Category Archives: Comparative Genomics

Evo-Devo and Arrival of the Fittest

The molecular mechanisms that bring about biological form in modern-day embryos … should not be confused with the causes that led to the appearance of these forms in the first place … selection can only work on what already exists. (G. B. Muller and S. A. Newman 2003: 3, Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology)

Cited in Minelli and Fusco 2008: xv. Evolving Pathways: Key Themes in Evolutionary Developmental Biology.

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The evolution of organismal form consists of a continuing production and ordering of anatomical parts: the resulting arrangement of parts is nonrandom and lineage specific. The organization of morphological order is thus a central feature of organismal evolution, whose explanation requires a theory of morphological organization. Such a theory will have to account for (1) the generation of initial parts; (2) the fixation of such parts in lineage-specific combinations; (3) the modification of parts; (4) the loss of parts; (5) the reappearance of lost parts [atavism]; and (6) the addition of new parts. Eventually, it will have to specify proximate and ultimate causes for each of these events as well.

Only a few of the processes listed above are addressed by the canonical neo-Darwinian theory, which is chiefly concerned with gene frequencies in populations and with the factors responsible for their variation and fixation. Although, at the phenotypic level, it deals with the modification of existing parts, the theory is intended to explain neither the origin of parts, nor morphological organization, nor innovation. In the neo-Darwinian world the motive factor for morphological change is natural selection, which can account for the modification and loss of parts. But selection has no innovative capacity; it eliminates or maintains what exists. The generative and the ordering aspects of morphological evolution are thus absent from evolutionary theory.

— Muller, Gerd B. (2003) Homology: The Evolution of Morphological Organization. In Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology. (eds., Gerd B. Muller and Stuart A. Newman). The Vienna Series in Theoretical Biology. MIT Press. p. 51.

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What is evo-devo? Undoubtedly this is a shorthand for evolutionary developmental biology. There, however, agreement stops. Evo-devo has been regarded as either a new discipline within evolutionary biology or simply a new perspective upon it, a lively interdisciplinary field of studies, or even necessary complement to the standard (neo-Darwinian) theory of evolution, which is an obligate step towards an expanded New Synthesis. Whatever the exact nature of evo-devo, its core is a view of the process of evolution in which evolutionary change is the transformation of (developmental) processes rather than (genetic or phenotypic) patterns. Thus our original question could be more profitably rephrased as: What is evo-devo for? (Minelli and Fusco 2008: 1)

(….) Evo-devo aims to provide a mechanistic explanation of how developmental mechanisms have changed during evolution, and how these modifications are reflected in changes in organismal form. Thus, in contrast with studies on natural selection, which aim to explain the ‘survival of the fittest’, the main target of evo-devo is to determine the mechanisms behind the ‘arrival of the fittest’. At the most basic level, the mechanistic question about the arrival of the fittest involves changes in the function of genes controlling developmental programs. Thus it is important to reflect on the nature of the elements and systems underlying inheritable developmental modification using an updated molecular background. (Minelli and Fusco 2008: 2)

The Evolution of the Genome

The biggest intellectual danger of any evolutionary research is the temptation to find satisfaction in ingenious “just so” stories. Devo-evo, as the youngest member of the evolutionary sciences, is in particular danger of falling into this trap, as other branches of evolutionary biology did in the past. (Laubichler and Maienschein 2007: 529).

(….) One of the main sources of intellectual excitement in devo-evo is the prospect of understanding major evolutionary transformations. If developmental evolution were to focus exclusively on microevolutionary processes, the field would abandon that major objective. In other words, even a very successful microevolutionary approach to developmental evolution would not fulfill the expectations that have been raised: bridging the gap between evolutionary genetics and macroevolutionary pattern. (Laubichler and Maienschein 2007: 530)

— Laubichler and Maienschein 2007: 529. In Embryology to Evo-Devo: A History of Developmental Evolution.

