Biology subjects

Rogers, R. L.

Publications and source records attributed to Rogers, R. L..

4 recordsLinked to original sources

bioRxiv2025

Genetic Novelty and Short-Term Evolutionary Dynamics in Drosophila yakuba mayottensis

1Understanding how genetic novelty arises and contributes to population divergence is central to evolutionary biology. On short evolutionary timescales, the relative roles of new mutations and standing variation remain underexplored among structural variation. Here, we compare the contributions of chromosomal rearrangements, tandem duplications, and single-nucleotide polymorphisms (SNPs) to early genomic differentiation in a recently colonized island population, Drosophila yakuba mayottensis, from the island of Mayotte. By comparing the relative impacts of these mutation classes, along with the involvement of transposable elements (TEs), we assess whether certain mutations are more likely to contribute to rapid divergence. We show that TEs are disproportionately involved in the formation of novel structural variants shortly after colonization, particularly through direct insertions. Our results suggest that TE-associated rearrangements may bypass the clocklike pace of SNP accumulation and divergence, where the contributions of coding SNPs, tandem duplications, and TE-facilitated ectopic recombination are constrained to standing variation on short timescales. Although TEs can drive the rapid emergence of novel variants, their full contribution to adaptation likely depends on evolutionary context and time since colonization. Together, our findings reveal time-dependent mutational dynamics and highlight the importance of structural variation, particularly TE-associated rearrangements, in shaping early genomic divergence following habitat shifts.

evolutionary biology↗

bioRxiv2024

The role of pigments in light color variation of the firefly Photinus pyralis

Fireflies use bioluminescent signals to communicate with their mates. Luciferase has been thought to be the sole contributor to light color; however, populations of the Photinus pyralis firefly display variation in the color of their emitted signals yet have identical luciferase sequences. Here, we examined whether pigments could be present in the light organs of the twilight-active species P. pyralis and contribute to this variation. We detected patterns of expression that suggest ommochrome and pterin screening pigments are expressed in P. pyralis light organs and could filter light emitted by luciferase and play a role in signal tuning. There were no significant differences between the pigment gene expression of P. pyralis individuals with yellower and greener signals. Our study provides alternative mechanisms that could influence pigments in P. pyralis light organs that could also play a role in modifying signal color.

evolutionary biology↗

bioRxiv2022

Genomic islands of divergence between Drosophila yakuba subspecies predominantly overlap with chromosomal inversions

During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs in Drosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 20 GIDs distinguishing D. y. mayottensis from generalist mainland populations of D. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome for D. y. mayottensis and identified five novel chromosomal inversions. Twelve GIDs ([~]72% of outlier windows) fell close to or within subspecies-specific inversions. However, three GIDs were in collinear, high recombining regions indicating strong signal of hard selective sweeps. Unlike D. y. mayottensis, D. sechellia, the only other noni-specialist, is homosequential with its generalist relatives. Thus, both selection and rearrangements shape GIDs and striking convergences can occur between species with distinct genomic architectures.

evolutionary biology↗

bioRxiv2016

Tandem duplications lead to novel expression patterns through exon shuffling in D. yakuba

One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this gene dosage hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5' and 3' UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution.\n\nAuthor SummaryThe enclosed work shows that whole gene duplications rarely affect gene expression, in contrast to widely held views that the adaptive value of duplicate genes is related to additive changes in gene expression due to gene copy number. We further explain how tandem duplications that create shuffled gene structures can force upregulation of gene sequences, de novo gene creation, and multifold changes in transcript levels.\n\nThese results show that tandem duplications can produce new genes that are a source of immediate novelty associated with more extreme expression changes than previously suggested by theory. Further, these gene expression changes are a potential source of both beneficial and pathogenic mutations, immediately relevant to clinical and medical genetics in humans and other metazoans.

evolutionary biology↗