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Revolutionary stirrings in Spain
M E E T I N G R E P O RT S
Revolutionary stirrings in Spain WORKSHOP: THE REVOLUTION IN SYSTEMATICS, FUNDACION RAMON ARECES, MADRID, SPAIN, 23–24 FEBRUARY 1998. The ‘revolution’ is the use of DNA sequences in the establishment of phylogeny and in the understanding of mechanisms of evolution. One theme was the use of molecular information to time speciation events. These included the nodes of speciation among Darwin’s finches of the Galapagos, described by Jan Klein (Max-Planck Inst., Tubingen, Germany), and the remarkably rapid speciation among the cichlid fishes of Lake Victoria. For the latter, new molecular evidence discussed by Axel Meyer (Konstanz, Germany) indicated that the 100+ species in this lake have arisen not merely in the last 200 000 years (the age of the lake) but possibly in the 12 000 years since the recent complete desiccation of the lake. DNA sequences can also reveal, however, that species are more ancient than morphological studies suggest. Robert Zink (Bell Museum of Natural History, Minnesota, USA) considered sister pairs of North American perching birds (passerines), which, on the basis of morphology, were all thought to have speciated during Pleistocene glaciations. In fact, mitochondrial DNA sequences imply that the times of speciation of the pairs were more or less continuously distributed throughout the past five million years1. Indeed,
FIGURE 1. A simple eukaryote: field emission SEM showing the dorsal and ventral surfaces of Giardia trophozoites displaying bilateral symmetry, four pairs of flagella, and the adhesive disk on the ventral surface (trophozoite at right). (Courtesy of P.T. Macechko and S.L. Erlandsen, Univ. of Minnesota.)
a drop in species diversity (through increased extinction or reduced speciation rates) seems to have occurred during the Pleistocene. The estimation of population sizes during speciation was another use for the measurement of DNA sequence diversity. Klein’s evidence for a large number of deep lineages of MHC alleles seen in Darwin’s finches suggested that the founding population that invaded the island group could not have been a few birds, but that at least 40 allelic lineages must have been present2. A more controversial method for estimating ancestral population sizes, using the variance in estimated times to common ancestry for different loci, was outlined by Naoyuki Takahata (Graduate Univ. for Advanced Studies, Kanagawa, Japan). This method often generates predictions of extreme molecular diversity in ancestral populations, which some fear might not be accurate. The size of the ancestral populations is relevant to one of the theories of speciation reviewed by Nick Barton (Univ. of Edinburgh, UK). This is that speciation might occur if a population moves to a new adaptive peak, an event that is only likely in a very small population. While a large taxonomic range of organisms were described, the most attention was paid to humans, and, perhaps surprisingly, the lower eukaryotes. The discovery that Giardia (which is suggested by 18S ribosomal RNA sequencing to be on the basal eukaryote branch) is primitively mitochondriate3 (Mitchell Sogin, Woods Hole, USA) has refocused attention on possible multiple gene transfers and symbioses established in the early eukaryotes (Fig. 1). Clues to these events come from molecules such as the mitochondrial DNA of Reclinomonas americana (described by Michael Gray, Dalhousie Univ., Halifax, Canada), which has retained far more genes from its ␣-purple bacterial ancestor than have been seen in any other mitochondrion4. An important issue is choosing the appropriate techniques to apply to phylogeny estimation from DNA sequence information. Masatoshi Nei (Univ. Park, Pennsylvania, USA) suggested that the techniques of maximum TIG MAY 1998 VOL. 14 NO. 5
Copyright © 1998 Elsevier Science Ltd. All rights reserved. 0168-9525/98/$19.00 PII: S0168-9525(98)01456-5
174
likelihood, maximum parsimony and neighbour-joining were approximately equally likely to produce the correct phylogeny when given artificially generated data. The nodes that differed between methods were generally those that were supported by a low proportion of bootstrap replicates, and so would have had little confidence placed in them anyway. James Lake (Univ. of California Los Angeles, USA) considered problems created by the attraction of long branches in phylogeny estimation. Long branch attraction is an artefact that arises when the standard techniques of phylogeny estimation are used on DNA data sets when two of the taxa differ very greatly from all the others. The artefact has the effect that, even if these taxa are not closely related, they tend to get clustered together by the tree-building programs. In the majority of nematode lineages, for example, the 18S ribosomal RNA sequence evolves quickly compared with other phyla, creating long branches. Choosing only slowly evolving nematode lineages generates a new phylogenetic position for the nematodes, within the protostomes, indeed within the arthropods, suggesting a common origin for all moulting animals5. The meeting reflected the increasing ability of DNA to resolve deep phylogenetic branchings in organisms with inadequate fossil records, a result springing largely from the confidence that, for DNA (and unlike morphology), convergent and parallel changes will be rare.
Further reading 1 Klicka, J. and Zink, R.M. (1997) Science 277, 1666–1669 2 Vincek, V. et al. (1997) Proc. R. Soc. London Ser. B 264, 111–118 3 Roger, A.W. et al. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 229–234 4 Lang, B.F. et al. (1997) Nature 387, 493–497 5 Aguinaldo, A.M.A. et al. (1997) Nature 387, 489–493
John F.Y. Brookfield [email protected] Division of Genetics, University of Nottingham, Queens Medical Centre, Nottingham, UK NG7 2UH.
