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Evolutionary and developmental geneticsThere is a growing awareness that recent advances in evolutionary genomics and developmental genetics can provide significant insights into evolution and the nature of biodiversity. This is the central theme of research in my lab. In one area of study. we use evolution-based strategies for investigating how molecular processes such as gene duplication and regulatory element (enhancer) evolution have shaped the genomes of higher organisms (e.g. human and zebrafish). We focus primarily on the HOX genes. which originated early in metazoan phylogeny and are distributed throughout the animal kingdom. HOX genes. which encode transcription factors that play an important role in embryonic development. are organized in clusters in the genome. These clusters display tandem gene duplication. gene loss. gene sequence divergence. functional divergence. and regulatory element evolution. HOX clusters also display the phenomenon of colinearity. in which the position of a gene in the cluster is related to its expression dynamics in the developing embryo. The study of HOX genes. therefore. provides the opportunity to understand the relationship between genome organization and gene expression. This research involves the construction of BAC genomic libraries. screening of BAC libraries. large scale DNA sequencing. and evolutionary sequence analysis. The second and related area of study is evolutionary developmental biology or "evo-devo". which seeks to explain the evolution and development of morphological characters as well as the evolution of their underlying genetic and developmental mechanisms using a comparative approach. We currently use the tetrapod limb as a model system. with focus on the genetic basis for evolutionary diversity in the hands and feet of primates. This research combines developmental biology methodologies using traditional animals models such as mouse and chick with functional tests to identify sequence changes in developmental patterning and growth genes that are associated with interspecific differences in adult primate limb morphologies. Selected PublicationsMulley JF, Chiu CH, Holland PW. (2006) Breakup of a homeobox cluster after genome duplication in teleosts. Proc Natl Acad Sci U S A. 103(27):10369-72. Chiu CH. Dewar K. Wagner GP. Takahashi K. Ruddle F. Ledje C. Bartsch P. Scemama JL. Stellwag E. Fried C. Prohaska SJ. Stadler PF. Amemiya CT. (2004) Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Res. 14(1):11-7. Chiu. C-H.. Dewar. K.. Wagner. G.P.. Takahashi. K.. Ruddle. F.. Ledje. C.. Bartsch. P.. Scemama. J.. Stellwag. E.. Fried. C.. Prohaska. S.. Stadler. P.F.. Amemiya. C.T. (2003) Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Research. in press. Chiu
C-H. Amemiya
CT
. Dewar K. Kim C-B. Ruddle FH. Wagner GP. (2002). Molecular evolution of the HoxA
cluster in the three major gnathostome lineages. Proc Natl Acad Sci
Chiu. C-H.. Hamrick. M.W. (2002). Evolution and development of the primate limb skeleton. Evolutionary Anthropology 11: 94-107. Wagner. G.P.. Chiu. C-H. (2001). The tetrapod limb: A hypothesis on its origin. Mol Dev Evol 291: 226-240. Wagner. G.P.. Chiu. C-H.. Laubichler. M. (2000). Developmental evolution as a mechanistic science: The inference from developmental mechanisms to evolutionary processes. Amer Zool 40: 819-831. Hansen. T.F.. Carter. A.. Chiu. C-H. (2000) Gene conversion may aid adaptive peak shifts. J Theoret Biol 207: 495-511. Chiu. C-H.. Nonaka. D.. Xue. L.. Amemiya. C.T.. Wagner. G.P. (2000) Evolution of hoxa11 in lineages phylogenetically positioned along the fin-limb transition. Mol Phyl Evol 17: 305-316. Chiu. C-H.. Amemiya. C.T.. Carr. J.L.. Bhargava. J.. Hwang. J.K.. Shashikant. C.S.. Ruddle. F.H.. Wagner. G.P. (2000). A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: construction and expression of a 100 kb zebrafish hoxa11b-lacZ reporter gene. Dev Genes Evol 210: 105-109. |
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