Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtail Xiphophorus nezahualcoyotl

Sex-linked traits are widespread, but their genetic architecture has been challenging to characterize, due in part to the repetitive and structurally complex nature of sex chromosomes. In swordtails a...

biorxiv.org

Structural variants are enriched in deleterious visible phenotypes in Drosophila

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation; yet, many evade discovery using short reads. While long-read sequencing can reveal hidden SVs, their role in organismal trait variation remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore Technologies long reads. These assemblies enable construction of a pangenome graph containing nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncover new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, the wing vein phenotype plexus (px1) links to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype links to a 7.5 kb DM412 retrotransposon disrupting the coding sequence of the muscle protein gene Strn-Mlck. We also identify a candidate intergenic enhancer for AblpeyD, a finding supported by CRISPR-Cas9. We also unveil 8 SV alleles of previously identified causal genes, including uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of genes causing phenotypic changes harbor candidate SVs >100 bp, whereas only 28% are expected based on euchromatic SVs. Together, our results indicate that SVs are strongly enriched among this class of large-effect, deleterious visible phenotypes in Drosophila.

genome.cshlp.org

Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments

Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...

journals.plos.org

Pervasive Fitness Trade‐Offs Revealed by Rapid Adaptation to Shifting Population Densities in Large Experimental Populations of Drosophila melanogaster

Trade-offs are an inherent feature of organismal biology and fundamental to the evolution of natural populations. Using experimental evolution in large, genetically diverse populations of Drosophila ...

onlinelibrary.wiley.com

Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore

Abstract. The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of popul

doi.org

High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation

The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...

doi.org

biorxiv.org

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

biorxiv.org

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Increased rates of hybridization in swordtail fish are associated with water pollution

Biodiversity loss can occur when disturbance compromises the reproductive barriers between species, causing them to collapse into a single population through hybridization. Recent research has documen...

biorxiv.org

Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin

The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the eff...

doi.org

pnas.org