- Email: [email protected]
Vertebrate evolution: recent perspectives from fish
Outlook
COMMENT
Recent perspectives from fish on vertebrate evolution
Vertebrate evolution recent perspectives from fish Recent progress in understanding the evolution of vertebrate genomes has been rapid, and previous notions that all such genomes could be regarded as equivalent in their gene content have been rendered outdated. This notion, often embodied in the representation that vertebrates possess four Hox complexes, still appears in contemporary textbooks of developmental biology. Recent data from the genomes of teleost fish show that this assumption is untrue and suggest that interesting situations might arise from the apparent proliferation of genes among fish.
T
Samuel Aparicio [email protected] CIMR, Wellcome/MRC Building, Addenbrookes, Cambridge, UK CB2 2XY. 54
he background to these recent studies begins with numerous observations that mammals (and probably all amniotes) possess four copies of genes that are normally found as single copies in invertebrates. How did this arise? That some existing species (especially fish and amphibia) are chromosomally tetraploid led to the suggestion some time ago that tetraploidy might also have been ancestral and that its subsequent fixation (diploidization) could lead to an effective duplication of the genome and increase in the number of genes. These copies are referred to as being paralogous, signifying that they have arisen from duplication in an ancestor, followed by speciation. (Orthologous genes exist as a direct result of speciation events and can be considered as ‘direct descendents’ of a single gene in the last common ancestor of two species.) The notion that at least two such rounds of duplication probably coincided with the appearance of vertebrates as the most complex metazoans and the increase of vertebrate species in the fossil records, has been discussed extensively (Refs 1–5). One piece of evidence that supports the notion that at least two rounds of genome duplication predated modern mammals, is the observation that the number of paralogous gene clusters in mammals is generally four (or less). This has often been exemplified with the case of the clustered homeodomain that contains the Hox genes, whose roles in patterning the anterior– posterior axis of invertebrate and vertebrate embryos have become one of the central axioms of the relationship between development and evolution. Mammals possess four Hox complexes (see Refs 6, 7 and references therein), whereas Amphioxus, an extant sister group to vertebrates, possess only one8 (Fig. 1). However, studies on two bony fishes (teleosts) suggest that this group of vertebrates have additional complexity in the form of an extra set of genes and indeed, an extra set of Hox complexes, probably resulting from an additional genome duplication after the divergence of teleosts and the tetrapod lineage. Classical studies on isoenzyme loci of several fish have long suggested that additional polyploidization events have taken place in fish (for examples see Refs 9–11). Recent work in constructing linkage maps for the teleost Danio rerio (Zebrafish) has placed these notions on a firmer footing12–14. Mapping of many Zebrafish genes has shown that there are several paralogous chromosomal segments with conserved synteny in this fish13,14. These studies have shown that, on average, for any four segments that are putatively orthologous to mammalian segments, TIG February 2000, volume 16, No. 2
there are probably three additional paralogous segments. The most parsimonious explanation for this is that the Zebrafish (a chromosomally diploid vertebrate) has an extra round fixed in its genome during evolution but subsequent gene loss has resulted in only partial retention of the extra gene copies (Fig. 1). The question here is whether the genome duplication that gives rise to the extra genes is a local phenomenon, peculiar to only certain lineages of teleost, or a fundamental event in an early ancestor of the teleosts. A strong insight into this question has resulted from recent comparative studies that have produced the only extensive chromosomal maps of Hox complexes in fish; namely those of Fugu rubripes (Japanese puffer fish) and Danio rerio.
