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Chapter 6 Intraspecific variation 鄭先祐 生態主張者:Ayo 工作室 Intraspecific variation Genetic mechanisms that affect variation Measuring genetic variation within and among populations The interaction of genetic and ecological process. Environmental application 生態學 2001 2 Intraspecific variation Until recently, direct measurement of the amount of genetic variation in natural populations was difficult. In the past 20 years, however, the revolution in molecular biology that has transformed much of biology has also had an impact on the study of ecology and evolution. By applying molecular technique, we can now study the interactions between ecological processes and their genetic and evolutionary bases. 生態學 2001 3 生態學 2001 4 Genetic mechanisms that affect variation Ultimately, genetic difference is derived from mutation of the DNA. A second mechanism that maintains variations is the phenomenon of heterozygote advantage, or heterosis. If the heterozygote has higher fitness than either homozygote, the heterozygote class protects deleterious recessives from elimination by selection. 範例:sickle-cell 生態學 2001 5 Decreasing the genetic variation Genetic drift has the effect of decreasing the total amount of genetic variation in a population. Inbreeding also affects variation. The major genetic effect of inbreeding is an increase in homozygosity. 生態學 2001 6 Inbreeding 的影響 (p2 + 2pg + q2) =1.0 (p2 + Fpq) + 2pq(1 - F) + (q2 + Fpg) =1.0 – Where F is the inbreeding coefficient. 基因組成 p 和 q 所佔的比率不變。 (p2 + Fpq) + (1/2) (2pq)(1-F) = p(p + q) = p Homozygosity increases and heterozygosity decreases, alleles are exposed more directly to selection, and this can lead to a decrease in genotypic variation. (Fig. 6.2) 生態學 2001 7 生態學 2001 8 Measuring genetic variation within and among populations Morphological variation 生態學 2001 9 農耕地 生態學 2001 地理變異的範例一 10 This significant increase in growth rate in the ab suggests that growth rate it plastic. 生態學 2001 11 地理變異的 範例二 位於高山的, 比較低矮。 生態學 2001 12 Plants from the high-altitude population(timberline) remain short in stature regardless of where they were grown. On the other hand, the lower-elevation populations exhibit some plasticity in growth, they are dwarfed at high elevation. 生態學 2001 13 Interaction of genetic and phenotypic response 範例:Intertidal snail, Littoria obtusata. – 生活於浪大的地區,和浪小的地區。 – 是否會被浪捲下去,取決於shell size and shape, 以及the strength of the foot。 – 於浪大的地區生活的snail ,都有較大的foot。 Trussell (1997) 將生活在不同浪大小地區的 snail 交換。(野外,且於實驗室內模擬)。 – 浪小地區生活的snail轉換至浪大地區,其foot 會轉變大。但是相反的轉換,卻不會縮小。 生態學 2001 14 有變異,未必然就有基因上的意義 有型態特徵的變異,未必然就有基因上的基礎。 譬如:seed size is clearly an important component of the reproductive strategy, we cannot necessarily assume that seed size is under simple genetic control such that it can be modified by natural selection. (Wolfe, 1995) In the biennial plant in which seed size varies by at least a factor of 2, Wolfe found that there is no variation on which natural selection can act to modify seed size. The seed size is affected by the light regime. 生態學 2001 15 Chromosomal variation There is considerable geographic variation in distribution of the chromosome types of 果蠅 D. psydoobscura. 生態學 2001 16 The white-footed mouse can be divided into two chromosomal races, distinguishable on the basis of Gbanded karyotypes. It do not show clines in chromosome types. 生態學 2001 17 Allozymes Protein electrophoresis has been used extensively to measure genetic variation. One advantage is that a large number of loci can be sampled Furthermore, we are measuring variation at the level of the cell’s proteins – one step closer to the DNA. 生態學 2001 18 生態學 2001 19 硬骨魚類 Fig. 6.8 Frequencies of polymorphisms for different taxonomic groups. 生態學 2001 20 Fig. 6.8 Frequencies of polymorphisms for different taxonomic groups. Bars represent the number of species in the group with that level of polymorphism for electrophoretic alleles. 生態學 2001 21 Fig. 6.8 Frequencies of polymorphisms for different taxonomic groups. Bars represent the number of species in the group with that level of polymorphism for electrophoretic alleles. 生態學 2001 22 Fig. 6.9 percent heterozygosity 生態學 per 2001 individual (H) 23 Fig. 6.9 percent heterozygosity 生態學 per 2001 individual (H) 24 Fig. 6.9 Frequencies of heterozygosity values for different taxonomic groups. Bar represent the number of species in the group with that proportion of heterozygous alleles. 生態學 2001 25 • Genetic similarity IN = (pix piy) / (pix2)(piy2) • genetic distance Dn = - ln IN 生態學 2001 26 FIt = FST + (1-FST) FIS 生態學 2001 27 FST ( variance among groups) 生態學 2001 28 DNA fingerprinting DNA fingerprinting has recently emerged as an additional technique of genetic analysis that holds great promise for ecological genetics. This technique is based on the present in DNA of socalled minisatellites, hypervariable regions that are composed of short segments containing multiple copies of a short sequence. It is thought that minisatellites are noncoding regions. 