bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/283390

Transposable elements and gene expression during the evolution of amniotes

Zeng, L.·Pederson, S.·Kortschak, D.·Adelson, D.
View original source ↗Export metadata ↓

Abstract

BackgroundTransposable elements (TEs) are primarily responsible for the changes in genome sequences that occur over time within and between species. TEs themselves evolve, with clade specific LTR/ERV, LINEs and SINEs responsible for the bulk of species specific genomic features. Because TEs can contain regulatory motifs, they can be exapted as regulators of gene expression. While TE insertions can provide evolutionary novelty for the regulation of gene expression, their overall impact on the evolution of gene expression is unclear. Previous investigators have shown that tissue specific gene expression in amniotes is more similar across species than within species, supporting the existence of conserved developmental gene regulation. In order to understand how species specific TE insertions might affect the evolution/conservation of gene expression, we have looked at the association of gene expression in six tissues with TE insertions in six representative amniote genomes (human, opossum, platypus, anole lizard, bearded dragon and chicken).\n\nResultsWe have used a novel bootstrapping approach to minimise the conflation of effects of repeat types on gene expression. We compared the expression of orthologs containing different types of recent TE insertions to orthologs that contained older TE insertions and found significant differences in gene expression associated with TE insertions. Likewise, we compared the expression of non-ortholog genes containing different types of recent TE insertions to non-orthologs with older TE insertions and found significant differences in gene expression associated with TE insertions. As expected TEs were associated with species-specific changes in gene expression, but the magnitude and direction of change of expression changes were unexpected. Overall, orthologs containing clade specific TEs were associated with lower gene expression, while in non-orthologs, non clade-specific TEs were associated with higher gene expression. Exceptions were SINE elements in human and chicken, which had an opposite association with gene expression compared to other species.\n\nConclusionsOur observed species-specific associations of TEs with gene expression support a role for TEs in speciation/response to selection by species. TEs do not exhibit consistent associations with gene expression and observed associations can vary depending on the age of TE insertions. Based on these observations, it would be prudent to refrain from extrapolating these and previously reported associations to distantly related species.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Zeng, L., Pederson, S., Kortschak, D., Adelson, D.. 2018-03-16. Transposable elements and gene expression during the evolution of amniotes. https://doi.org/10.1101/283390

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Efficient growth factor production stabilizes cooperation in a cellular public goods game

Eukaryotic cells secrete growth factors that facilitate the proliferation and survival of neighboring cells in a coordinated manner essential for tissue development, repair, and homeostasis. However, mutant cells that fail to produce these factors may exploit the benefits provided by neighboring producers, thereby gaining a proliferative advantage that could lead to the extinction of the producer clone. Evolutionary theory predicts that preventing this "tragedy of the commons" requires a fixed spatial structure or other mechanisms that enable cells to interact preferentially with copies of themselves. Contrary to this expectation, we found that, in competition experiments, cells producing the diffusible growth factor interleukin-3 (IL3) resist invasion by non-producing mutant cells even in well-mixed populations, and that non-producers are driven to extinction instead. Using evolutionary game theory, we show that this outcome arises when the cost-to-benefit ratio of growth factor production falls below a critical threshold. We derive this tipping point analytically across the full parameter space of benefit function shape and group size and confirm that IL3 production in our experimental system satisfies this condition with a production cost less than 0.1% of the benefit conferred. These results demonstrate that efficient public good production alone can resolve the tragedy of the commons in populations of cells, and potentially in other biological systems.

evolutionary biology↗
bioRxiv2026

Repeated Transitions in Migratory Behavior Across a Songbird Radiation Are Not Driven by Selection on Shared Variation in Candidate Genes

Understanding the mechanisms facilitating the repeated evolution of traits is a core question in evolutionary biology. While repeated evolution has been observed across many systems, behavioral phenotypes have been less well studied than morphological traits. Migration is a behavioral adaptation to seasonality that has evolved independently in many animals, and repeated gains and losses of migratory behavior have been especially prevalent throughout the diversification of birds. While migratory traits are heritable in many taxa and candidate genes underlying intraspecific variation in migratory behavior have been identified, whether similar genetic changes are responsible for the repeated evolution of migration remains poorly understood. We used a phylogenomic approach to investigate the relationship between variation in candidate genes and migratory propensity across nearly all species in the parulid warbler radiation (n = 101), a group of songbirds in which migratory behavior has been lost and gained multiple times. Comparisons of candidate gene tree topologies to the parulid warbler species tree revealed cases of discordance, though these were explained by differences in the number of phylogenetically informative sites among genes rather than by elevated genetic similarity among species sharing migratory strategies. Testing models of coding sequence evolution identified sites with elevated dN/dS in five candidate genes, suggestive of positive selection; however, variation at these sites showed no clear association with migratory strategy, nor did we detect recurrent selection across lineages where transitions in migratory behavior most likely occurred. Together, these results contradict the hypothesis that selection on shared variation (ancestral polymorphisms or introgressed alleles) facilitated the repeated evolution of migration in this clade.

evolutionary biology↗
bioRxiv2026

Why development time matters: temperature influences plasticity while nutritional stress reshapes selection and evolutionary potential

The time it takes organisms to reach adulthood is often considered a central life-history trait that influences fitness and is highly plastic across environments. Despite its importance, direct estimates of how selection on development time varies across combinations of environmental stressors remain rare, limiting our understanding of its role in population responses to environmental change. We reared 68 full-sibling families of the vinegar fly, Drosophila melanogaster, at two temperatures (14{degrees}C and 28{degrees}C) on two diets (standard and low-calorie), and measured development time, body size (mass and wing size), egg-to-adult viability and productivity (number of offspring). Temperature caused the largest plastic response, with development taking 4-5 times longer at 14{degrees}C, whereas the low-calorie diet extended development by 20-30%. Yet diet, not temperature, changed directional selection on development time. On the standard diet, faster development was associated with higher fitness at both temperatures. On the low-calorie diet, this advantage disappeared, and at 14{degrees}C slower-developing females tended to produce more offspring. Viability selection showed consistent patterns. The low-calorie diet also increased evolvability in development time c.10-16-fold at both temperatures, and genetic correlations between diets were close to zero, indicating strong genotype-by-environment interactions. Plasticity in development time was not associated with fitness in any treatment. Overall, we provide evidence that development time is a functional trait whose relationship with fitness depends on the environment. Nutritional stress induced a smaller plastic response in development time than temperature, but had a larger effect on directional selection and evolvability. The stressor causing the greatest plastic change in a functional trait is therefore not necessarily the one that shapes its selection and evolution.

evolutionary biology↗