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Codon Usage Bias

Codon Usage Bias   Reference library

Encyclopedia of Evolution

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Current Version:
2005

...melanogaster , that show aspects of both patterns. Table 2. Proportion of Leucine and Phenyalanine Codons Encoded By Their Synonymous Codons in Four Species Escherichia coli Saccharomyces cerevisiae Drosophila melanogaster Homo sapiens Codon (bacterium) (yeast) (fruit fly) (human) TTA 0.13 0.28 0.05 0.07 TTG 0.13 0.29 0.17 0.12 Leucine CTT 0.11 0.13 0.10 0.13 codons CTC 0.10 0.06 0.16 0.20 CTA 0.04 0.14 0.08 0.07 CTG 0.49 0.10 0.44 0.41 Phenylalanine TTT 0.57 0.59 0.34 0.44 codons TTC 0.43 0.41 0.66 0.56 Translational Patterns In a variety of...

Molecular Clock

Molecular Clock   Reference library

Encyclopedia of Evolution

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Subject Reference
Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
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2,874 words
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2

...17.16 ± 1.86 2 d 2 = 0.052 t 2 = 13 d 2 = 0.045 t 2 = 13 3 d 3 = 0.031 t 3 = 7.73 ± 1.03 d 3 = 0.029 t 3 = 8.38 ± 1.17 4 d 4 = 0.020 t 4 = 5.04 ± 0.86 d 4 = 0.019 t 4 = 5.60 ± 0.96 5 d 5 = 0.009 t 5 = 2.35 ± 0.64 d 5 = 0.009 t 5 = 2.65 ± 0.72 l −1796.12 −1795.35 r 1 1 1.36 Note . The data consist of the transfer RNA genes from five hominoid species: human, chimpanzee, gorilla, orangutan, and siamang. Alignment gaps are removed, with 759 nucleotides in the sequence. The model of nucleotide substitution accounts for different rates of transitions...

Fitness

Fitness   Reference library

Encyclopedia of Evolution

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Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
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2,777 words
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1

... Viability Selection on Lead Tolerance in a Plant Population Form of plant Tolerant Intolerant Numbers of seeds n 1 (50,000) n 2 (50,000) Frequencies among seeds n 1 /( n 1 + n 2 ) (0.5) n 2 /( n 1 + n 2 ) (0.5) Probabilities of surviving to maturity v 1 (0.04) v 2 (0.02) Numbers of survivors n 1 v 1 (2,000) n 2 v 2 (1,000) Frequencies among survivors n 1 v 1 /( n 1 v 1 + n 2 v 2 ) (0.667) n 2 v 2 /( n 1 v 1 + n 2 v 2 ) (0.333) Assume that tolerance is controlled by a single gene, with tolerance dominant to intolerance, and that the plant population...

Quantitative Genetics

Quantitative Genetics   Reference library

Encyclopedia of Evolution

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Subject Reference
Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
Length:
4,115 words
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4

...phenotypic variation, in combination with high V A . Table 1. Median CV A and h 2 Values and Predicted Relative Rates of Evolution under Three Kinds of Selection for Five Well-Studied Traits in Drosophila melanogaster Relative rate Trait h 2 CV A Truncation Linear Shift optimum Sternopleural bristles 0.44 8.39 1.00 0.49 0.02 Wing length 0.36 1.56 0.15 0.01 0.01 Fecundity 0.06 11.90 0.57 1.00 1.00 Longevity 0.11 9.89 0.54 0.69 0.04 Development time 0.28 2.47 0.20 0.04 0.02 source: Houle, 1992. Predicting the Response to Selection The usefulness of...

