Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate

By Paramvir S. Dehal, Jeffrey L. Boore. PLoS Biology, 2005

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The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish–tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d98e997c2729647a37c6c27afd750ea3aa19b0e4

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Citations in the corpus

TreeFam: a curated database of phylogenetic trees of animal gene families (2005, methodology): “TreeFam uses clusters of closely related animal and fungal genes from the PhIGs database [http://phigs.org; ( 22 )] as seeds for TreeFam-B families (Figure 1A).”
Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140 year old naturally established neo-allopolyploid monkeyflower (2016, background): “evolutionary history of eukaryotes (McLysaght et al., 2002; Dehal and Boore, 2005; Otto, 2007), 58 including having contributed to the origin of novel traits and shifts in net diversification rates (Levin, 59 1983; Wright et al.”
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, neutral): “Thus duplication of these genes is likely to have occurred in between the deuteros-tomes and vertebrate branches in the tree of life––perhaps as part of the 2R whole genome duplication at the basis of the vertebrates (24).”
The evolutionary significance of ancient genome duplications (2009, background): “However, all vertebrates seem to have shared two ancient WGD events, whereas all teleosts, and probably also eudicots, are derived from a lineage that experienced a WGD even”
Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. (2007, methodology): “Recently, Dehal and Boore showed that a large part of the human genome contains four-way paralogous chromosomal regions, which are traces of the 2R WGD (Dehal and Boore 2005).”
THE LOCUS OF EVOLUTION: EVO DEVO AND THE GENETICS OF ADAPTATION (2007, methodology): “We chose these examples because each demonstrates fairly rigorously both the adaptive nature of the genetic change as well as whether that change is cis-regulatory, structural, or both.”
Teleost fish with specific genome duplication as unique models of vertebrate evolution (2010, background): “…of their chromosomal locations, and evolutionary inferences of ancestral karyotypes have confirmed two rounds of WGD (i.e., first-round [1R]-WGD and second-round [2R]-WGD) in the ancestors of vertebrates (Dehal and Boore 2005; Panopoulou and Poustka 2005; Nakatani et al. 2007; Putnam et al. 2008).”
Widespread genome duplications throughout the history of flowering plants. (2006, background): “…and Hughes 2001; Makalowski 2001; Hughes and Friedman 2003), ancient polyploidy is supported by genetic and genomic investigations of individual gene families as well as large syntenic chromosomal segments (Abi-Rached et al. 2002; Gu et al. 2002; McLysaght et al. 2002; Dehal and Boore 2005).”
Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “In contrast, the most recent WGD event occurred approximately 450 MYA in the lineage leading to humans (Panopoulou et al., 2003; Dehal and Boore, 2005) and approximately 200 MYA in the budding yeast lineage (Wolfe and Shields, 1997; Kellis et al., 2004).”
The Human Transcription Factors. (2018, neutral): “The earlier wave, with duplications across diverse TF families, is consistent with the postulation that two rounds of whole-genome duplication occurred at or near the base of vertebrates (Dehal and Boore, 2005).”
The amphioxus genome and the evolution of the chordate karyotype (2008, background): “Louis MO 63130, USA [4] Division of Biology, California Institute of Technology, Pasadena CA 91125 [5] Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS UK [6] RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 2300045, Japan [7] Marine Biol”