Research Bibliographies, Page 3

This bibliography is like a glimpse into the past, an artefact of my time with BT’s Complex Systems Laboratory. Originally intended for internal use within a research group and later made available to the public, the bibliography has not been actively maintained since 2000.

Evolutionary Theory


Baatz, M. (1998) ‘Pleiotropy and the Evolution of Adaptability’, in Van de Vijver, et al. (1998), pp. 101-12.

Very interesting model of an evolvable epigenetic modifier system modulating pleiotropic and polygenic effects. This one merits a closer look than I’ve given it so far.

Cheverud, J. and E. Routman (1995) ‘Epistasis and its contribution to genetic variance components’, Genetics 130: 1455-61.

Principle point of interest for me is distinction between physiological and statistical views of dominance and epistasis. Physiological dominance is deviation of heterozygote phenotype value from average of the two homozygote phenotype values at one locus, while statistical dominance is taken as deviation from the linear model (deviation of single locus values from linear regression of composing alleles to genotypic values) and is dependent on genotype frequencies in the population.

Wagner, G.P.; M.D. Laubichler, and H. Bagheri-Chaichian (1998) ‘Genetic measurement theory of epistatic effects’, Genetica 102/103: 569-80. (available online)

Offers new approach to scaling of epistasis which is argued to be superior to normal treatment in population genetics, where epistasis “is often represented as a mere noise term in an additive model of gene effects” (p. 569). Includes a useful section on dominance, which begins with the distinction between the physiological and the statistical interpretation of dominance (noted, along with the analogous distinction between physiological and statistical interpretations of epistasis, by Cheverud and Routman1995).


Eigen, M. (1992) Steps Towards Life: A Perspective on Evolution. Oxford: Oxford University Press.

This is an excellent but regrettably brief book from one of the best authorities in the field. It’s organised into a series of ‘vignettes’ on theoretical issues and the details of areas of molecular biology.

Fisher, R.A. (1958) The Genetical Theory of Natural Selection, revised 2nd edn. New York: Dover Publications. (First edition published in 1929.)

One of the classics of modern evolutionary theory, this book covers areas from variation, sexual selection, and the evolution of dominance (this is the place to go for Fisher’s original position on the evolution of modifiers) to human society and social selection. There’s far too much here to cover in the time this popular book is available on interlibrary loan, so a better look will have to wait for a purchased copy.

Morowitz, H.J. (1968) Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics. London: Academic Press.

Broad early account applying, as the title suggests, principles of thermal physics to problems in biology. Introduces and justifies several important ideas, such as that energy flow alone can give rise to order in a system and that such order can only be maintained, once it arises, by continued energy flow. Includes an interesting but somewhat dated chapter on order, information and entropy.

Steele, E.J.; R.A. Lindley, R.V. Blanden, P. Davies (1998) Lamarck’s Signature: How Retrogenes are Changing Darwin’s Natural Selection Paradigm. Reading, Massachusetts: Perseus Books.

Evidence from the field of somatic hypermutation now strongly suggests that the so-called Weismann Barrier may be selectively permeable: information may flow from somatic to germline cells. More notes on this one to follow…

Stentiford, S. (to appear) ‘Evolution: The Best Possible Search Algorithm?’, to appear in Millenium Edition of the BT Technical Journal.

The question posed in the title does not find an answer in the article, although the author’s general predilection is definitely toward the affirmative. The article is principally a review of selected elements of Darwinism and basic molecular genetics, with some comments toward the end about evolution-inspired computer methods.

Life Histories

Stearns, S.C. (1992) The Evolution of Life Histories. Oxford: Oxford University Press.

This is an introductory text for life histories theory, with one half covering the basic elements of explanations of life history variation — demography, quantitative genetics, trade-offs, and lineage-specific effects — and the other covering the application of these to major life history traits — age and size at maturity, number and size of offspring, and reproductive lifespan and ageing. While certain areas are deliberately not covered (sex allocation theory, complex life histories, modular organisms, frequency-dependent life histories, etc.), the book nonetheless provides a very broad look at the field for anyone trying to understand the evolution of life history traits.


Also see sections on epistasis, on sex, and on speed of evolution, as well as section on multiploidy in GAs.

Kacser, H. and J.A. Burns (1981) ‘The molecular basis of dominance’, Genetics 97: 639-66.

Important theoretical account of dominance in terms of the kinetics of enzyme systems. Notes on this one to follow.

Kettlewell, H.B.D. (1955) ‘Selection experiments on industrial melanism in Lepidoptera’, Heredity 9: 323-42.

As far as I’m aware, this is the earliest original sources for the celebrated example of the peppered moth Biston betularia, whose rapid colour change in response to nineteenth century British industrial pollution occurred as a result of a dominance change in a single gene controlling wing colouration. The change from white wings with small black spots to black wings was not the result of a fortuitous mutation for black wings, but of the re-emergence of a previously evolved solution ‘stored’ as a recessive allele. Also see Kettlewell (1961).