Fish Hox complexes: an additional ancient genome duplication? Mapping of Hox genes from Fugu rubripes15 revealed the presence of four Hox complexes with several features that were distinct from tetrapod complexes. First, although three of the Hox complexes could be assigned as likely orthologues of tetrapod clusters, it was also clear that significant losses of genes had occurred. Second, although the fourth complex found was labelled D, it was not possible to assign the relationship between this complex and any known tetrapod complex at the time. The hypothesis was made, that as this complex had no true tetrapod counterpart, it was possible that it represented an ancestral copy of a Hox complex that was derived from additional duplication and that Fugu posessed no true orthologue of mammalian Hox D. The notion that other fish might possess additional complexes was also hinted at by the discovery of Hox sequences in Danio rerio that apparently did not fit into any of the tetrapod groups16,17. The recent definitive mapping of Hox genes in zebrafish18 has shown the presence of at least seven Hox complexes in Zebrafish and has confirmed gene loss as a dominant feature in the evolution both of tetrapod and of teleost Hox complexes. When the sequences and the cluster structures were compared with the Fugu complexes, it became clear that the divergent Fugu Hox ‘D’ complex was in fact an orthologue of the duplicated Zebrafish Hox–ab complex (Fig. 1). Therefore, because Fugu also possessed descendents of the same segments, the duplication was probably shared in a common ancestor of acanthopterygian (ray-finned) salt-water and fresh-water fish, over 150 million years ago (Fig. 1). 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(00)01934-4
COMMENT
Recent perspectives from fish on vertebrate evolution
Outlook
FIGURE 1. Genome duplications increase gene number in vertebrates
Ancestral ray-finned fish
Loss of 3–4 clusters and many genes
Teleosts (a)
Fugu
(b) Loss of several genes Ancestral Ancestral chordate jawless vertebrate
Ancestral jawed vertebrate
? Loss of 1 cluster and several genes
Zebrafish Tetrapods trends in Genetics
The model for extant genomes in vertebrates is shown schematically as the duplication of ancient genomes (represented as a schematic chromosome). The existence of a prototypical single chordate Hox complex (Amphioxus) is shown as a series of boxes in the chromosome. In (a), at least two (but possibly three) rounds of genome duplication produced a fourfold increase in genes in a jawed ancestor. Although tetrapods remained in this state (with some gene loss during evolution), teleosts underwent at least another round of genome duplication shown in (b). Alignment of informative sequences of Hox genes and comparison with other vertebrate Hox genes revealed that three of the Zebrafish Hox complexes represented additional paralogous clusters to those described in tetrapods, further confirming the observations of genome-wide maps that an additional duplication had taken place at least in the Zebrafish lineage. Fugu rubripes and Zebrafish have undergone differential loss of genes to arrive at the present state. By comparison, the Zebrafish complexes that are orthologous to tetrapod counterparts are known as Hox-aa, Hox-ba, Hox-ca and Hox-da, whereas the additional duplicated sister complexes are known as Hox-ab, Hox-bb, Hox-cb and Hox-db. The previously labelled Fugu Hox-d is, in fact, Hox-ab. Note that sufficient sampling of extant fishes has not been undertaken to resolve whether the ancestor of Fugu and Zebrafish had already lost a whole complex, or whether this has been a more recent occurrence. Similar comments apply to the stem jawless vertebrates.
Further studies on existing stem teleosts are needed urgently to determine the precise timepoint of the additional event after the divergence of tetrapods and teleosts. Such studies should also tackle the question of whether the additional duplication resulted from autopolyploidization (duplication in the same species) or, as has been proposed for the maize genome19, allopolyploidization (a fusion between two highly related species).
Additional gene duplication in fish Additional gene duplication in fish poses some interesting problems. The first question relates to the retention of additional copies of genes. Although there is a great deal of morphological diversity among fish, there appears to be no linear correlation between increased gene number and morphological complexity, the question therefore arises as to the mechanism by which genes are retained. Consider first the condition that the sequences have neutral value. This question has been examined in theoretical work on the parametric relationship between gene retention and mutation rates, population sizes and selection, in polyploidization events under various model assumptions11,20,21. There are at least four key parameters involved. For example, if the time between chromosomal
polyploidy and subsequent diploidization is long, then the rate at which genes are extinguished is low; if the effective population size is large then persistence will be apparent; and if the mutation rate is low then extinguishing of neutral sequences will take longer. In any single case, the ancestral values for such parameters are hard to estimate. Of greater interest is the condition that the duplicated sequences acquire some selective value before mutations render them non-functional. This could occur by at least two general pathways: (1) mutations in the coding sequences that alter protein function and confer selective advantage; and/or (2) mutations in regulatory sequences that alter expression patterns. This latter mechanism is appealing, because it means that relatively small changes in expression pattern could fix duplicated copies. This might occur in several ways; for example, by shifting the expression domain into incompletely overlapping domains, or by fractionating an essential expression domain into two or more contiguous subdomains. Another process might involve altering protein expression levels so that two duplicates account for an overall amount of protein. In each of these cases, although the protein coding functions of the genes would be the same, copies would be retained by virtue of their being required TIG February 2000, volume 16, No. 2
55
Outlook
COMMENT
Recent perspectives from fish on vertebrate evolution
FIGURE 2. Fractionating expression domains of duplicated genes can provide a mechanism for their retention
Gene A′
Genome duplication Gene A
Gene A′′
trends in Genetics
This schematic shows an imaginary vertebrate embryo in which the expression of a gene A is required for patterning of the developing central nervous system. After genome duplications, small changes in expression pattern could result in both copies, A9 and A99, being required as the expression domains no longer completely overlap in the domain that was originally patterned by only one gene.
