Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery

The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next‐generation sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analysed and 127 041 single‐nucleotide polymorphisms identified. This contig data set will contribute to improving our understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.     

Evaluating model transferability for a threatened species to adjacent areas: Implications for rock‐wallaby conservation

When modelling the distribution of a species, it is often not possible to comprehensively sample the whole distribution of the species and managers may have habitat models based on data from one area that they want to apply in other areas. Hence, an important question is: how accurate are models of the distributions of species when applied beyond the areas where they were developed? A first step in measuring model transferability could be testing models in adjacent areas. We predicted the habitat associations of the brush‐tailed rock‐wallaby (Petrogale penicillata) across two spatial scales in two neighbouring study areas in eastern Australia, south‐east Queensland and north‐east New South Wales. We used classification trees for exploratory data analysis of habitat relationships and then applied logistic regression models to predict species occurrence. We assessed the within‐area discriminative ability of the habitat models using cross‐validation and threshold plots, and tested the predictive ability of the models for adjacent areas using the receiver operating characteristic statistic to determine the area under the curve. We found that models performed well within an area and extrapolating them to adjacent areas resulted in good predictive performance at the site scale but substantially poorer predictive performance at the landscape scale. We conclude that distribution models for wildlife species should only be extrapolated to neighbouring areas with caution when using landscape‐scale environmental variables. Alternatively, only key habitat associations predicted by the models at this scale should be transferred across adjacent areas once verified against local knowledge of the ecology of the study species.     

南方红豆杉盆栽扦插育苗技术研究

南方红豆杉(Taxus chinensis var. mairei)是中国特有的国家一级保护植物。2009-2010年采用2年龄实生苗为采条母株进行室内盆栽扦插试验研究,结果表明:珍珠岩和河沙两种基质相比较,珍珠岩上生根率显著高于河沙,是更佳选择;用市售的"花语牌"快速促根剂配制成5、10、15、2 0mg/mL 4个浓度分别处理插穗基部并以蒸馏水作对照发现,10 mg/mL、15 mg/mL处理有利于生长,15 mg/mL处理后生根率显著高于5 mg/mL、10 mg/mL、20 mg/mL及对照。再以同一浓度生根粉分别浸泡4 h、8 h、10 h作对比发现,8 h和10 h处理后生长效果较好,10 h的生根率显著高于4 h、8 h。     

Home range dynamics of the yellow‐footed rock‐wallaby (Petrogale xanthopus celeris) in central‐western Queensland

Analyses of the interspecific differences in macropod home range size suggest that habitat productivity exerts a greater influence on range size than does body mass. This relationship is also apparent within the rock‐wallaby genus. Lim reported that yellow‐footed rock‐wallabies (Petrogale xanthopus xanthopus) inhabiting the semi‐arid Flinders Ranges (South Australia) had a mean home range of 170 ha. While consistent with the hypothesis that species inhabiting less productive habitats will require larger ranges to fulfil their energetic requirements, the ranges reported by Lim were considerably larger than those observed for heavier sympatric macropods. The aim of the current study was to document the home range dynamics of P. x. celeris in central‐western Queensland and undertake a comparison with those reported for their southern counterparts. Wallaby movements were monitored at Idalia National Park, between winter 1992 and winter 1994. Male foraging ranges (95% fixed kernel; 15.4 ha, SD = ±7.8 ha) were found to be significantly larger than those of female wallabies (11.3 ha, SD = ±4.9 ha). Because of varying distances to the wallabies' favoured foraging ground (i.e. an adjacent herb field), the direction in which the wallabies moved to forage also significantly affected range size. Mean home range size was estimated to be 23.5 ha (SD = ±15.2 ha; 95% fixed kernel) and 67.5 ha (SD = ±22.4 ha; 100% minimum convex polygon). The discrepancy between these two estimates resulted from the exclusion of locations, from the 95% kernel estimates, when the wallabies moved to a water source 1.5 km distant from the colony site. The observed foraging and home ranges approximated those that could be expected for a macropod inhabiting the semi‐arid zone (i.e. 2.4 times larger‐than‐predicted from body mass alone). Possible reasons for the disparity between the current study and that of Lim are examined.     

Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling—a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.     

