Eric R. Pianka -- Phylogenetic Reconstruction of Ancestral Traits

Phylogenetic Reconstruction of Ancestral Traits

© Eric R. Pianka

Modern molecular techniques now allow biologists to isolate, amplify and sequence DNA, which in turn can be used to reconstruct probable evolutionary trees -- existing traits can be plotted on such trees allowing biologists to infer probable ancestral states. These comparative methods now allow ecologists to deduce and trace the probable actual course of evolution. An example of such an analysis is shown below.

Figure. Active body temperatures in oC among seven genera of Australian skinks (Mabuya is a non-Australian 'outgroup' used to root the tree), showing inferred ancestral body temperatures at various nodes. Note the high body temperature of Ctenotus (far right) and lower body temperatures of its relatives Hemiergis, Eremiascincus, and Sphenomorphus. This phylogenetic analysis suggests that descendent lineages diverged from a common ancestor, which possessed a moderate active body temperature. Ctenotus has undergone an adaptive radiation and is much more species rich (about 100 species) than its three sister groups, perhaps as a consequence of attaining higher active body temperatures. [Adapted from Huey and Bennett (1987).].

Another interesting more recent phylogenetic analysis of horn lengths among horned lizards is shown in the above figure from Leache and Maguire (2006). The preferred phylogeny depicted for Phrynosoma is based on combined mtDNA and nuclear data. The most parsimonious reconstruction of antipredator blood-squirting is mapped on the phylogeny (black bars). This tree suggests that blood squirting behavior was ancestral and has been lost 4 times. Silhouettes of Phrynosoma heads are shown to illustrate the variation in cranial horn morphology and color coded to correspond to relative horn length (ancestral state reconstructions are shown with colors mapped on each node). The asterisk adjacent to P. taurus indicates that the effective length of the squamosal horns of this unusual species are longer than portrayed by the measuring technique employed. Four Phrynosoma clades, TAPAJA, ANOTA, DOLIOSAURUS, and BREVICAUDA are marked (from Leache and Maguire 2006).

Darren Nalsh plotted line drawings of heads of the seven genera of pygopodid lizards on a phylogenetic tree

Very recently, a detailed comparative phylogenetic analysis of adhesive toepads among geckos has shown numerous independent gains and losses of these morpholgical structures (Gamble et al. 2012). Control of adhesive toepads requires integration across a hierarchy of systems operating at very different scales from molecular bonds to locomotor control of the entire gecko incorporated across seven orders of magnitude of size (Russell 2002; Pianka and Sweet 2005).

Phylogenies have now been constructed for many lizard clades, allowing application of modern comparative methodology to elucidate probable actual courses of evolution. Phylogenies are now available for the Australian agamid genus Ctenophorus (Melville et al. 2001, 2006; Hugall et al. 2008), Varanus (Ast 2001), the scincid genera Ctenotus (Rabosky et al. 2007; Rabosky et al. 2011) and Egernia (Chapple and Keogh. 2004), pygopodids (6 genera, Jennings et al. 2003), and the gekkonid genera Diplodactylus and Strophurus (Melville et al. 2004).

Traits will be plotted on phylogenetic trees and probable ancestral states inferred using modern comparative methods. For these groups, I will analyze extensive data on evolution of the following traits: body size, relative leg and tail length, head proportions, toe lamellae condition, sexual dimorphisms, active body temperature, times of activity, dietary niche breadth, microhabitat niche breadth, and clutch sizes. Of course, the effects of size must be factored out in such analyses.

In collaboration with Drs. Laurie Vitt (University of Oklahoma) and Guarino Colli (Universidade de Brasilia), a phylogenetic analysis of the evolution of body size and shape in 180 species of neotropical and desert lizards in almost all recognized families will be undertaken to identify anatomical ecological equivalents that have undergone convergent evolution. These will then be compared ecologically using data on microhabitats and diets. This study will resemble Vitt and Pianka 2005, but will be more extensive.
Phylogenetic tree for pygopodid lizards.

