bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.25.754399

Benchmarking Universal Single-Copy Orthologs for Phylogenomics: The Impact of Paralogy

Aranda, M.·Kulikov, N.·Irisarri, I.
View original source ↗Export metadata ↓

Abstract

Universal Single-Copy Orthologs (USCOs) are taxonomically-defined gene sets originally proposed to evaluate completeness in genome assemblies. Due to their single- or low-copy nature, they have also been proposed as ideal markers for phylogenomics. Here, we test this assumption using two vertebrate datasets, mammals and ray-finned fish, and their corresponding USCO reference marker sets, actinopterygii_odb10 and mammalia_odb10. Our results show that although most USCO markers are single-copy, 85% and 91% respectively, empirical analyses using a large number of taxa are able to identify a non-negligible proportion of paralogs in the actinopterygii_odb10 and mammalia_odb10 BUSCO gene sets. Gene phylogenies show that several of these paralogs derive from ancient whole-genome duplication events, particularly the teleost-specific whole-genome duplication, and also more recent duplications such as those in salmonids and cyprinids. Paralogs do not reflect the organismal phylogeny but rather the history of gene duplications, so retaining paralogs in phylogenomic datasets can lead to inaccurate phylogenomic hypotheses. To test the effect of ignoring paralogy in BUSCO gene sets, we analyze the mammal and ray-finned fish datasets using concatenated maximum likelihood and summary coalescent methods by randomly choosing one paralog per locus if these are present. The resulting phylogenomic trees are overall consistent with the reference phylogenies, although small discrepancies were found. Phylogeny-guided paralogy removal also changes the sequences retained for many loci, but whether these changes alter the inferred species trees remains to be tested.

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Aranda, M., Kulikov, N., Irisarri, I.. 2026-10-01. Benchmarking Universal Single-Copy Orthologs for Phylogenomics: The Impact of Paralogy. https://doi.org/10.64898/2026.09.25.754399

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↗