Incorporating anthropogenic effects into trophic ecology: predator–prey interactions in a human-dominated landscape

Apex predators perform important functions that regulate ecosystems worldwide. However, little is known about how ecosystem regulation by predators is influenced by human activities. In particular, how important are top-down effects of predators relative to direct and indirect human-mediated bottom-up and top-down processes? Combining data on species'' occurrence from camera traps and hunting records, we aimed to quantify the relative effects of top-down and bottom-up processes in shaping predator and prey distributions in a human-dominated landscape in Transylvania, Romania. By global standards this system is diverse, including apex predators (brown bear and wolf), mesopredators (red fox) and large herbivores (roe and red deer). Humans and free-ranging dogs represent additional predators in the system. Using structural equation modelling, we found that apex predators suppress lower trophic levels, especially herbivores. However, direct and indirect top-down effects of humans affected the ecosystem more strongly, influencing species at all trophic levels. Our study highlights the need to explicitly embed humans and their influences within trophic cascade theory. This will greatly expand our understanding of species interactions in human-modified landscapes, which compose the majority of the Earth''s terrestrial surface.     

Land use legacy effects on woody vegetation in agricultural landscapes of south‐western Ethiopia

Aim

Past land use legacy effects—extinction debts and immigration credits—might be particularly pronounced in regions characterized by complex and dynamic landscape change. The aim of this study was to evaluate how current woody plant species distribution, composition and richness related to historical and present land uses.

Location

A smallholder farming landscape in south‐western Ethiopia.

Methods

We surveyed woody plants in 72 randomly selected 1‐ha sites in farmland and grouped them into forest specialist, generalist and pioneer species. First, we investigated woody plant composition and distribution using non‐metric multidimensional scaling. Second, we modelled species richness in response to historical and current distance from the forest edge. Third, we examined diameter class distributions of trees in recently converted vs. permanent farmland.

Results

Historical distance was a primary driver of woody plant composition and distribution. Generalist and pioneer species richness increased with historical distance. Forest specialists, however, did not respond to historical distance. Only few old individuals of forest specialist species remained in both recently converted and permanent farmlands.

Main conclusions

Our findings suggest that any possible extinction debt for forest specialist species in farmland at the landscape scale was rapidly paid off, possibly because farmers cleared large remnant trees. In contrast, we found substantial evidence of immigration credits in farmland for generalist and pioneer species. This suggests that long‐established farmland may have unrecognized conservation values, although apparently not for forest specialist species. We suggest that conservation policies in south‐western Ethiopia should recognize not only forests, but also the complementary value of the agricultural mosaic—similar to the case of European cultural landscapes. A possible future priority could be to better reintegrate forest species in the farmland mosaic.

     

An Algorithm to Automatically Generate the Combinatorial Orbit Counting Equations

Graphlets are small subgraphs, usually containing up to five vertices, that can be found in a larger graph. Identification of the graphlets that a vertex in an explored graph touches can provide useful information about the local structure of the graph around that vertex. Actually finding all graphlets in a large graph can be time-consuming, however. As the graphlets grow in size, more different graphlets emerge and the time needed to find each graphlet also scales up. If it is not needed to find each instance of each graphlet, but knowing the number of graphlets touching each node of the graph suffices, the problem is less hard. Previous research shows a way to simplify counting the graphlets: instead of looking for the graphlets needed, smaller graphlets are searched, as well as the number of common neighbors of vertices. Solving a system of equations then gives the number of times a vertex is part of each graphlet of the desired size. However, until now, equations only exist to count graphlets with 4 or 5 nodes. In this paper, two new techniques are presented. The first allows to generate the equations needed in an automatic way. This eliminates the tedious work needed to do so manually each time an extra node is added to the graphlets. The technique is independent on the number of nodes in the graphlets and can thus be used to count larger graphlets than previously possible. The second technique gives all graphlets a unique ordering which is easily extended to name graphlets of any size. Both techniques were used to generate equations to count graphlets with 4, 5 and 6 vertices, which extends all previous results. Code can be found at https://github.com/IneMelckenbeeck/equation-generator and https://github.com/IneMelckenbeeck/graphlet-naming.     

