|
ScienceWeek
2004 25 June A4 4. EVOLUTIONARY BIOLOGY: ON ANIMAL PHYLOGENY
The following points are made by Maximilian J. Telford (Current Biology 2004 14:R274):
1) One of the most important applications of research into model organisms such as the fruitfly Drosophila melanogaster and the nematode Caenorhabditis elegans is the extrapolation of findings about their biology to other species, perhaps most importantly to vertebrates such as ourselves. In order to make such inferences as rigorous as possible, however, it is important to know the pattern of relationships between the species involved. Considering the importance of this question, it is surprising that there is no consensus over how flies, nematodes and vertebrates are related to one another, and this state of affairs is all the more remarkable considering just how much we know about all three species. Recent phylogenetic analyses [1] comparing their completely sequenced genomes suggest a return to traditional views of their relationships.
2) For many years, most zoologists considered arthropods such as fruitflies to be more closely related to the vertebrates than to the nematodes. This possibility -- the Coelomata hypothesis -- is predicated on the assumption that the mesoderm-lined body cavity, or coelom, shared by arthropods and vertebrates, as well as by other phyla including annelids and molluscs, has a common origin. In contrast, the Introverta [2], the group of worms that includes nematodes, have a less sophisticated body cavity called a pseudocoelom.
3) For many years, the alternative hypothesis -- that arthropods are more closely related to nematodes than to vertebrates -- had few followers. But in 1997, careful analyses of small subunit ribosomal RNA (SSU) sequences upset this status quo, claiming strong support for an arthropod/nematode relationship [3]. According to this school, the arthropods and introvertans are linked in a group called the Ecdysozoa by the shared characteristic of periodic moulting of their cuticle, or ecdysis.
4) Following the SSU work, further studies claimed support for the Ecdysozoa hypothesis. Phylogenetic comparisons of Hox genes [4], large subunit rRNA (LSU) [5] and myosin gene sequences all corroborate the ecdysozoan clade, as does the more esoteric demonstration of the presence, peculiar to ecdysozoan nervous systems, of an epitope recognized by an anti-horseradish-peroxidase antibody. A multimeric form of the typically monomeric protein -thymosin, supposedly unique to nematodes and arthropods, has recently been found elsewhere, but this finding does not contradict what seems to be a widespread acceptance of the Ecdysozoa hypothesis.
References (abridged):
1 Wolf, Y.I., Rogozin, I.B., and Koonin, E.V. (2004). Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. Genome Res. 14, 29-36
2 Nielsen, C. (2001). Animal Evolution. Interrelationships of the living phyla. (2nd Edition) (Oxford: O.U.P.)
3 Aguinaldo, A.M.A., Turbeville, J.M., Linford, L.S., Rivera, M.C., Garey, J.R., Raff, R.A., and Lake, J.A. (1997). Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489-493
4 de Rosa, R., Grenier, J.K., Andreeva, T., Cook, C.E., Adoutte, A., Akam, M., Carroll, S.B., and Balavoine, G. (1999). Hox genes in brachiopods and priapulids and protostome evolution. Nature 399, 772-776
5 Mallatt, J. and Winchell, C.J. (2002). Testing the new animal phylogeny: First use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol. Biol. Evol. 19, 289-301
Current Biology http://www.current-biology.com
--------------------------------
Related Material:
EVOLUTION: ON INCONGRUENCE IN MOLECULAR PHYLOGENIES
In this context, the term "congruence" refers to congruent characters, i.e., shared features whose distribution among organisms fully corresponds to that in the same cladistic grouping
The following points are made by A. Rokas et al (Nature 2003 425:798):
1) Understanding the historical relationships between living organisms has been one of the principal goals of evolutionary research. Molecular phylogenetic data are instrumental in research on the history of life(1-3), the polarity of phenotypic and developmental evolution(4), and on the diversity of living organisms(5). Despite tremendous progress in recent years, phylogenetic reconstruction involves many challenges that create uncertainty with respect to the true historical associations of the taxa analyzed. One of the most notable difficulties is the widespread occurrence of incongruence between alternative phylogenies generated from single-gene data sets. Incongruence occurs at all taxonomic levels, from phylogenies of closely related species to relationships between major classes or phyla and higher taxonomic groups.
