Syst. Biol. 45(3):259--260, 1996

Phylogenies and Comparative Biology, Stage II: Testing Causal Hypotheses Derived From Phylogenies with Data from Extant Taxa

Jonathan Losos

Department of Biology, Washington Univeristy, St. Louis, MO 63130, USA

The revolution in comparative biology that occurred over the past 15 years stemmed from two related developments. In the early 1980's, a number of workers argued that macroevolutionary phenomena can be interpreted only in an explicitly historical context (e.g., Lauder, 1981; Cracraft, 1981; Gould and Vrba, 1982). Shortly thereafter, workers realized that as a result of shared ancestry, species are not statistically independent entities; consequently, statistical analyses of comparative data are invalid unless phylogenetic information is incorporated (e.g., Gittleman, 1981; Ridley, 1983; Felsenstein, 1985; Harvey and Pagel, 1991). The result is that workers in all fields of biology are now aware that phylogenetic information must be incorporated into any comparative study that investigates causal hypotheses (i.e., that are not purely descriptive). The extent to which one can find phylogenies in journal articles has increased substantially, not only in those journals traditionally devoted to evolutionary issues, but also in journals such as Animal Behavior, Ecology, and Development.

Nonetheless, the phylogenetic revolution is only half complete. Although workers now commonly use phylogenetic methods to evaluate hypotheses developed using other forms of data, the time has come to invert the process and to use phylogenies as the source of testable hypotheses about evolutionary patterns and processes. Phylogenies are statements not only of relationships among taxa, but also about the evolution of characters. These statements, in turn, may suggest causal hypotheses about why character change should occur in a particular manner. In many cases, hypotheses deduced from phylogenies make predictions that pertain both to historical events and contemporary phenomena. For example, phylogenetic analysis indicated that in ray-finned fishes, the hypochordal longitudinalis muscle arose prior to the evolution of an externally symmetrical tail (Lauder, 1989). One possible hypothesis derivable from this observation is that the muscle alters functional capacities of the tail in such a way as to favor a symmetrical tail, which might not have been beneficial previously. Functional studies of the hypochordal longitudinalis in extant fish support this hypothesis by revealing that the muscle qualitatively alters tail function (Lauder, 1989).

In a similar manner, testable hypotheses can be derived from phylogenies in many fields of comparative biology as the following four papers attest. The form that such tests will take, however, will vary from field to field. Laboratory examination and manipulations will be most appropriate to fields such as developmental biology, functional morphology, and endocrinoloy, whereas field observations and/or experiments may be more appropriate in ecological or behavioral studies. In addition, measures of genetic variation and constraint can be useful to test some hypotheses (e.g., Futuyma and McCafferty, 1990). In some situations, one can test hypotheses that certain traits are favored by natural selection in particular selective regimes (sensu Baum and Larson, 1991) as predicted based on phylogenetic evidence; multi-generation experiments can test whether selection leads to evolutionary change in the direction predicted by phylogenetic hypotheses. This approach applies to all fields of biology that have a comparative aspect; even in the area of conservation biology, this approach may prove useful in establishing priorities and conservation strategies (Brooks et al., 1992).

Although suggested by Hennig (1966), this approach to hypothesis generation and testing has been used only in the past few years (e.g., Lauder, 1989; Futuyma and McCafferty, 1990; Futuyma et al., 1994, 1995; McLennan, 1991; Basolo, 1995; Ryan and Rand, 1995). As these approaches become more widespread, workers will grapple with the situation in which a causal hypothesis developed from examination of a phylogeny is not supported by tests on extant taxa. Such a finding might indicate that the hypothesis is mistaken, but another possibility is that historical and present-day conditions are different in some important respect. Processes that operated in the diversification of a lineage might no longer be important agents of selection. For example, interspecific competition might lead to character displacement in early stages of adaptive radiation, but as species adapt to different niches, they might no longer compete with each other. Another possibility is that subsequent evolutionary change, such as the gain or loss of traits, the loss of genetic variation, or the establishment of genetic or functional correlations, may alter the way in which species within a lineage respond to a particular selective agent.

Thus, just as failure to reject a hypothesis does not prove that the hypothesis is correct, rejection of a phylogenetically-derived causal hypothesis through examination of extant taxa does not indicate that the hypothesis incorrectly describes the cause of historical events. Testing of historical processes must be seen as an iterative process in which the results of one round of testing inevitably lead to new investigative approaches.