I plan to collaborate with my former graduate student Dr. W. Bryan Jennings (Humboldt State University), in a phylogenetic analysis of evolution of body and head size and shape, as well as head and tail proportions among pygopodid lizards. Some species are fossorial, others terrestrial, and still others are arboreal. Tail length varies widely among species, with relatively short tails in fossorial species (in some, the tail is shorter than snout-vent length, SVL), terrestrial Pygopus have tails about twice as long as SVL, most Delma have tails about 3 times SVL, but exceedingly long tails up to 4 times SVL occur among two closely-related arboreal species (Delma concinna and Delma labialis).

Catscans of skulls of Pygopus and Lialis (latter from Digimorph web site).

Among the 6 genera, heads vary from shovel-like in fossorial species (Aprasia, Ophidiocephalus) to blunt snouts (Pygopus) to various degrees of long slender pointed snake-like noses (Delma, Lialis and Pletholax). Head morphologies will be related to ecologies (diets and microhabitats). We will exploit the phylogenetic trees reconstructed by Jennings et al. (2003) and Lee at al. (2009) to clarify deep phylogenetic relationships. Heads have been scanned in Dr. Timothy Rowe's Digimorph laboratory using 3-dimensional high-resolution digital catscans.


Ast, J. C. (2001): Mitochondrial DNA evidence and evolution in Varanoidea (Squamata). Cladistics 17: 211-226.

Chapple, D. G. and J. S. Keogh. 2004. Parallel adaptive radiations in arid and temperate Australia: molecular phylogeography and systematics of the Egernia whitii (Lacertilia: Scincidae) species group. Biological Journal of the Linnean Society 83: 157-173.

Gamble, T, E. Greenbaum, T. R. Jackman, A. P. Russell, and A. M. Bauer. 2012. Repeated Origin and Loss of Adhesive Toepads in Geckos. PLoS ONE 7(6): e39429.

Huey, R. B., and A. F. Bennett. 1987. Phylogenetic studies of co-adaptation: preferred temperatures versus optimal performance temperatures of lizards. Evolution 41:1098-1115. Download pdf

Huey, R. B., E. R. Pianka, and T. W. Schoener (eds.) 1983. Lizard Ecology: Studies of a Model Organism. Harvard University Press. 501 pp.

Huey, R. B., E. R. Pianka, and L. J. Vitt. 2001. How often do lizards 'run on empty?' Ecology 82: 1-7. Download pdf

Hugall, A. F., Foster, R., Hutchinson, M., and Lee, M. S. Y. 2008. Phylogeny of Australasian agamid lizards based on nuclear and mitochondrial genes: implications for morphological evolution and biogeography. Biological Journal of the Linnean Society. 93:343-358.

Jennings, W. B., E. R. Pianka, and S. Donnellan. 2003. Systematics of the lizard family Pygopodidae with implications for the diversification of Australian temperate biotas. Systematic Biology 52: 757-780. Download pdf

Leache, A.D. and J. A. McGuire. 2006. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: Evidence for a misleading mitochondrial gene tree. Molecular Phylogenetics and Evolution 39: 628-644.

Lee M.S.Y., P.M. Oliver, M.N. Hutchinson. 2009. Phylogenetic uncertainty and molecular clock calibrations: A case study of legless lizards (Pygopodidae, Gekkota). Molecular Phylogenetics and Evolution 50: 661-666.

Melville, J., J. A. Schulte, and A. Larson. 2001. A Molecular Phylogenetic Study of Ecological Diversification in the Australian Lizard Genus Ctenophorus. J. Exp. Zool. 291: 339-353.

Melville, J., J. A. Schulte, and A. Larson. 2004. A molecular study of phylogenetic relationships and evolution of antipredator strategies in Australian Diplodactylus geckos, subgenus Strophurus. Biological Journal of the Linnean Society 82: 123-138.

Melville, J., L. J. Harmon, and J. B. Losos. 2006. Intercontinental community convergence of ecology and morphology in desert lizards. Proc. R. Soc. B (2006) 273: 557-563.

