Extending phylogenetic studies of coevolution: secondary Brooks parsimony analysis, parasites, and the Great Apes (original) (raw)
Related papers
Cladistics, 2002
Brooks parsimony analysis and TreeMap are the two most commonly used methods and are tested using artificially evolved host-parasite associations with varying amounts of coevolutionary events occurring between the two ''phylogenies.'' The purpose is to test the precision with which each method recovers the true coevolutionary history. The reconstructions recovered by each method are compared against the original test case to determine how closely the reconstruction resembles the artificially created coevolutionary history. Brooks parsimony analysis is found to be consistently less prone to gross overestimation of coevolutionary events and misleading results. Brooks parsimony analysis performs better overall because it is more adept at dealing with hostswitching events, both between and within lineages leading to widespread parasite taxa, which provides enough evidence for implementing Brooks parsimony analysis instead of TreeMap in coevolutionary studies. Ó
A priori and a posteriori methods in comparative evolutionary studies of host-parasite associations
Cladistics, 2003
Brooks parsimony analysis (BPA) and reconciliation methods in studies of host-parasite associations differ fundamentally, despite using the same null hypothesis. Reconciliation methods may eliminate or modify input data to maximize fit of single parasite clades to a null hypothesis of cospeciation, by invoking different a priori assumptions, including a known host phylogeny. By examining the degree of phylogenetic congruence among multiple parasite clades, using hosts as analogs of taxa but not presuming a host phylogeny or any degree of cospeciation a priori, BPA modifies the null hypothesis of cospeciation if necessary to maintain the integrity of the input data. Two exemplars illustrate critical empirical differences between reconciliation methods and BPA: (1) reconciliation methods rather than BPA may select the incorrect general host cladogram for a set of data from different clades of parasites, (2) BPA rather than reconciliation methods provides the most parsimonious interpretation of all available data, and (3) secondary BPA, proposed in 1990, when applied to data sets in which host-switching produces hosts with reticulate histories, provides the most parsimonious and biologically realistic interpretations of general host cladograms. The extent to which these general host cladograms, based on cospeciation among different parasite clades inhabiting the same hosts, correspond to host phylogeny can be tested, a posteriori, by comparison with a host phylogeny generated from nonparasite data. These observations lead to the conclusion that BPA and reconciliation methods are designed to implement different research programs based on different epistemologies. BPA is an a posteriori method that is designed to assess the host context of parasite speciation events, whereas reconciliation methods are a priori methods that are designed to fit parasite phylogenies to a host phylogeny. Host-switching events are essential for explaining complex histories of host-parasite associations. BPA assumes coevolutionary complexity (historical contingency), relying on parsimony as an a posteriori explanatory tool to summarize complex results, whereas reconciliation methods, which embody formalized assumptions of maximum cospeciation, are based on a priori conceptual parsimony. Modifications of basic reconciliation methods, embodied in TreeMap 1.0 and TreeMap 2.02, represent the addition of weighting schemes in which the researcher specifies allowed departures from cospeciation a priori, with the result that TreeMap results more closely agree with BPA results than do reconciled tree analysis results.
Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data
Cladistics, 2011
The use of model-based methods to infer a phylogenetic tree from a given data set is frequently motivated by the truism that under certain circumstances the parsimony approach (MP) may produce incorrect topologies, while explicit model-based approaches are believed to avoid this problem. In the realm of empirical data from actual taxa, it is not known (or knowable) how commonly MP, maximum-likelihood or Bayesian inference are inaccurate. To test the perceived need for ''sophisticated'' model-based approaches, we assessed the degree of congruence between empirical phylogenetic hypotheses generated by alternative methods applied to DNA sequence data in a sample of 1000 recently published articles. Of 504 articles that employed multiple methods, only two exhibited strongly supported incongruence among alternative methods. This result suggests that the MP approach does not produce deviant hypotheses of relationship due to convergent evolution in long branches. Our finding therefore indicates that the use of multiple analytical methods is largely superfluous. We encourage the use of analytical approaches unencumbered by ad hoc assumptions that sap the explanatory power of the evidence.
The relationship between phylogenetic reconstruction and evolutionary theory is reassessed. It is argued here that phylogenies, and evolutionary principles, should be analysed initially as independently from each other as possible. Only then can they be used to test one another. If the phylogenies and evolutionary principles are totally consistent with one another, this consilience of independent lines of evidence increases confidence in both. If, however, there is a conflict, then one should assess the relative support for each hypothesis, and tentatively accept the more strongly supported one. We review examples where the phylogenetic hypothesis is preferred over the evolutionary principle, and vice versa, and instances where the conflict cannot be readily resolved. Because the analyses of pattern and process must initially be kept separate, the temporal order in which they are performed is unimportant. Therefore, the widespread methodology of always proceeding from cladogram to evolutionary ' scenario ' cannot be justified philosophically. Such an approach means that cladograms cannot be properly tested against evolutionary principles, and that evolutionary ' scenarios ' have no independent standing. Instead, we propose the ' consilience ' approach where phylogenetic and evolutionary hypotheses are formulated independently from each other and then examined for agreement.
