Matching roots to their environment

Background

Plants form the base of the terrestrial food chain and provide medicines, fuel, fibre and industrial materials to humans. Vascular land plants rely on their roots to acquire the water and mineral elements necessary for their survival in nature or their yield and nutritional quality in agriculture. Major biogeochemical fluxes of all elements occur through plant roots, and the roots of agricultural crops have a significant role to play in soil sustainability, carbon sequestration, reducing emissions of greenhouse gasses, and in preventing the eutrophication of water bodies associated with the application of mineral fertilizers.

Scope

This article provides the context for a Special Issue of Annals of Botany on ‘Matching Roots to Their Environment’. It first examines how land plants and their roots evolved, describes how the ecology of roots and their rhizospheres contributes to the acquisition of soil resources, and discusses the influence of plant roots on biogeochemical cycles. It then describes the role of roots in overcoming the constraints to crop production imposed by hostile or infertile soils, illustrates root phenotypes that improve the acquisition of mineral elements and water, and discusses high-throughput methods to screen for these traits in the laboratory, glasshouse and field. Finally, it considers whether knowledge of adaptations improving the acquisition of resources in natural environments can be used to develop root systems for sustainable agriculture in the future.     

BlackOPs: increasing confidence in variant detection through mappability filtering

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, for a given sample, are expected to be almost completely false positives. We show that these blacklist positions are specific to the alignment algorithm and read length used, and BlackOPs allows users to generate a blacklist specific to their experimental setup. We queried the dbSNP and COSMIC variant databases and found numerous variants indistinguishable from mapping errors. We demonstrate how filtering against blacklist positions reduces the number of potential false variants using an RNA-seq glioblastoma cell line data set. In summary, accounting for mapping-caused variants tuned to experimental setups reduces false positives and, therefore, improves genome characterization by high-throughput sequencing.     

Doing Sovereignty in Native North America: Anishinaabe Counter-Mapping and the Struggle for Land-Based Self-Determination

Beginning with the premise that sovereignty may be most constructively contemplated not as a definable object or objective but instead as a process, this article examines counter-mapping as a way for contemporary indigenous citizens to “do” sovereignty. It surveys three Anishinaabe/Ojibwe communities’ recent use of geographical techniques to communicate their own territorial claims and counter the competing claims of others. In a 21^st century context characterized by urgent extractive-industrial threats to indigenous landbases and lifeways, the cases presented here demonstrate that counter-mapping can serve as a powerful positive tool. Yet because the prevailing methods available to safeguard land-based self-determination also have the potential to undermine it, I conclude by considering some of the pitfalls that complicate counter-mapping’s ability to promote the sovereignty process. I suggest that indigenous people who choose to enact their sovereignty in this manner are indeed empowered, but only within an existing—and inequitable—socio-political system.     

A wingless alpine stonefly from New Zealand,and further information on genus Holcoperla (Plecoptera: Gripopterygidae)

Abstract

Holcoperla magna n.sp. is described and figured from material collected on Headlong Peak, Mt Aspiring National Park. New information is given on H. angularis (Wisely) and H. jacksoni McLellan, and the 3 species are compared. Larvae designated as type specimens of H. angularis are shown to be Apteryoperla monticola Wisely.     

Some aspects of the biology of the hedgehog (Erinaceus europaeus L.) in the Manawatu,New Zealand

In a study area of 16.3 ha of dairy pasture and pine plantations in the Manawatu region of the southern North Island, 150 hedgehogs were marked and 356 recaptures recorded between 1 January 1970 and 24 June 1971. Population density was estimated at between 1.1/ha in winter and 2.5/ha in summer and autumn. Only 11 females and 5 males were considered to be residents, and these used overlapping feeding ranges of similar extent. Concentrations of food organisms became foci of hedgehog activity. During winter, when an estimated 20% of the population died, movement was restricted to the vicinity of the nest site; the hedgehogs hibernated fitfully during July‐October. The breeding season as such extended at least from November to March; some breeding activity was observed in most months, however. The average life span of adults was 1.97 years. The causes of 6 natural deaths and the incidence of abscesses and external parasites were noted.