Mutation

Mutation   Reference library

Encyclopedia of Evolution

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Current Version:
2005
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Science and technology, Life Sciences, Social sciences, Anthropology
Length:
6,049 words
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3

...−5 0.15 1.10 × 10 −4 0.82 Measles virus 6.29 × 10 −5 1.00 Human rhinovirus 9.40 × 10 −5 0.67 Vesicular stomatitis virus b 9.94 × 10 −5 1.11 Retroelements Spleen necrosis virus 5.1 × 10 −6 0.04 Murine leukemia virus c 7.2 × 10 −6 ≥0.06 3.1 × 10 −5 0.26 Rous sarcoma virus 4.6 × 10 −5 0.43 Bovine leukemia virus 3.2 × 10 −6 0.027 Human immunodeficiency virus type 1 d 2.1 × 10 −6 0.19 S. cerevisiae Ty1 retrotransposon 1.9 × 10 −5 0.11 DNA based microbes Bacteriophage M13 7.2 × 10 −7 0.0046 Bacteriophage λ 7.7 × 10 −8 0.0038 Bacteriophages T2 and T4 2.4 × 10 −8 0...

Comparative Method

Comparative Method   Reference library

Encyclopedia of Evolution

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2005
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Science and technology, Life Sciences, Social sciences, Anthropology
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4,461 words
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4

...and Slopes of Regression Lines of Brain-Volume and Basal Metabolic Rate against Body Size in Mammals Variable Number of species Correlation GLS regression slope, 95% CI Theoretical expectation Brain volume 23 0.96 0.59 (0.52–0.67) 0.67–0.75 Basal metabolic rate 15 0.95 0.72 (0.60–0.84) 0.75 Correlated Evolution of Discrete Traits The discussion thus far has emphasized continuously evolving traits. In many instances, investigators wish to test hypotheses about discrete traits. Discrete or categorical-variable methods are applied to data that fall into a...

Vaccination

Vaccination   Reference library

Encyclopedia of Evolution

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Subject Reference
Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
Length:
2,814 words
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1

...Measles United Kingdom 1950s 5.0 70 15.0 93 Measles Senegal 1964 1.8 31 18.0 94 Smallpox West Africa 1960s 15.0 20 2.3 57 Smallpox India 1960s 12.5 30 3.4 70 Source: McLean, A. R. “Mathematical Modelling of the Immunization of Populations.” Reviews in Medical Virology 2 (1992): 141–152. The impact of perfect vaccines. The most straightforward situation is that of a vaccine that gives complete, lifelong protection in all recipients. While no such vaccine actually exists, the situation serves as a useful caricature in developing a theoretical description of...

Huxley, Thomas Henry

Huxley, Thomas Henry   Reference library

Encyclopedia of Evolution

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Current Version:
2005

...London, 1984. Huxley's use of fossils in the evolutionary debate. Di Gregorio, M. T. H. Huxley's Place in Natural Science . New Haven and London, 1984. The internal workings of Huxley's biology, with a detailed bibliography of Huxley's published writings. Huxley, L. , ed. Life and Letters of Thomas Henry Huxley . 2 vols. London, 1900. Original filial “life,” essential but dated. Jensen, J. V. Thomas Henry Huxley: Communicating for Science . Newark, Del., 1991. Manichean approach to Huxley's often anti-Anglican rhetoric. Lyons, S. L. Thomas Henry Huxley:...

Eugenics

Eugenics   Reference library

Encyclopedia of Evolution

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Current Version:
2005

...the only ones who may be selected against) is q 2 , which is very small when q is small. When selection discriminates perfectly and all those affected are prevented from having children, then the frequency in the subsequent generation is given by q ′ = q /(1 + q ): after n generations the frequency of q is given by q n = ( n + q −1 ) −1 . This latter formula was implicitly used in 1917 by Cambridge geneticist Reginald C. Punnett to show that, for example, a reduction in incidence from 0.1 to 0.01 percent would take about sixty-nine...

