Evolution of Three Parent Genes and Their Retrogene Copies in<i>Drosophila</i>Species
Bibliographic record
Abstract
Retrogenes form a class of gene duplicate lacking the regulatory sequences found outside of the mRNA-coding regions of the parent gene. It is not clear how a retrogene's lack of parental regulatory sequences affects the evolution of the gene pair. To explore the evolution of parent genes and retrogenes, we investigated three such gene pairs in the family Drosophilidae; in Drosophila melanogaster, these gene pairs are CG8331 and CG4960, CG17734 and CG11825, and Sep2 and Sep5. We investigated the embryonic expression patterns of these gene pairs across multiple Drosophila species. Expression patterns of the parent genes and their single copy orthologs are relatively conserved across species, whether or not a species has a retrogene copy, although there is some variation in CG8331 and CG17734. In contrast, expression patterns of the retrogene orthologs have diversified. We used the genome sequences of 20 Drosophila species to investigate coding sequence evolution. The coding sequences of the three gene pairs appear to be evolving predominantly under negative selection; however, the parent genes and retrogenes show some distinct differences in amino acid sequence. Therefore, in general, retrogene expression patterns and coding sequences are distinct compared to their parents and, in some cases, retrogene expression patterns diversify.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".