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      The origins of genome complexity.

      Science (New York, N.Y.)

      genetics, Vertebrates, Spliceosomes, Selection, Genetic, Recombination, Genetic, Population Density, Plants, Phylogeny, Mutation, Invertebrates, Introns, Interspersed Repetitive Sequences, Humans, Genome, Genetic Variation, Genetic Drift, Gene Silencing, Gene Duplication, Fungi, Evolution, Molecular, Eukaryota, Body Constitution, Bacteria, Animals, Alleles

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          Abstract

          Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.

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          Most cited references 18

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          Global dispersal of free-living microbial eukaryote species.

          The abundance of individuals in microbial species is so large that dispersal is rarely (if ever) restricted by geographical barriers. This "ubiquitous" dispersal requires an alternative view of the scale and dynamics of biodiversity at the microbial level, wherein global species number is relatively low and local species richness is always sufficient to drive ecosystem functions.
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            Alternative splicing: increasing diversity in the proteomic world.

            How can the genome of Drosophila melanogaster contain fewer genes than the undoubtedly simpler organism Caenorhabditis elegans? The answer must lie within their proteomes. It is becoming clear that alternative splicing has an extremely important role in expanding protein diversity and might therefore partially underlie the apparent discrepancy between gene number and organismal complexity. Alternative splicing can generate more transcripts from a single gene than the number of genes in an entire genome. However, for the vast majority of alternative splicing events, the functional significance is unknown. Developing a full catalog of alternatively spliced transcripts and determining each of their functions will be a major challenge of the upcoming proteomic era.
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              A common rule for the scaling of carnivore density.

              Population density in plants and animals is thought to scale with size as a result of mass-related energy requirements. Variation in resources, however, naturally limits population density and may alter expected scaling patterns. We develop and test a general model for variation within and between species in population density across the order Carnivora. We find that 10,000 kilograms of prey supports about 90 kilograms of a given species of carnivore, irrespective of body mass, and that the ratio of carnivore number to prey biomass scales to the reciprocal of carnivore mass. Using mass-specific equations of prey productivity, we show that carnivore number per unit prey productivity scales to carnivore mass near -0.75, and that the scaling rule can predict population density across more than three orders of magnitude. The relationship provides a basis for identifying declining carnivore species that require conservation measures.
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                Author and article information

                Journal
                10.1126/science.1089370
                14631042

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