生態學 2001 29 Fig. 6.12 The process of DNA fingerprinting (a) DNA is isolated from cells and cleaved at specific sites with an endonuclease. (b) The sample containing DNA fragments from each 生態學 2001 individual is placed in an elctrophoresis gel. 30 © The DNA fragments are then denatured into single-stranded segments and transferred to a nylon or nitrocellulose membrane by a Southern transfer. (e) A piece of X-ray film is placed over the membrane and exposed. 生態學 2001 31 生態學 2001 32 Michondrial DNA Population biologists have also made use of unique properties of mitochondrial DNA to measure genetic variation in natural populations. Mitochondria contain a small set of genes that are separate from the nuclear genes and thus do not undergo segregation at meiosis. 生態學 2001 33 The interaction of genetic and ecological processes Three fundamental interactions that affect variation: Selection Dispersal Population size 生態學 2001 34 A classic example land snail, Cepaea nemaralis The Intraspecific variation of the land snail is a product of selection for color matching to avoid predation. Colors of the shells show great variety, ranging from brown to yellow to pink, and the degree of banding also varies greatly. 生態學 2001 35 A strong association between particular shell patterns and certain habitat types. 生態學 2001 36 Ecotypes Geographic variants that result from adaptation to local conditions are called ecotypes. 範例: tickle grass (Agrostis scabra) grow at several sites near Sudbury, Ontrario, that are contaminated by heavy metals. Plants from contaminated sites show higher tolerance of heavy metals. (Fig. 6.15) 生態學 2001 37 Seed germination and root growth in the presence of heavy metals was higher in plants from contaminated sites than in plants from uncontaminated sites 生態學 2001 38 範例:The wild oat, Avena barbata Two electrophoretic genotypes associated with extreme mesic or xeric sites. Each genotype is based on the allozymes present at five loci. The mesic and xeric ecotypes can occur on a much smaller geographic scale (Table 6.6). 生態學 2001 39 The wild oat, Avena barbata 生態學 2001 40 Dispersal 範例:monarch butterfly (nonmigratory and migratory populations) FST ( variance among groups) 生態學 2001 41 範例:Pocket gopher (Thomomys bottae) The mean values of FST are significant and are considerable larger than those for migratory butterflies. 生態學 2001 42 範例:whitefooted mouse Ravines (深谷) and power line rights-of-way dissecting forest habitat act as barriers to dispersal in the white-footed mouse, a forest-dwelling mammal. (Table 6.8) 生態學 2001 43 F ( variance among groups) 生態學 ST2001 44 F生態學 variance among groups) ST (2001 45 範例:A perennial plant, the blazing star (Liatris cylindracea) Exhibits genetic subdivision on an extremely fine spatial scale. The entire population occupied only 600 square meters. It was quite dense– as many as 175 plants per square meter. The study population was divided into a series of 66 quadrates, each 3 meters square. Plants were sampled from these quadrates, and 27 allozymes were analyzed for each plant. 生態學 2001 46 blazing star The variance among subpopulations was significant. The values of FST, measured on a scale of only 600 square meters,were greater than those of the monarch butterfly measured across all of eastern North American. Why? Two factors result in extremely small dispersal distances: pollinator behavior and seed dispersal distances. 生態學 2001 47 blazing star 生態學 2001 48 範例:seed dispersal mechanism of three species of forest herbs Sanicular seeds attach easily and tighly to mammalian fur Cryptotaenia seeds fall relatively near the parent plant Osmorhiza seeds are intermediate. 生態學 2001 49 種子可散播最 遠的,其genetic distance 最低。 生態學 2001 50 範例:the mangrove (Avicennia marina) The potential for longdistance seed dispersal. This plant produces seeds that germinate on the tree and fall into the water where tides and currents disperse the seeds, potentially for great distances. 生態學 2001 紅樹林51 Genetic structuring in the Indo-West Pacific is characterized by sharp discontinuities in allele frequencies. 生態學 2001 52 紅樹林的 基因循流 途徑 生態學 2001 53 範例:sugar maples (Acer saccharum) The genetic structure of populations in patches of forest differs from the pattern in populations in large tracts of forest. 結果與原本的預期,Patch populations showed more genotypic variation than did large tracts of forest.,相反。 研究者的解釋:the patches of forest are subject to increased immigrant pollen and hence gene flow. 生態學 2001 54 於密度較低的樹林地,其 接觸外來花粉的機會較大。 生態學 2001 55 Population size 範例:California vole, a four-year cycle. During the peak of the population cycle, when dispersal and extensive gene flow have homogenized the population, FST is low. 生態學 2001 56 Small populations and extinction The small populations may be subject to loss of genetic variation by drift or inbreeding. Isolated populations may not have sufficient gene glow to maintain genetic variation. The loss of variation has three main detrimental effects: – 1. 對環境變動的適應潛能下降 – 2. Inbreeding depression. – 3. Fixation of new deleterious mutations. 