Comparative seed ecology of the endangered shrub, Pimelea spicata and a threatening weed, Bridal Creeper: Smoke, heat and other fire-related germination cues

Summary Pimelea spicata R. Br. is a nationally listed endangered Australian shrub threatened with extinction by habitat fragmentation and environmental weed invasion. Bridal Creeper (Asparagus asparagoides L. W. Wight) is the primary weed threat to the largest remaining populations of P. spicata in the Cumberland Plain. Fire, as part of an integrated pest management program, offers the potential to stimulate P. spicata populations while controlling Bridal Creeper. It is important, therefore, to understand how the components of fire affect the germination and growth of both species. Using laboratory experiments we investigated the effects of smoke, heat, ash and/or light on the germination of P. spicata and Bridal Creeper. We found a significant promotive effect of smoke and indication of an inhibitory heat shock (90°C for 10 min) effect on the germination of P. spicata seeds. The response of Bridal Creeper seeds to the same factors was complex; while the results of one experiment suggested an inhibitory effect of smoke and a promotive effect of heat, subsequent trials were contradictory, implying that Bridal Creeper, like many weeds, is able to germinate under a wide range of environmental conditions. Other experiments investigated the optimal germination temperature and innate dormancy of P. spicata in the absence of fire‐related germination cues. Of the incubation temperatures investigated, the optimal diurnally fluctuating regime for P. spicata germinations was 10°C and 20°C in the night and day, respectively. The innate dormancy of freshly produced seeds disappeared after 3 months. In contrast to Bridal Creeper, we found a persistent germinable seed bank of about 97 P. spicata seeds/m² located in the top 5 cm of the soil profile. While fire alone is unlikely to kill Bridal Creeper plants, fire may help to manage local infestations of the weed by limiting germination and providing opportunity for herbicide treatment of regrowth.     

Charging up Battery Recycling Policies: Extended Producer Responsibility for Single‐Use Batteries in the European Union,Canada, and the United States

Extended producer responsibility (EPR) policies have proven effective at raising consumer awareness, expanding waste collection infrastructure, and shifting costs of end‐of‐life (EOL) management from municipalities to stewardship organizations. Yet, such policies have been less successful in advancing waste management programs that ensure a net environmental benefit. This article analyzes how EPR policies for single‐use batteries in the European Union (EU), Canada, and the United States address the environmental costs and benefits of EOL management. Considering these EPR policies is instructive, because single‐use batteries have high collection costs and are of relatively low economic value for waste processors. Without deliberate planning, the environmental burdens of collecting and recycling such batteries may exceed the benefits. This article considers how EPR policies for single‐use batteries integrate performance requirements such as collection rates, recycling efficiencies, and best available techniques. It argues that for such policies to be effective, they need to be extended to address waste collection practices, the life cycle consequences of EOL management, and the quality of recovered materials. Such strategies are relevant to EPR policies for other products with marginal secondary value, including some textiles, plastics, and other types of electronic waste.     

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.     

Proteome plasticity in response to persistent environmental change

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Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field‐based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field‐based estimates of fitness components and approximate Bayesian computation (ABC) procedures to estimate habitat‐specific dispersal rates and characterize habitat quality in two‐toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field‐based observations indicated that birth and survival rates were similar in a sparsely shaded cacao farm and adjacent cattle pasture–forest mosaic. Sloth density was threefold higher in pasture compared with cacao, whereas home range size and overlap were greater in cacao compared with pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 single nucleotide polymorphism and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstorey can, in some cases, constitute lower‐quality habitat than pasture–forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field‐based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.     

^137Cs,^134Cs在人工海洋小生境中的行为

在自行建立的人工海洋小生境中,采用示踪法综合地研究~(137)Cs、~(134)Cs在人工小生境中的行为。结果表明,~(137)Cs和~(134)Cs具有共同的生理生态行为,并表现出相似的规律、沉积物对~(137)Cs、~(134)Cs的吸附能力甚低,~(137)Cs、~(134)Cs在海洋动物体内趋于全身性的分布。各主要生化物质均能检出~(137)Cs、~(134)Cs。排泄实验后,海洋动物的胃肠、肝(消化腺)~(137)Cs、~(134)Cs损失显著。沉积物表现为解吸-重吸附的过程。     

Aspects of the ecology of the spotted blindsnake,Typhlops punctatus punctatus in Port‐Harcourt,Nigeria

The ecology of the blindsnake, Typhlops punctatus punctatus in five selected study plots in the River Niger Delta (Port Harcourt, Nigeria) was investigated. A total of 207 specimens were collected, 43% occurring under stones, 30% under leaf litter and 15% under logs. The number of snakes found under cover objects was significantly influenced by the number of cover objects lifted up. GLM analysis revealed that there was no difference in terms of number of snakes observed, once the relative effect of the different number of cover objects lifted up was taken into account, either among study plots or among types of cover objects. These snakes appeared to have a strong affinity for loamy soils, with moisture content of 8–18%, high organic matter (1–6%) and slightly acid pH of 5.4–6.9. Stomach content analysis revealed that these snakes fed mainly upon ants and termites. A case of predation by the toad Bufo maculatus on a juvenile blindsnake was also reported.     

Consistent divergence times and allele sharing measured from cross‐species application of SNP chips developed for three domestic species

Recent advances in technology facilitated development of large sets of genetic markers for many taxa, though most often model or domestic organisms. Cross‐species application of genomic technologies may allow for rapid marker discovery in wild relatives of taxa with well‐developed resources. We investigated returns from cross‐species application of three commercially available SNP chips (the OvineSNP50, BovineSNP50 and EquineSNP50 BeadChips) as a function of divergence time between the domestic source species and wild target species. Across all three chips, we observed a consistent linear decrease in call rate (~1.5% per million years), while retention of polymorphisms showed an exponential decay. These results will allow researchers to predict the expected amplification rate and polymorphism of cross‐species application for their taxa of interest, as well as provide a resource for estimating divergence times.