@article {46535, title = {Genetic architecture and functional characterization of genes underlying the rapid diversification of male external genitalia between Drosophila simulans and Drosophila mauritiana.}, journal = {Genetics}, year = {2015}, month = {2015 Mar 16}, abstract = {

Male sexual characters are often among the first traits to diverge between closely related species and identifying the genetic basis of such changes can contribute to our understanding of their evolutionary history. However, little is known about the genetic architecture or the specific genes underlying the evolution of male genitalia. The morphology of the claspers, posterior lobes and anal plates exhibit striking differences between Drosophila mauritiana and Drosophila simulans. Using QTL and introgression-based high-resolution mapping, we identified several small regions on chromosome arms 3L and 3R that contribute to differences in these traits. However, we found that the loci underlying the evolution of clasper differences between these two species are independent from those that contribute to posterior lobe and anal plate divergence. Furthermore, while most of the loci affect each trait in the same direction and act additively, we also found evidence for epistasis between loci for clasper bristle number. In addition, we conducted an RNAi screen in D. melanogaster to investigate if positional and expression candidate genes located on chromosome 3L, are also involved in genital development. We found that six of these genes, including components of Wnt signaling and male-specific lethal 3 (msl3), regulate the development of genital traits consistent with the effects of the introgressed regions where they are located and that thus represent promising candidate genes for the evolution these traits.

}, issn = {1943-2631}, doi = {10.1534/genetics.114.174045}, author = {Tanaka, Kentaro M and Hopfen, Corinna and Herbert, Matthew R and Schl{\"o}tterer, Christian and Stern, David L and Masly, John P and McGregor, Alistair P and Nunes, Maria D S} } @article {45847, title = {Low affinity binding site clusters confer Hox specificity and regulatory robustness.}, journal = {Cell}, volume = {160}, year = {2015}, month = {2015 Jan 15}, pages = {191-203}, abstract = {

In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in\ vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in\ vivo, but multiple clustered sites were required for robust expression when embryos developed in\ variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.11.041}, author = {Crocker, Justin and Abe, Namiko and Rinaldi, Lucrezia and McGregor, Alistair P and Frankel, Nicol{\'a}s and Wang, Shu and Alsawadi, Ahmad and Valenti, Philippe and Plaza, Serge and Payre, Fran{\c c}ois and Mann, Richard S and Stern, David L} } @article {4650, title = {Morphological evolution caused by many subtle-effect substitutions in regulatory DNA.}, journal = {Nature}, volume = {474}, year = {2011}, month = {2011 Jun 30}, pages = {598-603}, abstract = {

Morphology evolves often through changes in developmental genes, but the causal mutations, and their effects, remain largely unknown. The evolution of naked cuticle on larvae of Drosophila sechellia resulted from changes in five transcriptional enhancers of shavenbaby (svb), a transcript of the ovo locus that encodes a transcription factor that governs morphogenesis of microtrichiae, hereafter called {\textquoteright}trichomes{\textquoteright}. Here we show that the function of one of these enhancers evolved through multiple single-nucleotide substitutions that altered both the timing and level of svb expression. The consequences of these nucleotide substitutions on larval morphology were quantified with a novel functional assay. We found that each substitution had a relatively small phenotypic effect, and that many nucleotide changes account for this large morphological difference. In addition, we observed that the substitutions had non-additive effects. These data provide unprecedented resolution of the phenotypic effects of substitutions and show how individual nucleotide changes in a transcriptional enhancer have caused morphological evolution.

}, keywords = {Animals, Base Sequence, Biological Evolution, Developmental, DNA-Binding Proteins, Drosophila, Drosophila melanogaster, Drosophila Proteins, Embryo, Enhancer Elements, Female, Gene Expression Regulation, Genetic, Larva, Male, Nonmammalian, Nucleic Acid, Phenotype, Sequence Alignment, Sequence Homology, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature10200}, author = {Frankel, Nicol{\'a}s and Erezyilmaz, Deniz F and McGregor, Alistair P and Wang, Shu and Payre, Fran\c cois and Stern, David L} } @article {4649, title = {Morphological evolution through multiple cis-regulatory mutations at a single gene.}, journal = {Nature}, volume = {448}, year = {2007}, month = {2007 Aug 2}, pages = {587-90}, 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.

}, keywords = {Alleles, Animals, Biological, Biological Evolution, Developmental, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Enhancer Elements, Evolution, Gene Expression Regulation, Genes, Genetic, Genetic Speciation, Models, Molecular, Mutation, Recombination, Reporter, Transcription Factors}, issn = {1476-4687}, doi = {10.1038/nature05988}, author = {McGregor, Alistair P and Orgogozo, Virginie and Delon, Isabelle and Zanet, Jennifer and Srinivasan, Dayalan G and Payre, Fran\c cois and Stern, David L} }