Evolutionary responses to persistent pathogen exposure can involve changes in immune regulation that vary among populations, sexes, and immune-related genes. We investigated the transcriptional response to long-term bacterial selection in two allopatric populations of Drosophila ananassae from the Indian subcontinent. Flies were subjected to continuous selection with Pseudomonas aeruginosa for 55 generations, while a separate relaxed-selection regime was initiated after generation 45 and maintained for a further 10 generations in the absence of bacterial challenge. The expression of nine immune-regulatory genes involved in melanization, immune signalling, and antimicrobial defence was quantified using RT-qPCR across generations, populations, and sexes. Continuous bacterial selection resulted in progressive changes in the expression of immune-related genes, although the magnitude and temporal pattern differed among genes, populations, and sexes. Different genes exhibited population specific trends in their changing expression level. Females generally showed greater transcriptional responses than males for several genes. Following removal of bacterial selection, expression of most genes declined toward control levels, although residual elevation persisted for several genes after ten generations of relaxed selection and the extent of reversion differed among genes and populations. These findings demonstrate that prolonged bacterial selection is associated with coordinated but gene-specific changes in immune gene expression in D. ananassae, together with population- and sex-dependent variation in transcriptional responses. The persistence and subsequent reversion of expression after removal of selection highlight the dynamic nature of immune regulation, while the underlying genetic, physiological, and epigenetic mechanisms remain to be determined. This study provides a molecular framework for investigating the evolution and regulation of immune responses under prolonged pathogen exposure and subsequent relaxation of selection.
Genes missing from a comparative matrix may be absent from the annotation rather than from the genome. We examined how incomplete gene records affect the interpretation of associations between gene representation and maximum lifespan in 68 amniotes. We grouped 200 genome maintenance genes into six modules and calculated the confidence-weighted fraction recovered in each species. Separate phylogenetic generalized least squares models found positive associations between all six scores and lifespan after accounting for body mass and clade. A separate principal component analysis showed that one component explained 99.01
Gamete recognition proteins are expressed on the surfaces of sperm and eggs, where they mediate interactions between gametes. The genetic basis for gamete recognition proteins, as well as their structure and interactions, have yet to be fully resolved. Using a new high-quality de novo genome assembly for the sea urchin Mesocentrotus franciscanus, we investigated the genomic structure, expression, and protein forms of several gamete recognition proteins: sperm bindin, egg receptor for sperm (HSP110), and egg bindin receptor (EBR1), as well as the receptor for egg jelly (REJ) and its paralogs. To inform future population genetic and evolutionary studies, we resolve the genomic structure of the large EBR1 protein, identifying fewer tandem CUB-TSP1 repeats in EBR1 compared to the initial characterization of this protein. As expected for an egg receptor for sperm, EBR1 is highly expressed in female reproductive tissues (eggs and female gonad), compared to other tissues. In contrast, HSP110 shows similar levels of expression across male and female reproductive tissues, as well as across non-reproductive tissues and development stages. HSP110 might be a pleiotropic gene that in part influences fertilization. Using protein structural modeling and functional domain predictions, we propose hypotheses about potential interactions among EBR1, bindin, and HSP110 proteins that may provide insight into sperm-egg interactions in sea urchins. Resolving the genomic structure of genes encoding gamete recognition proteins, in combination with functional annotations and protein structural modeling, enables deeper investigation into the consequences of variation in gamete recognition proteins and the evolution of reproductive isolation.
Different RNA sequences do not have equal access to nearby structural sequence space, but how strongly local sequence neighborhoods depend on starting-sequence identity and individual nucleotide positions remains unclear. Here, we compared the fully mutated neighborhoods of three isolated 20-nucleotide RNA seeds inspired by the P-site peptidyl transferase center, shifted P-loop, and A-site A-loop regions of the ribosomal core using ViennaRNA minimum-free-energy secondary-structure predictions. The seeds were treated as conceptual starting points for sequence-space exploration rather than exact residue-numbered extracts from a single modern rRNA. The three seeds generated reproducibly different predicted foldability landscapes, with the shifted P-loop-inspired seed consistently producing the highest foldability across independent pools and increasingly stringent MFE thresholds. Single-position retention revealed strong positional effects: retained guanine generally increased predicted foldability, but one retained-G position in each seed significantly outperformed other retained-G positions within the same sequence. Disabling G·U wobble pairing reduced the magnitude of these effects but preserved the retained-base hierarchy, the identity of all three positional anchors, and the overall seed ranking. Combinations of retained positions produced super-additive increases in predicted foldability, although structural-proximity analysis showed that these positions did not consistently form a single compact predicted structural core. Iterative computational selection for lower MFE progressively enriched all three neighborhoods for predicted structure, while six non-conserved biological control 20-mers generated even richer predicted foldability landscapes than the ribosome-inspired seeds. Together, these results show that local RNA sequence space is strongly shaped by starting-sequence identity, nucleotide position, and higher-order retained-position effects and cannot be explained by nucleotide composition or starting-seed structure alone. These conclusions are restricted to MFE-based secondary-structure predictions and do not establish tertiary folding, biochemical function, or experimentally populated structures.
The evolution of the human brain is characterized by profound changes in structure and function, despite relatively limited divergence in protein-coding genes compared to other primates. This paradox has led to increasing recognition of gene regulatory elements (GREs) as primary drivers of evolutionary innovation. In this review, we synthesize current knowledge on the role of conserved noncoding elements (CNEs), human accelerated regions (HARs), and transposable element (TE)-derived sequences in shaping gene regulatory networks (GRNs) underlying brain development. Comparative analyses across humans and closely related primates, including the chimpanzee, gorilla, and orangutan, reveal that while core regulatory architectures are highly conserved, subtle changes in regulatory elements drive species-specific gene expression patterns. We highlight how CNEs provide a stable regulatory framework, whereas HARs and TE-derived elements introduce lineage-specific modifications that fine-tune neurodevelopmental processes. Advances in functional genomics, including CRISPR-based perturbations, massively parallel reporter assays, and single-cell multi-omics, have enabled direct interrogation of regulatory function, linking sequence variation to cellular phenotypes. Furthermore, we discuss how regulatory evolution contributes to both cognitive innovation and susceptibility to neurological disorders. Despite significant progress, challenges remain in establishing causal relationships between regulatory variation and phenotypic outcomes. Future integration of multi-omics data and comparative models will be essential for resolving these complexities. Together, this review provides a comprehensive framework for understanding the molecular basis of primate brain evolution through the lens of gene regulation.
