bib gene duplication (2001)

Bibliography on gene and genome duplication (2001)

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G Achaz, P Netter, E Coissac (2001), "Study of intrachromosomal duplications among the eukaryote genomes", Molecular Biology and Evolution, 18:2280-2288.
[ abstract]
Ian Bancroft (2001), "Duplicate and diverge: the evolution of plant genome microstructure", Trends in Genetics, 17(2):89-93.
[ abstract]
edited, Per Erik Ahlberg (2001), Major Events in Early Vertebrate Evolution (CRC Press). ISBN: 0415233704
Jeffrey A Bailey, Amy M Yavor, Hillary F Massa, Barbara J Trask, Evan E Eichler (2001), "Segmental duplications: organization and impact within the current human genome project assembly", Genome Research, 11:1005-1017.
JS Conery, M Lynch (2001), "Nucleotide substitutions and the evolution of duplicate genes", Pacific Symposium on Biocomputing, 6:167-178.
[ PDF]
abstract: This paper describes software created to search for and analyze pairs of duplicate genes within a genome. The process is based on a program that uses aligned amino acid sequences to generate a corresponding alignment of the underlying nucleotide sequences and perform a codon by codon comparison of the nucleotides. Observed numbers of nucleotide substitutions can be used to make inferences about the ages of gene duplication events and the effects of natural selection acting on duplicate genes.
Evan Eichler (2001), "Recent duplication domain accretion and the dynamic mutation of the human genome", Trends in Genetics, 17(11):661-669.
[ abstract]
Martin F Flajnik, Masanori Kasahara (2001), "Comparative genomics of the MHC glimpses into the evolution of the adaptive immune system", Immunity, 15(3):351-362.
[ abstract]
R Friedman, AL Hughes (2001), "Gene duplication and the structure of eukaryotic genomes", Genome Research, 11:373-381.
abstract: A simple method for understanding how gene duplication has contributed to genomic structure was applied to the complete genomes of Caenorhabditis elegans, Drosophila melanogaster, and yeast Saccharomyces cerevisiae. By this method, the genes belonging to gene families (the paranome) were identified, and the extent of sharing of two or more families between genomic windows was compared with that expected under a null model. The results showed significant evidence of duplication of genomic blocks in both C. elegans and yeast. In C. elegans, the five block duplications identified all occurred intra-chromosomally, and all but one occurred quite recently. In yeast, by contrast, 39 duplicated blocks were identified, and all but one of these was inter-chromosomal. Of these 39 blocks, 28 showed evidence of ancient duplication, possibly as a result of an ancient polyploidization event. By contrast, three blocks showed evidence of very recent duplication, while seven others showed a mixture of ancient and recent duplication events. Thus, duplication of genomic blocks has been an ongoing feature of yeast evolution over the past 200-300 million years.
R Friedman, AL Hughes (2001), "Pattern and timing of gene duplication in animal genomes", Genome Research, 11:1842-1847.
abstract: Duplication of genes, giving rise to multigene families, has been a characteristic feature of the evolution of eukaryotic genomes. In the case of vertebrates, it has been proposed that an increase in gene number resulted from two rounds of duplication of the entire genome by polyploidization (the 2R hypothesis). In the most extensive test to date of this hypothesis, we compared gene numbers in homologous families and conducted phylogenetic analyses of gene families with two to eight members in the complete genomes of Caenorhabditis elegans and Drosophila melanogaster and the available portion of the human genome. Although the human genome showed a higher proportion of recent gene duplications than the other animal genomes, the proportion of duplications after the deuterostome-protostome split was constant across families, with no peak of such duplications in four-member families, contrary to the expectation of the 2R hypothesis. A substantial majority (70.9%) of human four-member families and four-member clusters in larger families showed topologies inconsistent with two rounds of polyploidization in vertebrates.
Brandon S Gaut (2001), "Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses", Genome Research, 11(1):55-66.
[abstract]
Mònica Gratacòs, Marga Nadal, Rocío Martín-Santos,Miguel Angel Pujana, Jordi Gago, Belén Peral, Lluís Armengol, Immaculada Ponsa, Rosa Miró, Antoni Bulbena, Xavier Estivill (2001), "A polymorphic genomic duplication on human chromosome 15 is a susceptibility factor for panic and phobic disorders", Cell, 106(3):367-379.
