Genetic Diversity 1.1 2003/07/23 14:03:42 GMT-5 2004/07/13 14:13:26.392 GMT-5 Ian Harrison harrison@amnh.org Melina Laverty laverty@amnh.org Eleanor Sterling sterling@amnh.org Ian Harrison harrison@amnh.org Nora Bynum nbynum@amnh.org Charlet Reedstrom charlet@rice.edu Melina Laverty laverty@amnh.org Eleanor Sterling sterling@amnh.org genetic diversity Genetic diversity refers to any variation in the nucleotides, genes, chromosomes, or whole genomes of organisms (the genome is the entire complement of DNA within the cells or organelles of the organism). Genetic diversity at its most elementary level is represented by differences in the sequences of nucleotides (adenine, cytosine, guanine, and thymine) that form the DNA (deoxyribonucleic acid) within the cells of the organism. The DNA is contained in the chromosomes present within the cell; some chromosomes are contained within specific organelles in the cell (for example, the chromosomes of mitochondria and chloroplast). Nucleotide variation is measured for discrete sections of the chromosomes, called genes. Thus, each gene compromises a hereditary section of DNA that occupies a specific place of the chromosome, and controls a particular characteristic of an organism. Most organisms are diploid, having two sets of chromosomes, and therefore two copies (called alleles) of each gene. However, some organisms can be haploid, triploid, or tetraploid (having one, three, or four sets of chromosomes respectively). Within any single organism, there may be variation between the two (or more) alleles for each gene. This variation is introduced either through mutation of one of the alleles, or as a result of sexual reproduction. During sexual reproduction, offspring inherit alleles from both parents and these alleles might be slightly different, especially if there has been migration or hybridization of organisms, so that the parents may come from different populations and gene pools. Also, when the offspring's chromosomes are copied after fertilization, genes can be exchanged in a process called sexual recombination. Harmless mutations and sexual recombination may allow the evolution of new characteristics (see the module on Microevolutionary processes for further discussion). Each allele codes for the production of amino acids that string together to form proteins. Thus differences in the nucleotide sequences of alleles result in the production of slightly different strings of amino acids or variant forms of the proteins.These proteins code for the development of the anatomical and physiological characteristics of the organism, which are also responsible for determining aspects of the behavior of the organism. Different species can have different numbers of genes within the entire DNA or genome of the organism. However, a greater total number of genes might not correspond with a greater observable complexity in the anatomy and physiology of the organism (i.e. greater phenotypic complexity). For example, the predicted size of the human genome is not much larger than the genomes of some invertebrates and plants, and may even be smaller than the Indian rice genome (see ). In humans, more proteins are encoded per gene than in other species (Rubin, 2001.). Comparison of Genome Sizes Species Organism common name Number of genes in genome Reference Arabidopsis thaliana thale cress 25,498 Arabidopsis Genome Initiative (2000) Oryza sativa (indica-cultivar subgroup) Indian rice 46,022-55,615 Yu et.al. (2002) Caenorhabditis elegans nematode 19,000 C. elegans Sequencing Consortium (1998) Drosophila melanogaster fruit fly 13,600 Adams et al. (2000) Homo sapiens human ca. 30,000-40,000 International Human Genome Sequencing Consortium (2001) Besides having distinct combinations of genes, species may also have variation in the shape and composition of the chromosomes carrying the genes in the total number of chromosomes present. Examination of these features of the chromosomes (termed karyology) provides another way of describing genetic diversity. Analyses of genetic diversity can be applied to studies of the evolutionary ecology of populations. Genetic studies can identify alleles that might affect the ability