I thank the National Science Foundation for supporting the symposium that led to these contributions and A. Larson for helpful comments on a previous draft of this introduction. This contribution was also supported by NSF DEB-9318642.

Literature Cited

Basolo, A.L. 1995. Phylogenetic evidence for the role of a pre-existing bias in sexual selection. Proc. R. Soc. Lond. 259:307-311.

Baum, D.A.and A. Larson. 1991. Adaptation reviewed: a phylogenetic methodology for studying character macroevolution. Syst. Zool. 40:1-18.

Brooks, D.R., R.C. Mayden, and D.A. McLennan. 1992. Phylogeny and biodiversity: converving our evolutionary legacy. Trends Ecol. Evol. 7:55-59.

Cracraft, J. 1981. The use of functional and adaptive criteria in phylogenetic systematics. Amer. Zool. 21: 21-3.

Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.

Futuyma, D.J., M.C. Keese, and D.J. Funk. 1995. Genetic constraints on macroevolution: the evolution of host affiliation in the leaf beetle genus Ophraella. Evolution 49:797-809.

Futuyma, D.J. and S.S. McCafferty. 1990. Phylogeny and the evolution of host plant associations in the leaf beetle genus Ophraella (Coleoptera, Chrysomelidae). Evolution 44:1885-1913.

Futuyma, D.J., J.S. Walsh, Jr., T. Morton, D.J. Fink, and M.C. Keese. 1994. Genetic variation in a phylogenetic context: responses of two specialized leaf beetles (Coleoptera: Chrysomelidae) to host plants of their congeners. J. Evol. Biol. 7:127-146.

Gittleman, J.L. 1981. The phylogeny of parental care in fishes. Anim. Beh. 29:936-941.

Gould, S.J., and E.S. Vrba. 1982. Exaptation--a missing term in the science of form. Paleobiology 8: 4-15.

Harvey, P.H.and M.D. Pagel. 1991. The comparative method in evolutionary biology. Oxford, Oxford Univ. Press.

Hennig, W. 1966. Phylogenetic systematics. Univ. Illinois Press, Urbana.

Lauder, G.V. 1981. Form and function: structural analysis in evolutionary morphology. Paleobiology 7:430-442.

Lauder, G.V. 1989. Caudal fin locomotion in ray-finned fishes: historical and functional analyses. Am. Zool. 29:85-102.

McLennan, D.A. 1991. Integrating phylogeny and experimental ethology: from pattern to process. Evolution 45: 1773-1789.

Ridley, M. 1983. The explanation of organic diversity: the comparative method and adaptations for mating. Oxford, Oxford Univ. Press.

Ryan, M.J., and A.S. Rand. 1995. Female responses to ancestral advertisement calls in Tūngara frogs. Science 269:390-392.

Syst. Biol. 45(3):261--277, 1996

Integrating phylogenetic and experimental analyses: the evolution of male and female nuptial coloration in the stickleback fishes (Gasterosteidae)

Deborah A. McLennan

Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada;

Abstract.---Both male and female gasterosteid fishes display nuptial coloration. Male nuptial coloration originated in the ancestor of the Pungitius ;pl Culaea ;pl Gasterosteus clade. Patterns of origin and diversification of characters involved in male--male, male--female, and parental interactions indicate that the evolution of male color was influenced by intersexual selection, natural selection during parental care, and intrasexual selection, in decreasing order of importance. This macroevolutionary hypothesis was corroborated by examining changes in male color across the breeding cycle for two stickleback species, Gasterosteus aculeatus and Culaea inconstans. Female nuptial coloration may have originated before the male signal. The phylogenetic diversification of the male and female signals are decoupled, suggesting that they have been subject to different selection pressures throughout their evolutionary histories. Macroevolutionary patterns and experimental studies indicate that color signal evolution has been more complex in this group of fishes than was previously thought. [Comparative biology; phylogeny; sexual selection; nuptial coloration; stickleback fishes.]