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Darwin has often been depicted as a radical selectionist at heart who invoked other mechanisms only in retreat, and only as a result of his age’s own lamented ignorance about the mechanisms of heredity. This view is false. Although Darwin regarded selection as the most important of evolutionary mechanisms (as do we), no argument from opponents angered him more than the common attempt to caricature and trivialize his theory by stating that it relied exclusively upon natural selection. In the last edition of the Origin, he wrote (1872, p. 395):

As my conclusions have lately been much misrepresented, and it has been stated that I attribute the modification of species exclusively to natural selection, I may be permitted to remark that in the first edition of this work, and subsequently, I placed in a most conspicuous position–namely at the close of the introduction—the following words: “I am convinced that natural selection has been the main, but not the exclusive means of modification.” This has been of no avail. Great is the power of steady misinterpretation.

Charles Darwin, Origin of Species (1872, p. 395)

— Gould, Stephen J., & Lewontin, Richard C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON, SERIES B, VOL. 205, NO. 1161, PP. 581-598.

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Dichotomy is both our preferred mental mode, perhaps intrinsically so, and our worst enemy in parsing a complex and massively multivariate world (both conceptual and empirical). Simpson, in discussing “the old but still vital problem of micro-evolution as opposed to macro-evolution” (ref. 10, p. 97), correctly caught the dilemma of dichotomy by writing (ref. 10, p. 97): “If the two proved to be basically different, the innumerable studies of micro-evolution would become relatively unimportant and would have minor value for the study of evolution as a whole.”

Faced with elegant and overwhelming documentation of microevolution, and following the synthesist’s program of theoretical reduction to a core of population genetics, Simpson opted for denying any distinctive macroevolutionary theory and encompassing all the vastness of time by extrapolation. But if we drop the model of dichotomous polarization, then other, more fruitful, solutions become available.

— Gould, Stephen Jay. Tempo and mode in the macroevolutionary reconstruction of Darwinism. National Academy of Sciences Colloquim “Tempo and Mode in Evolution”; 1994 Jul: 6767-6768. Emphasis added.

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If Darwin were alive today, I have no doubt his love of truth would lead him to follow the evidence—the facts—wherever they might chance to lead. Darwin was not a dogmatist, but he was dogged in pursuing facts and duly humble in his theoretical interpretations of them. The question of real import is not whether natural selection is a real phenomenon, for it is (aside from its reification into a ‘thing’, which it is not), but whether it is the source of novelty. There is no doubt that we can through artificial selection bring forth existing phenotypic plasticity (e.g., shifting the number of hairs on a fruit fly) ; but that is merely tweaking already existing features similar to how the environment brings about morphological changes due to phenotypic plasticity, the former being artificial, while the latter natural. Natural selection reveals how nature sifts the survival of the fittest, but theoretically speaking, tells us nothing when used as the basis for an unwarranted extrapolation about the arrival of the fittest. When science has mastered the arrival of the fittest we will have mastered evolution itself.

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At some point, such heritable regulatory changes will be created in a test animal in the laboratory, generating a trait intentionally drawing on various conserved processes. At that point, doubters [of organic evolution] would have to admit that if humans can generate phenotypic variation in the laboratory in a manner consistent with known evolutionary changes, perhaps it is plausible that facilitated variation has generated change in nature.

— Gerhart, C. and Kirschner Marc W. The Plausibility of Life: Resolving Darwin’s Dilemma. New Haven: Yale University Press; 2005; p. 237. Emphasis added.

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Natural selection does not act on anything, nor does it select (for or against), force, maximize, create, modify, shape, operate, drive, favor, maintain, push, or adjust. Natural selection does nothing. Natural selection as a natural force belongs in the insubstantial category already populated by the Becker/Stahl phlogiston or Newton’s “ether.” ….

Having natural selection select is nifty because it excuses the necessity of talking about the actual causation of natural selection. Such talk was excusable for Charles Darwin, but inexcusable for evolutionists now. Creationists have discovered our empty “natural selection” language, and the “actions” of natural selection make huge vulnerable targets. (Provine 2001: 199-200)

Provine, William B. The Origins of Theoretical Population Genetics. Chicago: Chicago University Press; 2001; c1971 pp. 199-200. Emphasis added.

