TY - JOUR AU - Grafen, A. AU - Ridley, M. PY - 1997 TI - A new model for discrete character evolution SP - 7-14 JF - Journal of Theoretical Biology VL - 184 IS - 1 Y2 - Jan 7 N1 - ISI:A1997WB69800002 N1 - KW - Correlated evolution; phylogenetic tree; copulation; inference N2 - The paper provides an explicit justification for the principle that a uniform taxon should contribute only one datapoint in comparative analyses with discrete variables. The justification is that phylogenetic patterns in variables unincluded in the proposed test vitiate the assumption of independence, both at the level of species and at the level of branch segments. The consequence is that a uniform taxon cannot safely be counted as more than one datapoint. The arguments use a branching discrete Markov process in continuous time, with the new feature that the tested variables are only a subset of the evolving characters. This model is proposed as a useful criterion for measuring the merit of proposed tests, and illustrates the necessity for models in evaluating comparative methods. (C) 1997 Academic Press Limited ID - 12 ER - TY - JOUR AU - Cunningham, C.W. AU - Omland, K.E. AU - Oakley, T.H. PY - 1998 TI - Reconstructing ancestral character states: a critical reappraisal SP - 361-366 JF - Trends in Ecology & Evolution VL - 13 IS - 9 Y2 - Sep N1 - ISI:000075606400010 N1 - KW - Evolutionary history; correlated evolution; phylogenetic methods; discrete characters; maximum-likelihood; trees; hypotheses; sequences; ribonuclease; nucleotide N2 - Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral states of a single character have received less attention than the much less challenging endeavor of reconstructing; phylogenetic trees from many characters. Recent research suggests that parsimony reconstructions are often sensitive to violations of the almost universal assumption of equal probabilities of gains and losses. In addition, maximum likelihood has been developed as an alternative to parsimony reconstruction, and has also revealed a surprising amount of uncertainty in ancestral reconstructions. ID - 11 ER - TY - JOUR AU - Pagel, M. PY - 1999 TI - Inferring the historical patterns of biological evolution SP - 877-884 JF - Nature VL - 401 IS - 6756 Y2 - Oct 28 N1 - ISI:000083464700048 N1 - KW - Phylogenetically independent contrasts; correlated evolution; molecular evidence; metazoan phyla; phylogenies; characters; sequences; reconstruction; rates; birds N2 - Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth. ID - 7 ER - TY - JOUR AU - Cunningham, C.W. PY - 1999 TI - Some limitations of ancestral character-state reconstruction when testing evolutionary hypotheses SP - 665-674 JF - Systematic Biology VL - 48 IS - 3 Y2 - Sep N1 - ISI:000083037700016 N1 - KW - Life-history evolution; marine-invertebrates; phylogenies; parsimony; nucleotide; likelihood; sequences; larvae; trees; bias ID - 10 ER - TY - JOUR AU - Omland, K.E. PY - 1999 TI - The assumptions and challenges of ancestral state reconstructions SP - 604-611 JF - Systematic Biology VL - 48 IS - 3 Y2 - Sep N1 - ISI:000083037700010 N1 - KW - Character states; evolution; phylogenies; likelihood; hypotheses; parsimony; history; bias; tree ID - 8 ER - TY - JOUR AU - Pagel, M. PY - 1999 TI - The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies SP - 612-622 JF - Systematic Biology VL - 48 IS - 3 Y2 - Sep N1 - ISI:000083037700011 N1 - KW - Sequences; evolution ID - 9 ER - TY - JOUR AU - Agapow, P.M. AU - Isaac, N.J.B. PY - 2002 TI - MacroCAIC: revealing correlates of species richness by comparative analysis SP - 41-43 JF - Diversity and Distributions VL - 8 IS - 1 Y2 - Jan N1 - ISI:000177683200005 N1 - KW - species richness; phylogeny; comparative analysis; independent contrasts; macroevolution N2 - Studies of species richness have been hampered by the use of methods that fail to account for phylogenetic non-independence of character states. MacroCAIC is a computer program that extends the method of phylogenetically independent contrasts to encompass species-richness data. It examines user-selected characters for correlation with species richness, thus allowing clearer identification of the factors driving large-scale patterns of diversity. ID - 6 ER - TY - JOUR AU - Huelsenbeck, J.P. AU - Rannala, B. PY - 2003 TI - Detecting correlation between characters in a comparative analysis with uncertain phylogeny SP - 1237-1247 JF - Evolution VL - 57 IS - 6 Y2 - Jun N1 - ISI:000183997400002 N1 - KW - Bayesian inference; comparative method; independent contrasts; Markov chain Monte Carlo; multivariate normal Maximum-likelihood approach; dna-sequences; mitochondrial-dna; molecular clock; evolution; trees; constraints; lizards; sites; model N2 - The importance of accommodating the phylogenetic history of a group when performing a comparative analysis is now widely recognized. The typical approaches either assume the tree is known without error, or they base inferences on a collection of well-supported trees or on a collection of trees generated under a stochastic model of cladogenesis. However, these approaches do not adequately account for the uncertainty of phylogenetic trees in a comparative analysis, especially when data relevant to the phylogeny of a group are available. Here, we develop a method for performing comparative analyses that is based on an extension of Felsenstein's independent contrasts method. Uncertainties in the phylogeny, branch lengths, and other parameters are accommodated by averaging over all possible trees, weighting each by the probability that the tree is correct. We do this in a Bayesian framework and use Markov chain Monte Carlo to perform the high-dimensional summations and integrations required by the analysis. We illustrate the method using comparative characters sampled from Anolis lizards. ID - 5 ER - TY - JOUR AU - Scotland, R.W. AU - Olmstead, R.G. AU - Bennett, J.R. PY - 2003 TI - Phylogeny