The groundwork of classical population genetics theory by Fisher, Wright, Haldane, and others formulated in mathematical language the forces underlying microevolution - mutation, natural selection, genetic drift, assortative mating, and migration. With later contributions, the theory would also incorporate the genetics of recombination and linkage, as well as the selective dynamics of frequency dependence and other complicating processes.
The question that remained to be answered was whether this impressive body of theory could account for all the phenomena of interest to evolutionary biologists. In terms of explaining the patterns of variation and rates of change in heritable traits within populations, microevolutionary theory made enormous headway. In the modeling and prediction of adaptive intraspecific change and variation, Neo-Darwinian theory was certainly a triumph and to this day is the foundation for active research programs directed toward explaining the enormous amount of information about intraspecific genetic variation at the molecular level that has recently become available.
Where traditional population genetic models were (at least initially) found wanting was in describing the origin of species and higher taxa. The first question, that of speciation, was reconciled with population genetics theory at a qualitative level in the writings of the 'new synthesis', most significantly in the writings of the new synthesis, most significantly in the work of T. Dobzhansky. More recently, the mechanisms of both allopatric and sympatric speciation have been given a firm mathematical foundation, one which represents the complicated interactions between assortative mating, migration, and frequency-dependent selection on phenotypic traits.
While the importance of allopatric versus sympatric speciation was broadly debated and the importance of genetic drift versus adaptation in species formation was a source of contention, it was widely recognized that the mechanisms driving speciation were entirely consistent with the processes of natural selection, assortative mating, and genetic drift in classical population genetics theory. Speciation could basically be understood as the origin of pre- or postzygotic isolating mechanisms through the standard processes of microevolution. Consequently, in the Neo-Darwinian worldview, speciation is a special case of microevolutionary change, and higher taxa are defined by the phenotypic changes associated with the origin of their ancestral species (i.e., since all monophyletic higher taxa begin as single species and the morphological or molecular traits that define that higher taxon originated in the 'stem' species of the clade).
Nevertheless, speciation introduces a new dimension into the evolutionary process. Since the local adaptive evolution during the history of an ancestral species can potentially be decoupled from the changes that take place during speciation (particularly in peripatric spe-ciation where the incipient species consists of a small, isolated subpopulation separated from the ancestor), some of the most visible recent challenges to the Neo-Darwinian worldview have focused on temporal patterns of speciation and cladogenesis in the fossil record.
It has long been observed in the fossil record that discontinuities between proposed ancestor and descendant species (and between closely related higher taxa) are quite prevalent. Paleontologists, following Darwin's own treatment of the subject, had traditionally assumed that this was due to the incompleteness of the fossil record itself.
Taking into consideration the implications of the peri-patric model of speciation, S. J. Gould and N. Eldredge proposed that the observed discontinuities are often not an artifact of gaps in the stratigraphic record, but rather reflect the logical consequences of a supposedly prevalent mode of speciation. If most new species arise from small peripheral isolates rather than through a gradual transformation of a large population, then the change from ancestral to descendant morphology can be independent of the adaptive trends within the mainstream of the ancestral species' population. Furthermore, because the speciation event will involve a comparatively small marginal subpopulation, the transition is unlikely to be captured in the fossil record. What one observes instead is an ancestral species with either a static morphology, or a history characterized by random changes in phenotype unrelated to the differences between it and its descendant form. The phenomenon, combined by the subsequent sudden appearance of the descendant species, was referred to as 'punctuated equilibrium' by Eldredge and Gould.
As an empirical observation, punctuated equilibrium has been supported by a number of examples in the fossil record, although cases of phyletic gradualism (gradual transformative phenotypic evolution, as contrasted in Figure 1) from one recognized morphology-defined species to another have also been documented in many fossil taxa.
Figure 1 A schematic illustrating the assumptions of how morphology changes through time under punctuated equilibrium (left) versus phyletic gradualism (right). In the former, most change in morphology is concentrated at speciation events; in the latter, speciation is a split in a lineage whose morphology has been evolving continuously.
The question remains whether this empirical observation constitutes a new model for evolutionary change inconsistent with population genetics theory. Following the arguments of C. H. Waddington on canalization and genetic assimilation, Eldredge and Gould postulated that the long periods of stasis reflect internal developmental homeostasis while the punctuations suggest a breaking of normally canalized development. Punctuated equilibrium proponents also argue that because of the supposed importance of non- or counteradaptive changes due to genetic drift during speciation (so-called 'founder flush' speciation leading to 'genetic revolutions'), the fact that most long-term trends in a lineage are due to speciation processes rather than a clade's history would imply that adaptation plays a limited role in macroevolutionary trends.
While acknowledging the empirical reality of punctuation in the fossil record, many population genetics theorists have convincingly argued that the punctuated equilibrium pattern does not require any exotic, hitherto-unknown processes in genetics or development. Though perhaps a small number of paleontologists and stratigra-phers may have naively assumed that Darwinian evolution requires gradual, constant-rate changes through time, there is nothing in the Neo-Darwinian paradigm or population genetics theory that requires this to be the case, making the notion of a constant rate of evolution a kind of straw man.
During their history, populations can be subject to conflicting selective pressures. A relatively stable environment (or an ability to track a changing environment by changes in distribution) imposes stabilizing selection and hence stasis on phenotype, while the selective pressures that drive speciation generally involve directional selection on isolates or disruptive selection during sympatry. Indeed, the very nature of species as self-contained gene pools imposes stasis as a default and speciation as a comparatively infrequent phenomenon. Counter to the claim that evolutionary trends are nonadaptive because specia-tion is nonadaptive, speciation due to genetic drift alone has been demonstrated to be improbable and at best a rare event from both theoretical and empirical considerations. The evolutionary changes that lead to allopatric and sympatric speciation alike are generally driven by natural or sexual selection, with genetic drift usually (though not necessarily) playing a confounding role.
Thus the mechanisms involved in speciation, allopa-tric or otherwise, do not demand 'genetic revolutions' (for which there is no real empirical evidence) or any assumptions about developmental constraints, so as such the phenomenon of punctuated equilibrium does not require an explanation beyond what standard evolutionary theory already provided. In fact, a number of the original proponents of the 'strong' form of punctuated equilibrium, such as Eldredge himself, have in recent writings shown favor of this more conventional, Neo-Darwinian understanding of stasis and punctuation.
Nevertheless, the discussion of punctuated equilibrium and the distinction between 'phyletic' and 'cladogenetic' evolutionary change did lead to an evolutionary model that could not be so readily reconciled with Neo-Darwinism: the notion that species, and possibly higher taxa as well, are themselves units of selection and evolution.
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