Topic 8 Lecture 14 Direct observations of past

Topic 8. Lecture 14. Direct observations of past evolution This topic can be viewed as a bridge connecting studies of past evolution and of Microevolution. Obviously, we cannot directly observe Macroevolution, because it is too slow, but even what can be observed is fascinating. We will treat the notion "direct observations" broadly and consider the following subjects: 1. Domestication 2. Selection experiments 3. Evolution of captive populations 4. Rapid evolution in the wild 5. Rapid evolution of human pathogens

1. Domestication The number of species of animals and plants that were domesticated long time ago and underwent substantial changes under artificial selection is not very large. Let us consider several examples of ancient and recent domestication. A. Goldfish The wild progenitor of domesticated goldfish Carassius auratus is a very common species in Eurasia.

A brief history of goldfish domestication During the Tang Dynasty (618 - 907), it was popular to raise Carassius auratus in ponds. As the result of a dominant mutation, one of these fishes displayed "gold" (actually yellowish orange) coloration. People began to breed the gold variety and began to display them in small containers. In 1162, the empress of the Song Dynasty (960 -1279) ordered the building of a pond to collect the red and gold variety. By this time, people outside the royal family were forbidden to keep goldfish of the gold (yellow) variety, yellow being the royal color. This probably is the reason why there are more orange goldfish than yellow goldfish, even though the latter are easier to breed. As time passed, more mutations occurred, producing new color variations, and fancier varieties of goldfish were developed. The occurrence of other colors was first recorded in 1276. The first occurrence of fancy tailed goldfish was recorded in the Ming dynasty (1368 - 1644). In 1502, goldfish were introduced to Japan, where the Ryukin and Tosakin varieties were developed. In 1611, goldfish were introduced to Portugal and from there to other parts of Europe. Obviously, strong artificial selection was applied to external morphology and color of domestic goldfish, usually in the direction opposite to that of natural selection.

A small sample of breeds of goldfish, starting from less derived ones:

None of these fishes would do well in the wild. Genetic variation on which artificial selection operated was partially present in the wild progenitor population and partially provided by new mutations in captivity. These patterns are typical for all domestic breeds.

B. Pigeon The wild progenitor of domestic pigeon breeds, the Rock Pigeon, has a restricted natural resident range in western and southern Europe, North Africa, and into southwest Asia. Its habitat is natural cliffs, usually on coasts. Rock Pigeons have been domesticated for several thousand years.

Darwin was an accomplished pigeon fancier: Believing that it is always best to study some special group, I have, after deliberation, taken up domestic pigeons. I have kept every breed which I could purchase or obtain, and have been most kindly favored with skins from several quarters of the world, more especially by the Hon. W. Elliot from India, and by the Hon. C. Murray from Persia. Many treatises in different languages have been published on pigeons, and some of them are. . . of considerable antiquity. I have associated with several eminent fanciers, and have been permitted to join two of the London Pigeon Clubs. The diversity of the breeds is something astonishing. Compare the English carrier and the short-faced tumbler, and see the wonderful difference in their beaks, entailing corresponding differences in their skulls. . In the skeletons of the several breeds, the development of the bones of the face, in length and breadth and curvature, differs enormously. The shape, as well as the breadth and length of the ramus of the lower jaw, varies in a highly remarkable manner. Altogether at least a score of pigeons might be chosen, which, if shown to an ornithologist, and he were told that they were wild birds, would certainly be ranked by him as well-defined species. Moreover, I do not believe that any ornithologist would in this case place the English carrier, the short-faced tumbler, the runt, the barb, pouter, and fantail in the same genus; more especially as in each of these breeds several truly-inherited sub-breeds, or species, as he would call them, could be shown him. Great as are the differences between the breeds of the pigeon, I am fully convinced that the common opinion of naturalists is correct, namely, that all are descended from the Rock Pigeon (Columba livia), including under this term several geographical races or sub-species, which differ from each other in the most trifling respects. ("Origin of Species", 1859, Chapter 1)

A small sample of breeds of domestic pigeon:

"Semi-wild" pigeons that live alongside humans are polymorphic, as some of them are wildtype and others have dark plumage (melanists). In rural habitats, the wild type is prevalent, but in big cities dark individuals are more common. This variation is due to 2 major genes and some minor genes. It is not clear how selection operates on this trait, but this selection must be strong, as urban pigeons in the Soviet Union evolved rapidly after World War II.