to fully encode a pre-existing function in the relevant tissues (Fig. 2). Seen from a different perspective, overlapping expression domains could produce a fine-graining of gene function that could have practical consequences for mutational screens. References 1 Ohno, S. (1970) Evolution by Gene Duplication, SpringerVerlag 2 Holland, P.W. and Garcia-Fernandez, J. (1996) Hox genes and chordate evolution. Dev. Biol. 173, 382–395 3 Lundin, L.G. (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16, 1–19 4 Pebusque, M.J. et al. (1998) Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145–1159 5 Skrabanek, L. and Wolfe, K.H. (1998) Eukaryotic genome duplication – where’s the evidence? Curr. Opin. Genet. Dev. 8, 694–700 6 Bailey, W.J. et al. (1997) Phylogenetic reconstruction of vertebrate Hox cluster duplications. Mol. Biol. Evol. 14, 843–853 7 Krumlauf, R. (1994) Hox genes in vertebrate development. Cell 78, 191–201 8 Garcia-Fernandez, J. and Holland, P.W. (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370, 563–566 9 Allendorf, F. et al. (1975) in Isoenzymes (Vol. 4) (Markert, C.L.,
56
One possibility is that the additional domains create, in effect, an evolutionary allelic series for each essential function in a screen. Some evidence for this fine-graining or subfunctionalization21 exists. For example, the expression of creatine kinase B duplicate loci in carps – one form, ckB1, is expressed predominantly in the eye, whereas the other, ckB2, is expressed predominantly in the heart22. More recent examples of engrailed23, hedgehog, FGF8 and pax gene duplicates24,25 have emerged from zebrafish mutational screens. In these cases, some evidence for overlapping expression domains exists and, in some cases, the extra copies have acquired separated functions. This is the case with three hedgehog homologues where one is expressed in the neural tube floor plate, one in the floor plate and notochord, and the other in the notochord only. In tetrapods, only one hedgehog (shh) is expressed in the floor plate and notochord (Refs 21, 26 and references therein). Another possibility however, is that some functions are masked from view because the phenotypic consequences of highly convergent expression domains are too subtle to be picked up easily. As none of the genome-wide screens have been pushed to saturation it is unclear how significant this effect might be. In any event, the additional redundancy of the basic set of required genes could result in more complex evolutionary features, for example, increasing the probability that one basis for assignment of functional orthology, namely genesequence identity, will break down. Finally, the question arises as to why so many genes have been retained in some species (e.g. Zebrafish), whereas in others (e.g. Fugu) apparently most of the extra genes have been lost. Is this loss entirely without consequence? Considering Hox complexes as an example, a large number of genes have been lost, especially in the Fugu lineage. The loss of genes in this case is a secondary or derived characteristic and it is noteworthy that these fish show extreme derived simplifications of their bony skeletons, completely lacking certain structures such as a pelvis and ribs. Although the precise relationship between Hox gene expression, function and skeletal morphology is sometimes contentious, it seems plausible that a general loss of genes that relate to skeletal patterning could account for the secondary simplifications of these fish skeletons. In this case, perhaps the redundancy produced by fractionation of gene functions into duplicate genes provides a buffering process of smaller steps by which simpler forms can evolve from those that are more complex.
