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At least 1.7 million species of living organisms have been discovered, and the list grows longer every year (especially of insects in the tropical rain forest). How are they to be classified?
Ideally, classification should be based on homology; that is, shared characteristics that have been inherited from a common ancestor. The more recently two species have shared a common ancestor,
Until recent decades, the study of homologies was limited to
The figure shows the bones in the forelimbs of three mammals: human, whale, and bat (obviously not drawn to the same scale!). Although used for such different functions as throwing, swimming, and flying, the same basic structural plan is evident in them all. In each case, the bone shown in color is the radius.Body parts are considered homologous if they have
It seems unlikely that a single pattern of bones represents the best possible structure to accomplish the functions to which these forelimbs are put. However, if we interpret the persistence of the basic pattern as evidence of inheritance from a common ancestor, we see that the various modifications are adaptations of the plan to the special needs of the organism. It tells us that evolution is opportunistic, working with materials that have been handed down by inheritance.
Here are two examples.
|Human beta chain||0|
|Sea slug (a mollusk)||127|
The numbers represent the number of amino acid differences between the beta chain of human hemoglobin and the hemoglobins of the other species. In general, the number is inversely proportional to the closeness of kinship.All the values listed are for the beta chain except for the last three, in which the distinction between alpha and beta chains does not occur.
The human beta chain contains 146 amino acid residues, as do most of the others.
Cytochrome c is found in the mitochondria of every aerobic eukaryote — animal, plant, and protist. The amino acid sequences of many of these have been determined, and comparing them shows that they are related.
Human cytochrome c contains 104 amino acids, and 37 of these have been found at equivalent positions in every cytochrome c that has been sequenced. We assume that each of these molecules has descended from a precursor cytochrome in a primitive microbe that existed over 2 billion years ago. In other words, these molecules are homologous.
The first step in comparing cytochrome c sequences is to align them to find the maximum number of positions that have the same amino acid. Sometimes gaps are introduced to maximize the number of identities in the alignment (none was needed in this table). Gaps correct for insertions and deletions that occurred during the evolution of the molecule.
This table shows the N-terminal 22 amino acid residues of human cytochrome c with the corresponding sequences from six other organisms aligned beneath. A dash indicates that the amino acid is the same one found at that position in the human molecule. All the vertebrate cytochromes (the first four) start with glycine (Gly). The Drosophila, wheat, and yeast cytochromes have several amino acids that precede the sequence shown here (indicated by <<<). In every case, the heme group of the cytochrome is attached to Cys-14. and Cys-17 (human numbering). In addition to the two Cys residues, Gly-1, Gly-6, Phe-10, and His-18 are found at the equivalent positions in every cytochrome c that has been sequenced.
We assume that the more identities there are between two molecules, the more recently they have evolved from a common ancestral molecule and thus the closer the kinship of their owners. Thus the cytochrome c of the rhesus monkey is identical to that of humans except for one amino acid, whereas yeast cytochrome c differs from that of humans at 44 positions. (There are no differences between the cytochrome c of humans and that of chimpanzees.)
The result is a phylogenetic tree. This one (the work of Walter M. Fitch and Emanuel Margoliash) shows the relationship between 20 species of eukaryotes. The numbers represent the minimum number of nucleotide substitutions in the gene for cytochrome c needed to produce these 20 proteins from a series of hypothetical ancestral genes at the various branching points (nodes).
The tree corresponds quite well to what we have long believed to be the evolutionary relationships among the vertebrates. But there are some anomalies. It indicates, for example, that the primates (humans and monkeys) split off before the split separating the kangaroo, a marsupial, from the other placental mammals. This is certainly wrong. But sequence analysis of other proteins can resolve such discrepancies.
Cytochrome c is an ancient molecule, and it has evolved very slowly. Even after more than 2 billion years, one-third of its amino acids are unchanged. This conservatism is a great help in working out the evolutionary relationships between distantly-related creatures like fish and humans.