生態學 2001 57 範例:受到人為影響的生物 marsh gentian (植物) In the Netherlands, this species was once common, but pollution of the soil and habitat loss have resulted in significant population declines. Raijman and colleagues (1994) examined allozymes from populations ranging from 1 to more than 50,000 individuals, they discovered that most of the populations did not contain any rare alleles, a result that suggests an overall loss of variation. The number of polymorphic loci and the average number of alleles per locus were positively correlated with population size, confirming the loss of variation in small populations. 生態學 2001 58 Fig. 6.24 genetic variation and population size in Gentiana. (a) proportion of polymorphic loci 生態學 2001 59 Fig. 6.24 genetic variation and population size in Gentiana. (b) mean number of alleles per locus 生態學 2001 60 範例:The northern elephant seal ( bottleneck effect ) One of the most extreme examples of the effects of very small population size on genetic variation. This species was hunted nearly to extinction in the 19th century – the population was reduced to only about 20 individuals. Although the species had recovered to more than 30,000 individuals by the middle of 20th century, there was no genetic variation at any of 24-electrophoretic loci analyzed. 生態學 2001 61 範例:the gray wolf ( Canis lupus) and the coyote ( C. latrans) Restriction analysis of mtDNA indicates that eh continent-wide coyote population is composed of a larger number of genotypes (32) than is the wolf population (18). Coyote populations are not highly genetically differentiated; their FST values were not significantly different from zero. FST values for the wolf, however, were large (0.76) and highly significant, which indicates that the North American population is highly subdivided into significantly different subpopulations. 生態學 2001 62 範例:The wild turkey ( Meleagris gallopavo ) The wild turkey populations were drastically reduced by the clearing of forest land in the eastern US in the 19th and 20th centuries. By the 1940s, the eastern populations had been extirpated from more than 80% of their original range. The remaining populations inhabit a highly fragmented forest landscape. An electrophoretic survey of turkeys revealed extremely high FST values. The mean FST value of 0.102 is one of the highest reported for any avian populations. 生態學 2001 63 範例:heath hens (prairie chicken) ( Tympanuchus cupido ) Bouzat et al. (1998) extracted and analyzed DNA from the feather roots of museum specimens of this species collected before the population reduction. These researchers used a relative new technique of genetic analysis, microsatellite DNA, to measure genetic variation. This technique is similar to DNA fingerprinting using minisatellite DNA. 生態學 2001 64 粗體字,代表於 museum specimens有,但於Illinois populations 沒有的 allele。 斜體字,代表只有museum specimens 才有的特殊 allele。 The museum specimens contained nine alleles not currently present in the Illinois populations. 生態學 2001 65 範例:the cheetah (Acinonyx jubatus) O’Brien and colleagues (1983) surveyed 47 allozyme systems in samples from populations form South Africa, they found that the 55 cheetahs in their samples were monomorphic for all 47 allozymes. Such extreme genetic uniformity has been found to include the major histocompatibility complex (MHC). This situation makes the cheetah extremely vulnerable to disease or to a change in the environment that would require selection to operate. 生態學 2001 66 Environmental application Subspecies, races, and the endangered species Act. In 1973 the US congress passed a piece of landmark conservation legislation, the endangered species Act. This legislation mandated that the Fish and Wildlife Service determine which species in the US are at risk of extinction. When a species is determined to be endangered, the government is required not only to protect the remaining individuals but also to develop and implement a recovery plan designed to move the species from the brink of extinction. 生態學 2001 67 保護的範圍包含亞種,甚至是族群 In addition, the Endangered Species Act recognizes the importance of protecting distinct subspecies, and even populations, in order to maintain the naturally occurring genetic diversity so important to species survival. This requirement has led to some practical problems in the implementation of the act. 生態學 2001 68 範例:a unique subspecies of the mountain lion (Filis concolor coryi) Once occupied much of the southeastern US. Today this subspecies, is critically endangered. Less than 40 individuals remain in the swamps of southern Florida. Recent genetic analysis has revealed that the subspecies is contaminated with genes from a South American subspecies, a few individuals of which were released in the late 1950s or 1960s. 生態學 2001 69 範例:the gray wolf (Canis lupus) Recent genetic analyses of this species have shown that it is contaminated by genes from coytes ( Canis latrans). These closely related species have very different ecological niches, but matings between them can produce viable, fertile hybrids. 因為環境的開發,gray wolf 和 coytes混交 持續增加。 → 是否要從保育類排除? 生態學 2001 70 問題與討論! [email protected] Ayo 文化站 http://faculty.pccu.edu.tw/~ayo 生態學 2001 71