2) Both analytical and biological factors may cause incongruence. Analytical factors affecting phylogenetic reconstruction include the choice of optimality criterion, limited data availability, taxon sampling, and specific assumptions in the modelling of sequence evolution. Biological processes such as the action of natural selection or genetic drift may cause the history of the genes under analysis to obscure the history of the taxa. The large number of potential explanations for the presence of incongruence in molecular phylogenetic analyses makes decisions on how to handle conflict in larger sets of molecular data difficult. For example, two genes with different evolutionary histories (for example, owing to hybridization or horizontal transfer) for a particular taxonomic group will by definition be incongruent while still depicting true histories. Data sets composed of genes showing heterogeneity in mode of sequence evolution may also compound bias rather than resolve the true history. Furthermore, because current tests are not always reliable, it has been difficult to estimate incongruence.
3) To overcome the effect of analytical and biological factors by increasing the signal-to-noise ratio, many researchers have attempted to address difficult phylogenetic questions by analysis of concatenated data sets(1). However, phylogenetic analyses of different sets of concatenated genes do not always converge on the same tree, and some studies have yielded results at odds with widely accepted phylogenies. Although theory suggests that a number of factors (such as gene number, sequence length, optimality criterion and rate of evolution) may influence phylogenetic reconstruction, the effect of these factors has not been systematically explored with large data sets derived from biological sequences. Recent progress in the genomics of the yeast genus Saccharomyces has presented an unprecedented opportunity to evaluate these issues in eukaryotic phylogenetics.
4) In summary: One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, the authors screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. The authors suggest their results indicate that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. The authors suggest these results have important implications for resolving branches of the tree of life.
References (abridged):
1. Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977 (2000)
2. Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. Universal trees based on large combined protein sequence data sets. Nature Genet. 28, 281-285 (2001)
3. Aguinaldo, A. M. A. et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489-493 (1997)
4. Knoll, A. H. & Carroll, S. B. Early animal evolution: emerging views from comparative biology and geology. Science 284, 2129-2137 (1999)
5. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734-740 (1997)
Nature http://www.nature.com/nature
--------------------------------
Related Material:
ON MODELS OF MOLECULAR EVOLUTION AND PHYLOGENY
The term "phylogeny" refers to the evolutionary history of a group of organisms, and the term "molecular phylogenetic relationships" refers especially to relationships between the DNA and proteins of one species and the DNA and proteins of other species, such relationships evidently derived from evolutionary relationships. Reconstructing evolutionary relationships is called "phylogenetic reconstruction", and this is a fast-growing field involving various statistical approaches and applications of findings in a broad range of biological specialties. Fundamental to the statistical approaches are mathematical models used to describe the patterns of DNA base substitution and protein amino acid replacement, and such models have potential as a basis for comparative genome research.
The following points are made by P. Lio and N. Goldman (Genome Research 1998 8:1233):
1) A geneticist reconstructs molecular phylogenetic relationships by proceeding hierarchically. The first step comprises DNA sequence selection and alignment to determine site-by-site homologies and to detect DNA (or amino acid) differences.
2) The second step is to build a mathematical model describing the evolution in time of the sequences. A model can be built empirically, using properties calculated through comparisons of observed sequences, or parametrically, using chemical or biological properties of DNA and amino acids (e.g., the *hydrophobicity values of each amino acid). Such models permit estimation of the genetic distance between two *homologous sequences, the distance measured by the expected number of nucleotide substitutions per site that have occurred between the genome of a species and the genome of its most recent common ancestor. Such distances may be represented as branch lengths in a phylogenetic tree: the extant sequences form the tips of the tree, whereas the ancestral sequences form the internal nodes and are generally not known.
3) The third step in molecular phylogenetic reconstruction involves applying an appropriate statistical method to find the tree topology and branch lengths that best describe the phylogenetic relationships of the sequences. The authors suggest that the modeling of processes of sequence evolution is a thriving field of research with two immediate and important benefits: a) an improved understanding of the biological processes that shape evolution at the molecular level, and b) an improved ability to infer from sequence data the story of the evolution of life on Earth.
Genome Research http://www.genome.org
--------------------------------
Notes by ScienceWeek:
hydrophobicity: In general, the term "hydrophobic" refers to a tendency not to dissolve in water, to have a low affinity for water, etc. In chemistry, a "hydrophobic interaction" is an association of nonpolar molecules or groups in aqueous media, the interaction resulting from the tendency of water molecules to exclude nonpolar species.
homologous sequences: In this context, the term "homologous" refers to DNA or protein macromolecules having the same or similar residues at corresponding positions.
ScienceWeek http://scienceweek.com
|