But what of humans and the great apes? Their cytochrome c molecules are identical and can tell us nothing about evolutionary relationships.
However, some proteins have evolved much more rapidly than cytochrome c, and these can be used to decipher recent evolutionary events. During blood clotting, short peptides are cut from fibrinogen converting it into insoluble fibrin. Once removed, these fibrinopeptides have no further function. They have been pretty much free from the rigors of natural selection and have, consequently, diverged rapidly during evolution. So they provide data useful in sorting out the twigs of phylogenetic trees of mammals, for example.
As we saw in the comparison of human and kangaroo cytochrome c, a single molecule provides only a narrow window for glimpsing evolutionary relationships.
The technique of DNA-DNA hybridization provides a way of comparing the total genome of two species. Let us examine the procedure as it might be used to assess the evolutionary relationship of species B to species A:
As the figure shows, the curve for A/B is to the left of A/A, i.e., duplexes of A/B separated at a lower temperature than those of A/A. The sequences of A/A are precisely complementary so all the hydrogen bonds between complementary base pairs (A-T, C-G) must be broken in order to separate the strands. But where the gene sequences in B differ from those in A, no base pairing will have occurred and denaturation is easier.
Thus DNA-DNA hybridization provides genetic comparisons integrated over the entire genome. Its use has cleared up several puzzling taxonomic relationships.
|Link to a phylogenetic tree of living hominoids based on DNA-DNA hybridization.|
DNA-DNA hybridization can also be used to compare genomes of mixed populations of organisms. For example,
The method is a modification of fluorescence in situ hybridization (FISH) and is also called Zoo-FISH.Chromosome painting has shown, for example, that large sections of human chromosome 6 (which includes hundreds of genes in the major histocompatibility complex (MHC) have their counterpart; i.e. homologous genes, in
Ideally, a system of classification should reflect the genealogies of the organisms. Darwin realized this when he wrote: "our classifications will come, as far as they can be so made, genealogies".
A classification based strictly on the rule that all members of a group must have shared a common ancestor more recently than they have with any species outside the group is called cladistics.
This phylogenetic tree or cladogram depicts the evolutionary relationships of 4 hypothetical species.
|Taxonomists who use cladistic methods have created an extraordinary vocabulary to help them (not necessarily us).
|Those taxonomists who are particularly impressed by the differences between species tend to increase the number of higher categories. Those with this bias are known fondly as "splitters". "Lumpers", those taxonomists who marvel at the uniformities they see among species, tend to create fewer higher categories. Thus, splitters might put each of the 4 species in separate genera while lumpers would put them in a single genus.|
|Scientific names. The Swedish naturalist Carolus Linnaeus — the "father of taxonomy" — created the system for naming species that is used by biologists throughout the world. The scientific name of each species consists of two parts:
|Here is a description of a common jellyfish as it appears in a Japanese guide to marine life. (Reprinted with permission from Hoikusha Publishing Co., Ltd., Tokyo, Japan.)|
Even Darwin recognized that kinship alone was not always enough for a sound taxonomy so he added a second criterion — degree of similarity — to be used in assigning species to a taxonomic category.
|Link to a list of some of the bacteria and archaea whose complete gene sequences are now known.|
There are many examples of marsupial mammals in Australia which bear a striking resemblance to placental mammals of Europe and North America. The North American woodchuck or groundhog and the Australian wombat (photo courtesy of the Australian News and Information Bureau), for examples, look superficially to be close relatives. But their similarities are analogous, not homologous, and have arisen as a result of similar selection pressures in similar ecological niches. The wombat has no placenta, cares for its young in a pouch as other marsupials do, and should be classified with them. In fact we are more closely related to the North American woodchuck than the wombat is!
In the language of cladistics, the wombat is placed in a clade with all marsupials because they share the marsupial pouch (an apomorphic trait) but are nonetheless mammals because they, too, have hair (a plesiomorphic trait).Convergent evolution also occurs at the level of molecules.