Cross section of a lily of the valley (Convallaria majalis) stem
100x (objective lens magnification)
Falco Krüger

Network motifs and their origins      

Lewi Stone, Daniel Simberloff, Yael Artzy-Randrup, 2019.

Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small “network motifs” that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. The concept of network motifs was introduced into Systems Biology by Milo, Alon and colleagues in 2002, quickly revolutionized the field, and it has had a huge impact in wider scientific domains ever since. Here, we argue that the same concept and tools for the detection of motifs were well known in the ecological literature decades into the last century, a fact that is generally not recognized. We review the early history of network motifs, their evolution in the mathematics literature, and their recent rediscoveries.

Network motif examples. Motifs in different contexts (right column) and example systems (left column). (A) Checkerboard motif. For example, 4 species (A–D) occupy 5 islands (I₁–I₅). The checkerboard motif highlighted in red represents 2 species that do not co-occur on the same island (here, B appears on I₅ but D does not, and conversely, D appears on I₃ but B does not), suggestive of competitive interactions. (B) Triadic clustering motif. For example, the motif represents cases in which an individual’s connected friends are also connected with each other, having significance, for example, in social networks and epidemiological contact networks. (C) Feed-forward loop motif. For example, a circuit in gene transcription networks, in which DNA target β can be activated only through simultaneous binding of two transcription factors A and B, and in which B depends on A initially binding to DNA targets α and β, suggesting regulatory control on transcription.

https://bit.ly/2UqRZ7v

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A mosquito’s foot at 800X magnification
by Steve Gschmeissner

Synchronized failure of global crop production

Zia Mehrabi and Navin Ramankutty, 2019.

Multiple breadbasket failure is a risk to global food security. However, there are no global analyses that have quantitatively assessed if global crop production has actually tended towards synchronized failure historically. We show that synchronization in production within major commodities such as maize and soybean has declined in recent decades, leading to increased global stability in production of these crops. In contrast, synchrony between crops has peaked, making global calorie production more unstable. Under the hypothetical event of complete synchronized failure we estimate simultaneous global production losses for rice, wheat, soybean and maize to lie between −17% and −34%. We find that offsetting these losses by reducing variation in production across all growing locations, and raising production ceilings in breadbaskets, are far more effective than strategies focused on reducing variability in breadbaskets alone or closing production gaps in low productive locations. Our findings sug-gest that maintaining asynchrony in the food system requires a central place in discussions of future food demand under mean climate change, population growth and consumption trends.

Local contributions to global variance of crop production between 1961 and 2008. a–h, Inset top left, maize; top right, rice; bottom left, soybean; bottom right, wheat. Each coloured pixel in the regional maps represents the percentage contribution to interannual global variance in crop production in a 100 km × 100 km grid cell between 1961 and 2008. Negative values (blue) show variance deflating (or stabilizing) locations and positive values (red) show variance inflating (or destabilizing) locations. Grey areas are non-cropped areas (that is, fractional area <1 created="" in="" maps="" r.="" span="" were="">

https://go.nature.com/2Pej3Wp 

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A Network Perspective for Community Assembly 
Ponisio et al., 2019

Species interactions are responsible for many key mechanisms that govern the dynamics of ecological communities. Variation in the way interactions are organized among species results in different network structures, which translates into a community's ability to resist collapse and change. To better understand the factors involved in dictating ongoing dynamics in a community at a given time, we must unravel how interactions affect the assembly process. Here, we build a novel, integrative conceptual model for understanding how ecological communities assemble that combines ecological networks and island biogeography theory, as well as the principles of niche theory. Through our conceptual model, we show how the rate of species turnover and gene flow within communities will influence the structure of ecological networks. We conduct a preliminary test of our predictions using plant-herbivore networks from differently-aged sites in the Hawaiian archipelago. Our approach will allow future modeling and empirical studies to develop a better understanding of the role of the assembly process in shaping patterns of biodiversity.

Conceptual figure illustrating the interplay of interaction niche overlap and interaction niche breadth in determining the arrangement of interactions in a community, and specifically nestedness and modularity (A–F). In the accompanying network figures, white circles represent one trophic level (e.g., pollinators) and dark squares represent the other trophic level (e.g., plants). Each color represents a species. Within our review, we could not find evidence of communities exhibiting a structure as depicted in (F).

https://bit.ly/2D68xMl

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The earth is what we all have in common 

Wendell Berry
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The poultry book  (1867)
By  W. B. Tegetmeier and W. Harrison. 
https://bit.ly/2uN4rE4
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Tulip mania (Dutch: tulpenmanie) 

 Jan Davidsz de Heem

Period in the Dutch Golden Age during which contract prices for some bulbs of the recently introduced and fashionable tulip reached extraordinarily high levels and then dramatically collapsed in February 1637.[2] It is generally considered the first recorded speculative bubble. For example, a tulip known as "the Viceroy" (shown below), was offered for sale for between 3,000 and 4,200 guilders (florins) depending on size (aase). A skilled craftsworker at the time earned about 300 guilders a year.

