A phylogeny results from evolutionary descent with modification. As such, a phylogeny is one kind of genealogy. At the level of biological organization of species and groups of species, a phylogeny results from a number of speciation events (new species evolving from ancestral species) that have happened over time. Biologists recognize that all living organisms are related to each other through this descent and that there is a single phylogeny, or Tree of Life, that exists objectively in nature and quite apart from our ability to discover it. In accepting this idea, biologists embrace the grand paradigm of evolution and reject both special creation and spontaneous generation.
Processes that generate the Tree of Life operate at several different levels. Reproduction, growth, and ontogeny (development of the individual) predominate at the level of individual organisms. Although natural processes operate on the level of individual organisms, processes such as natural selection, genetic drift, and migration, birth, and death, are best studied by considering entire populations. Speciation predominates at the level of lineages (species), which are composed of one to many populations.
Discovering the Tree of Life is one of the major preoccupations of systematic biologists. The origin of the term resides in the fact that early evolutionary biologists used the tree metaphor to characterize phylogeny. We should be careful to distinguish between the Tree of Life and our attempts to reconstruct the Tree of Life. The phylogenies presented by systematic biologists are hypotheses about the Tree of Life and not the thing itself. A useful metaphor is a roadmap. A roadmap may accurately present information on the location and intersections of roads, but it is a graphic representation, not the roads themselves. It represents many useful facts about roads using abstract symbols. Phylogenic hypotheses most frequently map the descent thought to have occurred between entire species or entire groups of species such as families, orders, or even phyla.
Phylogenetic tree hypotheses have very explicit meanings, and it is worth examining what is implied. Consider a tree hypothesis of some species. Like a real tree, tree hypotheses have branches, nodes, and internodes. In most cases branches and internodes are entire lineages (see below for the exception). Since species are the highest levels of individual organization on which forces of evolution can work (speciation), these branches and intern-odes are graphic representations of at least one species. In Figure 1 the branches are labeled with species names, forming a hypothesis of how they are related. Species who share a common ancestor not shared with any other species, such as the two in the hypothetical genus Aus, are termed sister species. Groups of species that share a common ancestor not shared with any other groups are termed sister groups. The branching events that separate the branches and internodes represent speci-ation events: cladogenesis. Cladogenesis is a term for a variety of modes of speciation that are characterized by a lineage being split to form two different lineages. Cladogenesis is probably the most common form of speciation. In parts of the tree where cladogenesis has occurred, the internodes are the symbolic representation of common ancestral species.
In some phylogenies, especially in higher plants, there can also be reticulations: individual organisms of different lineages interbreed, and the hydrids form a new, third, lineage. Although it is possible for two entire lineages to join to form a third, most of these kinds of events involve individual organisms from local populations. In these cases the internodes do not represent species but only parts of species. They are the graphic representation of the individual organisms that hybridize to produce the new species.
Systematic biologists reconstruct parts of the Tree of Life by studying the similarities and differences among organisms and attempting to sort out which of the similarities denote unique common ancestry. Traits may be the result of convergence, the independent origin of a similar trait. They may be homologous: traits that evolved in a common ancestor and were retained in descendants of that ancestor. For example, the body shape of sharks and dolphins are similar but convergent; the body shape of garter snakes and rattlesnakes are similar and homologous. Of course, the only reason we conclude that the body shapes of sharks and dolphins are convergent is that we already have a hypothesis of phylogeny: dolphins are more closely related to cows than to sharks.
So, how do we reconstruct phylogeny in the first place? The answer lies in the methods of phylogenetic systematics, a set of methods that allow systematists to use agreement among many characters to test different hypotheses about phylogeny. Initially, it might be quite reasonable to think that the body shapes of sharks and dolphins are homologous and thus derived from the same body shape in their common ancestor. But many other traits argue otherwise. We conclude that dolphins are mammals, and thus their body shape has evolved independently from that of sharks. To complicate things even more, not all homologous characters are equally useful for any particular phylogenetic problem. For example, the coelacanth is a living fossil fish that, like most other fishes, has a caudal fin. No one doubts that this caudal fin is homologous with the caudal fin of tunas. Humans don't have a caudal fin. In fact, humans even lose their tails as embryos. Does this mean that coelacanths are more closely
A Hypothetical Phylogeny of Five Species of Organisms Classified in Two Qenera, Aus and Xus
Sister Groups r
Sister Species Sister Species r i r i r i
Branch (A. aus through time)
Sister Species Sister Species r
Node (Special event)
Internode (ancestral species)
(Path to all other species)
Node (Special event)
Internode (ancestral species)
(Path to all other species)
Note: This figure illustrates some of the implied meaning of the graphic representation of a phylogenetic hypothesis.
related to tunas? No, as it turns out, coela-canths are more closely related to humans. They are one of the early branches in that part of the Tree of Life leading to the legged vertebrates, and they bear the mark of that common descent in other homologous features shared with humans, such as the presence of the vena cava as a major artery of the circulatory system leading from the heart.
The basic methods for reconstructing phy-logenies were formalized by the German entomologist Willi Hennig in the 1950s. The method consists of searching for patterns of potentially homologous characters and accepting only those phylogenetic tree hypotheses that contain the maximum number of homolo-gies and the minimum number of convergences. For example, if we accept that dolphins and cows are more closely related to each other than dolphins and sharks, then we can accept such traits as being warm-blooded, having a placenta, and having bone as homologous while rejecting only body shape as being convergent. Conversely, if we accepted the idea that sharks and dolphins were more closely related, we would have to accept a whole suite of mammalian traits as convergent. Although that is certainly a possibility, it is not very likely.
See also: Classification, Biological; Linnaean Hierarchy; Systematics
Brooks, Daniel R., and Deborah A. McLennan. 1991. Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology. Chicago: University of Chicago Press; Hennig, Willi. 1966. Phylogenetic Systematica. Urbana: University of Illinois Press; Kitch-ing, I. J., et al. 1998. Cladistics: The Theory and Practice of Parsimony Analysis, 2d ed. The Systematics Association Publ. No. 11. New York: Oxford University Press; Wiley, Edward O., et al. 1991. The Compleat Cladist: A Primer of Phylogenetic Systematica. Lawrence, KS: Museum of Natural History, University of Kansas.
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