Steps in Reconstructing Phylogenies

The first step in reconstructing a phylogeny is to select the group of organisms whose phylogeny is to be reconstructed—the ingroup—and an appropriate outgroup. The next step is to choose the characters that will be used in the analysis and to identify the possible forms of those characters (states or traits). A trait may be the presence or absence of a character, or one of the states a particular character may have, such as the number of body segments or number of appendages. The next, and usually the most difficult step, is to determine which traits are ancestral and which are derived. Finally, through phylogenetic analysis, systematists must distinguish homologous from homoplastic traits.

Because organisms differ in many ways, systematists use many characters to reconstruct phylogenies. Some of these characters, such as morphology, are readily preserved in fossils; others, such as behavior and molecular structures, rarely survive fossilization processes. Systematists use physiological, behavioral, molecular, and structural characters that can be assessed in both living and fossil organisms. The more characters that are measured, the more

Sarracenia purpurea likely it is that the phylogeny will reflect the actual evolutionary pattern.

Morphological and developmental traits are used in reconstructing phylogenies

An important source of information for systematists is morphology—that is, the sizes and shapes of body parts. Since living organisms have been studied for centuries, we have a wealth of recorded morphological data, as well as extensive museum and herbarium collections of organisms whose traits can be measured. Technological tools, such as the electron microscope and computer simulations, enable systema-tists to measure and analyze the structures of organisms at much finer scales, down to the level of molecules, than was formerly possible.

The early developmental stages of many organisms reveal similarities to other organisms, but those similarities may be lost during later development. For example, the larvae of marine creatures called sea squirts have a rod in the back—the notochord—that disappears as they develop into adults. All vertebrate animals also have a notochord at some time during their development (Figure 25.4). This shared structure is one of the reasons for believing that sea squirts are more closely related to vertebrates than would be suspected if only adult sea squirts were examined.

Fossils show us where and when organisms lived in the past and give us an idea of what they looked like. Fossils provide important evidence that helps us distinguish ancestral from derived traits. The fossil record also reveals when lineages diverged and began their independent evolutionary histories. However, few or no fossils have been found for some groups whose phylogeny we may wish to determine.

Sea squirt

(seen in section)

Sea squirt

(seen in section)

25.4 A Larva Reveals Evolutionary Relationships Sea squirt larvae, but not adults, have a well-developed notochord (orange) that reveals their evolutionary relationship to vertebrates, all of which have a notochord at some time during their life cycle. In adult vertebrates, the vertebral column replaces the notochord as the support structure.

25.4 A Larva Reveals Evolutionary Relationships Sea squirt larvae, but not adults, have a well-developed notochord (orange) that reveals their evolutionary relationship to vertebrates, all of which have a notochord at some time during their life cycle. In adult vertebrates, the vertebral column replaces the notochord as the support structure.

Molecular traits are also useful in reconstructing phylogenies

The molecules that make up organisms are also heritable traits that may diverge among lineages over evolutionary time. Molecular evolution will be discussed in detail in Chapter 26. Here we will briefly mention the molecular traits that are most useful for constructing phylogenies: the primary structures of proteins and nucleic acids (DNA and RNA).

protein primary structure. Relatively precise information about phylogenies can be obtained by comparison of the primary structures of proteins. We can measure genetic differences between two lineages by obtaining homologous proteins from both of them and determining the number of amino acids that have changed since the lineages diverged from a common ancestor.

dna base sequences. The base sequences of DNA provide excellent evidence of evolutionary relationships among organisms. The cells of eukaryotes have genes in their mitochondria as well as in their nuclei; plant cells also have genes in their chloroplasts. The chloroplast genome (cpDNA), which is used extensively in phylogenetic studies of plants, has changed little over evolutionarily time. Mitochondrial DNA (mtDNA) has been used extensively for studies of evolutionary relationships among animals (see Figure 25.10).

Relationships among the apes were investigated by sequencing more than 10,000 base pairs making up a segment of DNA that includes a hemoglobin pseudogene (a nonfunctional DNA sequence derived early in primate evolution by duplication of a hemoglobin gene). The outgroups for the analysis were Ateles, the spider monkeys of tropical America, and Macaca, the Rhesus monkey of Asia. The DNA data strongly indicate that chimpanzees and humans share a more recent ancestor than they do with gorillas, a conclusion supported by other types of molecular data.

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