@article {65362, title = {A large genomic insertion containing a duplicated follistatin gene is linked to the pea aphid male wing dimorphism.}, journal = {eLife}, volume = {9}, year = {2020}, month = {2020 Mar 06}, abstract = {

Wing dimorphisms have long served as models for examining the ecological and evolutionary tradeoffs associated with alternative phenotypes. Here, we investigated the genetic cause of the pea aphid () male wing dimorphism, wherein males exhibit one of two morphologies that differ in correlated traits that include the presence or absence of wings. We mapped this trait difference to a single genomic region and, using third generation, long-read sequencing, we identified a 120 kb insertion in the wingless allele. This insertion includes a duplicated gene, which is a strong candidate gene in the minimal mapped interval to cause the dimorphism. We found that both alleles were present prior to pea aphid biotype lineage diversification, we estimated that the insertion occurred millions of years ago, and we propose that both alleles have been maintained in the species, likely due to balancing selection.

}, issn = {2050-084X}, doi = {10.7554/eLife.50608}, author = {Li, Binshuang and Bickel, Ryan D and Parker, Benjamin J and Saleh Ziabari, Omid and Liu, Fangzhou and Vellichirammal, Neetha Nanoth and Simon, Jean-Christophe and Stern, David L and Brisson, Jennifer A} } @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 {45061, title = {Looking under the lamp post: neither fruitless nor doublesex has evolved to generate divergent male courtship in Drosophila.}, journal = {Cell Reports}, volume = {8}, year = {2014}, month = {2014 Jul 24}, pages = {363-70}, abstract = {

How do evolved genetic changes alter the nervous system to produce different patterns of behavior? We address this question using Drosophila male courtship behavior, which is innate, stereotyped, and evolves rapidly between species. D. melanogaster male courtship requires the male-specific isoforms of two transcription factors, fruitless\ and doublesex. These genes underlie genetic switches between female and male behaviors, making them excellent candidate genes for courtship behavior evolution. We tested their role in courtship evolution by transferring the entire locus for each gene from divergent species to D.\ melanogaster. We found that despite differences in Fru+ and Dsx+ cell numbers in wild-type species, cross-species transgenes rescued D.\ melanogaster courtship behavior and no species-specific behaviors were conferred. Therefore, fru and dsx are not a significant source of evolutionary variation in courtship behavior.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2014.06.023}, author = {Cande, Jessica and Stern, David L and Morita, Tomoko and Prud{\textquoteright}homme, Benjamin and Gompel, Nicolas} } @article {4648, title = {The loci of evolution: how predictable is genetic evolution?}, journal = {Evolution}, volume = {62}, year = {2008}, month = {2008 Sep}, pages = {2155-77}, abstract = {

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22\% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

}, keywords = {Animals, Evolution, Humans, Molecular, Phenotype, Regulatory Elements, Transcriptional}, issn = {0014-3820}, doi = {10.1111/j.1558-5646.2008.00450.x}, author = {Stern, David L and Orgogozo, Virginie} } @article {45751, title = {Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera).}, journal = {Genome Biol}, volume = {7}, year = {2006}, month = {2006}, pages = {R21}, abstract = {

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

}, keywords = {Animals, Aphids, Base Composition, Base Sequence, DNA, DNA, Complementary, Expressed Sequence Tags, Gene Library, Microsatellite Repeats, Peas, Phylogeny, Plant Diseases, Population Density, Transcription, Genetic}, issn = {1465-6914}, doi = {10.1186/gb-2006-7-3-r21}, author = {Sabater-Mu{\~n}oz, Beatriz and Legeai, Fabrice and Rispe, Claude and Bonhomme, Jo{\"e}l and Dearden, Peter and Dossat, Carole and Duclert, Aymeric and Gauthier, Jean-Pierre and Ducray, Dani{\`e}le Giblot and Hunter, Wayne and Dang, Phat and Kambhampati, Srini and Martinez-Torres, David and Cortes, Teresa and Moya, Andr{\`e}s and Nakabachi, Atsushi and Philippe, Cathy and Prunier-Leterme, Nathalie and Rahb{\'e}, Yvan and Simon, Jean-Christophe and Stern, David L and Wincker, Patrick and Tagu, Denis} }