Kettlewell, H.B.D. (1961) ‘The Phenomenon of Industrial Melanism in the Lepidoptera’, Annual Review of Entomology 6: 245-62.

Lewis, J. and L. Wolpert (1979) ‘Diploidy, Evolution and Sex’, Journal of Theoretical Biology 78: 425-38.

Excellent article contrasting the two paths by which haploid and diploid species may create a new gene for a new purpose through the mutation of an existing gene. Assuming that the new gene will be created on a duplicate of the old gene (since mutations which turn an existing functional gene into a new dual-purpose functional gene are rare), an important difference arises between the two cases: haploids must duplicate the original gene first and then mutate it, while the diploid can mutate an existing copy of the gene and duplicate it later during recombination. Thus, “an additional gene for a new purpose can become fixed in a haploid population only after a happy coincidence of two rare chances [duplication then mutation]; whereas in a diploid species the gene can become fixed by a two-step process, in which the two rare chances have merely to occur in sequence [mutation, then later duplication]” (p. 426). The authors observe further that “mutations which are forbidden as lethals in the haploid may be tolerated as recessive lethals in the diploid” (p. 426). The upshot is that diploids can enlarge their genomes much more easily than haploids. Later, “mutations preserved in balanced polymorphism act as a driving force for enlargement of the genome; through recombination, they lend their heterotic selective advantage to any duplication that may arise, and tend to carry it to fixation” (pp. 431-32).

Near the end of the article (pp. 432-33), the authors offer a fascinating line of reasoning about the different evolutionary pathways available to haploids and diploids with respect to gene control networks–such as may play an important role in the development of multicellular organisation. Consider a particular example where a need arises to control a gene H via an adjacent control locus L via the binding of a protein P (i.e., where the presence of such control would confer a selective advantage). They observe that there are two basic strategies: 1) evolve the original locus L0 adjacent to H so it will bind P or 2) mutate an original P0 so as to bind to locus L. The haploid will be best suited for option 1. For the diploid, however, option 2 will be available: there is already a copy of the gene responsible for P0 which can be mutated to create P without disrupting the existing function of P0. A heterozygote carrying a new variant P will be at an advantage, with the effect of the mutant P binding to control locus L ensuring dominance. Consideration of this process suggests that “haploids and diploids will gend to evolve differently in response to selection favouring the development of this sort of control over transcription” (p. 433).

Mayo, O. and R. B├╝rger (1997) ‘The Evolution of Dominance: A Theory Whose Time Has Passed?’, Biological Reviews 72: 97-110.

This comprehensive, if somewhat compressed, review article traces the idea of the evolution of dominance from R.A. Fisher in 1928 through to the present day. One upshot is that, contra Fisher, it cannot be correct “that dominance has always arisen through the accrual by natural selection of modifiers of heterozygotes” (p. 105, emphasis original). Yet at the same time, the theory of Kacser and Burns (1981), which suggests that there is no need at all to explain the phenomenon of dominance by inferring that it has evolved, also does not fully accommodate all the evidence. In the end, the authors conclude about the range of apparently conflicting available theories that they “provide explanations at different levels of the phenotype, and as such all may be of some use” (p. 105). This is an excellent entry point for the literature, with plenty of references to other important work in the history of ideas about the evolution of dominance.

Paquin, C. and J. Adams (1983) ‘Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations’, Nature 302: 495-500.

Contrasts two positions on adaptive significance of diploidy: 1) greater variability and 2) capacity to mask deleterious recessive mutations. Suggests instead that adaptive significance is the capacity for faster adaptation to new environments. Despite poorly justified assumption that >50% of adaptive mutations are expressed in the heterozygous state (on the grounds that advantageous mutations should be dominant — likely and probably true but in need of better justification than the authors provide), empirical data show a significantly higher fixation of adaptive mutations for diploids than haploids of the single-celled eukaryote Saccharomyces cerevisiae — which has both stable haploid and diploid phases. Includes interesting background on the tracking of selectively favoured genes through the observation of the frequency of an unrelated neutral mutation, thus making it possible to track adaptive mutations without knowing their phenotypic expressions.

Soltis, D.E. and P.S. Soltis (1999) ‘Polyploidy: Recurrent Formation and Genome Evolution’, Trends in Ecology & Evolution 14(9): 348-52.

Review of recent work on polyploidy suggesting that most polyploid species have formed multiple times from different populations of their diploid progenitors. Subsequent hybridization between populations of different origins can be a great source of variation. Authors suggest polyploidization may be viewed as transilience, “a period during which the genome is more amenable to or tolerant of change, such as recombination” (p. 351), noting that divergent genomes within a common polyploid nucleus may be a source of stress genomic stress which may facilitate rapid evolution. Article also discusses this process of rapid and radical genomic restructing after polyploidization and the role of transposons in the evolution of gene silencing mechanisms.