Convergent and Parallel Evolution

Convergent and Parallel Evolution   Reference library

Encyclopedia of Evolution

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Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
Length:
1,982 words
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3

...Gene of HIV-1 in Response to Drug Treatment in Patients Infected with HIV. Codon (nucleotides) Patient 10 (28–30) 54 (160–162) 71 (211–213) 82 (244–246) 90 (268–270) P4-0 CTC ATC GCT GTC TTG P4-75 ATC GTC GTT GCC ATG P5-0 CTT ATC GCT GTC TTG P5-59 ATT GTC GTT GCC ATG P6-0 CTC ATC GCT GTC TTG P6-71 ATC GTC GTT GCC ATG P7-0 CTC ATC GTT GTC TTG P7-60 ATC No change No change GCC ATG P8-0 ATC ATC GCT GTC TTG P8-72 GTC GTC No change GCC ATG Experimental Convergent Evolution One of the most exciting areas of research in convergent evolution comes from the field...

Heterozygote Advantage

Heterozygote Advantage   Reference library

Encyclopedia of Evolution

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Subject Reference
Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
Length:
4,349 words
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6

...advantage may accumulate (Mitton, 1997 ; Gillespie , 1991 ). Table 3. Heterozygous Advantage Can Accumulate from a Series of Selective Events Genotype w 1 w 2 w 3 w 4 w cum w rel AA 1.0 .4 1.0 .8 .3200 .85 Aa .7 .7 .8 .9 .3528 1.0 aa .4 1.0 .6 1.0 .2400 .68 note : w 1 through w 4 are fitnesses in selective events 1 through 4. Cumulative fitness, w cum , is the product of w 1 , w 2 , w 3 , and w 4 . Relative fitness, w rel , is obtained by dividing all of the w cum by the highest w cum . Note that the heterozygote has an intermediate...

Demography

Demography   Reference library

Encyclopedia of Evolution

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2005
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Science and technology, Life Sciences, Social sciences, Anthropology
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1,508 words
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2

...century, the population will grow or decline depending on whether λ is greater or less than one, and the population t time intervals in the future will be λ t N 0 , where N 0 is the population density at time zero. Especially when we add greater biological detail, it is often useful to replace λ by its natural logarithm r = ln(λ), in which case the population at time t is e rt N 0 . Thus when r is less than zero the population declines exponentially, while when r is greater than zero it increases exponentially. Age Structure and Stable...

Phylogenetic Inference

Phylogenetic Inference   Reference library

Encyclopedia of Evolution

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2005
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Science and technology, Life Sciences, Social sciences, Anthropology
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10,174 words
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4

...a way as to maximize L . This reveals the following values: L = 0.00325153   t 1 = 0.0000020 t 3 = 0.00000018 t 5 = 0.00000057 t 2 = 1.06  t 4 = 1.0 t 6 = 1.06 λ = 0.38 The estimated branch lengths are pleasing in that all three branches in which we infer a change to have occurred are estimated to have a length of approximately 1.0, and all the others are reconstructed to have a length of zero. The value of the rate parameter suggests a 0.5 probability of a change in a branch of length 0.548. It is easy to verify the overall likelihood and value of λ by...

Hominid Evolution

Hominid Evolution   Reference library

Encyclopedia of Evolution

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2005
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Science and technology, Life Sciences, Social sciences, Anthropology
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14,569 words
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...Homo erectus 1.9–?0.4 Myr Form of archaic Homo , known principally in Asia. Homo heidelbergensis 0.7–?0.2 Myr Robust Homo from Africa and Europe, strongly associated with mode 2 (Acheulean hand axes) technologies, showing considerable brain enlargement Homo antecessor ±0.8 Myr Controversial hominin with some modern features known from Spain Homo helmei 0.3–0.2 Myr Controversial species with larger brains and mode 3 technologies proposed as more derived ancestor of Neanderthals and modern humans Homo neanderthalensis ?0.20.027 Myr Among the best...

