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Paul-Michael Agapow

Publications and source records attributed to Paul-Michael Agapow.

9 recordsLinked to original sources
PubMed2005

The simplicity of metazoan cell lineages.

Developmental processes are thought to be highly complex, but there have been few attempts to measure and compare such complexity across different groups of organisms. Here we introduce a measure of biological complexity based on the similarity between developmental and computer programs. We define the algorithmic complexity of a cell lineage as the length of the shortest description of the lineage based on its constituent sublineages. We then use this measure to estimate the complexity of the embryonic lineages of four metazoan species from two different phyla. We find that these cell lineages are significantly simpler than would be expected by chance. Furthermore, evolutionary simulations show that the complexity of the embryonic lineages surveyed is near that of the simplest lineages evolvable, assuming strong developmental constraints on the spatial positions of cells and stabilizing selection on cell number. We propose that selection for decreased complexity has played a major role in moulding metazoan cell lineages.

Algorithms↗
PubMed2004

The fmo genes of Caenorhabditis elegans and C. briggsae: characterisation, gene expression and comparative genomic analysis.

The flavin-containing monooxygenase (FMO) gene family is conserved and ancient with representatives present in almost all phyla so far examined. The genes encode FAD-, NADP- and O(2)-dependent enzymes that catalyse oxygenation of soft-nucleophilic heteroatom centres in a range of substrates. Although usually classified as xenobiotic-metabolising enzymes, examples of FMOs exist that have evolved to metabolise specific endogenous substrates as part of a discrete physiological process. The genome of Caenorhabditis elegans contains five predicted genes encoding putative homologs of mammalian FMOs, K08C7.2, K08C7.5, Y39A1A.19, F53F4.5 and H24K24.5, which we have named fmo and numbered fmo-1 to fmo-5, respectively. As a first step towards determining their functional role(s), we have experimentally characterised these C. elegans fmo genes including analysing reporter gene expression patterns and RNAi phenotypes. Two major gene expression patterns were observed, either intestinal or hypodermal, but no gross RNAi phenotypes were found possibly due to functional redundancy. The internal structures of fmo-2, fmo-3 and fmo-4 have been compared with orthologs identified in the related nematode C. briggsae. For each orthologous pair, a global comparison of the paired upstream intergenic regions was performed and a number of conserved noncoding sequences, which may represent potential cis-regulatory elements, identified. Phylogenetic analysis reveals that several of the fmo homologs are the result of gene duplication along the lineage leading to the nematodes.

Amino Acid Sequence↗
PubMed2004

The impact of species concept on biodiversity studies.

Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48%) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.

Animals↗
PubMed2003

A tree island approach to inferring phylogeny in the ant subfamily Formicinae, with especial reference to the evolution of weaving.

The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been lost once. A maximum likelihood analysis showed that loss of the metapleural gland is significantly associated with the weaver life-pattern. The graph of the frequencies with which trees were discovered versus their likelihood indicates that trees with high likelihoods have much larger basins of attraction than those with lower likelihoods. While this result indicates that single searches are more likely to find high- than low-likelihood tree islands, it also indicates that searching only for the single best tree may lose important information.

Animals↗
PubMed2003

Phylogenetically nested comparisons for testing correlates of species richness: a simulation study of continuous variables.

Explaining the uneven distribution of species among lineages is one of the oldest questions in evolution. Proposed correlations between biological traits and species diversity are routinely tested by making comparisons between phylogenetic sister clades. Several recent studies have used nested sister-clade comparisons to test hypotheses linking continuously varying traits, such as body size, with diversity. Evaluating the findings of these studies is complicated because they differ in the index of species richness difference used, the way in which trait differences were treated, and the statistical tests employed. In this paper, we use simulations to compare the performance of four species richness indices, two choices about the branch lengths used to estimate trait values for internal nodes and two statistical tests under a range of models of clade growth and character evolution. All four indices returned appropriate Type I error rates when the assumptions of the method were met and when branch lengths were set proportional to time. Only two of the indices were robust to the different evolutionary models and to different choices of branch lengths and statistical tests. These robust indices had comparable power under one nonnull scenario. Regression through the origin was consistently more powerful than the t-test, and the choice of branch lengths exerts a strong effect on both the validity and power. In the light of our simulations, we re-evaluate the findings of those who have previously used nested comparisons in the context of species richness. We provide a set of simple guidelines to maximize the performance of phylogenetically nested comparisons in tests of putative correlates of species richness.

Phylogeny↗
PubMed2002

Evaluating phylogenetic tree shape: two modifications to Fusco & Cronk's method.

Measurement of the degree of asymmetry in phylogenetic trees is important because a tree's shape reflects the process by which it has grown. For example, highly asymmetric trees are evidence that species have had different potential for diversification. Of the tree shape measures in the literature, that proposed by Fusco & Cronk (J. theor. Biol.175, 235-243) appears to be particularly useful, because it does not require fully-resolved trees whose terminals are of equal taxonomic rank. The value of the asymmetry or imbalance at a node is intended to be independent of the number of species ultimately descended from the node. In this paper, however, we point out that the value does depend upon species number. We propose two modifications that remove the dependency and so increase the measure's usefulness. We illustrate the use of the modified measures, which are implemented in a freely-available program, MESA.

Animals↗
PubMed2002

Phylogeny imbalance: taxonomic level matters.

Two lines of evidence indicate that the degree of symmetry in phylogenetic topologies differs at different hierarchical levels. First, in a set of 61 phylogenies with superspecific taxa as their terminals, trees were on average more unbalanced (asymmetric) when the species richness of terminals was considered than when it was not. Second, nodes with a given number of higher taxa descended from them were on average more unbalanced than were nodes with the same number of species as descendants. There are several possible reasons--some biological, some artifactual--for the differences. Whatever the reason, these results caution against treating species-level and higher level phylogenies as equivalent when considering tree shape. The imbalance measure adopted here permits the use of trees that contain polytomies, facilitating a larger sample than has been achieved previously.

Animals↗
PubMed2002

Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis.

We used simulations to compare the relative power of eight statistical tests to detect imbalance in phylogenies that is too great to be ascribed to an equal-rates Markov null model. Three of these tests have never had their power assessed before. Our simulations are the first to assess performance under scenarios in which the speciation rates of various lineages can evolve independently. In one of the scenarios explored, rates depend upon the value of an evolving trait, whereas in the other the probability that a species will speciate declines with the time since it last did so. The results indicate that the relative performance of the methods depends upon how the imbalance is generated. Different types of processes lead to different imbalance signatures, i.e., different patterns of imbalance at different depths in the phylogeny, and the measures of tree shape differ in the depth of phylogeny at which they are most sensitive. Relative performance is also affected by tree size but does not appear to depend greatly upon the degree of speciation rate variation among lineages. Two of the indices (Colless's index I(c) and Shao and Sokal's Nmacr;) show reasonable performance throughout, but another (Shao and Sokal's B(2)) is never indicated to be a preferred method. Two tests that do not require completely resolved phylogenies, mean I' and mean I'(10), have reasonable power.

Biological Evolution↗