Catalog Verzameling van een Meenigte Tulipaanen (1637)

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https://en.wikipedia.org/wiki/Tulip_mania

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Scanning Electron Microscope pictures of plants

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https://www.eyeofscience.de/en/botany/
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Highland cattle 

(Scottish Gaelic: Bò Ghàidhealach; Scots: Heilan coo) 

They descend from the Hamitic Longhorn, which were brought to Britain by Neolithic farmers in the second millennium BC, as the cattle migrated northwards through Africa and Europe.

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https://en.wikipedia.org/wiki/Highland_cattle

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Plant-plant interactions and N fertilization shape soil bacterial and fungal communities 
Guo et al., 2019

Highlights  
•      Neighbor plant negatively affected plant growth, in particular for L. kaempferi. 
•      Inter-specific plant interactions raised bacterial and fungal diversity in added N. 
•      L. olgensis and N addition induced the dominance of the Basidiomycota community.
•      L. olgensis mainly affected microbial community in inter-specific associations.  

Abstract  

The impact of conspecific and heterospecific neighboring plants on soil bacterial and fungal communities has never been explored in a forest ecosystem. In the present study, we first investigated soil microbial communities in three plantations: Larix kaempferi monoculture, L. olgensis monoculture and their mixture. Then, a two-year growth experiment was conducted to investigate the effects of intra- and inter-specific interactions of L. kaempferi and L. olgensis on rhizosphere microbial communities at two different nitrogen levels. The results demonstrated clear differences in the beta-diversity and composition of bacteria and fungi among the three plantations, which implied the presence of different effects of plant-plant interactions on soil microbial communities. The results of the pot experiment showed that L. kaempferi suffered from greater neighbor effects from its conspecific neighbor regardless of N fertilization, although the effect declined when L. kaempferi was grown with L. olgensis under N fertilization. Changes in intra- and inter-specific plant interactions significantly impacted the chemical and biological properties of soil under N fertilization, with lower concentrations of NH4+, and lower soil microbial biomass (CMic) and soil carbon nitrogen biomass (NMic) under intra-specific plant interactions of L. kaempferi (KK) compared to inter-specific interactions of L. kaempferi and L. olgensis (KO). N fertilization increased bacterial and fungal alpha diversities in the rhizosphere soil of KO. For the beta diversity, the PERMANOVA results demonstrated that there was a significant impact of intra- and inter-specific plant interactions on soil microbial communities, with KK significantly differing from intra-specific plant interactions of L. olgensis (OO) and KO. The two plant species and N fertilization showed specific effects on the soil microbial composition, particularly on the fungal community. Both L. olgensis and N fertilization increased the abundance of Ascomycota but reduced that of Basidiomycota, and even shifted the dominance from Basidiomycota to Ascomycota under KO combined with N fertilization.

Bacterial (a) and fungal (b) taxa with different abundance changes in two-plant pots between N-treated (N+) and control (N-) soil, irrespective of plant-plant interactions (Class: N treatment; Subclass: Plant-plant interactions), as detected by LEfSe analysis. The taxa with the absolute LDA scores over 3 and P values less than 0.05 are shown.

https://bit.ly/2uIrXSS

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Karen Barad. Troubling Time/s and Ecologies of Nothingness. 
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Durum wheat genome highlights past domestication signatures and future improvement targets      

Maccaferri et al., 2019

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

https://www.nature.com/articles/s41588-019-0381-3

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Black Hole 

Kronos Quartet - Total Solar Eclipse Sonification | Exploratorium

Shepherds on stilts from the marshy region of Landes, France

Evolutionary agroecology: Trends in root architecture during wheat breeding 
Yong‐He Zhu Jacob Weiner Ming‐Xi Yu Feng‐Min Li

Root system characteristics determine soil space exploration and resource acquisition, and these characteristics include competitive traits that increase individual fitness but reduce population performance. We hypothesize that crop breeding for increased yield is often a form of “group selection” that reduces such “selfish” traits to increase population yield. To study trends in root architecture resulting from plant breeding and test the hypothesis that increased yields result in part from group selection on root traits, we investigated root growth and branching behavior in a historical sequence of wheat (Triticum aestivum) cultivars that have been widely grown in northwestern China. Plants were grown in gel‐filled chambers to examine growth angles, numbers, and lengths of seminal roots, and in soil‐filled chambers under eight soil resource levels for fractal analysis of root system architecture. Yield in field was evaluated at standard and low planting densities. Newer cultivars produced higher yields than older ones only at the higher sowing density, showing that increased yield results from changes in competitive behavior. Seminal root number and growth angles were negatively correlated with yield, while primary seminal root length was positively correlated with yield. Roots of higher‐yielding modern varieties were simpler and less branched, grew deeper but spread less laterally than modern varieties. The fractal dimension of root branching was negatively correlated with the yield of cultivars at all resource levels. Root:shoot ratio was negatively correlated with yield under high soil resource levels. The results are consistent with the hypothesis that the success of wheat breeding for higher yields over past 100 years in northwestern China has been in part due to unconscious group selection on root traits, resulting in smaller, less branched, and deeper roots, suggesting a direction for further increases in crop yield in the future.