C. Dog East Asian form of wolf, Canis lupus, the progenitor of domestic dogs.

A small sample of dog breeds:

A brief history of dog domestication Archaeological finds from Mesolithic sites around the world indicate that the dog was the first domestic animal. The earliest finds believed to be from domestic dogs are a single jaw from 14, 000 years before the present in Germany and an assemblage of small canids from 12, 000 yr B. P. in Israel. Genetic data firmly establish wolves as wild progenitor of dogs. Examination of the mitochondrial DNA sequence variation among 654 domestic dogs representing all major dog populations worldwide suggest a common origin from a single gene pool for all dog populations. A larger genetic variation in East Asia than in other regions and the pattern of phylogeographic variation suggest an East Asian origin for the domestic dog, ~15, 000 years ago. (Science 298, 1610 -1613, 2002).

Phylogenetic tree of all dog (unlabeled) and wolf (open squares) haplotypes. Six clades (A to F) of dog haplotypes are indicated. Branch lengths are according to the indicated scale; the branch leading to the outgroup (coyote) was reduced by 50%.

D. Experimental domestication of the fox, Vulpes vulpes wild foxes Domesticated foxes after 40+ generations of selection for tame behavior. (J. of Heredity 95, 185– 194, 2004).

The story of fox domestication: The silver fox, a color variation of the red fox (Vulpes vulpes), has been domesticated in an experiment at the Institute of Cytology and Genetics in Novosibirsk, Russia by D. K. Belyaev and L. N. Trut. Starting in 1959, and selected solely on behavioral criteria, a strain of foxes with behavior extremely similar to domestic dogs was produced. Tame foxes exhibit highly social behavior with both other members of their own species and humans in a playful, friendly manner. In contrast, foxes from an unselected population, or from a strain bred for aggressive behavior, avoid social interactions with humans. Although the heritability of these behavioral differences is well established, the molecular biological basis has not yet been determined. Forty years of determined selection in over 45 000 foxes produced a sizeable population of tamed foxes. As Belyaev predicted, a host of additional changes never deliberately selected for also appeared. They included piebald coat color, drooping ears, shorter, occasionally upturned tails, shortened snouts and shifts in the developmental timing of various other characteristics. As they aged, many of the fox pups began behaving in a manner similar to domestic dogs by barking, whining and licking their handlers. The Fox-Farm experiment conclusively demonstrated that consistent and prolonged selection for a single behavioral trait can radically alter not only the behavior and developmental characteristics of an animal, but its physical constitution as well. The tame foxes, with regard to nearly every affected trait, demonstrate a 'stretching' of those characteristics associated with the early stages of ontogeny, as well as an extension of juvenile traits into adulthood.

General patterns in animal domestication Several phenotypic traits appear independently in many domesticated animals. Usually, more than one substantially different genetic lineages of the wild progenitor is incorporated into domesticated breeds, indicating multiple domestication events (J. of Zoology 269, 261271, 2006).

E. Domestication of maize, Zea mays. Annual teosinte, the wild progenitor of maize. The photograph shows the robust vegetative habit and long branches with tassels at their tips.

