Functional composition drives ecosystem function through multiple mechanisms in a broadleaved subtropical forest

Understanding the role of biodiversity (B) in maintaining ecosystem function (EF) is a foundational scientific goal with applications for resource management and conservation. Two main hypotheses have emerged that address B-EF relationships: niche complementarity (NC) and the mass-ratio (MR) effect. We tested the relative importance of these hypotheses in a subtropical old-growth forest on the island nation of Taiwan for two EFs: aboveground biomass (ABG) and coarse woody productivity (CWP). Functional dispersion (FDis) of eight plant functional traits was used to evaluate complementarity of resource use. Under the NC hypothesis, EF will be positively correlated with FDis. Under the MR hypothesis, EF will be negatively correlated with FDis and will be significantly influenced by community-weighted mean (CWM) trait values. We used path analysis to assess how these two processes (NC and MR) directly influence EF and may contribute indirectly to EF via their influence on canopy packing (stem density). Our results indicate that decreasing functional diversity and a significant influence of CWM traits were linked to increasing AGB for all eight traits in this forest supporting the MR hypothesis. Interestingly, CWP was primarily influenced by NC and MR indirectly via their influence on canopy packing. Maximum height explained more of the variation in both AGB and CWP than any of the other plant functional traits. Together, our results suggest that multiple mechanisms operate simultaneously to influence EF, and understanding their relative importance will help to elucidate the role of biodiversity in maintaining ecosystem function

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

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

A Sentinel-2 Image-Based Irrigation Advisory Service: Cases for Tea Plantations

In this study, we aim to develop an inexpensive site-specific irrigation advisory service for resolving disadvantages related to using immobile soil moisture sensors and to the differences in irrigation needs of different tea plantations affected by variabilities in cultivars, plant ages, soil heterogeneity, and management practices. In the paper, we present methodologies to retrieve two biophysical variables, surface soil water content and canopy water content of tea trees from Sentinel-2 (S2) (European Space Agency, Paris, France) images and consider their association with crop water availability status to be used for making decisions to send an alert level. Precipitation records are used as auxiliary information to assist in determining or modifying the alert level. Once the site-specific alert level for each target plantation is determined, it is sent to the corresponding farmer through text messaging. All the processes that make up the service, from downloading an S2 image from the web to alert level text messaging, are automated and can be completed before 7:30 a.m. the next day after an S2 image was taken. Therefore, the service is operated cyclically, and corresponds to the five-day revisit period of S2, but one day behind the S2 image acquisition date. However, it should be noted that the amount of irrigation water required for each site-specific plantation has not yet been estimated because of the complexities involved. Instead, a single irrigation rate (300 t ha−1) per irrigation event is recommended. The service is now available to over 20 tea plantations in the Mingjian Township, the largest tea producing region in Taiwan, free of charge since September 2020. This operational application is expected to save expenditures on buying irrigation water and induce deeper root systems by decreasing the frequency of insufficient irrigation commonly employed by local farmers