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Phylogeny is the genealogy (i.e., “family tree”) of organism. In other words, the phylogeny represents the ancestor-descendant relationships. The inference of phylogeny is one of the foci of evolutionary biologists. It is also one of the most difficult tasks that these scientists undertake. Because one can never replay the “tape of history”, one can never “know” the true phylogeny. Species are subject to extinction and parallel evolution, and these phenomena obscure phylogeny. At best, a “phylogeny” is really a “phylogenetic hypothesis.” In no other field is appreciation of the strengths and weaknesses of the scientific method more appropriate.
The basis for inferring phylogeny is the synapomorphy = a shared derived characteristic. For example, the presence of a cranium (= skull) is a synapomorphy for the Vertebrata. No other animals have a skull. Thus, this synapomorphy supports a phylogenetic hypothesis that states that all vertebrates (fishes, mammals, amphibians, etc.) are more closely related to each other than to any other groups of animals. For example, fish and frogs are more closely related to each other than they are to crayfish.
To infer a synapomorphy, one must have some idea what the ancestral (plesiomorphic) state of that character is. For example, the ancestral amphibian had lungs. Because there is a large group of salamanders that do not have lungs, we call “lunglessness” a synapomorphy that unites all lungless salamanders into a single family. Lunglessness is a derived condition that all these species of salamanders share.
Using synapomorphies, one can place species on a “family tree” or phylogeny. Because traits are subject to natural selection, it is uncommon to find concrete synapomorphies that define 100% of the group.
Terrestrial vertebrates are called Tetrapoda in reference to a significant synapomorphy: presence of four limbs. However, snakes are a member of the Tetrapoda even though they lack external evidence of legs. Yet there are numerous other characteristics that clearly make snakes reptiles, thus members of the Tetrapoda. Use of only one characteristic (presence or absence of four limbs) would lead one to an incorrect phylogeny that did not include the snakes with the reptiles. Use of as many characters as possible is critical to developing a rigorous phylogenetic hypothesis.
Loss of legs (synapomorphy of tetrapods) in the snakes is an example of what is referred to as evolutionary reversal. The best phylogenetic hypothesis is one in which the number of evolutionary events (achievements, reversals etc.) is minimal. This is known as the principle of parsimony. There is a consensus among evolutionary biologists that the most parsimonious phylogenetic hypothesis is the one that is most likely to represent the true genealogy of a group of organisms.
Most organisms have common names, such as the “red maple” or the “red-winged blackbird”. However, these common names are often misleading. Many different species are called the same thing in different parts of world, and many identical species are called different names. Formal Latin names are used by scientists to establish a unique name for each species on the Earth: “red maple” is Acer rubrum whereas “red-winged blackbird” is Agelaius phoeniceus. Each Latin name is made, approved and used by scientists worldwide.
Every species name consists of two parts: the first part is the generic name (or genus, e.g., Homo); the second part is the specific epithet (e.g., sapiens.) This Linnaean binomial system of nomenclature was introduced by Carolus Linnaeus in the XVIII century and has been in use ever since.
The study and practice of biological classification is known as taxonomy. Species and genera are taxonomic groups (taxa). Taxonomic groups have ranks: they may be species, genera, families, orders, classes, phyla, kingdoms or stay between them like subclass or superfamily.
Biologists would like taxonomy to reflect phylogeny. For example, all the frogs in Ranidae are hypothesized to be more closely related to one another than to any frogs from other groups. However, because phylogeny is difficult to infer, taxonomy is always changing. As scientists’ opinions of phylogeny change, so does taxonomy. As more information is gathered, phylogenetic hypotheses may change; this often results in a change in taxonomy. This is the reason that textbooks often present different taxonomies. This is also the reason that the taxonomy presented in any textbook will not be the same one that is found in textbooks in 20 years.