ed.), pp. 415–432, Academic Press 10 Uyenyo, T. and Smith, G.R. (1972) Tetraploid origin of the karyotype of catostomid fishes. Science 175, 644–646 11 Bailey, G.S. et al. (1978) Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc. Natl. Acad. Sci. U. S. A. 75, 5575–5579 12 Knapik, E.W. et al. (1998) A microsatellite genetic linkage map for zebrafish (Danio rerio). Nat. Genet. 18, 338–343 13 Postlethwait, J.H. et al. (1998) Vertebrate genome evolution and the zebrafish gene map. Nat. Genet. 18, 345–349 14 Postlethwait, J.H. et al. (1998) Erratum. Nat. Genet. 19, 303 15 Aparicio, S. et al. (1997) Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet. 16, 79–83 16 van der Hoeven, F. et al. (1996) Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex. Mech. Dev. 54, 9–21 17 Prince, V.E. et al. (1998) Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk. Development 125, 407–420 18 Amores, A. et al. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711–1714 19 Gaut, B. and Doebley, J.F. (1997) DNA sequence evidence for
TIG February 2000, volume 16, No. 2
20
21
22
23
24 25
26
the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. U. S. A. 94, 6809–6814 Li, W.H. (1980) Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fishes. Genetics 95, 237–258 Force, A. et al (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1535 Ferris, S. and Whitt, G.S. (1979) Evolution of the differential regulation of duplicate genes after polyploidisation. J. Mol. Evol. 12, 267–317 Ekker, M. et al. (1992) Coordinate embryonic expression of three zebrafish engrailed genes. Development 116, 1001–1010 Nornes, S. et al. (1998) Zebrafish contain two pax6 genes involved in eye development. Mech. Dev. 77, 185–196 Lun, K. and Brand, M. (1998) A series of no isthmus (noi) alleles of the zebrafish pax2.1 gene reveals multiple signaling events in development of the midbrain–hindbrain boundary. Development 125, 3049–3062 Lewis, K.E. et al. (1999) Characterisation of a second patched gene in the zebrafish Danio rerio and the differential response of patched genes to Hedgehog signalling. Dev. Biol. 208, 14–29
COMMENT
Recent perspectives from fish on vertebrate evolution
Vertebrate evolution recent perspectives from fish Recent progress in understanding the evolution of vertebrate genomes has been rapid, and previous notions that all such genomes could be regarded as equivalent in their gene content have been rendered outdated. This notion, often embodied in the representation that vertebrates possess four Hox complexes, still appears in contemporary textbooks of developmental biology. Recent data from the genomes of teleost fish show that this assumption is untrue and suggest that interesting situations might arise from the apparent proliferation of genes among fish.
T
Samuel Aparicio [email protected] CIMR, Wellcome/MRC Building, Addenbrookes, Cambridge, UK CB2 2XY. 54
he background to these recent studies begins with numerous observations that mammals (and probably all amniotes) possess four copies of genes that are normally found as single copies in invertebrates. How did this arise? That some existing species (especially fish and amphibia) are chromosomally tetraploid led to the suggestion some time ago that tetraploidy might also have been ancestral and that its subsequent fixation (diploidization) could lead to an effective duplication of the genome and increase in the number of genes. These copies are referred to as being paralogous, signifying that they have arisen from duplication in an ancestor, followed by speciation. (Orthologous genes exist as a direct result of speciation events and can be considered as ‘direct descendents’ of a single gene in the last common ancestor of two species.) The notion that at least two such rounds of duplication probably coincided with the appearance of vertebrates as the most complex metazoans and the increase of vertebrate species in the fossil records, has been discussed extensively (Refs 1–5). One piece of evidence that supports the notion that at least two rounds of genome duplication predated modern mammals, is the observation that the number of paralogous gene clusters in mammals is generally four (or less). This has often been exemplified with the case of the clustered homeodomain that contains the Hox genes, whose roles in patterning the anterior– posterior axis of invertebrate and vertebrate embryos have become one of the central axioms of the relationship between development and evolution. Mammals possess four Hox complexes (see Refs 6, 7 and references therein), whereas Amphioxus, an extant sister group to vertebrates, possess only one8 (Fig. 1). However, studies on two bony fishes (teleosts) suggest that this group of vertebrates have additional complexity in the form of an extra set of genes and indeed, an extra set of Hox complexes, probably resulting from an additional genome duplication after the divergence of teleosts and the tetrapod lineage. Classical studies on isoenzyme loci of several fish have long suggested that additional polyploidization events have taken place in fish (for examples see Refs 9–11). Recent work in constructing linkage maps for the teleost Danio rerio (Zebrafish) has placed these notions on a firmer footing12–14. Mapping of many Zebrafish genes has shown that there are several paralogous chromosomal segments with conserved synteny in this fish13,14. These studies have shown that, on average, for any four segments that are putatively orthologous to mammalian segments, TIG February 2000, volume 16, No. 2