[ abstract]
T Ryan Gregory (2001), "Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma", Biological Reviews, 76:65-101.
[abstract]
Xun Gu (2001), "Maximum-likelihood approach for gene family evolution under functional divergence", Molecular Biology and Evolution, 18:453-464.
[abstract]
AL Hughes, J da Silva, R Friedman (2001), "Ancient genome duplications did not structure the human Hox-bearing chromosomes", Genome Research, 11:771-780.
abstract: The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the four Hox-bearing chromosomes (the chromosomes bearing the Hox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the human Hox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hox clusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.
IK Jordan, KS Makarova, JL Spouge, YI Wolf, EV Koonin (2001), "Lineage-specific gene expansions in bacterial and archaeal genomes", Genome Research, 11:555-565.
abstract: Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (~5%-33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size 20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.
Fyodor A Kondrashov and Eugene V Koonin (2001), "Origin of alternative splicing by tandem exon duplication", Human Molecular Genetics, 10(23):2661-2669.
[abstract]
Matthew J Kourakis, Mark Q Martindale (2001), "Hox gene duplication and deployment in the annelid leech Helobdella", Evolution & Development, 3(3):145-153.
WH Li, Z Gu, H Wang, A Nekrutenko (2001), "Evolutionary analyses of the human genome", Nature, 409:847-849.
[PDF]
DA Liberles, DR Schreiber, S Govindarajan, SG Chamberlin, SA Benner (2001),
"The adaptive evolution database (TAED)",
Genome Biology, 2(8):research0028.1-0028.6
related web page : http://www.sbc.su.se/~liberles/TAED.html
M Long (2001), "Evolution of novel genes", Current Opinion in Genetics and Development, 11:673-680.
[ abstract]
M Long, K Thornton (2001), "Gene duplication and evolution" (technical comments), Science, 293(5535):1551.
Arne Ludwig, Natalia M. Belfiore, Christian Pitra, Victor Svirsky, Ingo Jenneckens (2001), "Genome duplication events and functional reduction of ploidy levels in Sturgeon (Acipenser, Huso and Scaphirhynchus)", Genetics, 158:1203-1215.
[abstract]
M Lynch, M O'Hely, B Walsh, and A Force (2001), "The probability of preservation of a newly arisen gene duplicate", Genetics, 159(4):1789-1804.
[abstract]
Edward Malaga-Trillo, Axel Meyer (2001), "Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes", American Zoologist, 41(3):676-686.
AP Martin (2001), "Is tetralogy true? Lack of support for the 'one-to-four' rule" (Letter), Molecular Biology and Evolution, 18:89-93.
[html]
T Massingham, LJ Davies, P Lio (2001), "Analysing gene function after duplication", Bioessays, 23(10):873-876.
abstract: After gene duplication, mutations cause the gene copies to diverge. The classical model predicts that these mutations will generally lead to the loss of function of one gene copy; rarely, new functions will be created and both duplicate genes are conserved. In contrast, under the subfunctionalization model both duplicates are preserved due to the partition of different functions between the duplicates. A recent study provides support for the subfunctionalization model, identifying several expressed gene duplicates common to humans and mice that contain regions conserved in one duplicate but variable in the other (and vice versa). We discuss both the methodology used in this study and also how gene phylogeny may lead to additional evidence for the importance of subfunctionalization in the evolution of new genes.
J McClintock, R Carlson, D Mann, VE Prince (2001), "Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish hox paralogue group 1 genes", Development, 128:2471-2484.
Csaba Pal, Balazs Papp, Laurence D Hurst (2001), "Highly expressed genes in yeast evolve slowly" (letter to the editor), Genetics, 158:927-931.
[html]
J Piskur (2001), "Origin of the duplicated regions in the yeast genomes", Trends in Genetics, 17(6):302-303.
C Popovici, M Leveugle, D Birnbaum, F Coulier (2001), "Coparalogy: physical and functional clusterings in the human genome", Biochemical and Biophysical Research Communications, 288(2):493-493.
Marc Robinson-Rechavi, and Vincent Laudet (2001), "Evolutionary rates of duplicate genes in fish and mammals", Molecular Biology and Evolution, 18:681-683.
[abstract]
Marc Robinson-Rechavi, Oriane Marchand, Hector Escriva, Vincent Laudet (2001), "An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes", Current Biology, 11(12):R458-R459.