Organic biogeochemistry of groundwater at a mountain coal mine

Measurements of dissolved organic matter (DOM), humic and fulvic acids, carbohydrates, tannins + lignins, phenols and amino acids were made in the groundwater permeating Reclamation site 2 at the Canmore Coal Mine (Alberta, Canada). Estimates of the number of bacteria present in the groundwater were also made using plate and direct count techniques. Temperature, pH, Eh, and oxygen content of the groundwater were measured on two occasions. DOM was very low in concentration (av. 1.62 mg/liter) and consisted principally of fulvic acid. Humic acids formed about 20% of DOM, carbohydrates 6%, tannins + lignins 4%, and trace compounds (phenols, amino acids, and proteins) 2%. Seasonal variations were observed, with tannins + lignins and carbohydrates reaching their highest concentration in the summer, and humic and fulvic acids, and DOM peaking in the winter. The organic composition of the groundwater upstream of the reclamation site did not differ significantly from groundwater sampled from within the reclamation site. Differences were observed, however, between ground and surface waters draining the site. No correlation between concentration and depth was observed. Large numbers of bacteria were found in groundwater using both plate count and direct count methods. Populations were only modestly correlated with the concentrations of organic compounds (r<0.9). Heterotrophic bacteria must have been dependent upon organic matter (both as DOM and as insoluble organic matter in the spoil) for growth, however. The groundwater bacteria studied appeared to be characterized by slow growth under adverse geological conditions with only low concentrations of labile organic compounds present.     

Where are the glacial refugia in Europe? Evidence from pteridophytes

In this paper we demonstrate that, by investigating polyploid complexes in Asplenium, it is possible to locate the areas in Europe that are southern glacial rcfugia, and arc likely to have been so since the beginning of the Pleistocene during the consecutive cold and warm periods in Europe. Identification and conservation of these specific areas that serve as safe havens for plants, and perhaps animals, is of paramount importance for the maintenance of European biodiversity because Man's activities arc resulting in an ever-increasing loss of natural habitats and putting diversity at risk. The genus Asplenium in Europe comprises some 50 taxa: half of these are diploid while the other half arc polyploids derived from the diploids. All aspleniums in Europe are (small) rock ferns with high substrate specificity. Today, most of mainland Europe, Scandinavia and the British Isles has been colonized by polyploid Asplenium species, while the diploids that gave rise to these polyploids are distributed around (and more or less confined to) the Mediterranean Basin. In the tetraploids genetic variation is partitioned mostly between sites, whereas diploids show a high degree of genetic variation both within and between sites. The tctraploid taxa seem capable of single spore colonization via intragametophytic selfing, but the diploid taxa appear to be predominantly outbreeding. For most diploids at least two gametophytes, produced by different spores, have to be present to achieve fertilization and subsequent sporophyte formation for the successful colonization of a new site. This results in a slower rate of colonization. The formation of auto- and allopolyploid taxa from diploid communities appears to have been a recurrent and common feature in Europe. Minority cytotypc exclusion is likely to prevent the establishment of tetraploids within the diploid communities, but spores from tetraploids can establish populations outside the diploid communities. The differences between colonization abilities of tctraploid and ancestral diploid taxa, resulting from their different breeding systems, has prevented the merging and mingling of their ranges and led to the establishment of contact/ hybrid zones. This has resulted in the restriction of diploid populations to ancient glacial rcfugia and the colonization of the rest of Europe by polyploids. Mapping the current distribution of these diploid communities and comparing the genetic diversity within and between outbreeding diploid Asplenium taxa allows us to define the area, age and historical biogcography of these rcfugia and to assess their importance for present day genetic and species diversity in Europe.     

Novel polymorphic microsatellites for the red‐legged partridge (Alectoris rufa) and cross‐species amplification in Alectoris graeca

The red‐legged partridge, Alectoris rufa, is an endemic species of the southwestern Mediterranean, and the most popular game bird in the Iberian Peninsula. A total of 27 microsatellite loci was isolated from an enriched genomic library of A. rufa. Six perfect GT microsatellites were characterized and optimized in 45 individuals of A. rufa. All loci revealed high levels of polymorphism with a number of alleles that ranged from three to 13. Observed heterozygosity ranged from 0.2 to 0.6. Cross‐species amplification showed that all loci were also polymorphic in rock partridge, Alectoris graeca. The new markers will be useful in determining hybridization between both species of Alectoris.     

Food and feeding ecology of the rock fowl Picatthartes oreas in Old Oyo National Park, Nigeria

The rock fowl is an endangered species and its food and feeding ecology was studied in the forest zone of Old Oyo National Park, Nigeria. The methods used were direct observation, and fragmentation analysis of faecal and crop content of samples collected during both the wet and dry seasons. The results showed that rock fowl feed on a wide range of species of insects, fruits and flower buds. In the wet season, animal resources represented 54 and 62% of the adult and chick diet, respectively, whereas in the dry season, animal food resources represented about 60% of both adult and the chick diets. There was a significant difference (P < 0.05) in the food composition of the birds between the dry and wet seasons. There was also a significant (P < 0.05) difference in food preference between adults and chicks. Food sharing was not common, although it was observed between rock fowl cockerels and hens. Food search and selection indices were directly related to season and food availability. It was concluded that food scarcity may not be a serious contributory factor in the threat to the rock fowl.