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The Epigenetic System of Heredity and Phenotypic Variation

In response to various environmental stimuli metazoans develop a wide variety of discrete biological adaptations, new phenotypic characters, without changes in genes and genetic information. Such abrupt emergence or new morphological and life history (as well as physiological and behavioral) characters requires information. The fact that the genetic information does not change, implies that information of a type other than genetic information is responsible for the development of those characters.

(…) [T]he CNS, in response to external stimuli, releases specific chemical signals, which start signal cascades that result in adaptive morphological and physiological changes in various organ or parts of the body. In other words, information for those adaptations flows from the CNS to the target cells, tissues and organs. … [I]t was also proven the nongenetic, computational nature and origin of that information.

The CNS generates its information by processing the input of external stimuli. As defined in this work, a stimulus is a perceptible change in an environmental agent to which the CNS responds adaptively. Changes in the environment may be as big as to cause stress condition and radical changes in environment are often associated with adaptive changes in morphology. (Cabej 2004: 209)

Cabej, Nelson R. Neural Control of Development: The Epigenetic Theory of Heredity. New Jersey: Albanet; 2004; p. 209.

Natural selection is today, understood in the context of what we now know, a description of the relationship between an organism’s phenotypic plasticity and its environment. This relationship can be empirically observed, both in nature and the laboratory, shifting existing features and attributes of an organism, by selectively altering gene frequencies in the lab, or by observing phenotypic responses to environmental signals in nature.

Macroevolution and the Genome

There are many ways of studying the mechanisms and outcomes of evolution, ranging from genetics and genomics at the lowest scales through to paleontology at the highest. Unfortunately, the division into specialties according to scale has often led to protracted disagreement among evolutionary theorists from different disciplines regarding the nature of the evolutionary processes. Although the resulting debate has undoubtedly led to a refinement of the various theoretical approaches employed, it has also prevented the development of a complete and unified theory of evolution. Without such a theory, all evolutionary phenomena, including those involving features of the genome, will remain at best only partially understood. (….) The goal … is to provide an expansion, not a refutation, of existing evolutionary theory, and to build some much-needed bridges across traditionally disparate disciplines. (Gregory 2005: 679-680)

From Darwin to Neo-Darwinism

Charles Darwin did not invent the concept of evolution (“descent with modification” or “transmutation,” in the terminology of his time). In fact, the notion of evolutionary change long predates Darwin’s (1859) contributions in On the Origin of Species, which were essentially twofold: (1) providing extensive evidence, from a variety of sources, for the fact that species are related by descent, and (2) developing his theory of natural selection to explain this fact. Although quite successful in establishing the fact of evolution (the subsequent Creationist movement in parts of North America notwithstanding), Darwin’s explanatory mechanism of natural selection received only a lukewarm reception in contemporary scientific circles. (Gregory 2005: 680)

By the beginning of the 20th century, Darwinian natural selection had fallen largely out of favor, having been overshadowed by several other proposed mechanisms including mutationism, whereby species form suddenly by single mutations, with no intermediates; saltationism, in which major chromosomal rearrangements generate new species suddenly; neo-Lamarckism, which supposed that traits are improved directly through use and lost through disuse; and orthogenesis, under which inherent propelling forces drive evolutionary changes, sometimes even to the point of being maladaptive. Mutationism, in particular, gained favor after the rediscovery of Mendel’s laws of inheritance by Hugo de Vries and others, which showed heredity to be “particulate”—with individual traits passed on intact, even if hidden for a generation—rather than “blending,” as Darwin had believed. Particulate inheritance was taken by de Vries and others to imply that discontinuous variation in traits would be much more important than continuous variability expected under gradual Darwinian selection. (Gregory 2005: 680-681)

