Local extinction of a coral reef fish explained by inflexible prey choice

While global extinctions of marine species are infrequent, local extinctions are becoming common. However, the role of habitat degradation and resource specialisation in explaining local extinction is unknown. On coral reefs, coral bleaching is an increasingly frequent cause of coral mortality that can result in dramatic changes to coral community composition. Coral-associated fishes are often specialised on a limited suite of coral species and are therefore sensitive to these changes. This study documents the local extinction of a corallivorous reef fish, Oxymonacanthus longirostris, following a mass bleaching event that altered the species composition of associated coral communities. Local extinction only occurred on reefs that also completely lost a key prey species, Acropora millepora, even though coral cover remained high. In an experimental test, fish continued to select bleached A. millepora over the healthy, but less-preferred prey species that resisted bleaching. These results suggest that behavioural inflexibility may limit the ability of specialists to cope with even subtle changes to resource availability.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

Exotic plant species invade diversity hot spots: the alien flora of northwestern Kenya

We analysed the distribution of native and alien plant species across 20 ecogeographic zones of northwestern Kenya. The source pool for the majority of aliens was Europe and America. Thus, the source pool has a biogeographic bias which explains the low proportion of aliens in the tropics: most species in the European or American source pool are not well adapted to tropical conditions. As expected, native and alien plant species showed an area effect. Correcting for this area effect. species rich zones showed a higher proportion of alien plant species in their flora. At the analysed scale, species richness of native plant communities does not increase the resistance to invasions and alien plant species invade diversity hotspots. Compared to the other ecogeographic zone, the urban area around Nairobi showed an increased richness in alien and native plant species. This is very similar to findings in Europe, although the history of urbanisation is much shorter in Kenya. The species turnover between zones (β-diversity) shows a similar pattern in native and alien plant species. Within a very short time scale the alien plant species mapped the biogeographic patterns of natives, although the geography of human activities influences the propagule pressure.     

Phylogenetics of European cyprinids: insights from allozymes

Allozyme data from 23 central European cyprinid taxa suggest that the two sub-families Alburninae and Leuciscinae are paraphyletic. However together, both families seem to form a monophyletic group. By using a molecular clock, the radiation of this group is estimated to be as old as 20 million years. This is consistent with the fossil record. The genus Leuciscus is not monophyletic. The commonly used genus Blicca is a junior synonym to Abramis and both genera should become merged. The genus Tinca is rather distinct from the Alburninae Leuciscinae lineage and clearly does not belong to this group. These conclusions are consistent with published phylogenetic analyses of sequence data. These analyses underline that despite the developments in sequencing allozymes are a cheap and valuable tool in phylogenetics. Combining the estimate of the phylogenetic tree and biogeographic data, there was a decrease of distributional overlap when moving from the tips of the tree to the root. This pattern is consistent with sympatric speciation.     

Evolutionary processes,dispersal limitation and climatic history shape current diversity patterns of European dragonflies

We investigated the effects of contemporary and historical factors on the spatial variation of European dragonfly diversity. Specifically, we tested to what extent patterns of endemism and phylogenetic diversity of European dragonfly assemblages are structured by 1) phylogenetic conservatism of thermal adaptations and 2) differences in the ability of post‐glacial recolonization by species adapted to running waters (lotic) and still waters (lentic). We investigated patterns of dragonfly diversity using digital distribution maps and a phylogeny of 122 European dragonfly species, which we constructed by combining taxonomic and molecular data. We calculated total taxonomic distinctiveness and mean pairwise distances across 4192 50 × 50 km equal‐area grid cells as measures of phylogenetic diversity. We compared species richness with corrected weighted endemism and standardized effect sizes of mean pairwise distances or residuals of total taxonomic distinctiveness to identify areas with higher or lower phylogenetic diversity than expected by chance. Broken‐line regression was used to detect breakpoints in diversity–latitude relationships. Dragonfly species richness peaked in central Europe, whereas endemism and phylogenetic diversity decreased from warm areas in the south‐west to cold areas in the north‐east and with an increasing proportion of lentic species. Except for species richness, all measures of diversity were consistently higher in formerly unglaciated areas south of the 0°C isotherm during the Last Glacial Maximum than in formerly glaciated areas. These results indicate that the distributions of dragonfly species in Europe were shaped by both phylogenetic conservatism of thermal adaptations and differences between lentic and lotic species in the ability of post‐glacial recolonization/dispersal in concert with the climatic history of the continent. The complex diversity patterns of European dragonflies provide an example of how integrating climatic and evolutionary history with contemporary ecological data can improve our understanding of the processes driving the geographical variation of biological diversity.     

LiDAR‐derived canopy structure supports the more‐individuals hypothesis for arthropod diversity in temperate forests

Despite considerable progress in the ability to measure the complex 3‐D structure of forests with the improvement of remote‐sensing techniques, our mechanistic understanding of how biodiversity is linked to canopy structure is still limited. Here we tested whether the increase in arthropod abundance and richness in beech forest canopies with increasing canopy complexity supports the more‐individuals hypothesis or the habitat‐heterogeneity hypothesis. We used fogging to collect arthropod samples from 80 standardized plots from canopies of single‐ to multi‐layered mature montane European beech stands. Tree height and an independent measure of vertical heterogeneity – the vertical distribution ratio – on each arthropod sampling plot were derived from high‐resolution full‐waveform airborne laser scanning data. Mixed‐model path analysis based on almost 20 000 specimens of 762 species from 11 orders provided support for the more‐individuals hypothesis, with higher arthropod abundance but not higher species richness in stands with a more equal vertical distribution of plant biomass. By contrast, we found no support for the habitat‐heterogeneity hypothesis. The increase in the number of individuals with increasing vertical distribution of biomass might be caused either by increasing leaf area, as indicated by higher space filling and productivity in multi‐layered stands, or by higher persistence of arthropod populations owing to better shelter, reduced competition and more refuges under harsh conditions, or by both. High‐resolution airborne laser scanning, with its ability to penetrate dense canopies under leaf‐on conditions, has proved suitable for measuring vertical structures as a predictor for canopy diversity. Expanding combinations of remote‐sensing and canopy‐biodiversity data opens many avenues for improving our understanding of the link between diversity and forest structures.     

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Liposome fractionation and size analysis by asymmetrical flow field-flow fractionation/multi-angle light scattering: influence of ionic strength and osmotic pressure of the carrier liquid

Asymmetrical flow field-flow fractionation (AsFlFFF)/multi-angle light scattering (MALS) was employed for studying filter-extruded liposomes in carrier solutions with different ionic strength and osmolarity. By dilution of preformed liposome suspensions with different media, only the ionic strength in the external free aqueous phase was changed. Under such conditions the liposomes were found to elute at almost identical elution times, which is in contrast to earlier studies. This may be explained by two opposing effects: (a) modulation of inter-particulate and particle-wall-repulsion effects and (b) osmotic stress-induced changes in vesicle size. The latter effect was demonstrated when analysing liposomes upon dilution in media of constant ionic strength, but varying osmotic pressure (with or without 150 mmol L^?1 sucrose supplement). The osmotic stress-induced change in liposome size was found to be size dependent. Larger liposomes appeared to both shrink and swell when exposed to hyper- or hypoosmotic media, respectively. Smaller liposomes appeared to shrink but not to swell. The potential causes of this effect are discussed.