Testing the accuracy of methods for reconstructing ancestral states of continuous characters

Webster, Andrea J.; Purvis, Andy

doi:10.1098/rspb.2001.1873

Cited by 134 publications

(142 citation statements)

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“…see Laurin, 2004; K. E. Bonine, T. T. Gleeson and T. Garland, Jr, manuscript submitted for publication), but it must be kept in mind that most analytical procedures assume a simple evolutionary model, such as Brownian motion. If this assumption is invalid, as when evolutionary trends have occurred, then estimates may be quite misleading (for some empirical examples, see Oakley and Cunningham, 2000;Webster and Purvis, 2002). Comparative historical analysis can thus never really know ancestral or intermediate states, but only conjecture about them.…”

Section: Some Notes Of Cautionmentioning

confidence: 99%

Phylogenetic approaches in comparative physiology

Garland

Bennett

Rezende

2005

Journal of Experimental Biology

609

569

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SUMMARY Over the past two decades, comparative biological analyses have undergone profound changes with the incorporation of rigorous evolutionary perspectives and phylogenetic information. This change followed in large part from the realization that traditional methods of statistical analysis tacitly assumed independence of all observations, when in fact biological groups such as species are differentially related to each other according to their evolutionary history. New phylogenetically based analytical methods were then rapidly developed, incorporated into `the comparative method', and applied to many physiological, biochemical, morphological and behavioral investigations. We now review the rationale for including phylogenetic information in comparative studies and briefly discuss three methods for doing this(independent contrasts, generalized least-squares models, and Monte Carlo computer simulations). We discuss when and how to use phylogenetic information in comparative studies and provide several examples in which it has been helpful, or even crucial, to a comparative analysis. We also consider some difficulties with phylogenetically based statistical methods, and of comparative approaches in general, both practical and theoretical. It is our personal opinion that the incorporation of phylogeny information into comparative studies has been highly beneficial, not only because it can improve the reliability of statistical inferences, but also because it continually emphasizes the potential importance of past evolutionary history in determining current form and function.

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Section: Some Notes Of Cautionmentioning

confidence: 99%

Phylogenetic approaches in comparative physiology

Garland

Bennett

Rezende

2005

Journal of Experimental Biology

609

569

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“…9 However, we also know from the fossil record that trends in evolutionary direction occur commonly (e.g., Vermeij, 1987;McNamara, 1990). Because phylogenetic analyses usually are based only on extant taxa, such trends may be difficult or impossible to detect (Oakley and Cunningham, 2000;Webster and Purvis, 2002; but see Polly, 2001). For example, in a laboratory study in which a phylogeny was created by periodically dividing bacteriophage T7 colonies, a substantial decrease in the size of plaques on the lawn of E. coli occurred independently in all lineages.…”

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confidence: 99%

Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology

Losos

2011

The American Naturalist

244

241

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The last 30 years have seen a revolution in comparative biology. Prior to that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies is not only requisite in macroevolutionary studies, but has been applied to a wide range of topics and fields that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be all and end all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past-both pattern and process-is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process. 3I start with two observations about evolutionary biology. First, as attendance at the 2010 joint meeting of the American Society of Naturalists, the Society for the Study of Evolution, and the Society of Systematic Biologists attests, evolutionary biology is a thriving science. One sign of the health of this science, evident to any participant at the meeting, is the number of young people entering the field. This leads to my second observation. Evolutionary biology is inherently about history, the progression of life through time.Given these two points, I begin my essay by providing a service to the younger members of the field. In my ASN Presidential Address (from which this essay is adapted), I asked all members of the audience born since 1980 to raise their hands. My estimate, looking out upon the assembled masses, was that approximately 61.31% of the audience (was in this fledgling class. 1 These young workers, then, do not personally know the field of evolutionary biology before the year 2000 or so, much less what it was like in the 1970's, before their birth. So, in the spirit of a historical science, I briefly review what life was like in that ancient time. A Short History of Modern Comparative ApproachesAhh, the 1970's: bell bottoms and big hair. Disco, Abba and Led Zep. Happy Days, Grease, and Star Wars. Tricky Dick and Watergate. Not to mention the Oil Embargo (the result of a time when we relied on oil imported from the Middle East for much of our energy).But what about evolutionary biology? In particular, the more historical, systematic, macroevolutionary side of the field, which is so vibrant today. What was it like? In a word, it was non-existent. The importance of a historical, evolutionary perspective was realized, at least by some (e.g., Mayr, 1976), but systematics itself was a scientific backwater. The construction of phylogenies often was more an art than a science; evolutionary trees were constructed using simplistic algorithms or none at all. The use of phylogenies t...

