@article {65900, title = {Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait.}, journal = {Evolution}, year = {2020}, month = {2020 Dec 14}, abstract = {

Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as "trichomes," on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of dorsal trichomes, but a subset of these trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here, we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that a single large effect QTL, which includes svb, explains most of the trichome number difference between two D. virilis strains and that svb expression correlates with the trichome difference between strains. This QTL does not explain the entire difference between strains, implying that additional loci contribute to variation in trichome numbers. Thus, the genetic architecture of intraspecific variation exhibits similarities and differences with interspecific variation that may reflect differences in long-term and short-term evolutionary processes.

}, issn = {1558-5646}, doi = {10.1111/evo.14142}, author = {Soverna, Ana Faigon and Rodriguez, Nahuel Cabrera and Korgaonkar, Aishwarya and Hasson, Esteban and Stern, David L and Frankel, Nicol{\'a}s} } @article {49092, title = {Comprehensive analysis of a cis-regulatory region reveals pleiotropy in enhancer function.}, journal = {Cell Reports}, volume = {22}, year = {2018}, month = {2018 Mar 13}, pages = {3021-3031}, abstract = {

Developmental genes can have complex cis-regulatory regions with multiple enhancers. Early work revealed remarkable modularity of enhancers, whereby distinct DNA regions drive gene expression in defined spatiotemporal domains. Nevertheless, a few reports have shown that enhancers function in multiple developmental stages, implying that enhancers can be pleiotropic. Here, we have studied the activity of the enhancers of the shavenbaby gene throughout D.\ melanogaster development. We found that all seven shavenbaby enhancers drive expression in multiple tissues and developmental stages. We explored how enhancer pleiotropy is encoded in two of these enhancers. In one enhancer,\ the same transcription factor binding sites contribute to embryonic and pupal expression, revealing site pleiotropy, whereas for a second enhancer, these roles are encoded by distinct sites. Enhancer pleiotropy may be a common feature of cis-regulatory regions of developmental genes, and site pleiotropy may constrain enhancer evolution in some cases.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2018.02.073}, author = {Preger-Ben Noon, Ella and Sabar{\'\i}s, Gonzalo and Ortiz, Daniela M and Sager, Jonathan and Liebowitz, Anna and Stern, David L and Frankel, Nicol{\'a}s} } @article {45725, title = {Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution.}, journal = {Proc Natl Acad Sci U S A}, volume = {109}, year = {2012}, month = {2012 Dec 18}, pages = {20975-9}, abstract = {

Similar morphological, physiological, and behavioral features have evolved independently in different species, a pattern known as convergence. It is known that morphological convergence can occur through changes in orthologous genes. In some cases of convergence, cis-regulatory changes generate parallel modifications in the expression patterns of orthologous genes. Our understanding of how changes in cis-regulatory regions contribute to convergence is hampered, usually, by a limited understanding of the global cis-regulatory structure of the evolving genes. Here we examine the genetic causes of a case of precise phenotypic convergence between Drosophila sechellia and Drosophila ezoana, species that diverged ~40 Mya. Previous studies revealed that changes in multiple transcriptional enhancers of shavenbaby (svb, a transcript of the ovo locus) caused phenotypic evolution in the D. sechellia lineage. It has also been shown that the convergent phenotype of D. ezoana was likely caused by cis-regulatory evolution of svb. Here we show that the large-scale cis-regulatory architecture of svb is conserved between these Drosophila species. Furthermore, we show that the D. ezoana orthologs of the evolved D. sechellia enhancers have also evolved expression patterns that correlate precisely with the changes in the phenotype. Our results suggest that phenotypic convergence resulted from multiple noncoding changes that occurred in parallel in the D. sechellia and D. ezoana lineages.

}, keywords = {Animals, Developmental Biology, Drosophila, Drosophila melanogaster, Enhancer Elements, Genetic, Evolution, Molecular, Gene Expression Regulation, Genes, Reporter, Genetic Vectors, Models, Genetic, Molecular Sequence Data, Phenotype, Species Specificity, Transcription, Genetic}, issn = {1091-6490}, doi = {10.1073/pnas.1207715109}, author = {Frankel, Nicol{\'a}s and Wang, Shu and Stern, David L} }