The problem faced by proponents of Darwinism was to reconcile the concept of discrete hereditary units with the graded variation required by natural selection. This issue was settled in the 1930s and 1940s with the advent of population genetics, which provided mathematical models to describe the behavior of genic variants (“alleles”) within populations, and showed that a particulate mechanism of inheritance did not prohibit the action of natural selection. This new theoretical framework is generally know as “neo-Darwinism” or the “Modern Synthesis,” because it sought to synthesize (i.e., combine) Mendelian genetics and Darwinian natural selection. (Gregory 2005: 681)

The first stage in the development of population genetics was to determine how alleles segregate within populations under “equilibrium” conditions. The issue was addressed by H.G. Hardy and Wilhelm Weinberg, resulting in what is now know as the “Hardy-Weinberg equilibrium,” a null hypothesis about the behavior of alleles in population that are not subject to natural selection, genetic drift (random changes in allele frequencies, for example by the accidental loss of a subset of the population, passage through a population bottleneck, or the founding of a new population by an unrepresentative sample of the parental population), gene flow (an influx of alleles from other populations by migration), or mutation (the generation of new alleles). When populations are not in Hardy-Weinberg equilibrium, one can begin to investigate which of these processes is (or are) responsible. More complex population genetics models were developed for dealing with this issue, most notably by Ronald Fisher, Sewall Wright, and J.B. Haldane. Others, like Theodosius Dobzhansky and G.L. Stebbins, established that natural populations contain sufficient genetic variation for these new models to work. (Gregory 2005: 681)

According to Provine (1988), the Modern Synthesis was really more of a “constriction” than an actual “synthesis,” in which a major goal was the elimination of the non-Darwinian alternatives listed previously and the associated restoration of selection to prominence in evolutionary theory. In at least one important sense, the term “synthesis” is clearly a misnomer, given that there remained a highly acrimonious divide between Fisher, who favored models based on large populations with a dominant role for selection, and Wright, whose “adaptive landscape” model dealt primarily with small populations and emphasized genetic drift. Despite these divisions, neo-Darwinians did succeed in narrowing the range of explanatory approaches to those involving mutation, selection, drift, and gene flow. (Gregory 2005: 681)

Genomes, Fossils, and Theoretical Inertia

As far as genetics is concerned, evolutionary theory has always been far ahead of its time. Darwin’s theory of natural selection was developed in the absence of concrete knowledge of hereditary mechanisms, and the mathematical framework of neo-Darwinism was assembled before the structure of DNA had been established (and even before DNA was identified as the molecule of inheritance). As a consequence, numerous surprises, puzzles, and conflicts have emerged from new discoveries in genetics and genomics. Consider, for example, the recent findings of deep genetic homology undergirding “analogous” features of unrelated organisms, the role of clustered master control genes in regulating development, the remarkable low gene numbers in humans, the collapse of the “one gene-one protein” model, the extraordinary abundance of transposable elements in the genomes of humans and other species, and the increasing evidence for the role of large-scale genome duplications in evolution. Also recognized for decades (and still the subject of healthy debate) are the importance of smaller-scale gene duplications, the role recurrent hybridization and polyploidy, the preponderance of neutral evolution at the molecular level, and the initially quite alarming disconnect between genome size and organismal complexity. Advances in genetics and genomics have also provided revolutionary insights into the relationships among organisms, from the smallest scales (e.g., human-chimpanzee genetic similarity) to the largest (e.g., deep divergences between “prokaryote” groups). None of these was (or indeed, could have been) predicted or expected by the accepted formulation of evolutionary theory that preceded it. This historical record in evolutionary biology is that theories are developed under assumptions about the existence—or perhaps more commonly, the absence—of certain genetic mechanisms, and must later be revised as new knowledge comes to light regarding genomic structure, organization, and function. This mode of progress is not necessarily problematic, except when theoretical inertia forestalls the acceptance of the new information and its implications. (Gregory 2005: 682)

