Crop Biodiversity: An Unfinished Magnum Opus of Nature
Hufford et al, 2019.

Crop biodiversity is one of the major inventions of humanity through the process of domestication. It is also an essential resource for crop improvement to adapt agriculture to ever-changing conditions like global climate change and consumer preferences. Domestication and the subsequent evolution under cultivation have profoundly shaped the genetic architecture of this biodiversity. In this review, we highlight recent advances in our understanding of crop biodiversity. Topics include the reduction of genetic diversity during domestication and counteracting factors, a discussion of the relationship between parallel phenotypic and genotypic evolution, the role of plasticity in genotype × environment interactions, and the important role subsistence farmers play in actively maintaining crop biodiversity and in participatory breeding. Linking genotype and phenotype remains the holy grail of crop biodiversity studies.

https://bit.ly/2JpDQWr 

Photo:Aliza Sokolow

Asplenium rutifolium 
Transverse section through the petiole.
Photo: Olivier Leroux ‏ @Oli4_Leroux 
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Timothy Morton: Inside Big Botany

The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agroecosystem services across Europe
Martin et al., 2019.

Managing agricultural landscapes to support biodiversity and ecosystem services is a key aim of a sustainable agriculture. However, how the spatial arrangement of crop fields and other habitats in landscapes impacts arthropods and their functions is poorly known. Synthesising data from 49 studies (1515 landscapes) across Europe, we examined effects of landscape composition (% habitats) and configuration (edge density) on arthropods in fields and their margins, pest control, pollination and yields. Configuration effects interacted with the proportions of crop and non‐crop habitats, and species’ dietary, dispersal and overwintering traits led to contrasting responses to landscape variables. Overall, however, in landscapes with high edge density, 70% of pollinator and 44% of natural enemy species reached highest abundances and pollination and pest control improved 1.7‐ and 1.4‐fold respectively. Arable‐dominated landscapes with high edge densities achieved high yields. This suggests that enhancing edge density in European agroecosystems can promote functional biodiversity and yield‐enhancing ecosystem services.

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https://bit.ly/2DFxiiH
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Injurious insects in Formosa (1910-1914), by T. Shiraki and Hori. 
https://bit.ly/2PWeZuy
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The Garden of Death (1896) by Finnish symbolist painter Hugo Simberg.

Somehow, it reminds me of Bayer-Monsanto...
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Reconciling cooperation, biodiversity and stability in complex ecological communities      
Chengyi Tu, Samir Suweis, Jacopo Grilli, Marco Formentin & Amos Maritan

Empirical evidences show that ecosystems with high biodiversity can persist in time even in the presence of few types of resources and are more stable than low biodiverse communities. This evidence is contrasted by the conventional mathematical modeling, which predicts that the presence of many species and/or cooperative interactions are detrimental for ecological stability and persistence. Here we propose a modelling framework for population dynamics, which also include indirect cooperative interactions mediated by other species (e.g. habitat modification). We show that in the large system size limit, any number of species can coexist and stability increases as the number of species grows, if mediated cooperation is present, even in presence of exploitative or harmful interactions (e.g. antibiotics). Our theoretical approach thus shows that appropriate models of mediated cooperation naturally lead to a solution of the long-standing question about complexity-stability paradox and on how highly biodiverse communities can coexist.

Graphical representation of the model. (A,B) The population dynamics is stochastic: at each time step a randomly chosen individual of a given species (denoted by the color) die and it is replaced by another species that is also picked at random and give birth to an offspring. The species birth rate depends on the species population abundance and on the species interaction matrix (C).

The results of the mean field predictions. (A) Species interaction network for 7 species where each species i has one mutualistic partner j. (B) Time evolution of the populations of the 7 species as predicted by the mean field dynamics. (C) Species interaction network for 7 species where one species is not helped by any species and the iterative pruning process, as described in the main text, leads to a cascade of extinctions. (D) As the time evolution of the mean field Eq. , only one species dominates the community. (E) Nested structure for fruit eating birds community in Mexico^. (F) All species coexist, as predicted by our theoretical framework. In the ordinate axis use the notation 𝜂¯ and not η.

https://go.nature.com/2IWFFtG

Saturn's moon Hyperion

Plant behaviour in response to the environment: information processing in the solid state 
Salva Duran-Nebreda and George W. Bassel. 2019.

Information processing and storage underpins many biological processes of vital importance to organism survival. Like animals, plants also acquire, store and process environmental information relevant to their fitness, and this is particularly evident in their decision-making. The control of plant organ growth and timing of their developmental transitions are carefully orchestrated by the collective action of many connected computing agents, the cells, in what could be addressed as distributed computation. Here, we discuss some examples of biological information processing in plants, with special interest in the connection to formal computational models drawn from theoretical frameworks. Research into biological processes with a computational perspective may yield new insights and provide a general framework for information processing across different substrates.

Multicellular information processing in plants. (a) Stomata (dark cells) are dynamically open and closed in order to capture CO₂ and avoid excessive loss of water. (b) Thermal images of leaf surfaces showing the current state of stomata aperture within sectors. Patches of coordinated stomata activity are seen, indicating that collective dynamics of stomata are present in the form of excitable media-like waves that propagate through the leaf surface. (c) The hormone metabolic network underpinning the regulation of abscisic acid (ABA) and gibberellic acid (GA) levels in dormant Arabidopsis seeds. (d) Distribution of ABA and GA synthesis and response within distinct cell types of the dormant embryo radicle. (e) Spatial sites of ABA and GA responses within the dormant Arabidopsis embryo. (f) Attractor dynamics of the hormone metabolic interaction network in dormant Arabidopsis seeds when the distinct spatial embedding of hormone responses is taken into account.

