No abstract

The reconstruction of phylogenetic history is predicated on being able to accurately establish hypotheses of character homology, which involves sequence alignment for studies based on molecular sequence data. In an empirical study investigating nucleotide sequence alignment, we inferred phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based on complete small-subunit rDNA sequences, using six different multiple-alignment procedures: manual alignment based on the secondary structure of the 18S rRNA molecule, and automated similarity-based alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM computer programs. Trees were constructed using neighboring-joining, weighted-parsimony, and maximum-likelihood methods. All of the multiple sequence alignment procedures yielded the same basic structure for the estimate of the phylogenetic relationship among the taxa, which presumably represents the underlying phylogenetic signal. However, the placement of many of the taxa was sensitive to the alignment procedure used; and the different alignments produced trees that were on average more dissimilar from each other than did the different tree-building methods used. The multiple alignments from the different procedures varied greatly in length, but aligned sequence length was not a good predictor of the similarity of the resulting phylogenetic trees. We also systematically varied the gap weights (the relative cost of inserting a new gap into a sequence or extending an already-existing gap) for the ClustalW program, and this produced alignments that were at least as different from each other as those produced by the different alignment algorithms. Furthermore, there was no combination of gap weights that produced the same tree as that from the structure alignment, in spite of the fact that many of the alignments were similar in length to the structure alignment. We also investigated the phylogenetic information content of the helical and nonhelical regions of the rDNA, and conclude that the helical regions are the most informative. We therefore conclude that many of the literature disagreements concerning the phylogeny of the Apicomplexa are probably based on differences in sequence alignment strategies rather than differences in data or tree-building methods.

No abstract

Eire frequency is the number of fires experienced by a particular community within a given time period. This concept can potentially be resolved into a number of interacting variables, including: time since the most recent fire, the length of the inter-fire intervals, and the variability of the length of the inter-fire intervals. We estimated the effects of these three variables on the floristic composition of 65 samples from dry sclerophyll vegetation with different fire histories in Brisbane Water, Ku-ring-gai Chase and Royal National Parks near Sydney.Our analyses suggest that fire frequency may account for about 60% of the floristic variation among our samples. They confirm the hypothesis that the recent (<30 years) fire frequency produces effects on floristic composition of fire-prone communities that can recognizably be attributed both to the time since the most recent fire and to the length of the intervals between fires. These effects are equal in magnitude but are different in the nature of the floristic variation they are associated with. Increasing time-since-fire is associated with a decline in the evenness of fire-tolerant species, indicating that fewer of these species come to dominate the community in the prolonged absence of fire. Herbs and small shrubs decrease in abundance, while larger shrubs increase in abundance. Inter-fire intervals of decreasing length are associated with a decrease in the evenness of the fire-sensitive species, particularly those large Proteaceae shrubs that often dominate the community biomass in dry sclerophyll shrublands of southeastern Australia.Furthermore, the variation associated with inter-fire intervals is not necessarily solely related to the shortest inter-fire interval, but is related to combinations of inter-fire intervals through time. Thus, increasing variability of the length of the inter-fire intervals is associated with an increase in the species richness of both fire-sensitive and fire-tolerant species, implying that it may be variation of the inter-fire intervals through time that is primarily responsible for maintaining the presence of a wide variety of plant species in a particular community. Our results also suggest that the floristic variation associated with different inter-fire intervals decreases with increasing time-since-fire.

I have addressed the biological rather than bioinformatics aspects of molecular sequence alignment by covering a series of topics that have been under-valued, particularly within the context of phylogenetic analysis. First, phylogenetic analysis is only one of the many objectives of sequence alignment, and the most appropriate multiple alignment may not be the same for all of these purposes. Phylogenetic alignment thus occupies a specific place within a broader context. Second, homology assessment plays an intricate role in phylogenetic analysis, with sequence alignment consisting of primary homology assessment and tree building being secondary homology assessment. The objective of phylogenetic alignment thus distinguishes it from other sorts of alignment. Third, I summarise what is known about the serious limitations of using phenetic similarity as a criterion for automated multiple alignment, and provide an overview of what is currently being done to improve these computerised procedures. This synthesises information that is apparently not widely known among phylogeneticists. Fourth, I then consider the recent development of automated procedures for combining alignment and tree building, thus integrating primary and secondary homology assessment. Finally, I outline various strategies for increasing the biological content of sequence alignment procedures, which consists of taking into account known evolutionary processes when making alignment decisions. These procedures can be objective and repeatable, and can involve computerised algorithms to automate much of the work. Perhaps the most important suggestion is that alignment should be seen as a process where new sequences are added to a pre-existing alignment that has been manually curated by the biologist.