Morphological evolution through multiple cis-regulatory mutations at a single gene

Abstract

One central, and yet unsolved, question in evolutionary biology is the relationship between the genetic variants segregating within species and the causes of morphological differences between species. The classic neo-darwinian view postulates that species differences result from the accumulation of small-effect changes at multiple loci. However, many examples support the possible role of larger abrupt changes in the expression of developmental genes in morphological evolution. Although this evidence might be considered a challenge to a neo-darwinian micromutationist view of evolution, there are currently few examples of the actual genes causing morphological differences between species. Here we examine the genetic basis of a trichome pattern difference between Drosophila species, previously shown to result from the evolution of a single gene, shavenbaby (svb), probably through cis-regulatory changes. We first identified three distinct svb enhancers from D. melanogaster driving reporter gene expression in partly overlapping patterns that together recapitulate endogenous svb expression. All three homologous enhancers from D. sechellia drive expression in modified patterns, in a direction consistent with the evolved svb expression pattern. To test the influence of these enhancers on the actual phenotypic difference, we conducted interspecific genetic mapping at a resolution sufficient to recover multiple intragenic recombinants. This functional analysis revealed that independent genetic regions upstream of svb that overlap the three identified enhancers are collectively required to generate the D. sechellia trichome pattern. Our results demonstrate that the accumulation of multiple small-effect changes at a single locus underlies the evolution of a morphological difference between species. These data support the view that alleles of large effect that distinguish species may sometimes reflect the accumulation of multiple mutations of small effect at select genes.

Development and evolution of insect pigmentation: Genetic mechanisms and the potential consequences of pleiotropy

“…Such studies will reveal, for example, whether the predominant role of cisregulatory evolution observed for Drosophila melanin patterning is a general feature of insect pigmentation divergence. Studies of morphological traits controlled by pleiotropic developmental pathways in a variety of organisms suggest cis-regulatory changes are indeed a pervasive source of phenotypic diversification (examples in [87][88][89][90]; recent reviews [45,46]), while studies of variation in traits controlled by developmental systems with less pleiotropysuch as melanin synthesis activated by the dedicated Melanocortin 1 receptor in specialized vertebrate cells -suggest changes in amino acid sequence can be common as well [91].…”

The structure and evolution ofcis-regulatory regions: theshavenbabystory

“…Therefore, one possible explanation for the loss of svb expression in D. sechellia was that all of the enhancers that drive expression in quaternary cells had lost their activity in the D. sechellia lineage. To test this hypothesis, we cloned DNA fragments from D. sechellia homologous to the five enhancers of D. melanogaster that drive expression in quaternary cells [22,27]. These species diverged about 3 Myr ago and their genomes are sufficiently similar that these homologous regions could be identified unambiguously.…”

Naturally segregating loci exhibit epistasis for fitness

“…These details cannot be inferred from the between-population studies, because the alleles that differentiate populations or species may never have been simultaneously segregating in any population. Even if they had been, their effects would likely have changed substantially after many generations of isolation owing to the accrual of multiple mutations [14]. Natural assays estimating the magnitude and pattern of epistasis between segregating alleles are necessary to inform important issues such as the maintenance of genetic variation, and thus the evolutionary potential of populations.…”