Genomics is not the only field to have faced theoretical inertia. For decades, prominent paleontologists have argued that their observations of the fossil record fail to fit the expectations of strict Darwinian gradualism. Darwin’s view of speciation, sometimes labeled as “phyletic gradualism,” was based on the slow, gradual (but not necessarily constant) evolution of one species or large segments thereof into another through a series of imperceptible changes, often without any splitting of lineages (i.e., by “anagenesis”). By contrast, the theory of “punctuated equilibria” (“punk eek” to afficionados,” “evolution by jerks” to some critics) proposes that most species experience pronounced morphological stasis for most of their time, with change occurring only in geologically rapid bursts associated with speciation events (Eldredge and Gould, 1972; Gould and Eldredge, 1977, 1993; Gould, 1992, 2002). Moreover, speciation in this second case involves the branching off of new species (“cladogenesis”) via small, peripherally isolated populations rather than the gradual transformation of the parental stock itself. (Gregory 2005: 682-683)

Based on differences such as these, many of those who study evolutionary patterns in deep time have developed alternative theoretical approaches to account for the large-scale features of evolution. This, too, has generally proceeded with a minimal consideration of genomic information, and as such there is a need for increased communication between these two fields. In fact, despite their residence at opposite ends of the spectrum in evolutionary science, there is great potential for intergration between genomics and paleontology because ultimately both are concerned with variation among species and higher taxa. (Gregory 2005: 683-684)


Microevolution, Macroevolution, And Extrapolationism

The extent to which processes observable within populations and tractable in mathematical models can be extrapolated to explain patterns of diversification occurring in deep time remains one of the most contentious issues in modern evolutionary biology. This is a debate with a lengthy pedigree, extending back more than 75 years, and therefore long predating any of the issues of genome evolution … Nevertheless, genomes reside at an important nexus in this debate by containing the genes central to population-level discussions, but also having their own complex large-scale evolutionary histories. (Gregory 2005: 684)

Writing as an orthogeneticist in 1927, prior to the Modern Synthesis when Darwinian natural selection was largely eclipsed as a mechanism of evolutionary change, Iurii Filipchenko made the following argument:

Modern genetics doubtless represents the veil of the evolution of Jordanian and Linnaean biotypes (microevolution), contrasted with the evolution of higher systematic groups (macroevolution), which has long been of central interest. This serves to underline the above-cited consideration of the absence of any intrinisic connection between genetics and the doctrine of evolution, which deals particularly with macroevolution.

[Translation as in Hendry and Kinnison, 2001].

In modern parlance, microevolution represents the small-scale changes in allele frequencies that occur within populations (as studied by population geneticists and often observable over the span of a human lifetime), whereas macroevolution involves the generation of broad patterns above the species level over the course of Earth history (as studied in the fossil record by paleontologists, and with regard to extant taxa by systematists). … Dobzhansky (1937, p. 12) noted that because macroevolution could not be observed directly, “we are compelled at the present level of knowledge reluctantly to put a sign of equality between the mechanisms of macro- and micro-evolution.” However, although Dobzhansky was tentative in his assertion of micro-macro equivalence, the doctrine of “extrapolationism” was embraced as a fact by many other architects and early adherents of the Modern Synthesis. Thus as Mayr (1963, p. 586) later explained, “the proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and the events that take place within populations and species” (emphasis added). There was an obvious reason for this strict adherence to extrapolationism at the time, namely the belief that if micro- and macroevolution “proved to be basically different, the innumerable studies of micro-evolution would become relatively unimportant and would have minor value in the study of evolution as a whole” (Simpson, 1944, p. 97). As such, only proponents of non-Darwinian mechanisms, most notably the much-maligned saltationist Richard Goldschmidt (1940, p. 8), argued at the time that “the facts of microevolution do not suffice for an understanding of macroevolution.” (Gregory 2005: 684-685)

