The Nature and Analysis of Phenotype Transitions

“how do new traits arise from old phenotypes?”

“research on selection and adaptation may tell us why a trait persisted and spread, but it will not tell us where a trait came from”

“Of these three elements of evolutionary origin, transformational origin is the most neglected”

“how a phenotypic novelty–a trait that is new in composition or context of expression relative to established ancestral traits–can grow out of previous organization, and why a complex evolutionary change in the phenotype need not depend on a long series of genetic mutations. Because evolution can occur by reorganization, the phenotype divergence between populations or species need not be proportional to the genetic distance between them.”

categories of origins of novelty

  • hybridization between species [I would include introgression and admixture within species]
  • polyploidy [mostly plants, I would include any chromosomal transformation]
  • horizontal transfer of genes [multiple gene function by intron shuffling, gene duplication, random gene creation through action of retrotransposons, and random gene creation]
  • coupling and decoupling of modular traits – fusion, duplication, subdivision (decoupling)

“evolution is often and perhaps always combinatorial” [Algebraic Statistics for Computational Biology]

“Phenotype recombination can produce a new trait without loss of an old one, through repeated gene expression and novel epigenetic interactions.”

“increasing the phenotype repertoire of the genome … is a self-accelerating process that greatly augments the production of selectable variation”

not genetic recombination, a different process

two events in the origin of novel phenotypes:

  1. “new input in the form of a genetic mutation or an environmental change”
  2. “developmental response that produces a new phenotype”

need both

“How does the preexisting, ancestral phenotype get transformed into the descendent one?”

Development vs Selection

“Lack of clarity and disagreement about the relative importance of thee two contributions to novelty underlie the perennial debate over gradualism and saltation, and its modern manifestation, the division between those who see selection as paramount and those who focus on ‘developmental constraints’”

“Form always has a developmental origin, even though the spread and persistence of an adaptive variant are usually (though not necessarily) due to selection”

“A phenotype has to appear before it can affect fitness”

“One need only think of the striking sexual dimorphisms that exist in many species to realize that phenotype divergence does not depend upon breeding isolation between like phenotypes”

“It is important to acknowledge that there are small as well as large developmental variants and that all selectable phenotype variation, whether large or small, continuous or discontinuous, necessarily reflects developmental variation”

“Each time we define a trait of interest at a different level of organization, we alter the question of mode of origin. This need not be a paralyzing difficulty. It can be avoided by focusing on one developmentally defined trait and level of organization at a time”


“Detailed phenotype similarity is a commonly used criterion of homology between traits.”

“Developmental similarity is another type of resemblance that supports a homology hypothesis”

“Intraspecific alternative phenotypes or distinctive life-stage phenotypes can illuminate homology by showing that the same or similar phenotypes can be turned off and on during development, providing reason to expect the phylogenetically disjunct expression of a trait.”

difficult to tell between homology and convergence

Polarity – a trait can be derived from an ancestor trait or it can be lost

“Given that the transition is known to occur in both directions (e.g., in a polymorphic population), the question addressed here is how, in terms of phenotype reorganizartion and development, the transitions occur.”


“anomalies represent new options for evolution if they are recurrent enough to be modified by selection or if they happen to prove advantagous in conditions that were previously absent or rare.”

“computational studies of evolution and the Baldwin effect (Mitchell and Taylor, 1999)”

“phenotypes that appear in one species sometimes appear as widespread functional traits in others”

“Use of anomalies to illuminate common ancestry has a long history in evolutionary biology”

“in general, finding alternative states producible by the same individual demonstrates the potential for lability of switching from one to the other during the course of evolution”

“Recurrent, viable anomalies seem to appear wherever they are systematically sought”

“[mammals] Not a single skeleton was completely free of discrete variations”

“Thus, a trait that is a variable but frequent feature of one species is a low-frequency trait in the other and can be completely lost in individuals of a species where it is usually present.”

“Atavisms, as recurrent variants in a population, are material for the evolutionary establishment of a reversion. But evidence that this has actually occurred in nature requires an exceptional knowledge of phylogenetic relationships as well as attention to sporadic anomalies that indicate a capacity for coordinated reappearance of the trait”

“As would be expected if anomalies are in fact material for selection, anomalies of one species have been recorded to appear, as in the case of the iliofemoralis esternus muscle, as fixed traits in other species”

“Goldschmidt’s much maligned developmental constraints view seems closest to the modern one”

“But imprecision and noise are evidently common, at least in behavior, where even simple patterns are rarely exactly repeated, even by the same individual in the same conditions”

“To see pattern and extremes in variation is to glimpse the world as seen by natural selection. It is not a world of uniformly tiny, mutationally based, or exclusively quantitative variants. Rather, it is one full of recurrent developmental anomalies that vary in accord with the genetic makeup of individuals and also with their environmental circumstances.”

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