asian monsoon climate for the Tortonian (11–7 Ma) using the regional climate model CCLM3.2. We employ relatively high spatial resolution (1° × 1°) and adapt the physical boundary conditions such as topography, land-sea distribution and vegetation in the regional model to represent the Late Miocene. As climatological forcing, the output of a Tortonian run with a fully-coupled atmosphere-ocean general circulation model is used. Our regional Tortonian run shows a stronger-than-present East Asian winter monsoon wind as a result of the enhanced mid-latitude westerly wind of our global forcing and the lowered present-day northern Tibetan Plateau in the regional model. The summer monsoon circulation is generally weakened in our regional Tortonian run compared to today. However, the changes of summer monsoon precipitation exhibit major regional differences. Precipitation decreases in northern China and northern India, but increases in southern China, the western coast and the southern tip of India. This can be attributed to the changes in both the regional topography (e.g. the lower northern Tibetan Plateau) and the global climate conditions (e.g. the higher sea surface temperature). The spread of dry summer conditions over northern China and northern Pakistan in our Tortonian run further implies that the monsoonal climate may not have been fully established in these regions in the Tortonian. Compared with the global model, the high resolution regional model highlights the spatial differences of the Asian monsoon climate in the Tortonian, and better characterizes the convective activity and its response to regional topographical changes. It therefore provides a useful and compared to global models, a complementary tool to improve our understanding of the Asian monsoon evolution in the Late Miocene.
Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events.
The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex.
These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern.
Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area.
Acanthocephalans are attractive candidates as model organisms for studying the ecology and co-evolutionary history of parasitic life cycles in the marine ecosystem. Adding to earlier molecular analyses of this taxon, a total of 36 acanthocephalans belonging to the classes Archiacanthocephala (3 species), Eoacanthocephala (3 species), Palaeacanthocephala (29 species), Polyacanthocephala (1 species) and Rotifera as outgroup (3 species) were analyzed by using Bayesian Inference and Maximum Likelihood analyses of nuclear 18S rDNA sequence. This data set included three re-collected and six newly collected taxa, Bolbosoma vasculosum from Lepturacanthus savala, Filisoma rizalinum from Scatophagus argus, Rhadinorhynchus pristis from Gempylus serpens, R. lintoni from Selar crumenophthalmus, Serrasentis sagittifer from Johnius coitor, and Southwellina hispida from Epinephelus coioides, representing 5 new host and 3 new locality records. The resulting trees suggest a paraphyletic arrangement of the Echinorhynchida and Polymorphida inside the Palaeacanthocephala. This questions the placement of the genera Serrasentis and Gorgorhynchoides within the Echinorhynchida and not the Polymorphida, necessitating further insights into the systematic position of these taxa based on morphology.
Forest fragmentation and selective logging are two main drivers of global environmental change and modify biodiversity and environmental conditions in many tropical forests. The consequences of these changes for the functioning of tropical forest ecosystems have rarely been explored in a comprehensive approach. In a Kenyan rainforest, we studied six animal-mediated ecosystem processes and recorded species richness and community composition of all animal taxa involved in these processes. We used linear models and a formal meta-analysis to test whether forest fragmentation and selective logging affected ecosystem processes and biodiversity and used structural equation models to disentangle direct from biodiversity-related indirect effects of human disturbance on multiple ecosystem processes. Fragmentation increased decomposition and reduced antbird predation, while selective logging consistently increased pollination, seed dispersal and army-ant raiding. Fragmentation modified species richness or community composition of five taxa, whereas selective logging did not affect any component of biodiversity. Changes in the abundance of functionally important species were related to lower predation by antbirds and higher decomposition rates in small forest fragments. The positive effects of selective logging on bee pollination, bird seed dispersal and army-ant raiding were direct, i.e. not related to changes in biodiversity, and were probably due to behavioural changes of these highly mobile animal taxa. We conclude that animal-mediated ecosystem processes respond in distinct ways to different types of human disturbance in Kakamega Forest. Our findings suggest that forest fragmentation affects ecosystem processes indirectly by changes in biodiversity, whereas selective logging influences processes directly by modifying local environmental conditions and resource distributions. The positive to neutral effects of selective logging on ecosystem processes show that the functionality of tropical forests can be maintained in moderately disturbed forest fragments. Conservation concepts for tropical forests should thus include not only remaining pristine forests but also functionally viable forest remnants.
Globally, tropical forest soils represent the second largest source of N2O and NO. However, there is still considerable uncertainty on the spatial variability and soil properties controlling N trace gas emission. To investigate how soil properties affect N2O and NO emission, we carried out an incubation experiment with soils from 31 locations in the Nyungwe tropical mountain forest in southwestern Rwanda. All soils were incubated at three different moisture levels (50, 70 and 90% water filled pore space (WFPS)) at 17 °C. Nitrous oxide emission varied between 4.5 and 400 μg N m−2 h−1, while NO emission varied from 6.6 to 265 μg N m−2 h−1. Mean N2O emission at different moisture levels was 46.5 ± 11.1 (50% WFPS), 71.7 ± 11.5 (70% WFPS) and 98.8 ± 16.4 (90% WFPS) μg N m−2 h−1, while mean NO emission was 69.3 ± 9.3 (50% WFPS), 47.1 ± 5.8 (70% WFPS) and 36.1 ± 4.2 (90% WFPS) μg N m−2 h−1. The latter suggests that climate (i.e. dry vs. wet season) controls N2O and NO emissions. Positive correlations with soil carbon and nitrogen indicate a biological control over N2O and NO production. But interestingly N2O and NO emissions also showed a negative correlation (only N2O) with soil pH and a positive correlation with free iron. The latter suggest that chemo-denitrification might, at least for N2O, be an important production pathway. In conclusion improved understanding and process based modeling of N trace gas emission from tropical forests will not only benefit from better spatial explicit trace gas emission and basic soil property monitoring, but also by differentiating between biological and chemical pathways for N trace gas formation.