Stable transformation of eggplant (Solanum melongena L.) by cocultivation of tissues withAgrobacterium tumefaciens carrying a binary plasmid vector

Stable transformation of eggplant to kanamycin resistance was obtained by cocultivation of cotyledonary and young leaves with the hypervirulent, fully oncogenicAgrobacterium tumefaciens strain A281 carrying plasmid pGA472. No transformation was observed when using the disarmedA. tumefaciens LBA4404 strain carrying pGA472 or when using either strain for cocultivation with eggplant suspension cells.The NPTII enzyme and DNA dot blot assays performed on callus cells growing in the presence of kanamycin indicated both the presence and expression of the foreign gene. The highest proportion of transformed explants was obtained from intact cotyledonary leaf pieces while the highest NPTII enzyme specific activity was detected in callus cells originating from superficially wounded cotyledonary leaf pieces. Kanamycin-resistant plantlets were regenerated after six months in culture.Abbreviations CTAB Cetyltrimethylammonium Bromide - DTT Dithiothreitol - EDTA Ethylenediaminetetraacetic Acid - NAA Naphtaleneacetic Acid - 2,4-D 2,4-Dichlorophenoxyacetic Acid - NPT II Neomycin Phosphotransferase     

The use of intercalating dye molecules in the study of chromatin structure

This paper reviews the field of chromatin structure studied by means of dye molecules believed to intercalate within DNA. The emphasis is on dyes whose binding properties are the best characterized (ethidium bromide (EB). actinomycin D(AMD), proflavine (PF)) but studies in which less common dye molecules are used are also considered. A comparison is made between the binding of these dyes to purified DNA and to whole or partially deproteinized chromatin in order to investigate both the availability of DNA in chromatin and the localization of chromosomal proteins or the DNA backbone.     

Immunogenic (tum−) variants obtained by mutagenesis of mouse mastocytoma P815

Mutagen treatment of mouse mastocytoma P815 produces highly inununogenic tum^– variants. Most of these variants express potent transplantation antigens which are not present on the original P815 tumor cells. These tum^– antigens, which appear to be specific for each variant, elicit a strong cytolytic T lymphocyte (CTL) response, but do not seem to induce a specific antibody response. As a first step in the isolation of the gene of a tum^– antigen, we attempted DNA-mediated gene transfer. As a DNA recipient cell we used P1.HTR, a highly transfectable P815 cell line, whose selection has been previously described. For the detection of antigen-expressing cells in transfected populations we developed a procedure that relies on the ability of these cells to stimulate the proliferation of the relevant CTL. Using DNA from tum^– variant P91 mixed with a plasmid carrying an antibiotic resistance gene, we obtained several independent transfectants expressing a tum^– antigen, at a frequency of approximately 1 in 13 000 antibiotic-resistant transfectants. These transfectants express only one of the two tum^– antigens that were identified on P91, suggesting that these tum^– antigens correspond to different genes. We expect that the detection procedure described here will be-suitable for the identification of transfectants for any gene that determines the expression of an antigen recognized by CTL.     

Duplication of a 2,4-dichlorophenoxyacetic acid monooxygenase gene in Alcaligenes eutrophus JMP134(pJP4).

The Alcaligenes eutrophus JMP134 plasmid pJP4 contains genes necessary for the complete degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and 3-chlorobenzoic acid. tfdA encodes 2,4-D monooxygenase, the initial enzyme in the 2,4-D catabolic pathway. The tfdA locus has recently been localized to a region on pJP4 13 kilobases away from a cluster of five genes, tfdB to tfdF, which encode the enzymes responsible for the further degradation of 2,4-D to chloromaleylacetic acid (W.R. Streber, K. N. Timmis, and M. H. Zenk, J. Bacteriol. 169:2950-2955, 1987). A second, dissimilar locus on pJP4, tfdAII, has been observed which encodes 2,4-D monooxygenase activity. Gas chromatographic analysis of the 2,4-D metabolites of A. eutrophus harboring pJP4 or subclones thereof localized tfdAII to within a 9-kilobase SstI fragment of pJP4 which also carries the genes tfdBCDEF. This fragment was further characterized in Escherichia coli by deletion and subcloning analysis. A region of 2.5 kilobases, adjacent to tfdC, enabled E. coli extracts to degrade 2,4-D to 2,4-dichlorophenol. Hybridization under low-stringency conditions was observed between tfdA and tfdAII, signifying that the 2,4-D monooxygenase gene was present as two related copies on pJP4.