TY - JOUR A1 - Tong, Hao A1 - Nikoloski, Zoran T1 - Machine learning approaches for crop improvement BT - leveraging phenotypic and genotypic big data JF - Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants N2 - Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of the breeding cycle in major crops relevant for sustaining present demands for food, feed, and fuel. In contrast to classical approaches that emphasize the need for resource-intensive phenotyping at all stages of artificial selection, genomic selection dramatically reduces the need for phenotyping. Genomic selection relies on advances in machine learning and the availability of genotyping data to predict agronomically relevant phenotypic traits. Here we provide a systematic review of machine learning approaches applied for genomic selection of single and multiple traits in major crops in the past decade. We emphasize the need to gather data on intermediate phenotypes, e.g. metabolite, protein, and gene expression levels, along with developments of modeling techniques that can lead to further improvements of genomic selection. In addition, we provide a critical view of factors that affect genomic selection, with attention to transferability of models between different environments. Finally, we highlight the future aspects of integrating high-throughput molecular phenotypic data from omics technologies with biological networks for crop improvement. KW - genomic selection KW - genomic prediction KW - machine learning KW - multiple KW - traits KW - multi-omics KW - GxE interaction Y1 - 2020 U6 - https://doi.org/10.1016/j.jplph.2020.153354 SN - 0176-1617 SN - 1618-1328 VL - 257 PB - Elsevier CY - München ER - TY - GEN A1 - Romero-Munoz, Alfredo A1 - Fandos, Guillermo A1 - Benítez-López, Ana A1 - Kuemmerle, Tobias T1 - Habitat destruction and overexploitation drive widespread declines in all facets of mammalian diversity in the Gran Chaco T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57%, similar to 37%, and similar to 6% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23% of the Chaco would have to be protected to safeguard the top 17% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1370 KW - biodiversity facets KW - extinction drivers KW - functional diversity KW - functional richness KW - overhunting KW - phylogenetic diversity KW - taxonomic KW - diversity KW - traits Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-567696 SN - 1866-8372 IS - 4 ER - TY - JOUR A1 - Romero-Munoz, Alfredo A1 - Fandos, Guillermo A1 - Benítez-López, Ana A1 - Kuemmerle, Tobias T1 - Habitat destruction and overexploitation drive widespread declines in all facets of mammalian diversity in the Gran Chaco JF - Global change biology N2 - Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57%, similar to 37%, and similar to 6% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23% of the Chaco would have to be protected to safeguard the top 17% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them. KW - biodiversity facets KW - extinction drivers KW - functional diversity KW - functional richness KW - overhunting KW - phylogenetic diversity KW - taxonomic KW - diversity KW - traits Y1 - 2020 U6 - https://doi.org/10.1111/gcb.15418 SN - 1354-1013 SN - 1365-2486 VL - 27 IS - 4 SP - 755 EP - 767 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Lehmann, Anika A1 - Zheng, Weishuang A1 - Ryo, Masahiro A1 - Soutschek, Katharina A1 - Roy, Julien A1 - Rongstock, Rebecca A1 - Maaß, Stefanie A1 - Rillig, Matthias C. T1 - Fungal traits important for soil aggregation JF - Frontiers in microbiology N2 - Soil structure, the complex arrangement of soil into aggregates and pore spaces, is a key feature of soils and soil biota. Among them, filamentous saprobic fungi have well-documented effects on soil aggregation. However, it is unclear what properties, or traits, determine the overall positive effect of fungi on soil aggregation. To achieve progress, it would be helpful to systematically investigate a broad suite of fungal species for their trait expression and the relation of these traits to soil aggregation. Here, we apply a trait-based approach to a set of 15 traits measured under standardized conditions on 31 fungal strains including Ascomycota, Basidiomycota, and Mucoromycota, all isolated from the same soil. We find large differences among these fungi in their ability to aggregate soil, including neutral to positive effects, and we document large differences in trait expression among strains. We identify biomass density, i.e., the density with which a mycelium grows (positive effects), leucine aminopeptidase activity (negative effects) and phylogeny as important factors explaining differences in soil aggregate formation (SAF) among fungal strains; importantly, growth rate was not among the important traits. Our results point to a typical suite of traits characterizing fungi that are good soil aggregators, and our findings illustrate the power of employing a trait-based approach to unravel biological mechanisms underpinning soil aggregation. Such an approach could now be extended also to other soil biota groups. In an applied context of restoration and agriculture, such trait information can inform management, for example to prioritize practices that favor the expression of more desirable fungal traits. KW - soil aggregation KW - traits KW - saprobic fungi KW - random forest KW - biomass KW - density KW - leucine amino peptidases Y1 - 2020 U6 - https://doi.org/10.3389/fmicb.2019.02904 SN - 1664-302X VL - 10 PB - Frontiers Media CY - Lausanne ER -