[Tree of Life Home Page] [Previous] [Next]

Introduction to Phylogenetic Biology

What is phylogeny?

Throughout the evolutionary history of life many things have happened: organisms have consumed, been consumed, made babies, interacted with other organisms, and through the years, they have evolved. An important component of this evolutionary history is the passage of genetic information from parent to offspring.

The genetic connections among organisms within a species that reproduces sexually form a tangled web, through the generations of interbreeding. However, these genetic connections do not extend much between species, and so, through time, each species is descends like a bundle of genetic connections isolated from other such bundles.

Each species is therefore a reproductive community. Occasionally, by various causes, a species might be broken into two isolated reproductive communities. The two isolated reproductive communities become separate species, and each becomes its own isolated bundle of genetic connections.

One species makes two, those two each make more, and so on. This process gives rise of a tree of species lineages descending and splitting. At the same time, some of the species go extinct, thus pruning the growing tree. In the end, this process has produced the many species of organisms we see around us today.

The notion that all of life is genetically connected via a vast phylogenetic tree is one of the most romantic notions to come out of science. How wonderful to think of the common ancestor of humans and beetles. An ancestral worm species was divided in two. Little did they know those hundreds of million years ago that some of their number would end up evolving into beetles, while their brothers and sisters would end up as humans.

How much do we know about phylogeny?

[not yet written; for now browse through the Tree of Life reading the sections on Discussion of Phylogenetic Relationships!]

How are phylogenies inferred?

[not yet written; see references below and Information about computer programs for phylogenetic analysis.]

Why is knowledge of phylogeny important?

[not yet written; see references below]