reconstruction: The role of morphology SP - 539-548 JF - Systematic Biology VL - 52 IS - 4 Y2 - Aug N1 - ISI:000184072300008 N1 - KW - Seed plant phylogeny; 3 genomic compartments; dna-sequence data; nucleotide substitution; character states; molecular-data; likelihood approach; homology assessment; extant gymnosperms; evolutionary trees ID - 4 ER - TY - JOUR AU - Ronquist, F. PY - 2004 TI - Bayesian inference of character evolution SP - 475-481 JF - Trends in Ecology & Evolution VL - 19 IS - 9 Y2 - Sep N1 - ISI:000223899600008 N1 - KW - Phylogenetic analysis; correlated evolution; discrete characters; likelihood approach; maximum-likelihood; confidence-limits; ancestor states; bootstrap; support; reconstruction N2 - Much recent progress in evolutionary biology is based on the inference of ancestral states and past transformations in important traits on phylogenetic trees. These exercises often assume that the tree is known without error and that ancestral states and character change can be mapped onto it exactly. In reality, there is often considerable uncertainty about both the tree and the character mapping. Recently introduced Bayesian statistical methods enable the study of character evolution while simultaneously accounting for both phylogenetic and mapping uncertainty, adding much needed credibility to the reconstruction of evolutionary history. ID - 1 ER - TY - JOUR AU - Kirchoff, B.K. AU - Richter, S.J. AU - Remington, D.L. AU - Wisniewski, E. PY - 2004 TI - Complex data produce better characters SP - 1-17 JF - Systematic Biology VL - 53 IS - 1 Y2 - Feb N1 - ISI:000188895000001 N1 - KW - analytic processing; Banskia; character; character state; complexity; configural processing; Dubautia; holistic processing; phylogenetic analysis Expert object recognition; phylogenetic analysis; homology assessment; states; faces; proteaceae; banksia; memory N2 - Two studies were conducted to explore the use of complex data in character description and hybrid identification. In order to determine if complex data allow the production of better characters, eight groups of plant systematists were given two classes of drawings of plant parts, and asked to divide them into character states ( clusters) in two separate experiments. The first class of drawings consisted only of cotyledons. The second class consisted of triplets of drawings: a cotyledon, seedling leaf, and inflorescence bract. The triplets were used to simulate complex data such as might be garnered by looking at a plant. Each experiment resulted in four characters ( groups of clusters), one for each group of systematists. Visual and statistical analysis of the data showed that the systematists were able to produce smaller, more precisely defined character states using the more complex drawings. The character states created with the complex drawings also were more consistent across systematists, and agreed more closely with an independent assessment of phylogeny. To investigate the utility of complex data in an applied task, four observers rated 250 hybrids of Dubautia ciliolata X arborea based on the overall form ( Gestalt) of the plants, and took measurements of a number of features of the same plants. A composite score of the measurements was created using principal components analysis. The correlation between the scores on the first principal component and the Gestalt ratings was computed. The Gestalt ratings and PC scores were significantly correlated, demonstrating that assessments of overall similarity can be as useful as more conventional approaches in determining the hybrid status of plants. ID - 3 ER - TY - JOUR AU - Rheindt, F.E. AU - Grafe, T.U. AU - Abouheif, E. PY - 2004 TI - Rapidly evolving traits and the comparative method: how important is testing for phylogenetic signal? SP - 377-396 JF - Evolutionary Ecology Research VL - 6 IS - 3 Y2 - Mar N1 - ISI:000220685800004 N1 - KW - bird song; habitat; phylogenetic autocorrelation; phylogenetically based comparative methods; rapid evolution Correlated evolution; geographical variation; independent contrasts; body-size; zonotrichia-capensis; computer-simulation; passerine birds; species limits; song; sound N2 - The indiscriminate application of phylogenetically based comparative methods in cross-species correlated evolution analyses has been questioned. It has been argued that traits are not always significantly correlated to their phylogenetic history, and that correcting for phylogeny in these cases may be unnecessary and may even introduce statistical error. Statistical diagnostics to test for phylogenetic signal have recently been presented. Here, we investigate the relationship between habitat and vocal characters within a tropical bird community. We show that the bird song parameters investigated are not correlated to their phylogenetic history, indicating that certain aspects of bird song can be subject to rates of evolution that are much more rapid than speciation events. In contrast, we show that the habitat parameter is significantly correlated to its phylogenetic history. Previous comparative studies, which have not taken phylogenetic signal into account, show a significant association between habitat and song. With respect to our continuous data, we demonstrate that analyses which fail to correct for phylogeny in traits that show phylogenetic signal (i.e. habitat). or those that correct for phylogeny in traits that are phylogenetically independent (i.e. bird song parameters), support an association between habitat and song. Analyses that incorporate tests for phylogenetic signal, however, reject this association, and thus call for a re-evaluation of the evidence on correlated evolution of habitat and bird song. Therefore, using tests for phylogenetic signal before and after conducting a cross-species correlated evolution analysis is crucial to the outcome of a comparative study when analysing rapidly evolving traits. ID - 2 ER -