Islands,mainland, and terrestrial fragments: How isolation shapes plant diversity

The fragmentation of natural habitats is a major threat for biodiversity. However, the impact and spatial scale of natural isolation mechanisms leading to species loss, compared to anthropogenic fragmentation, are not clear, mainly due to differences between fragments and islands, such as matrix permeability. We studied a 500 km² Mediterranean region in France, including urban habitat fragments, continuous habitat, and continental‐shelf islands. On the basis of 295 floristic relevés, we built species–area relationships to compare isolation in fragments after urbanization, with continuous habitat and continental‐shelf islands. We assumed either no dispersal, infinite dispersal, or estimated intermediate levels of habitat reachability through graph theory. Isolation mechanisms occurred in fragments but with a lower strength than in near‐shore islands, and most importantly affected perennial plants. Annual plants were less affected, probably due to their smaller size and shorter life cycle. Isolation occurred at landscape level in fragments and at patch level in islands. The amount of reachable habitat (accounting for spatial configuration) explained local species richness in both systems, but the amount of habitat (no consideration of spatial configuration) was already a good predictor. These results suggest an important role of habitat amount around fragments in mitigating the isolation effects observed in near‐shore islands, and the importance of carefully considering different functional groups.     

Graph models of habitat mosaics

Graph theory is a body of mathematics dealing with problems of connectivity, flow, and routing in networks ranging from social groups to computer networks. Recently, network applications have erupted in many fields, and graph models are now being applied in landscape ecology and conservation biology, particularly for applications couched in metapopulation theory. In these applications, graph nodes represent habitat patches or local populations and links indicate functional connections among populations (i.e. via dispersal). Graphs are models of more complicated real systems, and so it is appropriate to review these applications from the perspective of modelling in general. Here we review recent applications of network theory to habitat patches in landscape mosaics. We consider (1) the conceptual model underlying these applications; (2) formalization and implementation of the graph model; (3) model parameterization; (4) model testing, insights, and predictions available through graph analyses; and (5) potential implications for conservation biology and related applications. In general, and for a variety of ecological systems, we find the graph model a remarkably robust framework for applications concerned with habitat connectivity. We close with suggestions for further work on the parameterization and validation of graph models, and point to some promising analytic insights.     

Feeding studies on gynoparae, males and apterous virginoparae of Myzus persicae on potato by electrical penetration graph

Abstract:  Feeding behaviour of parthenogenetic apterae, post-teneral gynoparae and males of a holocyclic parthenogenetic lineage of Myzus persicae (Sulzer) (Hem., Aphididae) was studied on potato plants, Solanum tuberosum L. (Solanaceae) by DC-electrical penetration graph recording. Differences were observed between morphs during the 7-h recordings, specifically in the first phase of subcuticular probing and in xylem and phloem-related activities. The time required for the first penetration and first cell puncture of the non-vascular tissues was shorter in apterae than in gynoparae and males. Apterae more often showed phloem activities and sustained sap ingestion (100%) than winged morphs ( ca. 25%). In addition, phloem ingestion was much longer in apterae than in winged morphs, 3458 s and 25–70 s respectively. In contrast, winged morphs spent 14–21% of the available time ingesting sap from xylem while in apterae xylem sap uptake was only for 2% of the time. Furthermore, the data showed that males perform in general all the feeding behaviours that other conspecific morphs exhibit. The differences in feeding behaviour among morphs of M. persicae are discussed in relation to host specialization and to their possible involvement in non-persistent transmission of viruses.     

Phloem specific aphid resistance in Cucumis melo line AR 5: effects on feeding behaviour and performance of Aphis gossypii

The feeding behaviour, excretion rate, and life history traits of the cotton-melon aphid, Aphis gossypii (Glover) (Homoptera, Aphididae), were measured on a resistant melon, Cucumis melo L., breeding line, AR 5. The site of resistance detection by the aphids was determined using the electrical penetration graph (EPG) technique. EPG recordings showed that resistance is expressed within the host plant, rather than on its surface, because the time to first stylet penetration was not significantly different between AR 5 and the closely related susceptible breeding line, PMR 5. EPG patterns associated with stylet pathway activities of the aphids were not significantly different between the resistant and susceptible lines. Significant behavioural differences were observed only after stylets contacted phloem sieve elements. On AR 5, the duration of salivation after sieve element puncture (waveform E1) was significantly longer, and the number of aphids showing phloem sap ingestion (waveform E2) was significantly reduced. We conclude that the resistance mechanism producing the effects seen in this study acts within the phloem sieve elements. Monitoring of excretion rates on the two genotypes showed that aphid feeding was delayed and greatly reduced on the resistant genotype. Comparisons of aphid life history traits and population development between host plant genotypes showed that the effects of resistance act throughout aphid development and are highly effective at slowing down population increase.     

