bib gene duplication (1996)

Bibliography on gene and genome duplication (1996)

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M Averof, R Dawes, D Ferrier (1996), "Diversification of arthropod Hox genes as a paradigm for the evolution of gene functions", Cell. Dev. Biology, 7:539-551.
IP Blair, J Nash, MJ Gordon, and GA Nicholson (1996), "Prevalence and origin of de novo duplications in Charcot-Marie-Tooth disease type 1A: first report of a de novo duplication with a maternal origin", American Journal of Human Genetics, 58(3):472-476.
J Garcia-Fernandez, PW Holland (1996), "Amphioxus Hox genes: insights into evolution and development", International Journal of Development Biology, (Suppl 1):71S-72S.
R Guigo, I Muchnik, TF Smith (1996), "Reconstruction of ancient molecular phylogeny", Molecular Phylogenetics and Evolution, 6:189-213.
[ abstract] abstract: Support for contradictory phylogenies is often obtained when molecular sequence data from different genes is used to reconstruct phylogenetic histories. Contradictory phylogenies can result from many data anomalies including unrecognized paralogy. Paralogy, defined as the reconstruction of a phylogenetic tree from a mixture of genes generated by duplications, has generally not been formally included in phylogenetic reconstructions. Here we undertake the task of reconstructing a single most likely evolutionary relationship among a range of taxa from a large set of apparently inconsistent gene trees. Under the assumption that differences among gene trees can be explained by gene duplications, and consequent losses, we have developed a method to obtain the global phylogeny minimizing the total number of postulated duplications and losses and to trace back such individual gene duplications to global genome duplications. We have used this method to infer the most likely phylogenetic relationship among 16 major higher eukaryotic taxa from the sequences of 53 different genes. Only five independent genome duplication events need to be postulated in order to explain the inconsistencies among these trees.
Peter WH Holland, Jordi G Garcia-Fernandez (1996), "Hox genes and chordate evolution", Developmental Biology, 173:382-395.
[ abstract]
[Comments by Sidow (1996): A comprehensive review of Hox cluster evolution from the authors who showed that amphioxus has a single cluster. Expression patterns of the AmphiHox genes in development indicates that the conserved and perhaps ancestral expression domain of the chordate Hox genes is in the neurectoderm and not in the mesoderm. Furthermore, the authors convincingly make the point that expression of orthologous marker genes - in this case, expression of amphihox 3 in the amphioxus nerve cord and expression of its vertebrate orthologs in the developing hindbrain-can be used to establish homology of developing tissues in the absence of obvious morphological similarity. ]
M Kasahara, M Hayashi, K Tanaka, H Inoko, K Sugaya, T Ikemura, T Ishibashi (1996), "Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex", Proceedings of National Academy of Sciences, 93(17):9096-9101.
SE Kearsey, D Maiorano, EC Holmes, IT Todorov (1996), "The role of MCM proteins in the cell cycle control of genome duplication", Bioessays, 18:183-190.
AC Sharman, PWH Holland (1996), "Conservation, duplication, and divergence of developmental genes during chordate evolution", Netherlands Journal of Zoology, 46:47-67.
Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996), "Genome duplication in soybean (Glycine subgenus soja)", Genetics, 144(1):329-338.
[abstract]
A Sidow (1996), "Gen(om)e duplications in the evolution of early vertebrates", Current Opinion in Genetics and Development, 6:715-722.
abstract: Phylogenetic analyses and sequence surveys of developmental regulator gene families indicate that two large-scale gene duplications, most likely genome duplications, occurred in ancestors of vertebrates. Relaxed constraints allowed duplicated and thus redundant genes to diverge in a two stage mechanism. Neutral changes dominated at first but then positively selected regulatory changes evolved the novel and increasingly complex vertebrate developmental program.
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		Bibliography on gene and genome duplication (1996)
	front page glossary 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1994 1993 1992 1991 1990 80s 70s 60s 50s 40s 30s 20s 10s	M Averof, R Dawes, D Ferrier (1996), "Diversification of arthropod Hox genes as a paradigm for the evolution of gene functions", Cell. Dev. Biology, 7:539-551. IP Blair, J Nash, MJ Gordon, and GA Nicholson (1996), "Prevalence and origin of de novo duplications in Charcot-Marie-Tooth disease type 1A: first report of a de novo duplication with a maternal origin", American Journal of Human Genetics, 58(3):472-476. J Garcia-Fernandez, PW Holland (1996), "Amphioxus Hox genes: insights into evolution and development", International Journal of Development Biology, (Suppl 1):71S-72S. R Guigo, I Muchnik, TF Smith (1996), "Reconstruction of ancient molecular phylogeny", Molecular Phylogenetics and Evolution, 6:189-213. [ abstract] abstract: Support for contradictory phylogenies is often obtained when molecular sequence data from different genes is used to reconstruct phylogenetic histories. Contradictory phylogenies can result from many data anomalies including unrecognized paralogy. Paralogy, defined as the reconstruction of a phylogenetic tree from a mixture of genes generated by duplications, has generally not been formally included in phylogenetic reconstructions. Here we undertake the task of reconstructing a single most likely evolutionary relationship among a range of taxa from a large set of apparently inconsistent gene trees. Under the assumption that differences among gene trees can be explained by gene duplications, and consequent losses, we have developed a method to obtain the global phylogeny minimizing the total number of postulated duplications and losses and to trace back such individual gene duplications to global genome duplications. We have used this method to infer the most likely phylogenetic relationship among 16 major higher eukaryotic taxa from the sequences of 53 different genes. Only five independent genome duplication events need to be postulated in order to explain the inconsistencies among these trees. Peter WH Holland, Jordi G Garcia-Fernandez (1996), "Hox genes and chordate evolution", Developmental Biology, 173:382-395. [ abstract] [Comments by Sidow (1996): A comprehensive review of Hox cluster evolution from the authors who showed that amphioxus has a single cluster. Expression patterns of the AmphiHox genes in development indicates that the conserved and perhaps ancestral expression domain of the chordate Hox genes is in the neurectoderm and not in the mesoderm. Furthermore, the authors convincingly make the point that expression of orthologous marker genes - in this case, expression of amphihox 3 in the amphioxus nerve cord and expression of its vertebrate orthologs in the developing hindbrain-can be used to establish homology of developing tissues in the absence of obvious morphological similarity. ] M Kasahara, M Hayashi, K Tanaka, H Inoko, K Sugaya, T Ikemura, T Ishibashi (1996), "Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex", Proceedings of National Academy of Sciences, 93(17):9096-9101. SE Kearsey, D Maiorano, EC Holmes, IT Todorov (1996), "The role of MCM proteins in the cell cycle control of genome duplication", Bioessays, 18:183-190. AC Sharman, PWH Holland (1996), "Conservation, duplication, and divergence of developmental genes during chordate evolution", Netherlands Journal of Zoology, 46:47-67. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996), "Genome duplication in soybean (Glycine subgenus soja)", Genetics, 144(1):329-338. [abstract] A Sidow (1996), "Gen(om)e duplications in the evolution of early vertebrates", Current Opinion in Genetics and Development, 6:715-722. abstract: Phylogenetic analyses and sequence surveys of developmental regulator gene families indicate that two large-scale gene duplications, most likely genome duplications, occurred in ancestors of vertebrates. Relaxed constraints allowed duplicated and thus redundant genes to diverge in a two stage mechanism. Neutral changes dominated at first but then positively selected regulatory changes evolved the novel and increasingly complex vertebrate developmental program. [ html ]