Microevolution

Microevolution   Reference library

Encyclopedia of Evolution

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2005

...no mutation and no selection. The Hardy–Weinberg principle states that, after one generation of mating under these circumstances, genotype frequencies in a population of diploid organisms will be p 2 + 2 pq + q 2 , where p and q refer to the properties of two different alleles at any one locus in the population, and q = 1 − p , such that p + q = 1, 0. Any significant deviation from this equilibrium distribution is an indication that microevolutionary processes are acting on the population. Five major processes contribute to microevolution:...

Prokaryotes and Eukaryotes

Prokaryotes and Eukaryotes   Reference library

Encyclopedia of Evolution

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2005
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Science and technology, Life Sciences, Social sciences, Anthropology
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2,740 words
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...S. L. , J. D. Palmer , and W. F. Doolittle . “ The Root of the Universal Tree and the Origin of Eukaryotes Based upon Elongation Factor Phylogeny. ” Proceedings of the National Academy of Sciences USA 93 (1996): 7749–7754. The analyses upon which Figure 2 in this article is based. Doolittle, W. F. “ Phylogenetic Classification and the Universal Tree. ” Science 284 (1999): 2124–2128. A beautifully written account of the author's view that horizontal gene transfer may make our attempts to produce phylogenies for organisms fundamentally flawed. Hirt, R....

Extinction

Extinction   Reference library

Encyclopedia of Evolution

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Current Version:
2005

... Table 1. Estimated Mean Duration (in Millions of Years) of Fossil Species Marine Duration (millions of years) Nonmarine Duration (million of years) Reef corals 25.0 Monocotyledonous plants 4.0 Bivalves 23.0 Horses 4.0 Benthic foraminferans 21.0 Dicotyledonous plants 3.0 Bryozoa 12.0 Freshwater fish 3.0 Gastropods 10.0 Birds 2.5 Planktic foraminiferans 10.0 Mammals 1.7 Echinoids 7.0 Primates 1.0 Crinoids 6.7 Insects 1.5 SOURCE: From compilation by M. L. McKinney .“Extinction Vulnerability and Selectivity: Combining Ecological and Paleontological Views.” ...

Transmission Dynamics

Transmission Dynamics   Reference library

Encyclopedia of Evolution

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Current Version:
2005

...but sparse in data. Cox, F. E. G. Modern Parasitology . 2d ed. Oxford, 1993. Parasitology textbook that contains detailed section on epidemiology and ecology. Levin, B. R. , M. Lipsitch , and S. Bonhoeffer . “ Population Biology, Evolution, and Infectious Disease: Convergence and Synthesis. ” Science 283 (1999): 806–809. Short review of recent applications of population biological modeling in medicine. Mims, C. , J. Playfair , I. Roitt , D. Wakelin , and R. Williams . Medical Microbiology . 2d ed. St. Louis, 1998. Short, but comprehensive, reference...

Prions

Prions   Reference library

Encyclopedia of Evolution

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Current Version:
2005

...Genetic Variation and Phenotypic Diversity. ” Nature 407 (2000): 477–483. Wickner, R. B. “ [URE3] As an Altered URE2 Protein: Evidence for a Prion Analog in Saccharomyces cerevisiae. ” Science 264 (1994): 566–569. Liming Li and Susan M. Uptain and Susan...

Bacteria and Archaea

Bacteria and Archaea   Reference library

Encyclopedia of Evolution

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Subject Reference
Current Version:
2005
Subject:
Science and technology, Life Sciences, Social sciences, Anthropology
Length:
3,133 words
Illustration(s):
2

...compounds like glucose (represented simply as CH 2 O in Figure 2), there is a broad spectrum of inorganic compounds that can be oxidized, and these oxidation reactions can be tied not only to the reduction of oxygen, but to the reduction of other inorganic and organic compounds (Figure 2). Figure 2. Microbial Respiration and Photosynthesis.Drawing by Thomas M. Schmidt. It has been suggested that the total number of bacterial and archaeal microbes on earth is approximately 10 30 , that is 1 with thirty 0s! Even if this estimate is off by several orders of...

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