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“…[17], requiring fossil calibration to improve accuracy in the reconstruction of directional deviations in trait value [19,20,21]. Independent contrasts, being nondirectional, have been considered more robust with respect to such sources of bias and error.…”

Section: Discussionmentioning

confidence: 99%

“…Based on an analysis of phenotypic change in a bacteriophage colony with known evolutionary history, Oakley and Cunningham [17] advocate "the use of independent contrasts in addition to or instead of the more error-prone ancestral estimation procedures", error they ascribe to the existence of a directional bias in the polarity of trait change over time in their dataset. Directional tendencies in the evolutionary process have been shown to reduce the accuracy of ancestral state estimation in studies using fossil calibration to assess reconstruction quality [18] and the quality of ancestral state reconstruction has been challenged in general [19,20,21].…”

Section: Introductionmentioning

confidence: 99%

Identical inferences about correlated evolution arise from ancestral state reconstruction and independent contrasts

Elliot

2015

Journal of Theoretical Biology

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Inferences about the evolution of continuous traits based on reconstruction of ancestral states has often been considered more error-prone than analysis of independent contrasts. Here we show that both methods in fact yield identical estimators for the correlation coefficient and regression gradient of correlated traits, indicating that reconstructed ancestral states are a valid source of information about correlated evolution. We show that the independent contrast associated with a pair of sibling nodes on a phylogenetic tree can be expressed in terms of the maximum likelihood ancestral state function at those nodes and their common parent. This expression gives rise to novel formulae for independent contrasts for any model of evolution admitting of a local likelihood function. We thus derive new formulae for independent contrasts applicable to traits evolving under directional drift, and use simulated data to show that these directional contrasts provide better estimates of evolutionary model parameters than standard independent contrasts, when traits in fact evolve with a directional tendency. The primary reason to select one class of method over another is thus not that they measure different things but that their estimators exhibit different statistical properties that may be more or less desirable [2]. In this sense, independent contrasts and phylogenetic generalized least squares models are generally favoured over ancestral state reconstruction. Pagel [2] argues that independent contrasts are best suited to the problem of identifying evolutionary correlation coefficients, since directional methods based on a tree with n tips count evolutionary changes on 2(n − 1) internal branches, meaning that "half of the variation that a directional method calculates is redundant because it overlaps with variation already calculated" yielding "results that seem more stable than they actually are", whereas independent contrasts, 3 based on values calculated at n − 1 internal nodes, "make use of all the variance in the data, but in a way that does not count any of it twice". Ackerly It is shown here that independent contrasts and maximum likelihood ancestral state reconstruction not only estimate the same underlying Brownian rate parameter for a univariate trait, but also -in studies of correlated evolution -yield numerically identical regression estimators for the gradient and 4 correlation coefficient of bivariate traits. As a consequence, inferences about correlated evolution derived from maximum likelihood ancestral state estimation are as valid as, and indeed identical to, those derived from independent contrasts procedures. We show that the independent contrast associated with a pair of sibling nodes in a phylogenetic tree can be expressed in terms of the Gaussian local likelihood function of the node that is the direct common ancestor of the pair. It thus transpires that the numerical calculations carried out in generating independent contrasts are identical to those carried out in maximum likelihood ances...

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Testing the accuracy of methods for reconstructing ancestral states of continuous characters

Cited by 134 publications

References 40 publications

Phylogenetic approaches in comparative physiology

Phylogenetic approaches in comparative physiology

Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology

Identical inferences about correlated evolution arise from ancestral state reconstruction and independent contrasts

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