Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.     

Tobacco blue mould disease caused by Peronospora hyoscyami f. sp. tabacina

Blue mould [ Peronospora hyoscyami f. sp. tabacina (Adam) Skalicky 1964] is one of the most important foliar diseases of tobacco that causes significant losses in the Americas, south-eastern Europe and the Middle East. This review summarizes the current knowledge of the mechanisms employed by this oomycete pathogen to colonize its host, with emphasis on molecular aspects of pathogenicity. In addition, key biochemical and molecular mechanisms involved in tobacco resistance to blue mould are discussed.
Taxonomy: Kingdom: Chromista (Straminipila); Phylum: Heterokontophyta; Class: Oomycete; Order: Peronosporales; Family: Peronosporaceae; Genus: Peronospora ; Species: Peronospora hyoscyami f. sp. tabacina .
Disease symptoms: The pathogen typically causes localized lesions on tobacco leaves that appear as single, or groups of, yellow spots that often coalesce to form light-brown necrotic areas. Some of the leaves exhibit grey to bluish downy mould on their lower surfaces. Diseased leaves can become twisted, such that the lower surfaces turn upwards. In such cases, the bluish colour of the diseased plants becomes quite conspicuous, especially under moist conditions when sporulation is abundant. Hence the name of the disease: tobacco blue mould.
Infection process: The pathogen develops haustoria within plant cells that are thought to establish the transfer of nutrients from the host cell, and may also act in the delivery of effector proteins during infection.
Resistance: Several defence responses have been reported to occur in the Nicotiana tabacum – P. hyoscyami f. sp. tabacina interaction. These include the induction of pathogenesis-related genes, and a correlated increase in the activities of typical pathogenesis-related proteins, such as peroxidases, chitinases, β-1,3-glucanases and lipoxygenases. Systemic acquired resistance is one of the best characterized tobacco defence responses activated on pathogen infection.     

On the Ecology of Coexistence in Parthenogenetic and Bisexual Lizards of the Genus Cnemidophorus

In the center of their distribution in North America, membersof a complex of parthenogenetic and bisexual lizards of thegenus Cnemidophorus may be found side by side with one or moreof the others in a bewildering variety of patterns and ecologicalassociations. Exactly why so many congeneric species are foundliving together and exactly what their ecological, physiologicaland geographical requirements are remains virtually unknown.Here 1 summarize all reported cases of sympatry among six speciesof Cnemidophorus and discuss in detail specific examples ofsome of these interactions based on several years of field collectionsand observations. In addition I present the first field experimentalstudy designed to understand the ecological relationships ofsympatry in Cnemidophorus.     

Chromosome characterization and biogeographic relations among three populations of the driftwood catfish Parauchenipterus galeatus (Linnaeus, 1766) (Siluriformes: Auchenipteridae) in Brazil

The present study employed basic and molecular cytogenetic methods to characterize three populations of Parauchenipterus galeatus from the basins of the Paraná and São Francisco Rivers, and a region of connection between the two basins. Although the diploid number was equal to 58 chromosomes, variations in karyotype formula were detected among the populations. B chromosomes were detected only in the population from the São Francisco River. Heterochromatin was located in the terminal position in almost all the chromosomes and in the pericentromeric position in some acrocentric chromosomes in the three populations. A single nucleolus organizer region was detected by silver nitrate and 18S rDNA‐fluorescent in situ hybridization in the short arm of one subtelocentric pair in the three populations, varying only in the chromosome pair bearing this site. The 5S rDNA sites were located in two submetacentric chromosome pairs in the three populations, varying only in the chromosome pairs bearing these sequences. Classic and molecular chromosome markers, along with the context of the natural history of the formation of hydrographic basins, ecological aspects, and the geographic isolation of populations between hydrographic basins and within the same basin, were important contributions to the discussion on possible biogeographic relations among the populations of Parauchenipterus galeatus. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 648–656.     

Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species’ genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well‐supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49 500 ¹⁴C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40 400 to 10 250 ¹⁴C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66–77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.     

Multiple pleurograms in Chamaecrista Moench (Leguminosae, Caesalpinioideae)

According to the literature, the seeds of Chamaecrista lack pleurograms and have pitted testas aligned in vertical lines. Preliminary observations have revealed that these small structures consist of superficial alterations of the testa that are coloured differently to the rest of the seed coat and stand out as pits. However, no anatomical inspection has yet determined the precise composition of these pits. The present work examined the morphology, surface micromorphology, anatomy, and histochemistry of the seed coat of mature seeds of C. desvauxii var. latistipula , C. flexuosa , and C. nictitans var. patellaria in order to elucidate the structural nature of the seed coat pits. For this, seed coats were studied using scanning electron microscopy and light microscopy. Structural modifications were examined in the seed coats of the studied species, and variations were noted in the mucilaginous layer, in the thickness of the palisade layer, and in the presence of larger hypodermic cells. Based on the anatomical features observed, and comparing these with published data on pleurograms in the Caesalpinioideae, it was determined that the structures referred to previously as tegumental pits on Chamaecrista seeds are actually small and numerous pleurograms, reported here for the first time.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 487–492.     

A comparative study of cannibalism and predation in seven species of flour beetle

Abstract 1. The present study quantified egg and pupal cannibalism, and interspecific predation on eggs and pupae, by larvae and adults of seven species of flour beetle (Tribolium spp.) under laboratory conditions: T. anaphe, T. brevicornis, T. castaneum, T. confusum, T. destructor, T. freemani, and T. madens. 2. Variation among species in cannibalism and predation propensities did not reflect taxonomic affinities within the genus, indicating that these behaviours were shaped by ecology at species level. 3. Within species, larvae and adults displayed different propensities for cannibalism and predation, leading to the conclusion that these behaviours evolve independently in the two life stages. 4. All species behaved as intraguild predators to some degree, especially in the adult stage. 5. Three general patterns of cannibalism and predation were described by principal component mapping and cluster analysis. 6. The first group comprised three cosmopolitan pest species that were more voracious as adults than as larvae: T. castaneum, T. confusum, and T. destructor. It is proposed that stored product environments select for high adult voracity because the costs associated with emigration from such rare, but resource‐rich, habitats intensifies interference competition among adults. 7. The second group consisted of species that inhabit natural environments and that were more voracious as larvae: T. anaphe, T. freemani, and T. madens. Habitats for these species are probably numerous, but generally poor in quality, a situation that intensifies larval competition, while favouring earlier adult emigration. 8. The largest species, T. brevicornis, demonstrated inconsistent voracity between life stages and was the only species with chemically defended pupae. 9. It is proposed that consumption of eggs provides primarily nutritional benefits, whereas consumption of pupae has a more important role in interference competition.     

Predicting the outcome of trophic manipulation in lakes—a comment on Harris (1994)

1. Harris ( Freshwater Biology , 32 , 143–160, 1994) asserts that while empirical modelling of lake ecosystem properties has yielded general predictions and useful explanations, research into the effects of food-web interactions has not. I provide an explicit example of a useful, quantitative prediction gleaned from experiments on food-web effects—the relationship between total phosphorus and the magnitude of response of algal biomass.
2. I further argue that Harris errs in asserting that food-web effects will be ineffective in eutrophic lakes. This error stems from a misconception about the relevance of ecosystem behaviour in unmanipulated systems for predictions of how an ecosystem will respond to manipulation. I cite empirical evidence demonstrating that, contrary to Harris's contention, the response of algal biomass to a change in food-web structure increases as lakes are enriched.