Genetic analysis of photosynthesis and productivity in corn

Summary The genetic relationships among different inbred stocks of corn with respect to different indices of photosynthetic efficiency and plant productivity was assessed by means of diallel graphs. The salient feature of the current study was apparent overdominance for some important indices of photosynthetic efficiency, viz. photosynthetic rate/unit leaf area (at the silking stage), total chlorophyll content and chlorophyll a content, as well as for total dry matter production and economic yield. The results could be explained in terms of complementary gene action and the multiplicative effects of the sub-components that comprise these traits. However, complete dominance was recorded for photosynthetic rate (at the grain filling period), leaf area/plant, number of leaves/plant, number of leaves above the ear, ratio of chlorophyll a/b and harvest index. In the majority of cases graphic analysis was possible only when a number of epistatic parents were omitted from the analysis. Although the position of the array points for different indices of photosynthetic efficiency was consistent across the years, the ontogenetic and seasonal differences in the genetic behaviour of parents, meaning thereby, different loci being active at different stages and seasons, was apparent. The same was true for the epistatic parents. Non-allelic interaction of the genes rather than the non-random distribution of the genes among the parents seemed to be the most common cause of disturbance in the W_r/V_r relationship.Inbred stock MG 115 was identified to be the most promising because it embodied an efficient photosynthetic machinery by virtue of increasing the number of alleles for a majority of the indices of photosynthetic efficiency, thereby enabling it to register the highest biological productivity and economic yield. Further, inbred stocks MG 138, MG 121, and MG 125 were also promising for different photosynthetic parameters.     

Bioinformatics analysis of alternative splicing

Over the past few years, the analysis of alternative splicing using bioinformatics has emerged as an important new field, and has significantly changed our view of genome function. One exciting front has been the analysis of microarray data to measure alternative splicing genome-wide. Pioneering studies of both human and mouse data have produced algorithms for discerning evidence of alternative splicing and clustering genes and samples by their alternative splicing patterns. Moreover, these data indicate the presence of alternative splice forms in up to 80 per cent of human genes. Comparative genomics studies in both mammals and insects have demonstrated that alternative splicing can in some cases be predicted directly from comparisons of genome sequences, based on heightened sequence conservation and exon length. Such studies have also provided new insights into the connection between alternative splicing and a variety of evolutionary processes such as Alu-based exonisation, exon creation and loss. A number of groups have used a combination of bioinformatics, comparative genomics and experimental validation to identify new motifs for splice regulatory factors, analyse the balance of factors that regulate alternative splicing, and propose a new mechanism for regulation based on the interaction of alternative splicing and nonsense-mediated decay. Bioinformatics studies of the functional impact of alternative splicing have revealed a wide range of regulatory mechanisms, from NAGNAG sites that add a single amino acid; to short peptide segments that can play surprisingly complex roles in switching protein conformation and function (as in the Piccolo C2A domain); to events that entirely remove a specific protein interaction domain or membrane anchoring domain. Common to many bioinformatics studies is a new emphasis on graph representations of alternative splicing structures, which have many advantages for analysis.     

Network representation of protein interactions—Experimental results

A graph theoretical analysis of nuclear magnetic resonance (NMR) data of six different protein interactions has been presented. The representation of the protein interaction data as a graph or network reveals that all of the studied interactions are based on a common functional concept. They all involve a single densely packed hub of functionally correlated residues that mediate the ligand binding events. This is found independent of the kind of protein (folded or unfolded) or ligand (protein, polymer or small molecule). Furthermore, the power of the graph analysis is demonstrated at the examples of the Calmodulin (CaM)/Calcium and the Cold Shock Protein A (CspA)/RNA interaction. The presented approach enables the precise determination of multiple binding sites for the respective ligand molecules.