Homology

Homology is used to describe two things that share a common evolutionary origin. In genetics and molecular biology, homology means that the sequences of two different genes or two different proteins are so similar that they must have been derived from the same ancestral gene or protein.

The word "homology" has several meanings in biology, each related to the word's origin, meaning "same knowledge." At a molecular level, the term "homology" describes sequences, either DNA or protein, that share a common evolutionary origin. On a larger scale, a pair of chromosomes from a diploid organism that have the same size and shape, are considered homologous chromosomes. Regions of each member of a chromosome pair, which carry the same set of genes, are homologous regions. Finally, physical features with a common evolutionary origin, such as the wing of bat and the hand of a human, are homologous structures.

Diversity and Natural Selection

Biologists have long been fascinated by the diversity of life. The amazing variety of living things makes it natural to wonder how so many different life-forms came to be. Physical characteristics that could be easily observed, such as the shape of wing, the structure of a shell, or the size of a beak, provided the first means to search for an answer. Recognition of the variation within a species (imagine a Chihuahua and a Great Dane) led Charles Darwin to propose that new species emerge when selection favors certain traits within a population.

Today's biologists continue to study the effects of natural selection on the evolution of species, but they are no longer limited to beak size and wing shape. Now they can compare the positions of genes on chromosomes, the amino acid sequences of proteins, and the nucleotide sequences of genes. With DNA or protein sequences from over 133,000 species represented in the taxonomy database at the National Center for Biotechnology Information (NCBI) and over 800 genome sequences either published or in progress, researchers have an unprecedented opportunity to study evolution at a molecular level.

Homology and Computer Analysis

To study homologous sequences, researchers use computer programs, such as BLAST (Basic Local Alignment Search Tool), to compare a DNA or protein sequence with a collection of other sequences. One such collection is GenBank, the genetic sequence database operated by the NCBI that contains all publicly available DNA and protein sequences. Biologists use databases such as GenBank to find out if a test sequence matches any known sequences, how well it matches, and which portions of the sequence match.

Computer programs identify matching sequences by similarity. However, similar sequences are not always homologous, because they may not have a common origin. Although many sequences that show similarity did evolve from a common ancestor, the appearance of similar sequences can also result from independent events. For example, mutations frequently occur in the gene for the envelope protein of the AIDS virus, HIV-1, changing the amino acid sequence of the protein. The human immune system recognizes and destroys unmutated viruses, while leaving unharmed (selecting for) those viruses that contain mutations that make them unrecognizable. As a result, viruses from different patients can show identical mutations in the envelope protein, even though the patients were infected by different strains of the virus.

Exploring the Mechanisms of Mutation

The ability to compare protein and DNA sequences not only shows us where evolution has occurred but provides insight into its mechanisms. By comparing genomes, we find that mutations can occur on a small scale: Even a single nucleotide change is a mutation. They can also occur on a large scale, as happens when sequences are inserted, deleted, duplicated, or moved between chromosomes.

Many mutations that replace single nucleotides have no effect because of the "degeneracy" or redundancy of the genetic code. The genetic code has more codons (sixty-four) than amino acids (twenty). As a consequence, most amino acids are specified by two to four different codons. Because of this, some mutations can be "silent," with one nucleotide replacing another but without changing the specified amino acid. Other mutations are said to be "conservative." This occurs when a mutation replaces one amino acid with another that has similar properties: They may be chemically similar sharing the same charge, shape, or polarity.

If, however, the mutation affects the function of an important protein, that mutation may result in an evolutionary dead end, because it is less likely to be passed on to a future generation. As a result, important sequences show fewer mutations, whereas less important sequences show more change. Such properties can be deduced by comparing sequences from different organisms. Proteins that interact with other molecules, such as DNA or RNA, tolerate fewer changes in structure, and show little change through evolution. The histone proteins that form the backbone of the eukaryotic chromosome are important examples.

Evolutionary Relatedness

The number and types of differences that accumulate between genes or proteins of two different species can be used to assess their evolutionary relatedness and the amount of time since they diverged from a common ancestor. Such studies, termed "molecular systematics ," can be used to show that humans are more closely related to chimps than to gorillas, for instance, and how long ago the split in these lineages occurred.

Homologous proteins that perform the same function in different species are called orthologs. For example, hemoglobin, a protein that transports oxygen, has a similar amino acid sequence in both horses and dogs. If the predicted amino acid sequence of a newly discovered protein is similar to a known protein in another species, researchers can make guesses about the function of the newly discovered gene. If the sequence of a newly discovered protein was similar to hemoglobin, one might guess that the new protein is able to bind to oxygen and function in transporting oxygen. In the way, orthologs help researchers about the functions of newly discovered genes.

Natural selection acts against harmful mutations in critical genes. Gene duplication, however, makes extra copies of less critical genes, which are more free to acquire mutations. Members of these gene families are known as paralogs. Researchers look for paralogs in order to find proteins with new abilities. Cytokine genes, for example, are all derived from the same ancestral gene and share common sequence motifs, yet they fill a variety of roles in the immune system. New members of the cytokine family might be valuable tools for fighting disease. Just as species diverge and fill new biological niches, genes become duplicated and acquire new functions. On a molecular scale, the evolution of the genome reflects the evolution of all living things.

see also Bioinformatics; Chromosome, Eukaryotic; Evolution of Genes; Molecular Anthropology; Mutation.

Sandra G. Porter

Bibliography

Lander, Eric, et al. "Intitial Sequencing and Analysis of the Human Genome." Nature 409 (2001): 860-921.

Strachan, Tom, and Andrew P. Read. Human Molecular Genetics, 2nd ed. New York: John Wiley & Sons, 1999.