there are probably three additional paralogous segments. The most parsimonious explanation for this is that the Zebrafish (a chromosomally diploid vertebrate) has an extra round fixed in its genome during evolution but subsequent gene loss has resulted in only partial retention of the extra gene copies (Fig. 1). The question here is whether the genome duplication that gives rise to the extra genes is a local phenomenon, peculiar to only certain lineages of teleost, or a fundamental event in an early ancestor of the teleosts. A strong insight into this question has resulted from recent comparative studies that have produced the only extensive chromosomal maps of Hox complexes in fish; namely those of Fugu rubripes (Japanese puffer fish) and Danio rerio.
Fish Hox complexes: an additional ancient genome duplication? Mapping of Hox genes from Fugu rubripes15 revealed the presence of four Hox complexes with several features that were distinct from tetrapod complexes. First, although three of the Hox complexes could be assigned as likely orthologues of tetrapod clusters, it was also clear that significant losses of genes had occurred. Second, although the fourth complex found was labelled D, it was not possible to assign the relationship between this complex and any known tetrapod complex at the time. The hypothesis was made, that as this complex had no true tetrapod counterpart, it was possible that it represented an ancestral copy of a Hox complex that was derived from additional duplication and that Fugu posessed no true orthologue of mammalian Hox D. The notion that other fish might possess additional complexes was also hinted at by the discovery of Hox sequences in Danio rerio that apparently did not fit into any of the tetrapod groups16,17. The recent definitive mapping of Hox genes in zebrafish18 has shown the presence of at least seven Hox complexes in Zebrafish and has confirmed gene loss as a dominant feature in the evolution both of tetrapod and of teleost Hox complexes. When the sequences and the cluster structures were compared with the Fugu complexes, it became clear that the divergent Fugu Hox ‘D’ complex was in fact an orthologue of the duplicated Zebrafish Hox–ab complex (Fig. 1). Therefore, because Fugu also possessed descendents of the same segments, the duplication was probably shared in a common ancestor of acanthopterygian (ray-finned) salt-water and fresh-water fish, over 150 million years ago (Fig. 1). 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(00)01934-4
COMMENT
Recent perspectives from fish on vertebrate evolution
Outlook
FIGURE 1. Genome duplications increase gene number in vertebrates
Ancestral ray-finned fish
Loss of 3–4 clusters and many genes
Teleosts (a)
Fugu
(b) Loss of several genes Ancestral Ancestral chordate jawless vertebrate
Ancestral jawed vertebrate
? Loss of 1 cluster and several genes
Zebrafish Tetrapods trends in Genetics
The model for extant genomes in vertebrates is shown schematically as the duplication of ancient genomes (represented as a schematic chromosome). The existence of a prototypical single chordate Hox complex (Amphioxus) is shown as a series of boxes in the chromosome. In (a), at least two (but possibly three) rounds of genome duplication produced a fourfold increase in genes in a jawed ancestor. Although tetrapods remained in this state (with some gene loss during evolution), teleosts underwent at least another round of genome duplication shown in (b). Alignment of informative sequences of Hox genes and comparison with other vertebrate Hox genes revealed that three of the Zebrafish Hox complexes represented additional paralogous clusters to those described in tetrapods, further confirming the observations of genome-wide maps that an additional duplication had taken place at least in the Zebrafish lineage. Fugu rubripes and Zebrafish have undergone differential loss of genes to arrive at the present state. By comparison, the Zebrafish complexes that are orthologous to tetrapod counterparts are known as Hox-aa, Hox-ba, Hox-ca and Hox-da, whereas the additional duplicated sister complexes are known as Hox-ab, Hox-bb, Hox-cb and Hox-db. The previously labelled Fugu Hox-d is, in fact, Hox-ab. Note that sufficient sampling of extant fishes has not been undertaken to resolve whether the ancestor of Fugu and Zebrafish had already lost a whole complex, or whether this has been a more recent occurrence. Similar comments apply to the stem jawless vertebrates.
