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Farfan-Pira, K. J.

Publications and source records attributed to Farfan-Pira, K. J..

2 recordsLinked to original sources

A cis-regulatory sequence of the wing selector gene, vestigial, drives the evolution of scaling relationships in Drosophila species

Scaling between specific organs and overall body size has long fascinated biologists because they are a primary mechanism through which organismal shapes evolve. Yet, the genetic mechanisms that underlie the evolution of allometries remain elusive. Here we measured wings and tibia lengths in four Drosophila species (D. melanogaster, D. simulans, D. ananassae, and D. virilis) and show that the first three of them follow a single evolutionary allometry. However, D. virilis exhibits a divergent wing-to-tibia allometry due to a dramatic underscaling of their wings with respect to their bodies compared to the other species. We asked whether the evolution of this scaling relationship could be explained by changes in a specific cis-regulatory regulatory region of the wing selector gene, vestigial (vg), whose function is broadly conserved in insects and its expression pattern determines wing size in D. melanogaster. To test this hypothesis directly, we used CRISPR/Cas9 to replace the DNA sequence of the predicted Quadrant Enhancer (vgQE) from D. virilis for the corresponding vgQE sequence in the genome of D. melanogaster. Strikingly, we discovered that D. melanogaster flies carrying the D. virilis vgQE sequence have wings that are much smaller with respect to controls, partially rescuing the wing-to-tibia ratio observed in D. virilis. Our results show that this cis-regulatory element in D. virilis contributes to the underscaling of wings in this species. This provides evidence that scaling relationships may be unconstrained and may evolve gradually through genetic variations in cis-regulatory elements. Summary statementUsing CRISPR/Cas9 replacement of a cis-regulatory element, this study suggests that changes within the vestigial Quadrant Enhancer sequence are responsible for the evolution of wing allometries in Drosophila species.

evolutionary biology↗

MAPPER: A new image analysis pipeline unmasks differential regulation of Drosophila wing features

Phenomics requires quantification of large volumes of image data, necessitating high throughput image processing approaches. Existing image processing pipelines for Drosophila wings, a powerful model for studying morphogenesis, are limited in speed, versatility, and precision. To overcome these limitations, we developed MAPPER, a fully-automated machine learning-based pipeline that quantifies high dimensional phenotypic signatures, with each dimension representing a unique morphological feature. MAPPER magnifies the power of Drosophila genetics by rapidly identifying subtle phenotypic differences in sample populations. To demonstrate its widespread utility, we used MAPPER to reveal new insights connecting patterning and growth across Drosophila genotypes and species. The morphological features extracted using MAPPER identified the presence of a uniform scaling of proximal-distal axis length across four different species of Drosophila. Observation of morphological features extracted by MAPPER from Drosophila wings by modulating insulin signaling pathway activity revealed the presence of a scaling gradient across the anterior-posterior axis. Additionally, batch processing of samples with MAPPER revealed a key function for the mechanosensitive calcium channel, Piezo, in regulating bilateral symmetry and robust organ growth. MAPPER is an open source tool for rapid analysis of large volumes of imaging data. Overall, MAPPER provides new capabilities to rigorously and systematically identify genotype-to-phenotype relationships in an automated, high throughput fashion. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/422888v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@bdbecdorg.highwire.dtl.DTLVardef@139a7fdorg.highwire.dtl.DTLVardef@43d5b9org.highwire.dtl.DTLVardef@1846af9_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