The impacts of human activities, notably the conversion of tropical forests into farmland habitat, has profound impacts on biological diversity and ecosystem functions (Millennium Ecosystem Assessment 2005). It is widely debated to what extent human modified landscapes can maintain tropical biodiversity and their ecosystem functionality (e.g. Waltert et al. 2004, Sekercioglu et al. 2007). In this thesis, I have used a huge and temporarily replicated dataset to assess the value of different habitat types differing in land-use intensities for bird communities in tropical East Africa. I investigated bird abundance and species richness along a forest-farmland habitat gradient and assessed spatial and temporal fluctuations of bird assemblages and their food resources.
I could show that forest and farmland habitats harbor distinct bird communities. Moreover, the protection of natural forests merits the highest priority for conserving the high diversity of forest-dependent bird species. My study, however, also shows that farmland habitats in the proximity of natural forest can support a high bird diversity. High bird diversity in tropical farmlands depends on a high structural complexity, such as in small-scale subsistence farmlands. From my findings, I conclude that the conversion of forest to farmland leads to substantial losses in bird diversity, in particular in specialized feeding guilds such as insectivores, while the conversion of structurally heterogeneous subsistence farmlands to sugarcane plantation causes erosion of bird diversity in agricultural ecosystems. Both findings are important for conservation planning in times when tropical forests and agroecosystems are under constantly high pressure due to increasing human population numbers and global demands for biofuel crops (Gibbs et al. 2008). From an ecosystem function perspective, my study demonstrates the potential of agroecosystems in supporting important ecosystem functions, such as seed dispersal by frugivorous birds and pest control by insectivorous birds. I could show that bird abundances in both frugivorous and insectivorous guilds were strongly predicted by their respective food resources, implying that seasonal shifts in fruit and invertebrate abundance at Kakamega forest and surrounding farmlands affect community dynamics and appear to influence local movement patterns of birds. The most interesting finding of this study was that feeding guilds responded idiosyncratically to resource fluctuations. Frugivore richness fluctuated asynchronously in forest and farmland habitats, suggesting foraging movements and fruit tracking across habitat borders. In contrast, I found that insectivores fluctuated synchronously in the two habitat types, suggesting a lack of inter-habitat movements. I therefore predict that insectivorous bird communities in this forest-farmland landscape may be more susceptible to the combined effects of land-use and climate change, due to their narrow habitat niche and limited capacity to track their resources.
The fact that a number of bird species regularly moved across the landscape mosaic in my study system implies that birds are able to provide long-distance seed dispersal across habitat borders. Thus, birds may enhance forest regeneration in human-modified landscapes, such as those in most parts of tropical Africa, given that forest remnants are protected within an agricultural habitat matrix. In order to effectively conserve tropical biodiversity within forest-farmland mosaics, this study advocates for conservation strategies that go beyond forest protection and explicitly integrate farmlands into forest management plans and policies. This should emphasize the retention of keystone habitat elements within tropical farmland landscapes, such as indigenous trees, forest galleries and hedgerows, whose presence enhance species diversity. Such grassroot-level approaches can be operationalized for instance through providing incentives to farmers to maintain their traditional subsistence land-use practices and through community-based livelihood projects aiming at enhancing local habitat heterogeneity and inter-habitat connectivity.
Stakeholder dialogues can be used not only to introduce and discuss the various demands of the participants. Under certain circumstances they can also serve to smoothen out and solve conflicts that arise in connection with the use and conservation of biodiversity. In order to be successful in this respect, it is crucial to create a situation enabling a process of joint learning. A positive effect might also be achieved by the formation of groups that evolve in the course of a succession of workshops as well as speeches and special items on the agenda. In order for the workshops to be successful, they should be supported by frequent stakeholder analyses. In this guideline we are listing related principles and indications from the literature as well as our own experiences geared towards jointly solving biodiversity conflicts and creating islands of consensus.
Temporal variation in the detectability of a species can bias estimates of relative abundance if not handled correctly. For example, when effort varies in space and/or time it becomes necessary to take variation in detectability into account when data are analyzed. We demonstrate the importance of incorporating seasonality into the analysis of data with unequal sample sizes due to lost traps at a particular density of a species. A case study of count data was simulated using a spring-active carabid beetle. Traps were ‘lost’ randomly during high beetle activity in high abundance sites and during low beetle activity in low abundance sites. Five different models were fitted to datasets with different levels of loss. If sample sizes were unequal and a seasonality variable was not included in models that assumed the number of individuals was log-normally distributed, the models severely under- or overestimated the true effect size. Results did not improve when seasonality and number of trapping days were included in these models as offset terms, but only performed well when the response variable was specified as following a negative binomial distribution. Finally, if seasonal variation of a species is unknown, which is often the case, seasonality can be added as a free factor, resulting in well-performing negative binomial models. Based on these results we recommend (a) add sampling effort (number of trapping days in our example) to the models as an offset term, (b) if precise information is available on seasonal variation in detectability of a study object, add seasonality to the models as an offset term; (c) if information on seasonal variation in detectability is inadequate, add seasonality as a free factor; and (d) specify the response variable of count data as following a negative binomial or over-dispersed Poisson distribution.
Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S - stands for small) basic region-leucine zipper (bZIP)-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT). It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF) found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5′-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5′-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3–4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content.