The history of maize domestication: Teosinte is a common name for a group of four annual and perennial species of the genus Zea native to Mexico and Central America. Teosinte plants are taller and broader-leaved than most grasses. Their general growth form is similar to that of maize, although they have much longer lateral branches. Phylogenetic analysis indicates that one form of teosinte, known as Z. mays ssp. parviglumis, shares a particularly close relationship with maize and is its direct ancestor. A single domestication event that produced maize can be pinpointed to a specific geographic locality. The region harboring those teosinte populations that are phylogenetically most closely allied with maize can be considered a candidate for the region in which maize was domesticated. Populations of teosinte from the central Balsas River drainage are basal to diversity of domestic maize, suggesting that this regions was the cradle of maize domestication. From the know rate of evolution of traits used for the phylogenetic reconstruction (microsatellite alleles), the time of divergence ssp. parviglumis and Mexican maize can be estimated as 9, 188 B. P. (95% confidence limits of 5, 689 -13, 093 B. P. ). (PNAS 99, 6080 -6084, 2002; Ann. Rev. of Genetics 38, 37 -59, 2004). Domesticated varieties of potato also originated monophyletically in the northern Peru, from a wild tuber-bearing Solanum (PNAS 102, 14694 -14699, 2005).

Geographic distribution of maize and teosinte used for the phylogenetic analysis of maize domestication. Inset shows the distribution of the 34 populations of ssp. parviglumis in southern Mexico with the populations that are basal to maize. The blue line is the Balsas River and its major tributaries.

Phylogenies of maize and teosinte based on 99 microsatellites. Dashed gray line circumscribes the monophyletic domestic maize lineage. Asterisks identify those populations of ssp. parviglumis basal to maize, all of which are from the central Balsas River drainage. (a) Individual plant tree based on 193 maize and 71 teosinte. (b) Tree based on 95 ecogeographically defined groups. The arrow indicates the position of Oaxacan highland maize that is basal to all of the other maize.

Genetics of maize domestication A substantial portion of the phenotypic differences between maize and teosinte is explained by variation in an enhancer of gene expression at the tb 1 (teosinte branched 1) locus. Intergenic sequences 58 -69 kb 5' to the tb 1 coding region confer pleiotropic effects on Z. mays morphology (Nature Genetics 38, 594 -597, 2006).

A cost of domestication? One can expect domestication to be involved with a substantial fitness cost, in the sense that domestic animals and plants would not do well in the wild. This cost can appear due to the following reasons: 1) Artificial selection for useless or even deleterious trait states (goldfish). 2) Artificial selection for useful trait states (a high yield of something) which, nevertheless, may reduce the overall fitness due to trade-offs. 3) Damaging side-effects of strong artificial selection, due to hitch-hiking of deleterious alleles. 4) Relaxation of negative selection protecting features that are important in the wild, but not in captivity. 5) Inbreeding. Genetic cost of domestication has recently been studied on dogs and rice.

Dogs have accumulated nonsynonymous substitutions in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome (Genome Research 16, 990 -994, 2006). Relative rates of nonsynonymous substitutions. Values for wolves are indicated in blue, for dogs in yellow, and for the divergence between a random wolf and coyote sequence in red. Ninety-five percent confidence intervals are also shown. A similar pattern has been observed in domesticated rice. Also, among non-synonymous substitutions fixed in the course of rice domestication, a fraction of radical substitutions, that involve two chemically dissimilar amino acids, is elevated (Trends in Genetics 22, 126131, 2006).

Thus, wild progenitors and relatives of domesticated animals and plants remain a very valuable genetical resource. Although lacking some specific desirable qualities, produced by artificial selection, wild progenitors have healthier genotypes and may possess alleles which were lost in domesticated varieties. Wild (left) and domesticated cultivars (center, right) of sunflower. Like maize and potato, domestication of sunflower was a single event (J. of Heredity 97, 403408, 2006).

2. Selection experiments Almost all attempts to select for something artificially were successful, in the sense that a substantial response to selection has been obtained. However, this response often diminishes with time - due to the population running out of genetic variation and/or to negative correlation between fitness and the trait states that are selected for. The numbers of abdominal and sternopleural bristles in Drosophila are two convenient and seemingly unimportant traits for artificial selection experiments.

