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

Abstract

Paralogous genes from several families were found in four human chromosome regions (4p16, 5q33-35, 8p12-21, and 10q24-26), suggesting that their common ancestral region underwent several rounds of large-scale duplication. Searches in the EMBL databases, followed by phylogenetic analyses, showed that cognates (orthologs) of human duplicated genes can be found in other vertebrates, including bony fishes. In contrast, within each family, only one gene showing the same high degree of similarity with all the duplicated mammalian genes was found in nonvertebrates (echinoderms, insects, nematodes). This indicates that large-scale duplications occurred after the echinoderms/chordates split and before the bony vertebrate radiation. It has been suggested that two rounds of gene duplication occurred in the vertebrate lineage after the separation of Amphioxus and craniate (vertebrates + Myxini) ancestors. Before these duplications, the genes that have led to the families of paralogous genes in vertebrates must have been physically linked in the craniate ancestor. Linkage of some of these genes can be found in the Drosophila melanogaster and Caenorhabditis elegans genomes, suggesting that they were linked in the triploblast Metazoa ancestor.

Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions

“…Evidence in favor of the 1-2-4 hypothesis is the observation that genes from the same gene family are often arranged in linked clusters that maintain the same gene order on different chromosomes (e.g. see [8]). This synteny of gene clusters (the location of two genes within a linkage group but on different chromosomes) is often retained across large evolutionary distances, such as between fish, mice and humans.…”

Timing and mechanism of ancient vertebrate genome duplications – the adventure of a hypothesis

“…The identification of three 'large' quadrupled regions in the unfinished human genome, namely the major histocompatibility complex (MHC; human chromosome (Hsa) l, 6, 9 and 19), an extended Hox (Hsa 2, 7, 12 and 17) and the fibroblast growth factor receptor (FGFR; Hsa 4, 5, 8 and l0) regions, which included genes duplicated w530-738 Mya strongly supported tetraploidy [5][6][7][8][9]. These rounds of duplication could have happened in short succession within 90-106 Mya [10].…”

Reconciliation with Non-Binary Species Trees

“…First, we confirmed that our non-binary algorithms perform identically to Least Common Ancestor reconciliation when applied to binary trees. We tested the new algorithms in NOTUNG on a benchmark of 15 wellstudied, binary trees 5,17,32,38 and verified that the results were the same as those generated by the binary version of NOTUNG, as well as those of the original authors. Second, we considered performance.…”