[ abstract]
Marc Robinson-Rechavi, Oriane Marchand, Héctor Escriva, Pierre-Luc Bardet, Dominique Zelus, Sandrine Hughes, Vincent Laudet (2001), "Euteleost fish genomes are characterized by expansion of gene families", Genome Research, 11:781-788.
[abstract]
D Sankoff (2001), "Gene and genome duplication", Current Opinion in Genetics and Development, 11:681-684.
[ abstract]
John S. Taylor, Henner Brinkmann (2001), "2R or not 2R?" (research update), Trends in Genetics, 17(9):488-489.
[ abstract]
J Taylor, Y Van de Peer, A Meyer (2001), "Genome duplication, divergent resolution and speciation", Trends in Genetics, 17:299-301.
J Taylor, Y Van de Peer, A Meyer (2001), "Revisiting a recent test of the ancient fish-specific genome duplication hypothesis", Current Biology, 11:R1005-R1007.
J Taylor, Y van de Peer, I Braasch, A Meyer (2001), "Comparative genomics provides evidence for an ancient genome duplication in fish", Philosophical Transactions of Royal Society B: Biological Sciences, 356:1661-1679.
[abstract]
Y van de Peer, J Taylor, I Braasch, A Meyer (2001), "The ghost of selection past: rates of evolution and functional divergence in anciently duplicated genes", Journal of Molecular Evolution, 53:434-444.
[ abstract]
A Wagner (2001), "Birth and death of redundant duplicate genes", Trends in Genetics, 17:237-239.
A Wagner (2001), "The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes", Molecular Biology and Evolution, 18:1283-1292.
KH Wolfe (2001), "Yesterday's polyploids and the mystery of diploidization", Nature Reviews Genetics, 2:333-341.
[PDF]
L Zhang, BS Gaut, TJ Vision (2001), "Gene duplication and evolution" (Comment), Science, 293(5535):1551.
Rongjia Zhou, Hanhua Cheng, Terrence R. Tiersch (2001), "Differential genome duplication and fish diversity", Reviews in Fish Biology and Fisheries, 11(4):331-337.
[ abstract]
Christian M Zmasek, Sean R Eddy (2001),
"A simple algorithm to infer gene duplication and speciation events on a gene tree",
Bioinformatics, 17:821-828.

		Bibliography on gene and genome duplication (2001)
	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	G Achaz, P Netter, E Coissac (2001), "Study of intrachromosomal duplications among the eukaryote genomes", Molecular Biology and Evolution, 18:2280-2288. [ abstract] Ian Bancroft (2001), "Duplicate and diverge: the evolution of plant genome microstructure", Trends in Genetics, 17(2):89-93. [ abstract] edited, Per Erik Ahlberg (2001), Major Events in Early Vertebrate Evolution (CRC Press). ISBN: 0415233704 Jeffrey A Bailey, Amy M Yavor, Hillary F Massa, Barbara J Trask, Evan E Eichler (2001), "Segmental duplications: organization and impact within the current human genome project assembly", Genome Research, 11:1005-1017. JS Conery, M Lynch (2001), "Nucleotide substitutions and the evolution of duplicate genes", Pacific Symposium on Biocomputing, 6:167-178. [ PDF] abstract: This paper describes software created to search for and analyze pairs of duplicate genes within a genome. The process is based on a program that uses aligned amino acid sequences to generate a corresponding alignment of the underlying nucleotide sequences and perform a codon by codon comparison of the nucleotides. Observed numbers of nucleotide substitutions can be used to make inferences about the ages of gene duplication events and the effects of natural selection acting on duplicate genes. Evan Eichler (2001), "Recent duplication domain accretion and the dynamic mutation of the human genome", Trends in Genetics, 17(11):661-669. [ abstract] Martin F Flajnik, Masanori Kasahara (2001), "Comparative genomics of the MHC glimpses into the evolution of the adaptive immune system", Immunity, 15(3):351-362. [ abstract] R Friedman, AL Hughes (2001), "Gene duplication and the structure of eukaryotic genomes", Genome Research, 11:373-381. abstract: A simple method for understanding how gene duplication has contributed to genomic structure was applied to the complete genomes of Caenorhabditis elegans, Drosophila melanogaster, and yeast Saccharomyces cerevisiae. By this method, the genes belonging to gene families (the paranome) were identified, and the extent of sharing of two or more families between genomic windows was compared with that expected under a null model. The results showed significant evidence of duplication of genomic blocks in both C. elegans and yeast. In C. elegans, the five block duplications identified all