Further studies on existing stem teleosts are needed urgently to determine the precise timepoint of the additional event after the divergence of tetrapods and teleosts. Such studies should also tackle the question of whether the additional duplication resulted from autopolyploidization (duplication in the same species) or, as has been proposed for the maize genome19, allopolyploidization (a fusion between two highly related species).
Additional gene duplication in fish Additional gene duplication in fish poses some interesting problems. The first question relates to the retention of additional copies of genes. Although there is a great deal of morphological diversity among fish, there appears to be no linear correlation between increased gene number and morphological complexity, the question therefore arises as to the mechanism by which genes are retained. Consider first the condition that the sequences have neutral value. This question has been examined in theoretical work on the parametric relationship between gene retention and mutation rates, population sizes and selection, in polyploidization events under various model assumptions11,20,21. There are at least four key parameters involved. For example, if the time between chromosomal
polyploidy and subsequent diploidization is long, then the rate at which genes are extinguished is low; if the effective population size is large then persistence will be apparent; and if the mutation rate is low then extinguishing of neutral sequences will take longer. In any single case, the ancestral values for such parameters are hard to estimate. Of greater interest is the condition that the duplicated sequences acquire some selective value before mutations render them non-functional. This could occur by at least two general pathways: (1) mutations in the coding sequences that alter protein function and confer selective advantage; and/or (2) mutations in regulatory sequences that alter expression patterns. This latter mechanism is appealing, because it means that relatively small changes in expression pattern could fix duplicated copies. This might occur in several ways; for example, by shifting the expression domain into incompletely overlapping domains, or by fractionating an essential expression domain into two or more contiguous subdomains. Another process might involve altering protein expression levels so that two duplicates account for an overall amount of protein. In each of these cases, although the protein coding functions of the genes would be the same, copies would be retained by virtue of their being required TIG February 2000, volume 16, No. 2
55
Outlook
COMMENT
Recent perspectives from fish on vertebrate evolution
FIGURE 2. Fractionating expression domains of duplicated genes can provide a mechanism for their retention
Gene A′
Genome duplication Gene A
Gene A′′
trends in Genetics
This schematic shows an imaginary vertebrate embryo in which the expression of a gene A is required for patterning of the developing central nervous system. After genome duplications, small changes in expression pattern could result in both copies, A9 and A99, being required as the expression domains no longer completely overlap in the domain that was originally patterned by only one gene.