of the organism to survive in its existing habitat, or might enable it to survive in more diverse habitats. This is the basis of natural selection; some alleles can confer a selective advantage on the host organism, such that it is more likely to survive than if it did not have the particular alleles. The presence of unique genetic characteristics distinguishes members of a given population from those of any other population. Large populations will usually have a greater diversity of alleles compared to small populations. This diversity of alleles indicates a greater potential for the evolution of new combinations of genes and, subsequently, a greater capacity for evolutionary adaptation to different environmental conditions. In small populations, the individuals are likely to be genetically, anatomically, and physiologically more homogeneous than in larger populations and less able to adapt to different environmental conditions (see Small population phenomena). Genetic diversity is, therefore, a key component for conservation efforts associated with population management (e.g., Andayani et al., 2001). The genetic constitution of an organism - the arrangement of the DNA into genes on the chromosomes - is also referred to as its genotype. Hence, variation that exists within the genetic constitution of an organism is often referred to as genotypic variation . Note, therefore, that genetic variation and genotypic variation are somewhat synonymous terms. However, the outward appearance of an organism is a product of its genotypic variation, and so some people may refer to the visually discernible product of genotypic variation (for example, variation in the coloration of the populations of the northern water snake, Nerodia sipedon) as a feature of genetic variation. This is discussed in more detail below. Phenotypic diversity: Genes code for the outward expression of physical traits of the organism but the environment can also modify the way in which the genes are physically expressed in the organism. The physical constitution of an organism that results from its genetic constitution (genotype), and the action of the environment on the expression of the genes, is termed the phenotype. Phenotypic variation (See Phenotypic Diversity), therefore, refers to the variation of the physical traits, or phenotypic characters of the organism, such as differences in anatomical, physiological, biochemical, or behavioral characteristics. As noted above, the phenotypic characters represent an important measure of the adaptation of the organism to its environment because it is these phenotypic characters that interact with biotic and abiotic (i.e. living and non-living) factors of the environment. Phenotypic diversity between individuals, populations, and species is usually described in terms of the variation in external morphology of individuals. Variation in physiological and biochemical characteristics of the organism are also important indicators of phenotypic diversity. Behavioral characteristics represent the way in which the organism interacts with its environment and are therefore the product of the anatomical, physiological, or biochemical traits that might be adaptations for environment. For example, the migration behavior of some birds or mammals, and the host specificity of parasites are closely linked with the ways in which the organisms use the environment to meet their physiological requirements. Thus, variation in behavioral characteristics may also be used to describe phenotypic diversity between individuals, populations, or species. Local environmental conditions can alter phenotypic characters. The physiological (and anatomical) characteristics of the kidney in fishes, for example, can vary depending on the environment. Rainbow trout (Oncorhynchus mykiss) and flounder (Platichthys flesus) filter fluid through their kidneys at different rates depending on the salinity of the water in which the fish are immersed (see Harrison, 1996 for references). In plants, leaf shape can show significant variability among individuals occupying different habitats (e.g., dry versus wet sites, or sunny versus shaded sites). Thus, any discussion of