Syst. Biol. 45(3):278--289, 1996

Phylogenies and physiological processes---The Evolution of Sexual Dimorphism in Southeast Asian Frogs

Sharon B. Emerson

Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA,
and Division of Amphibians and Reptiles, Field Museum of Natural History, Chicago, Illinois 60605, USA

Abstract.---There are a number of species of Southeast Asian Rana that are characterized by an unusual suite of sexually dimorphic features and derived reproductive modes. These frogs lack the usual secondary sexual characteristics of ranid frogs: nuptial pads, vocal sacs, and enlarged flexor muscles. Secondary sexual characteristics in frogs are under androgenic control. Phylogenetic analyses using morphological and molecular data indicate that a drop in androgen level and;shor a shift in androgen sensitivity may have been involved in the evolution of male parental care and the loss of the common suite of secondary sexual characteristics in these Asian frogs. Phylogenetic analyses also provide important information on experimental design by indicating the most appropriate taxa to use in the exploration of physiological processes controlling the expression of sexual dimorphism. This work is an example of how emergent properties from phylogenetic analyses can be used to formulate and test hypotheses of process and pattern of evolutionary change. [Frog; hormone; sexual dimorphism; parental care.]

Syst. Biol. 45(3):290--307, 1996

The Phylogenetic Distribution of a Female Preference

Alexandra L. Basolo

Nebraska Behavioral Biology Group, University of Nebraska, Lincoln, Nebraska 68510, USA;

Abstract.---Robust phylogenetic information can be instrumental to the study of the evolution of female mating preferences and preferred male traits. In this paper, the evolution of a preexisting female bias favoring a sword in male swordtail fish and the evolution of the sword, a complex character, are used to demonstrate how the evolution of mating preferences and preferred traits can be examined in a phylogenetic context. Phylogenetic information suggests that a preference for a sword arose prior to the evolution of the sword in the genus Xiphophorus and that the sword was adaptive at its origin. A phylogenetic approach to the study of female preferences and male traits can also be informative when used in conjunction with mate choice theory in making predictions about evolutionary changes in an initial bias, both prior to the appearance of the male trait it favors and subsequent to the appearance of the trait. [Mate choice; female preference; preexisting biases; swordtail; sword.]

Syst. Biol. 45(3):308--322, 1996

Parallel Evolution of Nonfeeding Larvae in Echinoids

Gregory A. Wray

Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794-5245, USA;

Abstract.---The switch from feeding to nonfeeding larvae is an ecologically important transformation that has evolved on several separate occasions within the echinoids. In each case, this life history transformation has been accompanied by extensive changes in larval morphology. A phylogenetic approach is used here to reconstruct these morphological changes, to begin asking why they have taken the particular forms observed, and to assess the degree of parallel transformation in separate cases. Both traditional character mapping and a less usual aggregate analysis indicate massively parallel transformations in larval morphology associated with, and only with, this particular life history transformation. Some of these parallel morphological transformations may be due to relaxed functional constraints associated with the ancestral life history mode, but many are probably the result of new functional constraints associated with the derived mode. The comparative data suggest a simple and testable model for the switch from feeding to nonfeeding larvae involving three sequential steps. [Larva; life history evolution; developmental evolution; disparity; Echinoidea.]

Syst. Biol. 45(3):323--334, 1996

The Triples Distance for Rooted Bifurcating Phylogenetic Trees

Douglas E. Critchlow, Dennis K. Pearl, and Chunlin Qian

Department of Statistics, Ohio State University, Columbus, Ohio 43210, USA;
E-mail: (D.K.P.)

Abstract.---We investigated the triples distance as a measure of the distance between two rooted bifurcating phylogenetic trees. The triples distance counts the number of subtrees of three taxa that are different in the two trees. Exact expressions are given for the mean and variance of the sampling distribution of this distance measure. Also, a normal approximation is proved under the class of label-invariant models on the distribution of trees. The theory is applied to the usage of the triples distance as a statistic for testing the null hypothesis that the similarities in two trees can be explained by independent random structures. In an example, two phylogenies that describe the same seven species of chloroccalean zoosporic green algae are compared: one phylogeny based on morphological characteristics and one based on ribosomal RNA gene sequence data. [Tree comparison metrics; random trees; label-invariant models; hypothesis test.]

Syst. Biol. 45(3):335--343, 1996

Matrix Correspondence Tests on the DNA Phylogeny of the Tenerife Lacertid Elucidate Both Historical Causes and Morphological Adaptation

Roger S. Thorpe, Heather Black, and Anita Malhotra

School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, Wales, UK;
E-mail: (R.S.T.)