Philosophical Emphasis

Dennett, D.C. (1995) Darwin’s Dangerous Idea: Evolution and the Meanings of Life. London: Simon & Schuster.

Uncharacteristically wordy treatment of evolution by natural selection with a pan-adaptationist flavour. A few technical pitfalls mar what is an otherwise useful text, even if it does unwittingly rehash Schilcher and Tennant (1984) somewhat. See the 1997 Philosophical Books 38(2): 81-89 for my review of the book, with Dennett’s reply pp. 89-92.

Gray, R.D. (to appear) ‘Selfish genes or developmental systems? Evolution without replicators and vehicles’, to appear in Singh, et al.

Extended philosophical critique of genic selectionism from the viewpoint of developmental systems theory. Apart from some comments in the last few pages partly directed at Philip Kitcher, it is unclear how seriously Gray expects practicing scientists to take the debate; it is tempting to think the arguments will attract the interest mainly of philosophers, although Gray does offer a few thoughts as to why research scientists might care as well.

Gray, R.; P. Griffiths, and S. Oyama (2000) Cycles of Contingency. Cambridge: MIT Press.

von Schilcher, F. and N. Tennant (1984) Philosophy, Evolution and Human Nature. London: Routledge & Kegan Paul.

Now looking a little dated, this book was well ahead of its time and anticipated many of the ideas later explored to good effect in Dennett (1995). Written by a biologist and a philosopher, the book is by no means of interest just to philosophers. More than one third of the book is devoted to introducing and explicating the modern theory of evolution by natural selection, and for this reason it makes a very useful introduction to the field and its theoretical terrain. The remaining three chapters after the introduction to evolution cover sociobiology, evolutionary epistemology, and the evolution of language.

Singh, R.; K. Krimbas, D. Paul and J. Beatty, eds. (to appear) Thinking about Evolution: Historical, Philosophical and Political Perspectives: Festschrift for Richard Lewontin. Cambridge: Cambridge University Press.

Sterelny, K. (2000) ‘Niche Construction, Developmental Systems and the Extended Replicator’, to appear in Gray, et al. (2000).

This is an outstanding example of how clear philosophical/theoretical analysis can bear usefully on scientific thinking about evolution. Sterelny outlines a set of properties characterising evolvable inheritance systems and then analyses both genetic mechanisms and environmental engineering within the context of those properties, with extra attention to the extent to which such mechanisms may be interpreted as information carriers. This is an excellent critical introduction to ideas from developmental systems theory and to ideas related to the view of genetic inheritance as information flow.

Van de Vijver, G.; S.N. Salthe and M. Delpos, eds. (1998) Evolutionary Systems. Dordrecht: Kluwer Academic.

This collection has many very promising titles, but many of the articles themselves turn out to be too short on quantitative conclusions to excite too much interest from those approaching evolutionary systems from a scientific perspective.

Population Genetics

Hartl, D.L. and A.G. Clark (1989) Principles of Population Genetics, 2nd edition. Sunderland, Massachusetts: Sinauer Associates.

Source for viability selection model which allows exploration of selection-based behaviour while avoiding complexities introduced by fitness. Appealed to in Bidwell’s (1996) treatment of diploidy in GAs.

RNA Folding & Neutrality

For references on neutrality specifically in an artificial, as opposed to natural setting, please see entries under Evolutionary Algorithms.

Schuster, P. (1997) ‘Landscapes and molecular evolution’, Physica D 107: 351-65.

Very straightforward & easy to understand article reporting on modelling & analysis of the space of 2D RNA secondary structure (i.e., mathematically simpler pseudo-structure of folded RNA sequences) and how it relates to sequence space. Sequences folding into the same secondary structure are nearly randomly distributed in sequence space. This, combined with the fact that some 93% of the sequence space analysed folded into a set of ‘common’ structures — where ‘common’ denotes a structure formed by more sequences than the average structure — means that within a comparatively small Hamming radius of a given sequence, there exists on average at least one sequence for every common structure. This radius grows linearly with chain length, with a coefficient of about 1/4. Thus while the number of sequences within the radius grows exponentially with sequence length, it also shrinks exponentially as a fraction of the total sequence space. Persuasive observations on the crucial role of neutral evolution.

Wolynes, P.G. and W.A. Eaton (1999) ‘The Physics of Protein Folding’, Physics World 12(9): 39-44.

Discusses experimental and theoretical approaches to understanding how a single amino acid sequence can fold into myriad different 3D conformations. Particularly interesting is the description of energy landscapes, frustration, and single dominant energy funnels (for proteins which easily acquire a particular conformation) vs. complex funnels with many local minima.