to fully encode a pre-existing function in the relevant tissues (Fig. 2). Seen from a different perspective, overlapping expression domains could produce a fine-graining of gene function that could have practical consequences for mutational screens. References 1 Ohno, S. (1970) Evolution by Gene Duplication, SpringerVerlag 2 Holland, P.W. and Garcia-Fernandez, J. (1996) Hox genes and chordate evolution. Dev. Biol. 173, 382–395 3 Lundin, L.G. (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16, 1–19 4 Pebusque, M.J. et al. (1998) Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145–1159 5 Skrabanek, L. and Wolfe, K.H. (1998) Eukaryotic genome duplication – where’s the evidence? Curr. Opin. Genet. Dev. 8, 694–700 6 Bailey, W.J. et al. (1997) Phylogenetic reconstruction of vertebrate Hox cluster duplications. Mol. Biol. Evol. 14, 843–853 7 Krumlauf, R. (1994) Hox genes in vertebrate development. Cell 78, 191–201 8 Garcia-Fernandez, J. and Holland, P.W. (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370, 563–566 9 Allendorf, F. et al. (1975) in Isoenzymes (Vol. 4) (Markert, C.L.,
56
One possibility is that the additional domains create, in effect, an evolutionary allelic series for each essential function in a screen. Some evidence for this fine-graining or subfunctionalization21 exists. For example, the expression of creatine kinase B duplicate loci in carps – one form, ckB1, is expressed predominantly in the eye, whereas the other, ckB2, is expressed predominantly in the heart22. More recent examples of engrailed23, hedgehog, FGF8 and pax gene duplicates24,25 have emerged from zebrafish mutational screens. In these cases, some evidence for overlapping expression domains exists and, in some cases, the extra copies have acquired separated functions. This is the case with three hedgehog homologues where one is expressed in the neural tube floor plate, one in the floor plate and notochord, and the other in the notochord only. In tetrapods, only one hedgehog (shh) is expressed in the floor plate and notochord (Refs 21, 26 and references therein). Another possibility however, is that some functions are masked from view because the phenotypic consequences of highly convergent expression domains are too subtle to be picked up easily. As none of the genome-wide screens have been pushed to saturation it is unclear how significant this effect might be. In any event, the additional redundancy of the basic set of required genes could result in more complex evolutionary features, for example, increasing the probability that one basis for assignment of functional orthology, namely genesequence identity, will break down. Finally, the question arises as to why so many genes have been retained in some species (e.g. Zebrafish), whereas in others (e.g. Fugu) apparently most of the extra genes have been lost. Is this loss entirely without consequence? Considering Hox complexes as an example, a large number of genes have been lost, especially in the Fugu lineage. The loss of genes in this case is a secondary or derived characteristic and it is noteworthy that these fish show extreme derived simplifications of their bony skeletons, completely lacking certain structures such as a pelvis and ribs. Although the precise relationship between Hox gene expression, function and skeletal morphology is sometimes contentious, it seems plausible that a general loss of genes that relate to skeletal patterning could account for the secondary simplifications of these fish skeletons. In this case, perhaps the redundancy produced by fractionation of gene functions into duplicate genes provides a buffering process of smaller steps by which simpler forms can evolve from those that are more complex.
ed.), pp. 415–432, Academic Press 10 Uyenyo, T. and Smith, G.R. (1972) Tetraploid origin of the karyotype of catostomid fishes. Science 175, 644–646 11 Bailey, G.S. et al. (1978) Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc. Natl. Acad. Sci. U. S. A. 75, 5575–5579 12 Knapik, E.W. et al. (1998) A microsatellite genetic linkage map for zebrafish (Danio rerio). Nat. Genet. 18, 338–343 13 Postlethwait, J.H. et al. (1998) Vertebrate genome evolution and the zebrafish gene map. Nat. Genet. 18, 345–349 14 Postlethwait, J.H. et al. (1998) Erratum. Nat. Genet. 19, 303 15 Aparicio, S. et al. (1997) Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes. Nat. Genet. 16, 79–83 16 van der Hoeven, F. et al. (1996) Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex. Mech. Dev. 54, 9–21 17 Prince, V.E. et al. (1998) Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk. Development 125, 407–420 18 Amores, A. et al. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711–1714 19 Gaut, B. and Doebley, J.F. (1997) DNA sequence evidence for
TIG February 2000, volume 16, No. 2
20
21
22
23
24 25
26
the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. U. S. A. 94, 6809–6814 Li, W.H. (1980) Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fishes. Genetics 95, 237–258 Force, A. et al (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1535 Ferris, S. and Whitt, G.S. (1979) Evolution of the differential regulation of duplicate genes after polyploidisation. J. Mol. Evol. 12, 267–317 Ekker, M. et al. (1992) Coordinate embryonic expression of three zebrafish engrailed genes. Development 116, 1001–1010 Nornes, S. et al. (1998) Zebrafish contain two pax6 genes involved in eye development. Mech. Dev. 77, 185–196 Lun, K. and Brand, M. (1998) A series of no isthmus (noi) alleles of the zebrafish pax2.1 gene reveals multiple signaling events in development of the midbrain–hindbrain boundary. Development 125, 3049–3062 Lewis, K.E. et al. (1999) Characterisation of a second patched gene in the zebrafish Danio rerio and the differential response of patched genes to Hedgehog signalling. Dev. Biol. 208, 14–29