Algorithms of Evolution

Evolutionary mechanisms have inspired mathematical modeling, and computational methods underpin investigations into bioinformatics and biological evolution.

duplications of gene & genome

Modeling gene and genome duplications in eukaryotes. modified:
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been associated with important evolutionary transitions or major leaps in development and adaptive radiations of species. Here, we present an evolutionary model that simulates the duplication dynamics of genes, considering genome-wide duplication events and a continuous mode of gene duplication. Modeling the evolution of the different functional categories of genes assesses the importance of different duplication events for gene families involved in specific functions or processes. By applying our model to the Arabidopsis genome, for which there is compelling evidence for three whole-genome duplications, we show that gene loss is strikingly different for large-scale and small-scale duplication events and highly biased toward certain functional classes. We provide evidence that some categories of genes were almost exclusively expanded through large-scale gene duplication events. In particular, we show that the three whole-genome duplications in Arabidopsis have been directly responsible for >90% of the increase in transcription factors, signal transducers, and developmental genes in the last 350 million years. Our evolutionary model is widely applicable and can be used to evaluate different assumptions regarding small- or large-scale gene duplication events in eukaryotic genomes.
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. Modeling gene and genome duplications in eukaryotes. (Free Full Text Article) Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5454-9. Epub 2005 Mar 30.

The hidden duplication past of Arabidopsis thaliana. [Proc Natl Acad Sci U S A. 2002] PMID: 12374856
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. [Genome Biol. 2006] PMID: 16507168
Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome. [Nucleic Acids Res. 2003] PMID: 12582254
Investigating ancient duplication events in the Arabidopsis genome. [J Struct Funct Genomics. 2003] PMID: 12836691
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. [Trends Genet. 2004] PMID: 15363896
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Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity.
Controversy surrounds the apparent rising maximums of morphological complexity during eukaryotic evolution, with organisms increasing the number and nestedness of developmental areas as evidenced by morphological elaborations reflecting area boundaries. No "predictable drive" to increase this sort of complexity has been reported. Recent genetic data and theory in the general area of gene dosage effects has engendered a robust "gene balance hypothesis," with a theoretical base that makes specific predictions as to gene content changes following different types of gene duplication. Genomic data from both chordate and angiosperm genomes fit these predictions: Each type of duplication provides a one-way injection of a biased set of genes into the gene pool. Tetraploidies and balanced segments inject bias for those genes whose products are the subunits of the most complex biological machines or cascades, like transcription factors (TFs) and proteasome core proteins. Most duplicate genes are removed after tetraploidy. Genic balance is maintained by not removing those genes that are dose-sensitive, which tends to leave duplicate "functional modules" as the indirect products (spandrels) of purifying selection. Functional modules are the likely precursors of coadapted gene complexes, a unit of natural selection. The result is a predictable drive mechanism where "drive" is used rigorously, as in "meiotic drive." Rising morphological gain is expected given a supply of duplicate functional modules. All flowering plants have survived at least three large-scale duplications/diploidizations over the last 300 million years (Myr). An equivalent period of tetraploidy and body plan evolution may have ended for animals 500 million years ago (Mya). We argue that "balanced gene drive" is a sufficient explanation for the trend that the maximums of morphological complexity have gone up, and not down, in both plant and animal eukaryotic lineages.Freeling M, Thomas BC. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 2006 Jul;16(7):805-14.

Modeling gene and genome duplications in eukaryotes. [Proc Natl Acad Sci U S A. 2005] PMID: 15800040 Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. [Genome Res. 2006] PMID: 16760422 Widespread genome duplications throughout the history of flowering plants. [Genome Res. 2006] PMID: 16702410 New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. [Genome Res. 2003] PMID: 12799346 See all Related Articles...

Extensive genomic duplication during early chordate evolution.Opinions on the hypothesis that ancient genome duplications contributed to the vertebrate genome range from strong skepticism to strong credence. Previous studies concentrated on small numbers of gene families or chromosomal regions that might not have been representative of the whole genome, or used subjective methods to identify paralogous genes and regions. Here we report a systematic and objective analysis of the draft human genome sequence to identify paralogous chromosomal regions (paralogons) formed during chordate evolution and to estimate the ages of duplicate genes. We found that the human genome contains many more paralogons than would be expected by chance. Molecular clock analysis of all protein families in humans that have orthologs in the fly and nematode indicated that a burst of gene duplication activity took place in the period 350 650 Myr ago and that many of the duplicate genes formed at this time are located within paralogons. Our results support the contention that many of the gene families in vertebrates were formed or expanded by large-scale DNA duplications in an early chordate. Considering the incompleteness of the sequence data and the antiquity of the event, the results are compatible with at least one round of polyploidy.
McLysaght A, Hokamp K, Wolfe KH. Extensive genomic duplication during early chordate evolution. Nat Genet. 2002 Jun;31(2):200-4. Epub 2002 May 28. Comment in: Nat Genet. 2002 Jun;31(2):128-9.
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. [Mol Biol Evol. 2004] PMID: 15014147 New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. [Genome Res. 2003] PMID: 12799346 Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. [Mol Biol Evol. 1998] PMID: 9729879 Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. [J Exp Zoolog B Mol Dev Evol. 2003] PMID: 14508816 Phylogenetic analysis of T-Box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome. [Genetics. 2000] PMID: 11063699See all Related Articles...

Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis.Complete genome doubling has long-term consequences for the genome structure and the subsequent evolution of an organism. It has been suggested that two genome duplications occurred at the origin of vertebrates (known as the 2R hypothesis). However, there has been considerable debate as to whether these were two successive duplications, or whether a single duplication occurred, followed by large-scale segmental duplications. In this article, we review and compare the evidence for the 2R duplications from vertebrate genomes with similar data from other more recent polyploids.
Panopoulou G, Poustka AJ. Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis. Trends Genet. 2005 Oct;21(10):559-67

Evolution and diversity of fish genomes. [Curr Opin Genet Dev. 2003] PMID: 14638319
Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. [Proc Natl Acad Sci U S A. 2004] PMID: 14757817Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. [Mol Biol Evol. 2004] PMID: 15014147 Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. [Nature. 2004] PMID: 15496914 See all Related Articles...
Turning the clock back on ancient genome duplication. [Curr Opin Genet Dev. 2003] PMID: 14638327 Were vertebrates octoploid? [Philos Trans R Soc Lond B Biol Sci. 2002] PMID: 12028790 Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference. [Mol Biol Evol. 2004] PMID: 14694077 Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. [J Exp Zoolog B Mol Dev Evol. 2003] PMID: 14508816 Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. [Mol Biol Evol. 2002] PMID: 12200472See all Related Articles...

~ Basic mechanisms of evolution ~ Duplication ^ Population Genetics Tables  Mechanisms of Biological Evolution :  Gene Regulation in E.coli :

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