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Concerning the representation of organisms, evolutionary trees may represent the hypothetical relationships among the entire biodiversity or among members of a kingdom such as the animals.
Unfortunately, conclusions on the generality of Rapoport's rule are precluded by the uneven taxonomic and latitudinal representation of organisms examined thus far [24] [28].
However, we note that tRNA molecules in part 2 are unbalanced in term of representation of organisms in superkingdoms (e.g., overrepresentation of Haloarchaea in archaeal tRNAs, or Saccharomyces in eukaryal tRNAs) or in isoacceptor composition (e.g., underrepresentation of tRNACys).
While studies of Haldane's rule have included a small, but diverse phylogenetic representation of organisms (flies, birds, butterflies and moths, and mammals), perhaps such a limited taxonomic sample has lead to generalizations for a pattern that some organisms ignore due to other mechanisms (e.g. sex determination lability).
For the tree of [ 47], we made the representation of organisms non-redundant at the genus level, with a small number of exceptions for fast-evolving genera, and recomputed the best Maximum Likelihood tree, while keeping fixed the original topology of the published tree ('constraints' in RAxML).
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It has two semantic zoom levels: a general representation of organism's pathways (nodes represent pathways, the edges connect the related ones); and submaps showing the details of each of the pathways, including compartmentalization. Several levels of geometric zoom are available on both semantic zoom levels.
Cell cell aggregation and cell substratum adhesion are modeled by generating appropriate binding forces between discrete representations of organisms that may hold them together, or if fluid stresses are large, may yield and release the organisms.
Individual-based models (IBMs) are based on the explicit representation of individual organisms.
Perhaps the most famous example in biology is the comprehensive taxonomical representation of living organism phylogeny [9].
Ideally, if all the possible relationships among genes could be obtained, this network should be a full-information representation of an organism.
This first draft can be used to formulate a mathematical representation of an organism's metabolism, termed as genome-scale model (GSM).
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