Peter W H Holland

..Since Hh-C and Hoglet-C are homologous, but Hh-N and Hoglet-N are not, we argue that metazoan hedgehog genes evolved by fusion of two distinct genes...

..In the next century this should give us far greater mechanistic insight into how evolution has produced the vast diversity of living organisms, past and present...

..These data confirm that vertebrates have more genes than their closest invertebrate relatives, acquired through gene duplication...

..A novel hypothesis for the evolution of ParaHox gene expression in deuterostomes is presented...

..I also outline the major unresolved questions in the study of gene duplication, and its relevance to evolution and development...

..One of the many surprises is that this strange fish has lost an unusually large number of Hox genes...

..These roles were elaborated following Otx gene duplication in vertebrates, accompanied by regulatory and structural divergence, particularly of Otx1 descendant genes...

..Therefore, placodes are not likely to be a newly acquired feature in vertebrates, but may have already been possessed by the earliest chordates...

..Finally, our molecular phylogenetic analysis strongly supports the presence of a single Emx gene in the ancestor of chordates and gene duplication along the vertebrate lineage...

..We propose a new homeobox class, Mnx, to include AmphiMnx, HB9, MNR2 and their Drosophila and echinoderm orthologues; we suggest that vertebrate HB9 is renamed Mnx1 and MNR2 be renamed Mnx2...

..We propose that early vertebrates passed through an autoautooctoploid phase in the evolution of their genomes...

..We also show that the HMG1/2 family originated before the protostomes and deuterostomes diverged, over 525 million years ago...

..Using robust Bayesian statistical analysis of 18S ribosomal DNA, mitochondrial genes and nuclear protein-coding DNA, we find strong support for a hemichordate-echinoderm clade, and for monophyly of the cyclostomes...

..This disintegration may be mediated by the invasion of transposable elements into the clusters, and subsequent genomic rearrangements...

..This evolutionary pattern is in marked contrast to the Hox and ParaHox gene clusters, which are compact in amphioxus and vertebrates, but have been disrupted in Drosophila...

..These results suggest that dorsal specification in the neural tube by Pax-3/7 subfamily genes was established in the ancestors of extant chordates during emergence of the dorsal tubular nervous system...

..Furthermore, it implies that the ParaHox genes are of sufficient functional importance in both protostomes and deuterostomes that they have all been conserved in both of these bilaterian clades...

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..Comparative molecular and developmental data give new insights into the evolutionary origins of these characteristics and the complexity of the vertebrate body...

..The characterization of Hox-like genes from Hydra, sea anemones and jellyfish has revealed that a Hox gene cluster is extremely ancient, having originated even before the divergence of these basal animals...

..We infer that animals and at least some choanoflagellates are part of a clade that excludes the fungi. This is consistent with the origin of animals from a choanoflagellate-like ancestor...

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..Unusually for homeobox genes, there is no orthologue in the Drosophila or Caenorhabditis genomes; we argue this reflects secondary loss...

..Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described...

..We propose that this homeobox gene cluster is held together in chordates by the existence of interdigitated control regions that could be separated after locus duplication in the teleost fish...

..Comparison with hemichordates suggests that anterior Otx and posterior Gbx domains were probably overlapping in the ancestral deuterostome and came to abut at the MHB early in the chordate lineage before MHB organizer properties evolved...

..This active muscular worm increases the known diversity in cnidarian body plans and demonstrates that a muscular, wormlike form can evolve in the absence of overt bilateral symmetry...

..We suggest that 14 is the end...

..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...

..We discuss the evolution of midbrain development in relation to the ancestry of the tripartite neural ground plan and the origin of the MHB organiser...

..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...

..The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence...

..Deducing the evolutionary origins of these genes is not straightforward, but we propose that TPRX1, DPRX and DUXA are highly divergent derivatives of the CRX gene, itself a member of the Otx homeobox gene family...

..Furthermore, our phylogenetic analyses suggest that hagfishes may have diverged from the vertebrate lineage before the duplications, which created the multiple ParaHox clusters in jawed vertebrates...

..Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes ('EuHox' genes)...

..Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community...

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..The homeobox and kinase gene families have been further analysed in basal animals, although more data are required to enable detailed comparison with Bilateria...

..We argue that understanding evolutionary history is important for establishing consistent gene nomenclature, and for comparing gene expression patterns and gene functions between species and between gene families...

..The mouse genome has two processed pseudogenes, which are not clear orthologues of the primate pseudogenes...

..The composition of the MHC-linked genomic region, therefore, pre-dates vertebrate origins...

..Although homeobox genes have been the subject of many studies, little is known about the main amino acid changes that occurred early in the evolution of genes belonging to different classes...