Abstract.---Previous studies using partial regression Mantel tests of matrix correspondence on within-island geographic variation in the color pattern of the Tenerife (Canary Islands) lacertid lizard (Gallotia galloti) support natural selection for different north--south climatically determined biotopes but do not support any historical cause. However, tests on the DNA phylogeny based primarily on population data from 57 localities on Tenerife support the hypothesis that there were populations on two putative precursor islands that have come into secondary contact and introgressed after these islands were joined to form Tenerife by the eruption of the Ca;atnadas edifice. Subsequent partial Mantel tests continue to support the hypothesis that color pattern is adapted to the climatic biotopes even when this phylogenetic information is taken into account by (1) testing for color pattern adaptation separately within each lineage and (2) testing for color pattern adaptation across the entire island while considering the molecular phylogenetic relationships as representing an alternative explanation. Selection has largely expunged any trace of the geological history from current morphological variation, and the introgression of these island populations after an estimated 0.7 million years of separation gives an insight into the relationships between allopatric divergence and reproductive isolation. [Partial Mantel tests; molecular phylogeny; historical hypotheses; lineage introgression; cytochrome b sequence; DGGE; Canary Island lizards; Lacertidae; Gallotia galloti.]

Syst. Biol. 45(3):344--362, 1996

Morphometric Analysis of Old World Talpidae (Mammalia, Insectivora) Using Partial-Warp Scores

F. James Rohlf 1, Anna Loy 2, and Marco Corti 2

1 Department of Ecology and Evolution, University of New York, Stony Brook, New York 11794-5245, USA;
2 Department of Animal and Human Biology, University of Rome "La Sapienza," 50 Via Borelli, 00161 Rome, Italy

Abstract.---We illustrate one approach to bridging the gap between the statistical methodology of multivariate morphometrics and the graphically oriented methods of geometric morphometrics for landmark data. Partial-warp scores (elements of the weight matrix from relative-warp analysis) are used as variables to describe nonaffine shape variation. The results of various multivariate analyses can the be visualized by reconstruction of images as weighted linear combinations of thin-plate splines. The method was applied to data on seven species of Old World moles of the family Talpidae. There was no evidence for sexual dimorphism or any interaction between sex differences with respect to nonaffine shape differences (local deformations). Small but statistically significant differences were found among species with respect to the uniform component of shape variation. [Landmark data; geometric morphometrics; thin-plate spline; relative warps; Talpidae; Insectivora.]

Syst. Biol. 45(3):363--374, 1996

General Inconsistency Conditions for Maximum Parsimony: Effects of Branch Lengths and Increasing Numbers of Taxa

Junhyong Kim

Department of Biology, Yale University, New Haven, Connecticut 06511, USA;
E-mail: junhyong;

Abstract.---Inconsistency of phylogenetic estimations refers to the propensity of certain estimation methods to converge on the positively wrong estimate with increasing amounts of data. This propensity, at least with respect to the maximum parsimony method, has been given the catch phrase "long branches attract." It has also been suggested that this problem can be alleviated by inclusion of more taxa to break up the long branches. Unfortunately, these observations have been based on computations for trees with small numbers of taxa. Here, I present a decomposition equation that allows determination of inconsistency conditions for large numbers of taxa. I show by counterexamples that long branches are a poor predictor of inconsistent conditions and that even trees with equal branch lengths can produce inconsistent estimates. I also tested the idea of breaking up long branches with additional taxa. The addition of taxa alleviates the inconsistency problem only if the average rate of change in the added taxa is low. If the rate is high, the inconsistency problem can become worse. Sampling of random tree models indicates that the inconsistency problem becomes increasingly acute as the number of taxa becomes larger. Conclusions: (1) low rates of change are of paramount importance if the inconsistency problem is to be avoided, (2) if the evolutionary question of interest does not require large numbers of taxa, it seems best to use fewer taxa because larger trees are more likely to contain inconsistent branches, and (3) if taxa are added to counter inconsistency problems, the added taxa should have low rates of change and be close to the common ancestor of the clade (which may be measured by comparison with the outgroup taxa). Longer branches require large numbers of added taxa, but such additions should only be used to resolve the particular branch of interest. Other parts of the tree, especially the branches within the added taxa, may still be inconsistently estimated. [Maximum parsimony; inconsistency; large phylogenies; long branches.]