Artificial selection for seemingly unimportant traits Replicated divergent artificial selection for abdominal and sternopleural bristle number from a highly inbred strain of Drosophila melanogaster resulted in an average divergence after 125 generations of selection of 12. 0 abdominal and 8. 2 sternopleural bristles from the accumulation of new mutations affecting bristle number. Responses to selection were highly asymmetrical, with greater responses for low abdominal and high sternopleural bristle numbers. Decelerating responses to selection and rapid responses to reverse selection suggest new mutations affecting bristle number on average have deleterious effects on fitness (Genetics 136, 937 -951, 1994).

Responses to 125 generations of selection for abdominal bristle number from an inbred base population. Closed symbols and solid lines give generation means of high bristle number replicates, and open symbols and dashed lines represent generation means of low bristle number replicates. Circles, triangles and squares indicate replicates 1, 2 and 3, respectively.

Responses to 125 generations of selection for sternopleural bristle number from an inbred base population. Closed symbols and solid lines give generation means of high bristle number replicates, and open symbols and dashed lines represent generation means of low bristle number replicates. Circles, triangles and squares indicate replicates 1, 2 and 3, respectively.

The Illinois Long-Term Selection Experiment This experiment on artificial selection for grain protein and oil concentration in maize (Zea mays) is the longest continuous genetics experiment in higher plants. A total of 105 generations of selection have produced nine related populations that exhibit phenotypic extremes for grain composition and a host of correlated traits. The most striking observation in the Illinois Long-Term Selection Experiment is the significant degree of genetic variation remaining in these populations after more than 100 generations of selection. Selection response continues in all the populations except ILO and ILP, which have probably reached lower biological limits for these traits owing to their poor germination frequencies and lack of change in recent cycles. Further evidence for significant genetic variation is provided by the reverse selection experiments initiated at cycle 48 (Trends in Plant Science 9, 358 -364, 2004).

Selection responses in the Illinois Protein Strains (a). Selection has been performed for 103 cycles in the Illinois High Protein (IHP) and Illinois Low Protein (ILP) strains. Selection was reversed in these strains beginning at cycle 48 to produce the Reverse High Protein (RHP) and Reverse Low Protein (RLP) strains. Reverse Low Protein 2 (RLP 2) strain was initiated from ILP at cycle 90. Each cycle measured grain from 60– 120 plants, with seeds from the highest or lowest 20% (depending on the direction of selection) selected to form the next generation.

Selection responses in the Illinois Oil Strains (b). Selection has been performed for 103 cycles in the Illinois High Oil (IHO) and Illinois Low Oil (ILO) strains. Selection was reversed in these strains beginning at cycle 48 to produce the Reverse High Oil (RHO) and Reverse Low Oil (RLO) strains. The Switchback High Oil (SHO) strain was initiated from RLO at cycle 55. Each cycle measured grain from 60– 120 plants, with seeds from the highest or lowest 20% (depending on the direction of selection) selected to form the next generation.

Artificial selection for a certainly deleterious trait state It is possible to artificially select Drosophila melanogaster males for reduced sexual activity. In one such experiment, only those males who do not mate with any of the 4 virgin females in 30 minutes were allowed to reproduce (eventually). After several generations of such selection flies were in a rather bad shape - they hardly moved (Genetica 52 -53, 165 -181, 1980; PNAS 102 Suppl. 1, 6622 -6629, 2005). Response to 280 generations of selection for low sexual activity. The ordinate shows the fraction of males that did not mate after 30 minutes.

3. Evolution of captive populations In addition to experiments on active artificial selection, it is also possible to maintain a captive population, and to allow its individuals to perform selection on their own. Often, such experimental populations undergo substantial evolution. Obviously, such experiments can be performed only on organisms with short generation time, in particular on bacteria and viruses. Data of such experiments are usually consistent with expectations. Experimental evolution of Escherichia coli 1. Adaptation to a new environment. The dynamics of adaptation to a new environment of experimental populations of E. coli. Bacteria lived in a hemostat on a minimal medium with glucose as the only source of carbon. Fitness decelerated as the population approached a fitness peak (Nature 407, 736 -739, 2000).