Some References about Phylogeny

Baum, D. A. and A. Larson. 1991. Adaptation reviewed: A phylogenetic 
          methodology for studying character macroevolution. 
          Syst. Zool., 40:1-18.
Brooks DR, McLennan DA. 1991. "Phylogeny, Ecology and Behavior: 
          A Research Program in Comparative Biology." Chicago: 
          Univ. Chicago Press.
Carpenter, J. M. 1989. Testing scenarios: Wasp social behavior. 
          Cladistics, 5:131-144.
Coddington, J. A. 1988. Cladistic tests of adaptational hypotheses. 
          Cladistics, 4:3-22.
Donoghue, M. J. 1989. Phylogenies and the analysis of evolutionary 
          sequences, with examples from seed plants. Evolution, 
          43:1137-1156.
Edwards, A. W. F., and L. L. Cavalli-Sforza. 1964. Reconstruction 
          of evolutionary trees. Pp. 67-76 in V. H. Heywood and 
          J. McNeill (eds.), Phenetic and Phylogenetic Classification. 
          Systematics Assoc., Publ. No. 6, London.
Eldredge, N., and J. Cracraft. 1980. Phylogenetic Patterns and 
          the Evolutionary Process: Method and Theory in Comparative 
          Biology. Columbia Univ. Press, N.Y. 
Farrell BD, Mitter C, Futuyma DJ. 1992.  Diversification at the 
          insect-plant interface: Insights from phylogenetics. 
          Bioscience 42: 34-42.
Farris JS. 1970. Methods for computing Wagner Trees. Syst Zool, 
          19: 83-92.
Farris, J. S. 1983. The logical basis of phylogenetic analysis. 
          Pp. 7-36 in N. I. Platnick and V. A. Funk (eds.), Advances 
          in Cladistics, Vol. 2. Proceedings of the Second Meeting 
          of the Willi Hennig Society. Columbia Univ. Press, 
          N.Y.
Felsenstein J. 1985. Phylogenies and the comparative method. 
          Am Nat, 125: 1-15.
Felsenstein, J. 1979. Alternative methods of phylogenetic inference 
          and their interrelationship. Syst. Zool., 28:49-62.
Felsenstein, J. 1988a. Phylogenies from molecular sequences: 
          Inference and reliability. Ann. Rev. Genet., 22:521-565.
Felsenstein, J. 1988b. Phylogenies and quantitative characters. 
          Ann. Rev. Ecol. Syst., 19:445-471.
Fink, W. L. 1982. The conceptual relationship between ontogeny 
          and phylogeny. Paleobiology, 8:254-264.
Fitch, W. M. 1971. Toward defining the course of evolution: Minimal 
          change for a specific tree topology. Syst. Zool., 20:406-416.
Futuyma DJ, McCafferty SS. 1991. Phylogeny and the evolution 
          of host plant associations in the leaf beetle genus 
          Ophraella (Coleoptera, Chrysomelidae). Evolution, 44: 
          1885-1913. 
Futuyma, D. J. 1988. Sturm und Drang and the evolutionary synthesis. 
          Evolution, 42:217-226.
Gittleman, J. L. 1988. The comparative approach in ethology: 
          Aims and limitations. Perspect. Ethol., 8:55-83.
Golding, B., and J. Felsenstein. 1990. A maximum likelihood approach 
          to detection of selection from a phylogeny. J. Mol. 
          Evol., 31:511-523.
Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda 
          G. 1979. Fitting the gene lineage into its species 
          lineage, a parsimony strategy illustrated by cladograms 
          constructed from globin sequences. Syst Zool 28: 132-163.
Greene, H. 1986. Diet and arboreality in the Emerald Monitor, 
          Varanus prasinus, with comments on the study of adaptation. 
          Fieldiana Zool., New Series,  31:1-12.
Harvey, P. H., and M. D. Pagel. 1991. The Comparative Method 
          in Evolutionary Biology. Oxford Univ. Press, Oxford.
Hennig, W. 1966. Phylogenetic Systematics. Univ. Illinois Press, 
          Urbana. 
Hillis DM. 1987. Molecular versus morphological approaches to 
          systematics. Ann Rev Ecol Syst, 18: 23-42.
Hillis DM, Huelsenbeck JP, Cunningham CW. 1994.  Application 
          and accuracy of molecular phylogenies.  Science 264: 
          671-677.
Hillis DM, Moritz G (eds). 1990.  "Molecular Systematics." Sunderland, 
          Massachusetts: Sinauer Associates.
Huey, R. B., and A. F. Bennett. 1987. Phylogenetic studies of 
          coadaptation: Preferred temperatures versus optimal 
          performance temperatures of lizards. Evolution, 41:1098-1115.
Larson, A. 1984. Neontological inferences of evolutionary pattern 
          and process in the salamander family Plethodontidae. 
          Evol. Biol., 17:119-217.
Lauder, G. V. 1982. Historical biology and the problem of design. 
          J. Theor. Biol., 97:57-67.
Maddison DR. 1994.  Phylogenetic methods for inferring the evolutionary 
          history and processes of change in discretely valued 
          characters.  Ann Rev Entomology  39: 267-292.
Maddison WP. 1990.  A method for testing the correlated evolution 
          of two binary characters: Are gains or losses concentrated 
          on certain branches of a phylogenetic tree?  Evolution 
          44: 539-557.
Maddison WP, Maddison DR . 1992.  "MacClade 3: Analysis of phylogeny 
          and character evolution."  Sunderland, Massachusetts: 
          Sinauer Associates.
Mitter C, Farrell B, Wiegemann B. 1988. The phylogenetic study 
          of adaptive zones: Has phytophagy promoted insect diversification? 
          Am Nat 132: 107-128.
Nelson G, Platnick NI. 1981.  "Systematics and biogeography: 
          Cladistics and vicariance."  New York: Columbia Univ. 
          Press.
O'Hara, R. J. 1988. Homage to Clio, or, Toward an historical 
          philosophy for evolutionary biology. Syst. Zool., 37:142-155.
Pagel M. 1994.  Detecting correlated evolution on phylogenies: 
          A general-method for the comparative analysis of discrete 
          characters.  Proc Royal Soc London B, Biol Sci 255: 
          37-45.
Ridley, M. 1983. The Explanation of Organic Diversity. Oxford 
          Univ. Press, Oxford.
Rosen, D. E. 1978. Vicariant patterns and historical explanation 
          in biogeography. Syst. Zool., 27:159-188.
Saitou, N., and M. Nei. 1987. The neighbor-joining method: A 
          new method for reconstructing phylogenetic trees. Mol. 
          Biol. Evol., 4:406-425.
Sessions, S. R., and A. Larson. 1987. Developmental correlates 
          of genome size in plethodontid salamanders and their 
          implications for genome evolution. Evolution, 41:1239-1251.
Sillén-Tullberg, B. 1988. Evolution of gregariousness in aposematic 
          butterfly larvae: A phylogenetic analysis. Evolution, 
          42:293-305. 
Swofford DL, Maddison WP. 1992.  Parsimony, character-state reconstructions, 
          and evolutionary inferences.  In Mayden RL (ed. "Systematics, 
          historical ecology, and North American freshwater fishes." 
          Stanford: Stanford University Press, pp 187 - 223.
Swofford DL, Olsen GJ. 1990. Phylogeny reconstruction. In Hillis 
          DM, Moritz G (eds. "Molecular Systematics."  Sunderland, 
          Massachusetts: Sinauer Associates, pp. 411-501.
Wake, D. B., and A. Larson. 1987. Multidimensional analysis of 
          an evolving lineage. Science, 238:42-48.
Wanntorp, H.-E., D. R. Brooks, T. Nilsson, S. Nylin, F. Ronquist, 
          S. C. Stearns, and N. Wedell. 1990. Phylogenetic approaches 
          in ecology. Oikos, 57:119-132.
Wiley, E. O. 1981. Phylogenetics. The Theory and Practice of 
          Phylogenetic Systematics. Wiley, N.Y.
Copyright © 1994 by David R. Maddison and Wayne P. Maddison
All rights reserved.