Extensive genomic duplication during early chordate evolution

  title={Extensive genomic duplication during early chordate evolution},
  author={Aoife McLysaght and Karsten Hokamp and Kenneth H. Wolfe},
  journal={Nature Genetics},
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… 

Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate

The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, and the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage is highlighted.

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement.

It is proposed that the vertebrate whole genome duplication events may have been symptoms of a preexisting predisposition toward genomic structural change, and it is found that the early vertebrate WGD events were not followed by increased rates of genome rearrangement.

Multiple Chromosomal Rearrangements Structured the Ancestral Vertebrate Hox-Bearing Protochromosomes

A phylogenetic analysis of the vertebrate Hox clusters and several linked genes is presented and it is shown that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes, suggesting that a period of genome reorganization occurred after genome duplications in early vertebrates.

Inference of gene loss rates after whole genome duplications at early vertebrates through ancient genome reconstructions

A combined perspective of phylogenetic and genomic homology to revisit the hypothesis of 2R whole genome duplications and reconstructions provide convincing evidence for the 2R hypothesis, and may provide further insights in vertebral evolution.

Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution.

It is argued that a "phylogenomic" approach, which compares paralogous clusters of linked genes from complete amphioxus and human genome sequences, will be required if the pattern and process of early chordate genome evolution is ever to be reconstructed.

Phylogenomic analysis reveals ancient segmental duplications in the human genome.

Functional Evolution of the Vertebrate Myb Gene Family

The utility of genetic complementation in Drosophila to explore the functional evolution of duplicated genes in vertebrates is demonstrated and it is suggested that B-Myb and Dm- myb share essential conserved functions that are required for cell proliferation.

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes.

The results favor at least one large duplication event at the origin of vertebrates, followed by smaller scale duplication closer to the bird-mammalian split, and model based calculations of the codon substitution rate of the human genes included in these segments agree with the molecular clock duplication time-scale prediction.

Computational Analyses of Ancient Polyploidy

A review of a wide array of computational methods of ever-increasing sophistication developed to identify the obscured traces of ancient polyploidy events in genomic sequences, including comparative genomics, phylogenetics and molecular clock analyses.



Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution.

It was shown that cognates (orthologs) of human duplicated genes can be found in other vertebrates, including bony fishes, and that large-scale duplications occurred after the echinoderms/chordates split and before the bony vertebrate radiation.

Pattern and timing of gene duplication in animal genomes.

Although the human genome showed a higher proportion of recent gene duplications than the other animal genomes, the proportion of duplications after the deuterostome-protostome split was constant across families, with no peak of such duplications in four-member families, contrary to the expectation of the 2R hypothesis.

Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution

It is indicated that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution to build the current hierarchy of the human proteome.

Ancient genome duplications did not structure the human Hox-bearing chromosomes.

The results indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

Molecular evidence for an ancient duplication of the entire yeast genome

A model is proposed in which this species is a degenerate tetraploid resulting from a whole-genome duplication that occurred after the divergence of Saccharomyces from Kluyveromyces, and protein pairs derived from this duplication event make up 13% of all yeast proteins.

Gene duplications and the origins of vertebrate development.

From amphioxus and vertebrate homeobox gene expression patterns, it is suggested that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations.

Coparalogy: physical and functional clusterings in the human genome.

Two rounds of large-scale duplications are thought to have occurred in early vertebrate ancestry; this is now known as the "2R hypothesis." They have led to the constitution of subfamilies of

Vertebrate genome evolution: a slow shuffle or a big bang?

With more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters.

Divergence pattern of animal gene families and relationship with the Cambrian explosion

  • T. MiyataH. Suga
  • Biology
    BioEssays : news and reviews in molecular, cellular and developmental biology
  • 2001
A molecular phylogeny‐based analysis of several animal‐specific gene families has revealed that gene diversification by duplication occurred during two active periods interrupted by a long intervening quiescent period, indicating that there is no direct link between the first burst of gene diversifying and the Cambrian explosion itself.

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.