2. Decline of unused functions. The decline of catabolitic functions in the course of evolution with glucose as the only source of carbon, when these functions are not directly used. As expected, they declined, and this decline was faster in populations that acquired high mutation rate (dashed line) than in populations that kept low ancestral mutation rate (solid line). However, the difference was only marginal. Thus, direct selection against unused functions, due to antagonistic pleiotropy, played a substantial role in their decline.

3. Homoplasy (parallelism) and unpredictability. Twelve initially identical populations of Escherichia coli evolved in identical environments for 20, 000 cell generations. Mutations of unknown effect had been discovered in one population at four loci (pyk. F, nad. R, pbp. A-rod. A, and hok. B/sok. B). Two of these genes, pyk. F and nad. R, had substitutions in all 11 other populations, and the other two in several populations. There were only very few cases, however, in which the exact same mutations were fixed. Adaptation by natural selection probably drove the parallel evolution of these four genes (PNAS 103, 9107 -9112, 2006). Mutations fixed by 20, 000 generations in 12 experimental populations of E. coli. Lighter regions indicate protein-coding four sequences for pyk. F (A), nad. R (B), pbp. A-rod. A (C), and hok. B/sok. B (D). Each arrow marks a mutation; the number shows the affected population.

4. Cladogenesis and speciation. Two ecologically and morphologically distinct types, designated L (large) and S (small) based on their colony morphology, arose by generation 6000 in an experimental population of Escherichia coli and coexisted for more than 12, 000 generations thereafter. The derived S morph was monophyletic, indicating a long history of coexistence with L. Two factors enabled the stable coexistence of L and S, despite the fact that L grows exponentially about 20% faster than S. First, L excretes a metabolite that differentially promotes the growth of S. Second, L experiences increased death during the stationary phase (i. e. , after glucose is depleted) when S is present. The relationship between the morphs was dynamic through time, with the frequency of S rising and falling several times between about 10– 20% and 50– 90% of the total population. Both lineages continued to adapt, and their evolution contributed to fluctuations in their relative abundance. Based on their phylogenetic history and independent evolutionary trajectories, S and L can be viewed as two sympatric asexual populations and different asexual species (J. of Molecular Evolution 61, 171 -180, 2005).

L and S individuals from different generations each form their own clade, demonstrating phylogenetic continuity of each lineage. Here, paleontological record is perfect, and is maintained in a freezer. Thus, we can reject the upper scenario. Instead, both L and S are two phylogenetically continuous lineages, derived once from a basal group.

Trajectories of genetic diversity within the S and L lineages. The data for L are shown as circles and solid lines; the data for S are shown as squares and dashed lines. Significant declines in genetic variation between consecutive samples are indicated by asterisks. Each lineage underwent periods of sharp decline in genetic variation, indicating selective sweeps due to fixations of beneficial mutations within the lineage. Thus, both L and S lineages continued to adapt following their origin. However, adaptation of one lineage did not cause extinction of the other lineage. Thus, S and L are distinct, sympatric populations.

Experimental evolution of a phage Bacteriophage f. X 174 evolved on a continuous supply of sensitive hosts for 180 days (~13, 000 phage generations). The average rate of nucleotide substitution was nearly 0. 2% (11 substitutions)/20 days, and substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. Perhaps, continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genotypes competing within the same cell (Genetics 170, 19– 31, 2005). Changes in the f. X 174 hemostat population. Solid diamonds show the number of differences between each sequenced isolate and the ancestral sequence. Open triangles show the distance between pairs of isolates from the same time point.

4. Rapid evolution in the wild Rapid evolution is often triggered by rapid changes of the environment. The most salient cases are due to changes induced by humans, although rapid evolution in the wild due to natural causes has also been observed. Peppered moth Biston betularia Two extreme morphs of Biston betularia, typica (light) and carbonaria (dark).