Rational Disagreements in Phylogenetics
Acta biotheoretica, 2009
This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court.
Phylogeny, specialization, and brood parasite--host coevolution: some possible pitfalls of parsimony
Behavioral Ecology, 2002
Coevolutionary hypotheses (COEV) predict that parasitic birds become more specialized in host selection over time as more host species evolve defenses. A contrasting model, PHYLO, suggests that brood parasites exhibit a phylogenetic trajectory toward increasing generalization because there is a positive correlation between present-day numbers of host species and the branching order of parasitic cowbird species in a DNA-based phylogeny. However, this apparent phylogenetic pattern does not conflict with COEV, as some have concluded. Assuming allopatric speciation, which is supported by an area cladogram, COEV predicts a correlation between branching order and host number because the potential hosts of the earliest cowbirds to branch off have had the greatest amount of time to evolve defenses. Although PHYLO is more parsimonious than COEV, the difference is trivial, with the latter requiring only one more evolutionary change in the entire cowbird clade to produce the pattern that exists today. Support for COEV over PHYLO comes from brood parasitic cuckoos, which are much more specialized than parasitic cowbirds and represent an older clade, as shown by new DNA data. Cuckoos also have lower interspecific variance in host numbers than do cowbirds, which conflicts with PHYLO. Unlike COEV, which assumes that the number of hosts a parasite uses is related at least as much to present ecological conditions as to phylogenetic history, PHYLO assumes that current host numbers reflect historical character states. However, host number is labile, with as much variation within as between species. Nor are published host numbers reliable measures of parasite host selectivity, as they are due in part to researcher effort and range size. Although the comparative approach can provide insights into evolutionary history, some coevolved features may be too dynamic to retain a phylogenetic signature, and, in the case of parasitic birds, neither PHYLO nor COEV can be invalidated, although the latter is more consistent with available evidence. Strict adherence to parsimony may often be inappropriate when assessing coevolved characters.
Ideas in Ecology and Evolution
The ever increasing number of computer programs developed for phylogenetic research does not necessarily facilitate the construction of biologically relevant phylogenies. Regardless of the algorithm utilized by new software, the vast majority result in treelike graphs. We suggest that a new, more inclusive framework for phylogenetic studies needs to be developed, which includes trees as an alternative in the absence of conflicting signals in the sequence data set. Conflicts are caused by noisy phylogenetic signal deriving from hybridization, allopolyploidy and lateral gene transfer—biological processes that undermine the construction of simple dichotomic bifurcating graphs. A robust framework for determining biologically relevant phylogenetic relationships should include quality analysis of the phylogenetic signal, a thorough determination of homology, analyses for phylogenetic networks, and exploration of the data for character or tree conflicts.
Parasites and the Evolutionary Diversification of Primate Clades
The American Naturalist, 2004
Coevolutionary interactions such as those between hosts and parasites have been regarded as an underlying cause of evolutionary diversification, but evidence from natural populations is limited. Among primates and other mammalian groups, measures of host diversification rates vary widely among lineages, but comparative studies have not yet identified a reliable explanation for this variation. In this study, we used a comprehensive data set of diseasecausing organisms from free-living primates to illustrate how phylogenetic comparative methods can be used to examine mammalian lineage diversity in relation to parasite species richness. Our results provide evidence that the phylogenetic diversity of primate clades is correlated positively with the number of parasite species harbored by each host and that this pattern is largely independent of other host traits that have been shown to influence diversification rates and parasite species richness in primates. We investigated two possible mechanisms that could explain this association, namely that parasites themselves drive host evolutionary diversification through processes linked with sexual selection and that host shifts or host sharing increases parasite species richness among diverse primate $15.00. All rights reserved.
Evaluating strategies of phylogenetic analyses by the coherence of their results
I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more it reflects the historical signal common to the analysed data. Under this hypothesis, the capacity of an analytical strategy to extract historical signal should correlate positively with the coherence of the obtained results. I apply this approach to a series of analyses on empirical data, basing the coherence measure on the Robinson-Foulds distances between the obtained trees. At first approximation, the analytical strategies most suitable for the data produce the most coherent results. However, risks of false positives and false negatives are identified, which are difficult to rule out.