Revolutionary stirrings in Spain WORKSHOP: THE REVOLUTION IN SYSTEMATICS, FUNDACION RAMON ARECES, MADRID, SPAIN, 23–24 FEBRUARY 1998. The ‘revolution’ is the use of DNA sequences in the establishment of phylogeny and in the understanding of mechanisms of evolution. One theme was the use of molecular information to time speciation events. These included the nodes of speciation among Darwin’s finches of the Galapagos, described by Jan Klein (Max-Planck Inst., Tubingen, Germany), and the remarkably rapid speciation among the cichlid fishes of Lake Victoria. For the latter, new molecular evidence discussed by Axel Meyer (Konstanz, Germany) indicated that the 100+ species in this lake have arisen not merely in the last 200 000 years (the age of the lake) but possibly in the 12 000 years since the recent complete desiccation of the lake. DNA sequences can also reveal, however, that species are more ancient than morphological studies suggest. Robert Zink (Bell Museum of Natural History, Minnesota, USA) considered sister pairs of North American perching birds (passerines), which, on the basis of morphology, were all thought to have speciated during Pleistocene glaciations. In fact, mitochondrial DNA sequences imply that the times of speciation of the pairs were more or less continuously distributed throughout the past five million years1. Indeed,
FIGURE 1. A simple eukaryote: field emission SEM showing the dorsal and ventral surfaces of Giardia trophozoites displaying bilateral symmetry, four pairs of flagella, and the adhesive disk on the ventral surface (trophozoite at right). (Courtesy of P.T. Macechko and S.L. Erlandsen, Univ. of Minnesota.)
a drop in species diversity (through increased extinction or reduced speciation rates) seems to have occurred during the Pleistocene. The estimation of population sizes during speciation was another use for the measurement of DNA sequence diversity. Klein’s evidence for a large number of deep lineages of MHC alleles seen in Darwin’s finches suggested that the founding population that invaded the island group could not have been a few birds, but that at least 40 allelic lineages must have been present2. A more controversial method for estimating ancestral population sizes, using the variance in estimated times to common ancestry for different loci, was outlined by Naoyuki Takahata (Graduate Univ. for Advanced Studies, Kanagawa, Japan). This method often generates predictions of extreme molecular diversity in ancestral populations, which some fear might not be accurate. The size of the ancestral populations is relevant to one of the theories of speciation reviewed by Nick Barton (Univ. of Edinburgh, UK). This is that speciation might occur if a population moves to a new adaptive peak, an event that is only likely in a very small population. While a large taxonomic range of organisms were described, the most attention was paid to humans, and, perhaps surprisingly, the lower eukaryotes. The discovery that Giardia (which is suggested by 18S ribosomal RNA sequencing to be on the basal eukaryote branch) is primitively mitochondriate3 (Mitchell Sogin, Woods Hole, USA) has refocused attention on possible multiple gene transfers and symbioses established in the early eukaryotes (Fig. 1). Clues to these events come from molecules such as the mitochondrial DNA of Reclinomonas americana (described by Michael Gray, Dalhousie Univ., Halifax, Canada), which has retained far more genes from its ␣-purple bacterial ancestor than have been seen in any other mitochondrion4. An important issue is choosing the appropriate techniques to apply to phylogeny estimation from DNA sequence information. Masatoshi Nei (Univ. Park, Pennsylvania, USA) suggested that the techniques of maximum TIG MAY 1998 VOL. 14 NO. 5
Copyright © 1998 Elsevier Science Ltd. All rights reserved. 0168-9525/98/$19.00 PII: S0168-9525(98)01456-5
174
likelihood, maximum parsimony and neighbour-joining were approximately equally likely to produce the correct phylogeny when given artificially generated data. The nodes that differed between methods were generally those that were supported by a low proportion of bootstrap replicates, and so would have had little confidence placed in them anyway. James Lake (Univ. of California Los Angeles, USA) considered problems created by the attraction of long branches in phylogeny estimation. Long branch attraction is an artefact that arises when the standard techniques of phylogeny estimation are used on DNA data sets when two of the taxa differ very greatly from all the others. The artefact has the effect that, even if these taxa are not closely related, they tend to get clustered together by the tree-building programs. In the majority of nematode lineages, for example, the 18S ribosomal RNA sequence evolves quickly compared with other phyla, creating long branches. Choosing only slowly evolving nematode lineages generates a new phylogenetic position for the nematodes, within the protostomes, indeed within the arthropods, suggesting a common origin for all moulting animals5. The meeting reflected the increasing ability of DNA to resolve deep phylogenetic branchings in organisms with inadequate fossil records, a result springing largely from the confidence that, for DNA (and unlike morphology), convergent and parallel changes will be rare.
Further reading 1 Klicka, J. and Zink, R.M. (1997) Science 277, 1666–1669 2 Vincek, V. et al. (1997) Proc. R. Soc. London Ser. B 264, 111–118 3 Roger, A.W. et al. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 229–234 4 Lang, B.F. et al. (1997) Nature 387, 493–497 5 Aguinaldo, A.M.A. et al. (1997) Nature 387, 489–493
John F.Y. Brookfield [email protected] Division of Genetics, University of Nottingham, Queens Medical Centre, Nottingham, UK NG7 2UH.