Also see section on multiploidy.

Brooks, R. and M.D. Jennions (1999) ‘The Dark Side of Sexual Selection’, Trends in Ecology & Evolution 14(9): 336-37.

This ‘News & Comment’ section from TREE reviews recent work on the hidden costs of sexual selection in terms of intersexual conflict.

Crow, J.F. and M. Kimura (1965) ‘Evolution in Sexual and Asexual Populations’, American Naturalist 99: 439-50.

This very cleanly written article compares evolution in sexual and asexual populations vis-a-vis the rate at which favourable gene combinations can be fixed, considering the effects of gene interaction, mutation rate, population size, and magnitude of a mutation’s effect. Observes that “the advantage of a reproductive system that permits free recombination is greatest for the incorporation of mutant genes with individually small effects, occurring at relatively high rates, and in large population” (p. 443). Also, “sexual reproduction can be a disadvantage if evolution progresses mainly by putting together groups of individually deleterious, but collectively beneficial mutations. …if this type of gene action were the limiting factor in evolution at the time sexual reproduction first evolved, sexual recombination might never have been ‘invented'” (p. 445). And “The type of gene that is most efficiently selected in a sexual population is one that is beneficial in combination with a large number of genes” (p. 446). On haploidy vs. diploidy, “when the population has reached equilibrium as a haploid, a change to diploidy offers an immediate advantage (Muller 1932). …when the population reaches a new diploid equilibrium the advantage is lost. …Thus, it is easy to see how diploidy might evolve from haploidy, even if the population did not gain any permanent benefit therefrom” (p. 448, emphasis my own). Also mentions possibility that diploidy functions to protect against effects of somatic mutation, protection which would be more important for organisms which are large and complicated.

Muller, H.J. (1932) ‘Some Genetic Aspects of Sex’, American Naturalist 8: 118-38.

Mentioned by Crow and Kimura (1965) as an earlier source for the idea that a change to diploidy offers an immediate advantage for a population which has reached equilibrium as a haploid.

Speed of Evolution

Also see section on multiploidy in evolution as well as section on information, complexity and entropy.

Reznick, D.N.; F.H. Shaw, F.H. Rodd, R.G. Shaw (1997) ‘Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata)’, Science 275: 1934-36.

Report on extended studies of guppy populations in Trinidad reveals a capacity for much higher rates of evolutionary adaptation than that normally inferred from the fossil record. As they put it, “sustained directional selection can support far more rapid directional change than seen in the fossil record” (p. 1936). Authors suggest that results are entirely compatible with the low rate evidenced by the fossil record because such records are effectively averages over periods which might include periods of stasis, periods of rapid change, and even periods of reversal of change. Note that differences in rate of evolution explored here are principally attributable to differences in heritabilities of the traits under selection; fastest evolution was a result of their being more genetic variation on which natural could act.

Wagner, G.P. (1981) ‘Feedback selection and the evolution of modifiers’, Acta Biotheoretica 30: 79-102.

Author notes that modifier theory may be viewed as “a population genetic prerequisite for an explanation of so-called major evolutionary steps” (p. 100), citing work by Frazzetta, by Rechenberg, and by Reidl in support of the view that “the evolution of complex morphological characters is only possible if the structure of the genome is currently optimized in order to allow a maximum speed of adaptation” (p. 100). Wagner suggests that ‘feedback selection’, a positive feedback loop between the evolution of a phenotypic character and the speed of evolution of that character, fills this role. Paper considers view that modifier evolution may be interpreted as a result of selection for adaptation speed in populations far from equilibrium. This ‘feedback selection’ occurs when the “modifying influence of the secondary allele…enhance[s] the selection of its primary allele. This advantage feeds back on the selection of the modifier gene, forming a positive feedback loop” (p. 81). The general model of feedback selection depends on the notion of ‘dispositive genes’ which influence the disposition of a population in response to a particular variety of selection pressure. Wagner defines the dispositive gene as a genetic unit which “i) is able to enhance the speed of certain genetic adaptation processes and ii) has virtually no influence on the mean fitness of the population after the adaptation process is completed” (p. 81).

Worden, R.P. (1995) ‘A Speed Limit for Evolution’, Journal of Theoretical Biology 176: 137-52.

Derives very restrictive upper bound on the rate of a population’s accumulation of information about the environment as displayed in spread of phenotypic characteristics (“genetic information in the phenotype”, or GIP). The treatment rests on a partitioning of phenotypic characteristics which would be challenging to apply in empirical settings, and the notion of GIP does not appear to distinguish between full allele fixation on a sub-optimal local fitness peak and fixation on a global optimum. More complete critical review of this work is included in a paper currently under development.

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