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In a nested network, species with fewer interactions are connected to a subset of the partners of species with more interactions.
Introducing pseudo species causes a problem, as now two network species represent the same molecular entity.
The first label is a network species, and the second label is a positive integer.
Three network species (PI3K, MEK and PLCγ1) were chosen for in silico knockout.
This is easily implemented by assigning a unique identifier to each network species in the initial state and to each reaction product of every reaction instance.
Interaction diversity metrics at the network, species and guild levels correspond to elements of α-diversity, such as species richness and evenness within and across hierarchical levels.
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FASTA-format sequence files containing amino acid sequences for enzymes in Plant Metabolic Network species-specific databases (e.g., AraCyc and GrapeCyc) were downloaded in July 2013 and combined into one database.
Prior to the era of planetwide transportation networks, species routinely took millennia to establish themselves in new places.
In general, the lower VA of larger networks is sufficient in slow-changing environments, while the lower VP ensures that a large-network species is better adapted.
In contrast, the higher VA conferred by smaller networks is required in fast-changing environments; the small-network species does not adapt as well (higher VP), but it does not need to because the large-network species cannot adapt quickly enough.
In contrast, populations persist indefinitely regardless of the details of genetic architecture when the rate of environmental change is slow, and even large-network species can achieve high trait heritability.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com