Venter, J. C., et al. "The Sequence of the Human Genome." Science 291 (2001): 1304-1351.

Internet Resource

National Center for Biotechnology Information. <http://www.ncbi.nlm.nih.gov>.

Homology

The term "homology" was defined in 1843 by Richard Owen, a noted British paleontologist, as the "same organ under every variety of form and function." Thus homologous structures can be defined in an evolutionary context as elements whose similarity in various taxa derives from their common origin in a shared ancestor. Homology may be based on:

1. similarities in structure, or how an organ is shaped;
2. topography, or the location of an organ;
3. associations with other structures, an example of which would be bone-muscle relationships;
4. development, including shared expression patterns of homologous genes .

The concept of homology is fundamental to comparative biology and phylogenetics systematics. Homology has historically been defined in terms of inheritance of a structure, with more or less modification, from a common ancestor. In this sense, attributes of two organisms are homologous when they are derived from an equivalent characteristic of the common ancestor. For example, whale flippers, bat wings, and human hands are homologous with respect to one another despite obvious differences in size, structure, and function. Whales, bats, and humans are descendants of a common mammalian ancestor, and their specialized appendages are simply modifications of the ancestral forelimb.

If two or more species have a similar trait that was not inherited from their common ancestor, the traits are said to be homoplastic . For example, insect wings, bird wings, and bat wings are considered to be homoplastic with respect to one another despite that they are all specialized appendages used for flight. The common ancestor of insects and amniotes (terrestrial vertebrates, including mammals and birds) did not have wings. Specialized appendages used in flight have evolved several times independently in the history of metazoans (multicellular animals). The developmental origins and underlying structural patterns are very different in these two groups of organisms. Insects and amniotes acquire wings in different ways during development and, despite similarities in the early development of bats and birds, the common ancestor of birds and bats did not have wings but rather some other type of forelimb. In addition, insect wings are foils made up primarily of chitin , a type of tissue, while bird and bat wings are highly complex with various tissue types organized into different structures such as feathers, skin, bone, blood, muscle, and nerves.

The question of whether an identical trait shared by two or more taxa is the result of homology or homoplasy usually cannot be decided based on a single character alone. In the above examples, one might be misled by grouping organisms based solely on the presence or absence of "wings." Rather, multiple characters are needed to provide an accurate hypothesis of relationships. Whales, bats, and humans have many more traits in common than are shared by bats, birds, and insects despite the fact that the latter three have wings. Therefore, mammals are considered to be a natural group and the forelimbs of mammals are considered homologous, whereas the wings of birds, bats, and insects (an unnatural group whose members do not share a common, winged ancestor) are considered homoplastic. It is the pattern of relationships among taxa with the trait in question that determines the nature of the similarity.

see also Phylogenetic Relationships of Major Groups; Phylogenetics Systematics.

Andrew G. Gluesenkamp

Bibliography

Futuyma, Douglas J. Evolutionary Biology. Sunderland, MA: Sinauer Associates, Inc.,1986.

Gould, Stephen J. Ontogeny and Phylogeny. Cambridge, MA: Harvard University Press, Belknap Press, 1977.

McKinney, Michael L. Evolution of Life. Englewood Cliffs, NJ: Prentice Hall, 1993.

Raff, Rudolf A. The Shape of Life. Chicago: University of Chicago Press, 1996.

homologous
1. (in biology) Describing a character that is shared by a group of species because it is inherited from a common ancestor. Such characters, called homologies, are used in cladistics to determine the evolutionary relationships of species or higher taxa. They are divided into two types: a shared derived homology (see apomorphy) is unique to a particular group and may be used to define a monophyletic group; a shared ancestral homology (see plesiomorphy) is not unique to the group, or may not be exhibited by all descendants of the ancestor in which it arose (see paraphyletic). Even though homologous features share the same evolutionary origin, they may have developed different functions. For example the wings of a bat, the flippers of a dolphin, and the arms of a human are homologous organs, having evolved from the paired pectoral fins of a fish ancestor. Compare analogous.

2. (in molecular biology) Describing sequences of nucleotides (or amino acids) at corresponding sites of different nucleic acids (or proteins) that show similarity because the molecules are descended from a common ancestral molecule. The term is sometimes used more loosely, but incorrectly, to describe sequences that are merely similar, when no evolutionary relationship is implied or can be established. See orthologous; paralogous. See also conserved sequence.

homologous A term applied to organs or chromosomes. An organ of an animal is said to be homologous with that of another when both are thought to have the same evolutionary origin, although their functions may differ widely. Homology is generally deduced from similarity of structure and/or position of the organ relative to other organs, seen particularly during embryonic development; e.g., in the plant kingdom the fertilization of the lower plants (e.g. Bryophyta) is often effected by motile male gametes; this is homologous to the male gamete of Spermatophytes which is non-motile and transferred in the pollen grain. Homologous chromosomes are those that contain identical linear sequences of genes, and which pair during meiosis. Each homologue is therefore a duplicate of one of the chromosomes contributed by one of the parents; and each pair of homologous chromosomes is normally identical in shape and size.

homologous
1. Applied to an organ of one animal that is thought to have the same evolutionary origin as an organ of another animal, although the functions of the two organs may differ widely. Homology is generally deduced from similarity of structure and/or position of the organ relative to other organs, seen particularly during embryonic development (e.g. the ear ossicles of a mammal, which are homologous with certain bones involved in the articulation of the jaw in fish).

2. Applied to chromosomes that contain identical linear sequences of genes, and which pair during meiosis. Each homologue is therefore a duplicate of one of the chromosomes contributed by one of the parents; and each pair of homologous chromosomes is normally identical in shape and size. Compare HETEROLOGOUS.