https://onlinelibrary.wiley.com/doi/10.1111/eva.12749#.XJ-SptfPftk.twitter 

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Opuntia aciculata 
Photo: Sadie Barber

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Regresar a la naturaleza tiene para mí un solo sentido: vivenciarnos como naturaleza

Rafael Cadenas
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Plant diversity alters the representation of motifs in food webs      
Giling et al. 2019

Changes in the diversity of plant communities may undermine the economically and environmentally important consumer species they support. The structure of trophic interactions determines the sensitivity of food webs to perturbations, but rigorous assessments of plant diversity effects on network topology are lacking. Here, we use highly resolved networks from a grassland biodiversity experiment to test how plant diversity affects the prevalence of different food web motifs, the smaller recurrent sub-networks that form the building blocks of complex networks. We find that the representation of tri-trophic chain, apparent competition and exploitative competition motifs increases with plant species richness, while the representation of omnivory motifs decreases. Moreover, plant species richness is associated with altered patterns of local interactions among arthropod consumers in which plants are not directly involved. These findings reveal novel structuring forces that plant diversity exerts on food webs with potential implications for the persistence and functioning of multitrophic communities.

Three-species motifs in food webs. a The 13 possible connected triads, which may contain only single feeding links (labelled with ‘s’) or at least one double feeding link (‘d’). The common motifs are shown in colour: tri-trophic chains (e.g. a plant fed on by a herbivore which is then preyed upon by a predator; s1), omnivory (the species at the top of the food chain feeds on both other species; s2), apparent competition (two resources that are fed on by the same consumer; s4) and exploitative competition (a resource shared by two consumers; s5). b A hypothetical example of the consumer community (grey nodes) observed on a plot with two plant species (white nodes) and a node for detritus (black node). Coloured links show examples of the common triads that reoccur within the larger network. In this case, the omnivory (s2; blue) and exploitative competition (s5; pink) motifs are grounded (i.e. connected to a basal resource), while the tri-trophic chain (s1; green) and apparent competition (s4; orange) motifs are free floating (i.e. not connected to a basal resource).

https://www.nature.com/articles/s41467-019-08856-0 

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Suriname toad after an illustration by J.G. Prêtre from Jussieu's “Dictionnaire des Sciences Naturelles” [1816-1830.]

A meta‐food web for invertebrate species collected in a european grassland 
Jes Hines et al. 2019

Patterns of feeding interactions between species are thought to influence the stability of communities and the flux of nutrients and energy through ecosystems. However, surprisingly few well‐resolved food webs allow us to evaluate factors that influence the architecture of species interactions. We constructed a meta‐food web consisting of 714 invertebrate species collected over nine years of suction and pitfall sampling campaigns in the Jena Experiment, a long‐term grassland biodiversity experiment located in Jena, Germany. In this paper, we summarize information on the 51,496 potential trophic links, which were established using information on diet specificity and species traits that typically constrain feeding interactions (trophic group, body size, and vertical stratification). The list of species identities, traits, and link‐derivation rules will be useful not only for tests of plant diversity effects on food web structure within the Jena Experiment, but also for considering consistent construction of food webs from empirical data, and for comparisons of network structure across ecosystems.

https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecy.2679

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Areas of farming and herding in 1000 C.E.
Green - Farming societies 
Yellow - Pastoral nomadic herding societies 
Red - Foraging societies 
Arrows - Pastoral nomadic encounters with settled farming societies

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Ha muerto Paulino Núñez… 

Una figura fundamental, emblemática del ambientalismo en Venezuela. 
Luchador incansable por la agroecología. 
Un entrañable maestro para mí.


                    In Memoriam

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Review: Alternate grassy ecosystem states are determined by palatability-flammability trade-offs 

(Trends Ecol Evol) March 8, 2019/in Plant Science Research Weekly /by Rebecca Hayes

Grassy ecosystems tend towards two stable states. One, the grazing-lawn state, is dominated by shoter grasses that thrive when grazed by herbivores, and the other, the fire-grass state, is dominated by taller grasses thrive when periodically controlled by burning. The flux between fire-grass and grazing-lawn ecosystems can be attributed to the positive feedbacks promoted by the respective environmentally-adaptive traits of the inhabitant grasses. Since grazing-lawn grasses grow low to the ground, grazing is necessary to provide adequate light. These grasses promote grazing by offering ample nutritious and easy-to-forage leaf material, which in turn allows stems and roots to remain unharmed and continue to proliferate. Fire-grasses are sturdy and resist decomposition, resulting in a buildup of dead biomass that shades competitors and provides fuel for fires. Fire-grasses are well protected from fires and are quick to reestablish and proliferate after a burn, unlike their competitors. Although the underlying systems are different, the dynamics of the fire-grass vs. grazing-lawn and forest vs. savanna alternate stable states both display the impact initial conditions and lag effects have on ecological succession. A precise description of the cycle between these ecosystem states is yet unknown, however the importance of grasses and their varied traits is apparent.

 

 (Summary by Rebecca Hayes) Trends Ecol. Evol. 10.1016/j.tree.2019.01.007

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Nature is a mutable cloud which is always and never the same.

Ralph Waldo Emerson
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