Obviously, the “present level of knowledge” is not the same today as it was in Dobzhansky’s time. A great deal of new information has since been gleaned—and continues to accrue—regarding the mechanisms of heredity and the major patterns of evolutionary diversification. Considering Mayr’s statement, it is now clear that not all relevant genetic changes are small (cf., genome duplications), nor is all change guided by natural selection (cf., neutral molecular evolution), nor do all relevant processes operate within populations and species (cf., hybridization). In one of the more notorious exchanges on the subject, Gould (1980) went so far as to declare this simple version of the neo-Darwinian synthesis as “effectively dead, despite its persistence as textbook orthodoxy.”1 To be more specific, this applies not to the Modern Synthesis at large, but to strict extrapolationism. Using a far less aggressive tone, another prominent macroevolutionist put it as follows: “The advances in molecular biology contribute to the need for a formal expansion of evolutionary theory is an exigency we can hardly hold against the early architects of the synthesis” (Eldredge, 1985, p. 86), it is interesting to imagine the view that Fisher, Dobshansky, Haldane, Wright, or even Darwin might have taken had they been privy to modern insights. (Gregory 2005: 685-686)

Simpson’s (1944) account of the threat to the relevance of microevolution is also in need of revision. It is simply not the case that a mechanistic disconnect between micro- and macroevolution would render microevolutionary study obsolete. Far from it, because any genomic changes, regardless of the magnitude of their effects, must still pass through the filters of selection and drift to reach a sufficiently high frequency if they are to be of evolutionary significance. So, even if understanding this filtration process does not, by itself, provide a complete understanding of macroevolution, it would still be a crucial component of an expanded evolutionary theory. Consider, for example, the topic of major developmental regulation genes, which involves at least four different questions, all mutually compatible, studied by four different disciplines: (1) Evolutionary developmental biology (“evo-devo”)—How do such genes act to produce observed phenotypes? (2) Comparative genomics—What is the structure of these genes, and what role did processes like gene (or genome) duplication play in their evolution? (3) Population genetics—How would such genes have been filtered by selection, drift, and gene flow to reach their current rate of fixation? (4) Paleontology—What is the relevance of these genes for understanding the emergence of new body plans and thus new macroevolutionary trajectories (e.g., Carroll, 2000; Erwin, 2000; Jablonski, 2000; Shubin and Marshall, 2000)? (Gregory 2005: 686)

Though the protagonists have often been divided along these professional lines, the micro-macro debate is not between paleontologists and population geneticists per se. Rather, it is between strict extrapolationists who argue that all evolution can be understood by studying population-level processes and those who argue that there are additional factors to consider. Members of this latter camp may come from all quarters of evolutionary biology, from genome biologists to paleontologists, although the latter have been by far the most vocal proponents of an expanded outlook. For strict extrapolationists, there may be little value in pursuing this debate. But for those open to a more pluralistic approach who seek a resolution to the issue, there is much value in understanding the arguments presented in favor of a distinct macroevolutionary theory that coexists with, but is not subsumed by, established microevolutionary principles. (Gregory 2005: 686)

Critiques of Strict Extrapolationism

1 Of course, far from simply mourning their loss, microevolutionists responded to this charge with some vigor (e.g., Stebbins and Ayala, 1981; Charlesworth et al., 1982; Hecht and Hoffman, 1986), perhaps overlooking the fact that only the strict extrapolationist definition given by Mayr (1963), and not the synthesis in its entirety, was proclaimed deceased (see Gould, 2002). Although some may argue that Mayr’s (1963) definition was already outdated by this time, and that Gould’s (1980) criticism was therefore misplaced, it bears noting that such a definition had been in common use throughout the period in question and well beyond (e.g., Mayr, 1980; Ruse, 1982; Hecht and Hoffman, 1986). As for Gould’s (1980) claim of “‘textbook orthodoxy,’ one may consider Freeman and Herron’s (1998) recent textbook, which considers the Modern Synthesis to be composed of two main postulates: “[1] Gradual evolution results from small genetic changes that are acted upon by natural selection. [2] The origin of species and higher taxa, or macroevolution, can be explained in terms of natural selection acting on individuals, or microevolution.” Futuyma’s (1998) more advanced text provides a much more detailed description of the Modern Synthesis but the fundamental extrapolationist point remains.