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https://royalsocietypublishing.org/doi/10.1098/rstb.2018.0370

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Collecting Dry Red Chillies 
Photo and caption by MD Tanveer Rohan 
https://on.natgeo.com/2Dbtqpg 

Structural equation modeling of a winnowed soil microbiome identifies how invasive plants re-structure microbial networks      
Mamet et al., 2019

The development of microbial networks is central to ecosystem functioning and is the hallmark of complex natural systems. Characterizing network development over time and across environmental gradients is hindered by the millions of potential interactions among community members, limiting interpretations of network evolution. We developed a feature selection approach using data winnowing that identifies the most ecologically influential microorganisms within a network undergoing change. Using a combination of graph theory, leave-one-out analysis, and statistical inference, complex microbial communities are winnowed to identify the core organisms responding to external gradients or functionality, and then network development is evaluated against these externalities. In a plant invasion case study, the winnowed microbial network became more influential as the plant invasion progressed as a result of direct plant-microbe links rather than the expected indirect plant–soil–microbe links. This represents the first use of structural equation modeling to predict microbial network evolution, which requires identification of keystone taxa and quantification of the ecological processes underpinning community structure and function patterns.

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https://go.nature.com/2TPOasb

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Graham Harman: Morton’s Hyperobjects and the Anthropocene

Pseudosalix handleyi
a 48 million year old fossils plant relative of willows 
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Basic Principles of Temporal Dynamics      

Ryo et al., 2019

Temporal dynamics are inherently complex.

Concepts and techniques have flourished to understand ecological temporal dynamics in recent years.

A key finding of recent studies is that driver–response relationships are not necessarily constant through time, but rather, that they are conditioned by the recent and historical past.

Basic principles of temporal dynamics need to be summarized to increase the understanding and predictability of complex temporal dynamics in ecology and evolution.

All ecological disciplines consider temporal dynamics, although relevant concepts have been developed almost independently. We here introduce basic principles of temporal dynamics in ecology. We figured out essential features that describe temporal dynamics by finding similarities among about 60 ecological concepts and theories. We found that considering the hierarchically nested structure of complexity in temporal patterns (i.e. hierarchical complexity) can well describe the fundamental nature of temporal dynamics by expressing which patterns are observed at each scale. Across all ecological levels, driver–response relationships can be temporally variant and dependent on both short- and long-term past conditions. The framework can help with designing experiments, improving predictive power of statistics, and enhancing communications among ecological disciplines.

Hierarchical Complexity. The idea deals with driver–response relationships in time-series across three levels of complexity. The levels are hierarchically nested, as single-event (i.e., one driver and one response) is a subset of multiple events that are a part of the trajectory. The key property is that driver–response relationships are not necessarily constant through time, but they can change over time due to recent and historical past experience. Hierarchical complexity can be observed at any scale. Temporal dynamics at each of the levels affect each other.

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https://bit.ly/2GzDaMb

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Album Benary (1876-1882)
Ernst Benary

Meta‐ecosystem processes alter ecosystem function and can promote herbivore‐mediated coexistence 
Justin N. Marleau Frederic Guichard, 2019

Herbivory and dispersal play roles in the coexistence of primary producers with shared resource limitation by imposing trade‐offs either through apparent competition or dispersal limitation. These mechanisms of coexistence can further interact with meta‐ecosystem effects, which results in spatial heterogeneity through the movement of herbivores and nutrients. Here, we investigate how herbivores influence autotroph coexistence through a meta‐ecosystem effect, and how this effect couples mechanisms of coexistence to ecosystem structure and functioning. We articulate this framework through a parameterized one resource‐k producer‐one herbivore meta‐ecosystem model. The results show that herbivore movement with nutrient recycling can generate spatial heterogeneity to allow coexistence where the well‐mixed system predicts competitive exclusion. Furthermore, the presence of movement alters local and regional ecosystem functioning even when coexistence would occur without movement. These results highlight how meta‐ecosystem theory can provide a mechanistic context for the observed complexity of biodiversity‐ecosystem function relationships.

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https://bit.ly/2VY79CL

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James Collier
https://bit.ly/2UYEOe4
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Structure, spatial dynamics, and stability of novel seed dispersal mutualistic networks in Hawaiʻi      

Vizentin-Bugoni et al., 2019

When humans introduce exotic species to sensitive ecosystems, invasion and extinction of native species often follow. The resulting ecological communities can develop unusual interactions between the survivors and newcomers. Vizentin-Bugoni et al. analyzed the structure of seed dispersal networks in Hawai'i, where native bird species have been mostly replaced by invaders. They found that the native plants now depend on the invasive birds for seed dispersal. The network of dispersal interactions is complex and stable, which are features of native seed-dispersal networks in other parts of the world. It appears that introduced species may, in some circumstances, become integrated into native ecosystems

Abstract

Increasing rates of human-caused species invasions and extinctions may reshape communities and modify the structure, dynamics, and stability of species interactions. To investigate how such changes affect communities, we performed multiscale analyses of seed dispersal networks on Oʻahu, Hawaiʻi. Networks consisted exclusively of novel interactions, were largely dominated by introduced species, and exhibited specialized and modular structure at local and regional scales, despite high interaction dissimilarity across communities. Furthermore, the structure and stability of the novel networks were similar to native-dominated communities worldwide. Our findings suggest that shared evolutionary history is not a necessary process for the emergence of complex network structure, and interaction patterns may be highly conserved, regardless of species identity and environment. Introduced species can quickly become well integrated into novel networks, making restoration of native ecosystems more challenging than previously thought.

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https://science.sciencemag.org/content/364/6435/78

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Hungarian Racka Sheep 

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FOREST by Carol Ann Duffy