Urban Biodiversity and Landscape Ecology: Patterns, Processes and Planning

Effective planning for biodiversity in cities and towns is increasingly important as urban areas and their human populations grow, both to achieve conservation goals and because ecological communities support services on which humans depend. Landscape ecology provides important frameworks for understanding and conserving urban biodiversity both within cities and considering whole cities in their regional context, and has played an important role in the development of a substantial and expanding body of knowledge about urban landscapes and communities. Characteristics of the whole city including size, overall amount of green space, age and regional context are important considerations for understanding and planning for biotic assemblages at the scale of entire cities, but have received relatively little research attention. Studies of biodiversity within cities are more abundant and show that longstanding principles regarding how patch size, configuration and composition influence biodiversity apply to urban areas as they do in other habitats. However, the fine spatial scales at which urban areas are fragmented and the altered temporal dynamics compared to non-urban areas indicate a need to apply hierarchical multi-scalar landscape ecology models to urban environments. Transferring results from landscape-scale urban biodiversity research into planning remains challenging, not least because of the requirements for urban green space to provide multiple functions. An increasing array of tools is available to meet this challenge and increasingly requires ecologists to work with planners to address biodiversity challenges. Biodiversity conservation and enhancement is just one strand in urban planning, but is increasingly important in a rapidly urbanising world

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

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Biodiversity responses to vegetation structure in a fragmented landscape: ant communities in a peri-urban coastal dune system

© 2016 Springer International Publishing Switzerland. Habitat fragmentation often results in significant degradation of the structure and composition of remnant natural vegetation, leading to substantial biodiversity decline. Ants are an ecologically dominant faunal group known to be sensitive to vegetation degradation following fragmentation. We examined ant diversity and composition in relation to changes in vegetation structure in remnant coastal vegetation in the global biodiversity hotspot of southwestern Western Australia. The key features of vegetation structure driving the species and functional diversity and composition of ant communities were measures of cover of vegetation and bare ground. However, these effects were highly idiosyncratic at the species level. Cluster analyses based on plant species composition classified plots into two groups corresponding to relatively intact and degraded vegetation respectively. Although systematic changes in plant diversity and vegetation structure were observed between the two groups, key features from an ant perspective (native plant cover and bare ground) remained unchanged. Vegetation degradation consequently had little overall effect on ant species composition and functional diversity. The major disturbance–related impact on ant communities was through invasion by exotic ants, especially Pheidole megacephala; however, this occurred only in close proximity to development. Our results suggest that the priority for conserving ant diversity in our coastal dune system is the prevention of invasion by exotic species

Systematic landscape restoration in the rural-urban fringe: meeting conservation planning and policy goals

The original publication is available at www.springerlink.comMany landscapes that straddle the rural/urban divide suffer from low levels of species diversity following extensive clearing and fragmentation of native vegetation communities and conversion of land to agriculture. Further pressures are placed on remnant vegetation by encroaching urban expansion. These landscapes now exhibit a mosaic of small, patchy vegetation remnants that are under considerable pressure from housing and light-industrial development. Furthermore, agriculture in these landscapes tends to be of high economic value from uses such as intensive horticulture. Concerted and well-planned efforts are needed to balance the many conflicts of interest and competing demands for land with the need to restore landscapes for the protection of biodiversity. There has been a recent move in Australia toward regional biodiversity planning and goal setting, however specific detail on how to plan for achieving targets in complex landscapes is lacking. This paper applies a systematic landscape restoration model to a mixed-use, peri-urban landscape on the northern fringes of Adelaide, South Australia. The region contains fragments of remnant vegetation amongst a mosaic of high-value horticulture, light industry and urban development. Models produce maximally efficient solutions that meet comprehensive, adequate and representative conservation targets. Further constraints are added to the model to take into account the value of agricultural output, the biodiversity value of remnants, and property size and tenure. The effects on solution efficiencies as the number of constraints increase are investigated. This paper demonstrates the flexibility found in applying a systematic landscape restoration methodology. The process we present can be transferred to any rural-urban fringe region. © 2007 Springer Science+Business Media, Inc.Neville D. Crossman, Brett A. Bryan, Bertram Ostendorf and Sally Collin