Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants

The population genetic mechanisms governing the preservation of gene duplicates, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy serves to reduce gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such an accuracy in the phenotype yields a selective advantage in the order of 0. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we discuss how the genome rearrangement rates greatly condition the eventual fixation of duplicates. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication. Gene duplication has enthralled researchers for decades due to its link to the emergence of major evolutionary innovations in organisms of ranging complexity Ohno, The key aspect to deeply understand this process concerns the early stage, when the fate of the new-born gene is decided Innan and Kondrashov,

NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees

Microduplications are changes in chromosomes where small segments of DNA are copied or duplicated. This alters the translation of gene into protein, causing a loss of function. Frameshift mutations resulting from microduplications cause as many as different diseases, including limb-girdle muscular dystrophy, Hermansky-Pudlak syndrome, and Tay-Sachs.

In order to reduce the errors of molecular clock for our model, we developed a strict pipeline to build gene families and date the age of duplications based on.

A team led by scientists at The Scripps Research Institute has shown that an extra copy of a brain-development gene, which appeared in our ancestors’ genomes about 2. What genetic changes account for the vast behavioral differences between humans and other primates? Researchers so far have catalogued only a few, but now it seems that they can add a big one to the list.

Surprisingly, the added copy doesn’t augment the function of the original gene, SRGAP2, which makes neurons sprout connections to neighboring cells. Instead it interferes with that original function, effectively giving neurons more time to wire themselves into a bigger brain. Polleux is the senior author of the new report, which was published online ahead of print on May 3, by the journal Cell.

Gene Duplication

If the address matches an existing account you will receive an email with instructions to reset your password. If the address matches an existing account you will receive an email with instructions to retrieve your username. Large scale gene duplication is a major force driving the evolution of genetic functional innovation.

Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast, and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process.

Date de début 1 Janvier Date de fin 31 Decembre I propose that the opposing constraints on gene-by-gene duplications as compared to WGD.

Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast and vertebrate genomes.

The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process. View on ACM. Save to Library. Create Alert. Launch Research Feed.

Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach

Our certification programmes ensure certified labs offer the highest quality service on our sequencing platforms. Discuss your bespoke training, project support or consultancy needs with us so we can offer the right solution for you. Designed to ensure your instrument is performing optimally by providing the most up-to-date hardware and software.

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking.

Notung: dating gene duplications using gene family trees Large scale gene duplication is a major force driving the evolution of genetic functional innovation.

Howard University , United States of America. Genes may be altered before or after the duplication pro Genes may be altered before or after the duplication process thereby undergoing neofunctionalization, thus creating in time new organisms which populate the Earth. By Owen Z. Woody and Brendan J. By Klas Hatje and Martin Kollmar. Mar Alba. By Galina Zhouravleva and Stanislav Bondarev. By Venu Vuppu and Nicola Mulder. By Manoj Majee and Harmeet Kaur.

By Felipe Merino and Victoria Guixe. By Shiyang Kwong and R. Manjunatha Kini. Morris and Dangqun Cui.

NOTUNG: a program for dating gene duplications and optimizing gene family trees

Metrics details. The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity.

Dating endosymbiosis events with cross-calibration the potential of duplicated gene families to refine disputed dates of major evolutionary.

Duplicate genes are important in disease, are a hugely important source of evolutionary novelty, and for many years we thought we understood them. We thought that duplication relieved selective constraints. We thought that gene knockout neutrality was due to redundancy. We thought that a duplicate is a duplicate is a duplicate.

Evidence is accumulating challenging each of these views. Rather than being the result of an unbiased process, the genes that tend to duplicate in our genome and others are quickly evolving, non-essential genes, irrespective of current duplication status. Conversely, genes retained after whole genome duplication WGD are slowly evolving, important genes. I propose that different resolution of the evolutionary constraints imposed by the demands of gene expression can explain these contrasting relationships.

Date of large-scale gene duplication or whole-genome duplication

Vertebrates originated in the lower Cambrian. Their diversification gene morphological dating have been attributed to large-scale gene or for duplications at the origin of gene group. Under such models, gene genes that are duplicated in all vertebrates should have originated during the same period. Previous work has shown that indeed duplications started after the speciation between vertebrates and dating closest invertebrate, amphioxus, duplications have not set a clear ending.

Consideration of chordate phylogeny immediately shows the key position gene cartilaginous vertebrates Chondrichthyes to answer this question. Although the time interval is relatively short, it is crucial to understanding the events at the origin of vertebrates.

Description. Modified version of commons file Image: Source. commons file Image: Date. Author.

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Very low gene duplication rate in the yeast genome.

Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process.

Many studies in the molecular evolution literature have used this approach on small data sets, using analyses performed by hand.

Duplicate genes were preferentially retained for specific functions, such as Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential.

Gene duplication has certainly played a major role in structuring vertebrate genomes but the extent and nature of the duplication events involved remains controversial. A recent study identified two major episodes of gene duplication: one episode of putative genome duplication ca. We confirm this pattern using methods not reliant on molecular clocks for individual gene families.

However, analysis of a simple model of the birth—death process suggests that the apparent recent episode of duplication is an artefact of the birth—death process. We show that a constant-rate birth—death model is appropriate for gene duplication data, allowing us to estimate the rate of gene duplication and loss in the vertebrate genome over the last Myr 0. Finally, we show that increasing rates of gene loss reduce the impact of a genome-wide duplication event on the distribution of gene duplications through time.

Gene duplications are probably the major source of novel genetic material Ohno ; Holland et al. The arrival of genome-scale sequence data for vertebrates in recent years has prompted a number of investigations of gene duplications in vertebrates e. Gu et al. In particular, Gu et al. Gu, personal communication. These two datasets have difference strengths and weaknesses: while Gu et al.

Notung: dating gene duplications using gene family trees

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This study used a phylogeny of yeast species to date gene duplications, which enabled the authors to estimate the rate of duplications in the.

Through phylogeny reconstruction we identified 49 genes with a single copy in man, mouse, and chicken, one or two copies in the tetraploid frog Xenopus laevis , and two copies in zebrafish Danio rerio. For 22 of these genes, both zebrafish duplicates had orthologs in the pufferfish Takifugu rubripes. For another 20 of these genes, we found only one pufferfish ortholog but in each case it was more closely related to one of the zebrafish duplicates than to the other.

Forty-three pairs of duplicated genes map to 24 of the 25 zebrafish linkage groups but they are not randomly distributed; we identified 10 duplicated regions of the zebrafish genome that each contain between two and five sets of paralogous genes. Ohno proposed that without duplicated genes the creation of metazoans, vertebrates and mammals from unicellular organisms would have been impossible Ohno Such big leaps in evolution, Ohno argued, required the creation of new gene loci with previously nonexistent functions.

Because complete genome duplication increases gene number without upsetting gene dosage, it was advanced as the primary source of redundant genes. Ohno was not the first to suggest that genome-wide redundancy could lead to new evolutionary opportunities. Almost 20 years earlier, Stephens recognized that mutations were likely to impair original gene function, and he concluded that a mechanism in which a new function could be attained only at the price of discarding an old one would not be an efficient way of effecting evolutionary progress.

Christians Shouldn’t Think About Evolution