occurred intra-chromosomally, and all but one occurred quite recently. In yeast, by contrast, 39 duplicated blocks were identified, and all but one of these was inter-chromosomal. Of these 39 blocks, 28 showed evidence of ancient duplication, possibly as a result of an ancient polyploidization event. By contrast, three blocks showed evidence of very recent duplication, while seven others showed a mixture of ancient and recent duplication events. Thus, duplication of genomic blocks has been an ongoing feature of yeast evolution over the past 200-300 million years. R Friedman, AL Hughes (2001), "Pattern and timing of gene duplication in animal genomes", Genome Research, 11:1842-1847. abstract: Duplication of genes, giving rise to multigene families, has been a characteristic feature of the evolution of eukaryotic genomes. In the case of vertebrates, it has been proposed that an increase in gene number resulted from two rounds of duplication of the entire genome by polyploidization (the 2R hypothesis). In the most extensive test to date of this hypothesis, we compared gene numbers in homologous families and conducted phylogenetic analyses of gene families with two to eight members in the complete genomes of Caenorhabditis elegans and Drosophila melanogaster and the available portion of the human genome. Although the human genome showed a higher proportion of recent gene duplications than the other animal genomes, the proportion of duplications after the deuterostome-protostome split was constant across families, with no peak of such duplications in four-member families, contrary to the expectation of the 2R hypothesis. A substantial majority (70.9%) of human four-member families and four-member clusters in larger families showed topologies inconsistent with two rounds of polyploidization in vertebrates. Brandon S Gaut (2001), "Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses", Genome Research, 11(1):55-66. [abstract] Mònica Gratacòs, Marga Nadal, Rocío Martín-Santos,Miguel Angel Pujana, Jordi Gago, Belén Peral, Lluís Armengol, Immaculada Ponsa, Rosa Miró, Antoni Bulbena, Xavier Estivill (2001), "A polymorphic genomic duplication on human chromosome 15 is a susceptibility factor for panic and phobic disorders", Cell, 106(3):367-379. [ abstract] T Ryan Gregory (2001), "Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma", Biological Reviews, 76:65-101. [abstract] Xun Gu (2001), "Maximum-likelihood approach for gene family evolution under functional divergence", Molecular Biology and Evolution, 18:453-464. [abstract] AL Hughes, J da Silva, R Friedman (2001), "Ancient genome duplications did not structure the human Hox-bearing chromosomes", Genome Research, 11:771-780. abstract: The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the four Hox-bearing chromosomes (the chromosomes bearing the Hox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the human Hox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hox clusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes. IK Jordan, KS Makarova, JL Spouge, YI Wolf, EV Koonin (2001), "Lineage-specific gene expansions in bacterial and archaeal genomes", Genome Research, 11:555-565. abstract: Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (~5%-33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size 20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss. Fyodor A Kondrashov and Eugene V Koonin (2001), "Origin of alternative splicing by tandem exon duplication", Human Molecular Genetics, 10(23):2661-2669. [abstract] Matthew J Kourakis, Mark Q Martindale (2001), "Hox gene duplication and deployment in the annelid leech Helobdella", Evolution & Development, 3(3):145-153. WH Li, Z Gu, H Wang, A Nekrutenko (2001), "Evolutionary analyses of the human genome", Nature, 409:847-849. [PDF] DA Liberles, DR Schreiber, S Govindarajan, SG Chamberlin, SA Benner (2001), "The adaptive evolution database (TAED)", Genome Biology, 2(8):research0028.1-0028.6 related web page : http://www.sbc.su.se/~liberles/TAED.html M Long (2001), "Evolution of novel genes", Current Opinion in Genetics and Development, 11:673-680. [ abstract] M Long, K Thornton (2001), "Gene duplication and evolution" (technical comments), Science, 293(5535):1551. Arne Ludwig, Natalia M. Belfiore, Christian Pitra, Victor Svirsky, Ingo Jenneckens (2001), "Genome duplication events and functional reduction of ploidy levels in Sturgeon (Acipenser, Huso and