Milstead, W. W. (ed.). 1966. Lizard Ecology: A Symposium. University of Missouri Press, Columbia. 300 pp.

Morton, S. R., and C. D. James. 1988. The diversity and abundance of lizards in arid Australia: a new hypothesis. American Naturalist. 132: 237-256.

Pianka, E. R. 1966. Convexity, desert lizards, and spatial heterogeneity. Ecology 47: 1055-1059. Download pdf

Pianka, E.R. 1967. On lizard species diversity: North American flatland deserts. Ecology 48: 333-351. Download pdf

Pianka, E.R. 1969. Habitat specificity, speciation, and species density in Australian desert lizards. Ecology 50: 498-502. Download pdf

Pianka, E.R. 1971. Lizard species density in the Kalahari desert. Ecology 52: 1024-1029. Download pdf

Pianka, E. R. 1973. The structure of lizard communities. Annual Review of Ecology and Systematics 4: 53-74. Selected as "This Week's Citation Classic" in Current Contents (Agriculture, Biology & Environmental Sciences) (1988), volume 19 (number 35): page 18.) Download pdf

Pianka, E. R. 1975. Niche relations of desert lizards. Chapter 12 (pp. 292-314) in M. Cody and J. Diamond (eds.) Ecology and Evolution of Communities. Harvard University Press.

Pianka, E. R. 1986. Ecology and Natural History of Desert Lizards. Analyses of the Ecological Niche and Community Structure. Princeton University Press, Princeton, New Jersey.

Pianka, E. R. 1989. Desert lizard diversity: additional comments and some data. American Naturalist 134: 344-364. Download pdf.

Pianka, E. R. 1995. Evolution of body size: Varanid lizards as a model system. American Naturalist 146: 398-414. Download pdf.

Pianka, E. R. 1996. Long-term changes in Lizard Assemblages in the Great Victoria Desert: Dynamic Habitat Mosaics in Response to Wildfires. Chapter 8 (pp. 191-215) in M. L. Cody and J. A. Smallwood (eds.) Long-term studies of vertebrate communities. Academic Press. Download pdf

Pianka, E. R. 2001. The role of phylogenetics in evolutionary ecology. Pp. 1-20 in Herpetologia Candiana. P. Lymberakis, E. Valakos, P. Pafilis, and M. Mylonas (eds), Natural History Museum of Crete, Societas Europaea Herpetologica, Irakleio Crete 2001. Download pdf

Pianka, E. R. and S. S. Sweet. 2005. Integrative biology of sticky feet in geckos. BioEssays 27: 647-652. Download pdf

Rabosky, D. L., S. C. Donnellan, A. L. Talaba, and I. J. Lovette. 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proc. R. Soc. B. 274: 2915-2923.

Rabosky, D. L., M. A. Cowan, A. L. Talaba, and I. J. Lovette. 2011. Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from Arid Australia. Amer. Natur. 178(5): 579-95.

Russell A.P. 2002. Integrative functional morphology of the gekkotan adhesive system (Reptilia: Gekkota). Integrative and Comparative Biology 42: 1154-163.

Thompson, G. G., S. A. Thompson, P. C. Withers and E. R. Pianka. 2003 Diversity and abundance of pit-trapped reptiles of arid and mesic habitats in Australia: Biodiversity for Environmental Impact Assessments. Pacific Conservation Biology 9: 120-135. Download pdf

Vitt, L. J. and E. R. Pianka (eds.) 1994. Lizard Ecology: Historical and Experimental Perspectives. Princeton University Press. 403 pp.

Vitt, L. J. and E. R. Pianka. 2005. Deep history impacts present day ecology and biodiversity. Proc. Nat. Acad. Sci. 102: 7877-7881. Download pdf

Winemiller, K. O., E. R. Pianka, L. J. Vitt, and A Joern. 2001. Food web laws or niche theory? six independent empirical tests. American Naturalist 158: 193-199. Download pdf

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