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Schubert, M, Yu JK, Holland ND, Escriva H, Laudet V, Holland LZ.  2005.  Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus. Development. 132:61-73.   10.1242/dev.01554   AbstractWebsite

In the invertebrate chordate amphioxus, as in vertebrates, retinoic acid (RA) specifies position along the anterior/posterior axis with elevated RA signaling in the middle third of the endoderm setting the posterior limit of the pharynx. Here we show that AmphiHox1 is also expressed in the middle third of the developing amphioxus endoderm and is activated by RA signaling. Knockdown of AmphiHox1 function with an antisense morpholino oligonucleotide shows that AmphiHox1 mediates the role of RA signaling in setting the posterior limit of the pharynx by repressing expression of pharyngeal markers in the posterior foregut/midgut endoderm. The spatiotemporal expression of these endodermal genes in embryos treated with RA or the RA antagonist BMS009 indicates that Pax1/9, Pitx and Notch are probably more upstream than Otx and Nodal in the hierarchy of genes repressed by RA signaling. This work highlights the potential of amphioxus, a genomically simple, vertebrate-like invertebrate chordate, as a paradigm for understanding gene hierarchies similar to the more complex ones of vertebrates.

Mazet, F, Yu JK, Liberles DA, Holland LZ, Shimeld SM.  2003.  Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria. Gene. 316:79-89.   10.1016/s0378-1119(03)00741-8   AbstractWebsite

The Forkhead or Fox gene family encodes putative transcription factors. There are at least four Fox genes in yeast, 16 in Drosophila melanogaster (Dm) and 42 in humans. Recently, vertebrate Fox genes have been classified into 17 groups named FoxA to FoxQ [Genes Dev. 14 (2000) 142]. Here, we extend this analysis to invertebrates, using available sequences from D. melanogaster, Anopheles gambiae (Ag), Caenorhabditis elegans (Ce), the sea squirt Ciona intestinalis (Ci) and amphioxus Branchiostoma floridae (Bf), from which we also cloned several Fox genes. Phylogenetic analyses lend support to the previous overall subclassification of vertebrate genes, but suggest that four subclasses (FoxJ, L, N and Q) could be further subdivided to reflect their relationships to invertebrate genes. We were unable to identify orthologs of Fox subclasses E, H, I, J, M and Q1 in D. melanogaster, A. gambiae or C. elegans, suggesting either considerable loss in ecdysozoans or the evolution of these subclasses in the deuterostome lineage. Our analyses suggest that the common ancestor of protostomes and deuterostomes had a minimum complement of 14 Fox genes. (C) 2003 Elsevier B.V. All rights reserved.

Yu, JK, Holland ND, Holland LZ.  2002.  An amphioxus winged helix/forkhead gene, AmphiFoxD: Insights into vertebrate neural crest evolution. Developmental Dynamics. 225:289-297.   10.1002/dvdy.10173   AbstractWebsite

During amphioxus development, the neural plate is bordered by cells expressing many genes with homologs involved in vertebrate neural crest induction. However, these amphioxus cells evidently lack additional genetic programs for the cell delaminations, migrations, and differentiations characterizing definitive vertebrate neural crest. We characterize an amphioxus winged helix/forkhead gene (AmphiFoxD) closely related to vertebrate FoxD genes. Phylogenetic analysis indicates that the AmphiFoxD is basal to vertebrate FoxD1, FoxD2, FoxD3, FoxD4, and FoxD5. One of these vertebrate genes (FoxD3) consistently marks neural crest during development. Early in amphioxus development, AmphiFoxD is expressed medially in the anterior neural plate as well as in axial (notochordal) and paraxial mesoderm; later, the gene is expressed in the somites, notochord, cerebral vesicle (diencephalon), and hindgut endoderm. However, there is never any expression in cells bordering the neural plate. We speculate that an AmphiFoxD homolog in the common ancestor of amphioxus and vertebrates was involved in histogenic processes in the mesoderm (evagination and delamination of the somites and notochord); then, in the early vertebrates, descendant paralogs of this gene began functioning in the presumptive neural crest bordering the neural plate to help make possible the delaminations and cell migrations that characterize definitive vertebrate neural crest. (C) 2002 Wiley-Liss, Inc.

Holland, LZ, Holland ND.  1998.  Developmental gene expression in amphioxus: New insights into the evolutionary origin of vertebrate brain regions, neural crest, and rostrocaudal segmentation. American Zoologist. 38:647-658. AbstractWebsite

Amphioxus is widely held to be the closest invertebrate relative of the vertebrates and the best available stand-in for the proximate ancestor of the vertebrates. The spatiotemporal expression patterns of developmental genes can help suggest body part homologies between vertebrates and amphioxus, This approach is illustrated using five homeobox genes (AmphiHox1, AmphiHox2, AmphiOtx, AmphiDll, and AmphiEn) to pro,ide insights into the evolutionary origins of three important vertebrate features: the major brain regions, the neural crest, and rostrocaudal segmentation. During amphioxus development, the neural expression patterns of these genes are consistent with the presence of a forebrain (detailed neuroanatomy indicates that the forebrain is all diencephalon without any telencephalon) and an extensive hindbrain; the possible presence of a midbrain requires additional study. Further, during neurulation, the expression pattern of AmphiDll as web as migratory cell behavior suggest that the epidermal cells bordering the neural plate may represent a phylogenetic precursor of the vertebrate neural crest. Finally, when the paraxial mesoderm begins to segment, the earliest expression of AmphiEn is detected in the posterior part of each nascent and newly formed somite, This pattern recalls the expression of the segment-polarity gene engrailed during establishment of the segments of metameric protostomes. Thus, during animal evolution, the role of engrailed in establishing and maintaining metameric body plans may have arisen in a common segmented ancestor of both the protostomes and deuterostomes.

Holland, PWH, Holland LZ, Williams NA, Holland ND.  1992.  An Amphioxus Homeobox Gene - Sequence Conservation, Spatial Expression During Development and Insights into Vertebrate Evolution. Development. 116:653-&. AbstractWebsite

The embryology of amphioxus has much in common with vertebrate embryology, reflecting a close phylogenetic relationship between the two groups. Amphioxus embryology is simpler in several key respects, however, including a lack of pronounced craniofacial morphogenesis. To gain an insight into the molecular changes that accompanied the evolution of vertebrate embryology, and into the relationship between the amphioxus and vertebrate body plans, we have undertaken the first molecular level investigation of amphioxus embryonic development. We report the cloning, complete DNA sequence determination, sequence analysis and expression analysis of an amphioxus homeobox gene, AmphiHox3, evolutionarily homologous to the third-most 3' paralogous group of mammalian Hox genes. Sequence comparison to a mammalian homologue, mouse Hox-2.7 (HoxB3), reveals several stretches of amino acid conservation within the deduced protein sequences. Whole mount in situ hybridization reveals localized expression of AmphiHox3 in the posterior mesoderm (but not in the somites), and region-specific expression in the dorsal nerve cord, of amphioxus neurulae, later embryos and larvae. The anterior limit to expression in the nerve cord is at the level of the four/five somite boundary at the neurula stage, and stabilises to just anterior to the first nerve cord pigment spot to form. Comparison to the anterior expression boundary of mouse Hox-2.7 (HoxB3) and related genes suggests that the vertebrate brain is homologous to an extensive region of the amphioxus nerve cord that contains the cerebral vesicle (a region at the extreme rostral tip) and extends posterior to somite four. This proposed homology implies that the vertebrate brain probably did not evolve solely from the cerebral vesicle of an amphioxus-like ancestor, nor did it arise entirely de novo anterior to the cerebral vesicle.