In peppered moth, the ancestral phenotype is light-gray (morph typica), which provides some protection against birds on tree trunks that are covered by lichens. In the XIX century, pollution due to coal burning killed lichens over much of England, and morph carbonaria became common in the affected areas. The difference between carbonaria and typica is due to one locus, and the dark-color allele is dominant. At mid-20 th century a steep cline of carbonaria frequency running from the north of Wales to the southern coast of England separated a region of <5% to west from >90% to northeast. At that time pollution was greatly reduced. By the 1980 s the plateau of 90% frequency of carbonaria had contracted to northern England. The frequency has since continued to drop so that the maximum is now less than 50% and in most places below 10%. There have been similar declines in Europe and North America. Evidence from surveys shows that the observed changes require 5%20% selection against carbonaria. Experiments to investigate predation by birds show a net advantage to carbonaria morphs in regions where typica frequencies were low at the time of the experiment, and a disadvantage where typica frequencies were high. This would be expected if environment and frequency were associated, and selective predation played a part in generating the association. The advantage of carbonaria was large in areas of heavy pollution where typica frequencies were 20% or less. Quart. Rev. Biol. 78, 399 -417, 2003. carbonaria frequencies at three successive times: (a) Mid-20 th century; (b) 19831984; (c) 1987 -1999.

Rapid evolution of plants Mining and industry create high local levels of soil pollution with a number of metals, including zinc, copper, and lead. A wide variety of plant species rapidly adapt to this pollution, and acquire the ability to thrive in the presence of high concentrations of metals that would be lethal to ancestral genotypes. Let us consider just one example. Arabidopsis halleri, a species that now contains a number of metallophyte (M) populations that can grow in the presence of heavy metals, as well as ancestral NM populations that cannot. Geographically isolated M populations were more genetically related to their closest NM populations than to each other. Thus, M populations have been founded separately from distinct NM populations and the evolution towards increased tolerance observed in the distinct M population groups occurred independently. This is one more example of homoplasy.

Geographic distribution of Arabidopsis halleri genotypes. Metallophyte populations are shown in red, nonmetallophyte ones in blue (Molecular Ecology 14, 4403 -4414, 2005; Genetica 112– 113, 165– 182, 2001).

Multiple origin of metallophyte Arabidopsis halleri (Brassicaceae) in central Europe. Populations of Arabidopsis halleri that are geographically close to each other are also tightly related. Thus, the ability to tolerate zinc evolved many times independently.

5. Rapid evolution of human pathogens Both emergence of new pathogens and evolution of existing pathogens are very important. Emergence of new pathogens A relatively new human pathogen Mycobacterium leprae is undergoing a massive pseudogenesation. From the outside: circles 1 and 2 (clockwise and anticlockwise) genes on the - and + strands, respectively; circles 3 and 4, pseudogenes; 5 and 6, M. leprae specific genes; 7, repeat sequences; 8, G+C content; 9, G/C bias (G+C)/(G-C).

Emergence of an infectious disease. New pathogens emerge from animal reservoirs when ecological changes increase the pathogen's opportunities to enter the human population and to generate subsequent human-to-human transmission. Effective human-to-human transmission requires that the pathogen's basic reproductive number, R 0, should exceed one, where R 0 is the average number of secondary infections arising from one infected individual in a completely susceptible population. Introductions from the reservoir are followed by chains of transmission in the human population. Infections with the introduced strain (open circles) have R 0 < 1. Pathogen evolution generates an evolved strain (filled circles) with R 0 > 1. The infections caused by the evolved strain can go on to cause an epidemic. Daggers indicate no further transmission (Nature 426, 658 -661, 2003).

Evolution of SARS coronavirus Coronavirus that causes severe acute respiratory syndrome (SARS) in humans is a pathogen of palm civets. Phylogenetic analysis suggests that there were two independent transmissions of the virus to humans, one that caused 2002 -2003 epidemic and the other that caused 2003 -2004 outbreak in the city of Guangzhou. The virus evolves very rapidly within both hosts, and the ratio of nonsynonymous/synonymous nucleotide substitution is very high, suggesting rapid adaptation of viral proteins. Major genetic variations in some critical genes, particularly the Spike gene, are essential for the transition from animal-tohuman transmission to human-to-human transmission, which eventually caused the first severe acute respiratory syndrome epidemic of 2002/2003 (PNAS 102, 2430 -2435, 2005). PC prefix is for viruses isolated from palm civet and HP for viruses isolated from human patients. Both of them were suffixed with 03 or 04 to specify the 2002– 2003 or 2003– 2004 epidemics, respectively.