phenotypic diversity should account for the interrelationships between anatomical structure and function for organisms living in different habitats. Indeed, phenotypic characters are the product of complex interrelationships between the form and function of various body tissues and organs. For example, the physical properties of light limit the minimum size for vertebrate eyes, consequently the eyes are relatively large in minute vertebrates (such as species of amphibians and fishes). This, in turn, may affect the development and function of adjacent organs in the head, where there is a "competition" for headspace (Hanken, 1983; Harrison, 1996). The extent to which genetic variation between organisms is expressed in their phenotypes can be quite variable for different characteristics. Genetic variation between some features might be expressed as very subtle differences in their phenotype. For example, populations and subspecies of the herring gull (Larus argentatus) and the lesser black-backed gull (Larus fuscus) are distinguished by very slight differences in the coloration of individuals. In some cases these differences can be difficult to detect. On the other hand, genetic variation within a species can be quite extensive, particularly in cultured plants or domesticated animals where particular features have been artificially selected in different strains or breeds. For example, broccoli, cabbage, and kale are morphologically quite diverse but are all considered to be subspecies of Brassica oleracea. Behavioral characteristics - which are part of phenotypic diversity - are also important aspects of population, community, and ecosystem diversity. The herding behavior of some mammals such as elephants, or wildebeest, helps determine the size and activity of populations. Moreover, the activity of these herds (e.g. seasonal migrations) can significantly affect the overall ecology of an ecosystem. Behavioral patterns are also associated with landscape/seascape and biogeographic diversity. According to Tsukamoto and Aoyama (1998) some species of eels that inhabit temperate waters of the Indo-Pacific (the Japanese eel, Anguilla japonica) and temperate waters of the Atlantic (the European eel, A. anguilla and the American eel A. rostrata) are descended from tropical dwelling ancestors that may have undergone short spawning migrations between freshwater and sea water. However, Tsukamoto and Aoyama (1998) suggest that, in order for these species to maintain their habit of spawning in warmer waters, their spawning migrations have increased in length with the evolution and movement of the Philippine and Atlantic lithospheric plates. Note however that this evolutionary scenario is a hypothesis that requires further testing (see Biogeographic Diversity for further discussion). Genetic diversity refers to any variation in the nucleotides, genes, chromosomes, or whole genomes of organisms Genome the entire complement of DNA within the cells or organelles of the organism Genotype the genetic constitution of an organism that results from the arrangement of the DNA within the cell or organelles. Genotypic Variation the variation that exists between the genetic constitution of different individuals. Phenotypic Variation the variation of the physical traits, or phenotypic characters of the organism, such as differences in anatomical, physiological, biochemical, or behavioral characteristics. Phenotype the physical constitution of an organism that results from its genetic constitution (genotype), and the action of the environment on the expression of the genes Lithospheric Plates the large, mobile pieces of the Earth's lithosphere, which is the upper ca. 100 km of the mantle and crust of the Earth where the rocks are rigid compared to those deeper below the Earth's surface). Williams P.H. and C. J. Humphries Comparing character diversity among biotas. Biodiversity: a biology of numbers and difference Blackwell Science Ltd. 1996 K.J. Gaston 54-76 Oxford, U.K. Andayani, N., J.C. Morales, M.R.J. Forstner, J. Supriatna, D.J. Melnick Genetic variability in mtDNA of the silvery gibbon: implications for the conservation of a critically endangered species. Conservation