Comparative analyses of the scaling diversity index and its applicability

As well as the newly developed scaling diversity index, there are also eleven traditional diversity indices to be found in the literature. Analyses show that these eleven traditional indices are unable to formulate the richness component of diversity. In particular, the most widely used index, the Shannon-Weiner index, cannot express the evenness component. On the contrary, the scaling diversity index is able to formulate both the richness aspect and the evenness aspect of diversity. The scaling diversity index has been applied to developing scenarios of ecological diversity at different spatial resolutions and spatial scales. A case study in Fukang in the Xinjiang Uygur Autonomous Region in China shows that the scaling diversity index is sensitive to spatial resolution and is easy to understand. It is scientifically sound and could be operated at affordable cost

Neue linguistische Methoden und arbeitstechnische Verfahren in der Erschliessung der ägyptischen Grammatik

15 páginas, 1 tabla, 6 figuras.Does diversity beget diversity? Diversity includes a diversity of concepts because it is linked to variability in and of life and can be applied to multiple levels. The connections between multiple levels of diversity are poorly understood. Here, we investigated the relationships between genetic, bacterial, and chemical diversity of the endangered Atlanto-Mediterranean sponge Spongia lamella. These levels of diversity are intrinsically related to sponge evolution and could have strong conservation implications. We used microsatellite markers, denaturing gel gradient electrophoresis and quantitative polymerase chain reaction, and high performance liquid chromatography to quantify genetic, bacterial, and chemical diversity of nine sponge populations. We then used correlations to test whether these diversity levels covaried. We found that sponge populations differed significantly in genetic, bacterial, and chemical diversity. We also found a strong geographic pattern of increasing genetic, bacterial, and chemical dissimilarity with increasing geographic distance between populations. However, we failed to detect significant correlations between the three levels of diversity investigated in our study. Our results suggest that diversity fails to beget diversity within a single species and indicates that a diversity of factors regulates a diversity of diversities, which highlights the complex nature of the mechanisms behind diversityResearch funded by grants from the Agence Nationale de la Recherche (ECIMAR), from the Spanish Ministry of Science and Technology SOLID (CTM2010-17755) and Benthomics (CTM2010-22218-C02-01) and the BIOCAPITAL project (MRTN-CT-2004-512301) of the European Union. This is a contribution of the Consolidated Research Group ‘‘Grupo de Ecologı´a Bento´nica,’’ SGR2009-655.Peer reviewe

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