Implicit in the work of Eldredge and Gould's original papers and explicit in S. M. Stanley's treatment of the subject is the connection of punctuated equilibrium with the concept of 'species selection'. The basic argument is that just like genes and individual organisms, species can reproduce (through speciation) and exhibit heritable variation (i.e., covariance between ancestral and descendant species traits). The basic idea is that certain traits relating to dispersal ability, tendencies toward habitat specificity, etc., predispose some taxa to have high rates ofspeciation, while other taxa have ecological or behavioral traits that make speciation infrequent.
From this perspective, the reason some clades have been species rich throughout their history and others species poor is not due to members of one clade having traits that lead to higher Darwinian fitness at the individual or population level, but rather because the species-rich clade consists of species that themselves are likely to speciate at an enhanced rate. At some level, the argument has intuitive appeal - it makes little sense to argue that individuals from species-rare 'living fossils' such as horseshoe crabs are 'unfit' when compared to individuals from, for example, species-rich beetles. It is more likely that there is something about the ecology of phytophagous insects that makes them speciate at higher rates than generalist benthic marine invertebrates. D. Jablonski and other paleontologists have proposed that generalist or eurytopic taxa will tend to be less species rich than specialist or stenotopic taxa. Specific habitat requirements tend to lead to strong competitive exclusion and character displacement, low rates of gene flow, and consequently high rates of speciation rates in specialists relative to general-ists. It could also be argued that many observed long-term evolutionary trends, such as the increase in average body size observed in many lineages, occur not because of strong selection for the trait in question during the history of individual species or during speciation, but because taxa with the trait in question simply speciate at a higher rate.
Species selection has certainly been demonstrated to be a theoretical possibility based on the fact that any kind of heritable variation can be selected. However, species selection as a major force in evolution runs into the same problems as group or interdemic selection: the generation time of individual organisms is usually several orders of magnitude shorter than the 'generation time' for species. The former is generally on the scale of months or years, the latter on the scale of hundreds of thousands if not millions of years. The very argument that suggests species selection as a theoretical possibility, namely a decomposition of heritable variation into components following Price's equation (see Units of Selection), is what makes it of limited scope in practice. Specifically, rapid natural selection at the intraspecific level eliminates variance in trait at the interspecific level before higher-level selection can act.
Consequently, if a certain trait in an organism leads to a higher propensity to speciation, but is selected against among individuals in a population, then the trait in question will generally be lost prior to any speciation events. In recent studies, such as those of Sean Rice, it has been shown that under conditions when individual generation times are very long and speciation rates are very high, species selection can run counter to intraspecific selection, but these circumstances are probably exceptional.
Realistically, species selection may be important for traits that are on average neutral at the individual and genic (intraspecific) level. The possibility ofspecies selection being important in such neutral traits remains an interesting empirical question, albeit one that is difficult to answer because in many cases it is impossible to disentangle the history of selection on a trait from its fossil or phylogenetic history.
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