Detailed phylogeny of SARS-Co. V covering the epidemics from 2002 to 2004.

Evolution of HIV Origin Because both the human immunodeficiency virus type 1 (HIV-1) and HIV-2 lineages (red branches) fall within the simian immunodeficiency viruses (SIVs) that are isolated from other primates, they represent independent cross-species transmission events. The tree and other evidence also indicate that HIV-1 groups M, N and O represent separate transfers from chimpanzees (SIVcpz), again because there is a mixing of the HIV-1 and SIV lineages. Similarly, HIV-2 seems to have been transferred from sooty mangabey monkeys (SIVsm) on many occasions (Nature Reviews Genetics 5, 5261, 2004).

Evolution After HIV was transmitted to humans, its rapid evolution, driven by immune response of infected persons, became crucial. Patterns of intra- and inter-host evolution of HIV are very different. The tree was constructed using the envelope gene-sequence data that was taken from nine HIV-infected patients (a total of 1, 195 sequences, 822 base pairs in length), with those viruses sampled from each patient depicted by a different color. Intra-host HIV evolution is characterized by continual immune-driven selection, such that there is a successive selective replacement of strains through time, with relatively little genetic diversity at any time point. By contrast, there is little evidence for positive selection at the population level (bold lines connecting patients), so that multiple lineages are able to coexist at any time point. A major bottleneck is also likely to occur when the virus is transmitted to new hosts. Progression of HIV infection to AIDS is an evolutionary phenomenon.

Evolution of Neisseria meningitidis This is a typical example of rapid evolution of a bacterial pathogen, also driven by human immune response. Some residues in the surface loops of the variable outer membrane proteins Por. B and Por. C are under very strong positive selection whereas amino acids within the loops and the membrane-spanning regions of the protein are under purifying selection, presumably because of structural constraints (Molecular Biology and Evolution 19, 1686 -1694, 2002). Ribbon diagrams of Por. B 2 (top) and Por. B 3 (bottom) with superposition of residues subject to positive selection. Residues under strong selection are shown in red and residues under weak selection are shown in yellow.

Selection among cells and cancer Within-organism selection among cancerous cells plays a key role in progression of tumors, that makes them more malignant and may be fatal. Also, selection can be used as an experimental tool for studying cancer. The most damaging change during cancer progression is the switch from a locally growing tumor to a metastatic killer. This switch is believed to involve numerous genetic changes that allow tumor cells to complete the complex series of events needed for metastasis. An in vivo selection scheme was used to select highly metastatic melanoma cells. Cells with metastatic phenotype have enhanced expression of several genes involved in extracellular matrix assembly and of genes that regulate, either directly or indirectly, the actin-based cytoskeleton. One of these, the GTPase Rho. C, enhances metastasis when overexpressed, whereas a dominant-negative Rho inhibits metastasis. (Nature 406, 532 -535, 2000). Poorly metastatic melanoma cells (line A 375 or B 16) were injected into the tail veins of host mice and pulmonary metastases were isolated. These metastases were minced and grown in tissue culture (to be injected into additional host mice). The procedure to select for highly metastatic tumor cells was repeated three times.

When mice were injected intravenously with human A 375 tumor cells, relatively few pulmonary metastases were observed. When these rare metastases were dissected free from the lungs and the cells grown in tissue culture, however, the resulting cells showed enhanced metastatic capacity, confirming that highly metastatic cells can be selected from a heterogeneous population of poorly metastatic tumor cells. Pulmonary metastases in lungs of mice injected with tumor cell lines. a, A 375 cells; b, A 375 M cells, that went through three rounds of selection. Arrows indicate representative metastatic nodules. Scale bar, 1 mm.

Quiz: What are the differences between how selection operates in the course of a) domestication, b) selection experiments, and c) evolution of captive populations?