Biology 2001 15(3) 1545-1548 Rubin, G.M. The draft sequences: comparing species. Nature 2001 409 820-821 Hanken, J. Miniturization and its effects on cranial morphology in plethodontid salamanders, genus Thorius (Amphibia: Plethodontidae): II. The gate of the brain and sense organs and their role in skull morphogenesis and evolution Journal of Morphology 1983 177 255-268 The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Nature 2000 408 796-815 Yu, J., S. Hu, J. Wang, G. Ka-Shu Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, M. Cao, J. Liu, J. Sun, J. Tang, Y. Chen, X. Huang, W. Lin, C. Ye, W. Tong, L. Cong, J. Geng, Y. Han, L. Li, W. Li, G. Hu, X. Huang, W. Li, J. Li, Z. Liu, L. Li, J. Liu, Q. Qi, J. Liu, L. Li, T. Li, X. Wang, H. Lu, T. Wu, M. Zhu, P. Ni, H. Han, W. Dong, X. Ren, X. Feng, P. Cui, X. Li, H. Wang, X. Xu, W. Zhai, Z. Xu, J. Zhang, S. He, J. Zhang, J. Xu, K. Zhang, X. Zheng, J. Dong, W. Zeng, L. Tao, J. Ye, J. Tan, X. Ren, X. Chen, J. He, D. Liu, W. Tian, C. Tian, H. Xia, Q. Bao, G. Li, H. Gao, T. Cao, J. Wang, W. Zhao, P. Li, W. Chen, X. Wang, Y. Zhang, J. Hu, J. Wang, S. Liu, J. Yang, G. Zhang, Y. Xiong, Z. Li, L. Mao, C. Zhou, Z. Zhu, R. Chen, B. Hao, W. Zheng, S. Chen, W. Guo, G. Li, S. Liu, M. Tao, J. Wang, L. Zhu, L. Yuan, and H. Yang. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica). Science 2002 296 79-92 The C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998 282 2012-2018 Adams, M.D., S.E. Celniker, R.A. Holt, C.A. Evans, J.D. Gocayne, P.G. Amanatides, S.E. Scherer, P.W. Li, R.A. Hoskins, R.F. Galle, R.A. George, S.E. Lewis, S. Richards, M. Ashburner, S.N. Henderson, G.G. Sutton, J.R. Wortman, M.D. Yandell, Q. Zhang, L.X. Chen, R.C. Brandon, Y-H. C. Rogers, R.G. Blazej, M. Champe, B.D. Pfeiffer, K.H. Wan, C. Doyle, E.G. Baxter, G. Helt, C.R. Nelson, G.L. Gabor Miklos, J.F. Abril, A. Agbayani, H-J. An, C. Andrews-Pfannkoch, D. Baldwin, R.M. Ballew, A. Basu, J. Baxendale, L. Bayraktaroglu, E.M. Beasley, K.Y. Beeson, P. V. Benos, B.P. Berman, D. Bhandari, S. Bolshakov, D. Borkova, M.R. Botchan, J. Bouck, P. Brokstein, P. Brottier, K.C. Burtis, D.A. Busam, H. Butler, E. Cadieu, A. Center, I. Chandra, J.M. Cherry, S. Cawley, C. Dahlke, L.B. Davenport, P. Davies, B. de Pablos, A. Delcher, Z. Deng, A.D. Mays, I. Dew, S.M. Dietz, K. Dodson, L.E. Doup, M. Downes, S. Dugan-Rocha, B.C. Dunkov, P. Dunn, K.J. Durbin, C.C. Evangelista, C. Ferraz, S. Ferriera, W. Fleischmann, C. Fosler, A.E. Gabrielian, N.S. Garg, W.M. Gelbart, K. Glasser, A. Glodek, F. Gong, J.H. Gorrell, Z. Gu, P. Guan, M. Harris, N.L. Harris, D. Harvey, T.J. Heiman, J.R. Hernandez, J. Houck, D. Hostin, K.A. Houston, T.J. Howland, M-H. Wei, C. Ibegwam, M. Jalali, F. Kalush, G.H. Karpen, Z. Ke, J.A. Kennison, K.A. Ketchum, B.E. Kimmel, C.D. Kodira, C. Kraft, S. Kravitz, D. Kulp, Z. Lai, P. Lasko, Y. Lei, A.A. Levitsky, J. Li, Z. Li, Y. Liang, X. Lin, X. Liu, B. Mattei, T.C. McIntosh, M.P. McLeod, D. McPherson, G. Merkulov, N.V. Milshina, C. Mobarry, J. Morris, A. Moshrefi, S.M. Mount, M. Moy, B. Murphy, L. Murphy, D.M. Muzny, D.L. Nelson, D.R. Nelson, K.A. Nelson, K. Nixon, D.R. Nusskern, J.M. Pacleb, M. Palazzolo, G.S. Pittman, S. Pan, J. Pollard, V. Puri, M.G. Reese, K. Reinert, K. Remington, R.D.C. Saunders, F. Scheeler, H. Shen, B.C. Shue, I. Sidn-Kiamos, M. Simpson, M.P. Skupski, T. Smith, E. Spier, A.C. Spradling, M. Stapleton, R. Strong, E. Sun, R. Svirskas, C. Tector, R. Turner, E. Venter, A.H. Wang, X. Wang, Z-Y. Wang, D.A. Wassarman, G.M. Weinstock, J. Weissenbach, S.M. Williams, T. Woodage, K.C. Worley, D. Wu, S. Yang, Q.A. Yao, J. Ye, R-F. Yeh, J.S. Zaveri, M. Zhan, G. Zhang, Q. Zhao, L. Zheng, X.H. Zheng, F.N. Zhong, W. Zhong, X. Zhou, S. Zhu, X. Zhu, H.O. Smith, R.A. Gibbs, E.W. Myers, G.M. Rubin, J.C. Venter. The Genome Sequence of Drosophila melanogaster Science 2002 287 2185-2195 International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature 2001 409 860-921 Harrison, I.J Interface areas in small fish Symposia of the Zoological Society of London 1996 69 15-45 Tsukamoto, K., J. Aoyama Evolution of freshwater eels of the genus Anguilla: a probable scenario. Environmental Biology of Fishes 1998 52 139-148