Scaphirhynchus)", Genetics, 158:1203-1215. [abstract] M Lynch, M O'Hely, B Walsh, and A Force (2001), "The probability of preservation of a newly arisen gene duplicate", Genetics, 159(4):1789-1804. [abstract] Edward Malaga-Trillo, Axel Meyer (2001), "Genome duplications and accelerated evolution of Hox genes and cluster architecture in teleost fishes", American Zoologist, 41(3):676-686. AP Martin (2001), "Is tetralogy true? Lack of support for the 'one-to-four' rule" (Letter), Molecular Biology and Evolution, 18:89-93. [html] T Massingham, LJ Davies, P Lio (2001), "Analysing gene function after duplication", Bioessays, 23(10):873-876. abstract: After gene duplication, mutations cause the gene copies to diverge. The classical model predicts that these mutations will generally lead to the loss of function of one gene copy; rarely, new functions will be created and both duplicate genes are conserved. In contrast, under the subfunctionalization model both duplicates are preserved due to the partition of different functions between the duplicates. A recent study provides support for the subfunctionalization model, identifying several expressed gene duplicates common to humans and mice that contain regions conserved in one duplicate but variable in the other (and vice versa). We discuss both the methodology used in this study and also how gene phylogeny may lead to additional evidence for the importance of subfunctionalization in the evolution of new genes. J McClintock, R Carlson, D Mann, VE Prince (2001), "Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish hox paralogue group 1 genes", Development, 128:2471-2484. Csaba Pal, Balazs Papp, Laurence D Hurst (2001), "Highly expressed genes in yeast evolve slowly" (letter to the editor), Genetics, 158:927-931. [html] J Piskur (2001), "Origin of the duplicated regions in the yeast genomes", Trends in Genetics, 17(6):302-303. C Popovici, M Leveugle, D Birnbaum, F Coulier (2001), "Coparalogy: physical and functional clusterings in the human genome", Biochemical and Biophysical Research Communications, 288(2):493-493. Marc Robinson-Rechavi, and Vincent Laudet (2001), "Evolutionary rates of duplicate genes in fish and mammals", Molecular Biology and Evolution, 18:681-683. [abstract] Marc Robinson-Rechavi, Oriane Marchand, Hector Escriva, Vincent Laudet (2001), "An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes", Current Biology, 11(12):R458-R459. [ abstract] Marc Robinson-Rechavi, Oriane Marchand, Héctor Escriva, Pierre-Luc Bardet, Dominique Zelus, Sandrine Hughes, Vincent Laudet (2001), "Euteleost fish genomes are characterized by expansion of gene families", Genome Research, 11:781-788. [abstract] D Sankoff (2001), "Gene and genome duplication", Current Opinion in Genetics and Development, 11:681-684. [ abstract] John S. Taylor, Henner Brinkmann (2001), "2R or not 2R?" (research update), Trends in Genetics, 17(9):488-489. [ abstract] J Taylor, Y Van de Peer, A Meyer (2001), "Genome duplication, divergent resolution and speciation", Trends in Genetics, 17:299-301. J Taylor, Y Van de Peer, A Meyer (2001), "Revisiting a recent test of the ancient fish-specific genome duplication hypothesis", Current Biology, 11:R1005-R1007. J Taylor, Y van de Peer, I Braasch, A Meyer (2001), "Comparative genomics provides evidence for an ancient genome duplication in fish", Philosophical Transactions of Royal Society B: Biological Sciences, 356:1661-1679. [abstract] Y van de Peer, J Taylor, I Braasch, A Meyer (2001), "The ghost of selection past: rates of evolution and functional divergence in anciently duplicated genes", Journal of Molecular Evolution, 53:434-444. [ abstract] A Wagner (2001), "Birth and death of redundant duplicate genes", Trends in Genetics, 17:237-239. A Wagner (2001), "The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes", Molecular Biology and Evolution, 18:1283-1292. KH Wolfe (2001), "Yesterday's polyploids and the mystery of diploidization", Nature Reviews Genetics, 2:333-341. [PDF] L Zhang, BS Gaut, TJ Vision (2001), "Gene duplication and evolution" (Comment), Science, 293(5535):1551. Rongjia Zhou, Hanhua Cheng, Terrence R. Tiersch (2001), "Differential genome duplication and fish diversity", Reviews in Fish Biology and Fisheries, 11(4):331-337. [ abstract] Christian M Zmasek, Sean R Eddy (2001), "A simple algorithm to infer gene duplication and speciation events on a gene tree", Bioinformatics, 17:821-828.