Biology subjects

Danis, T.

Publications and source records attributed to Danis, T..

5 recordsLinked to original sources

bioRxiv2026

Processed pseudogenes as dynamic substrates of vertebrate genome evolution

Pseudogenes, gene copies presumed nonfunctional, are widespread products of genome evolution, yet their retention under selection and functional significance across vertebrate diversity remain poorly understood. Here, by analyzing 244 high-quality, chromosome-scale genomes from the Vertebrate Genomes Project spanning seven major vertebrate lineages, we show that the most abundant class of pseudogenes, processed pseudogenes (retrocopies), is a dynamic substrate for evolutionary innovation rather than an inert relic. Retrocopy abundance varies by more than an order of magnitude across lineages, closely tracks autonomous retrotransposon content, and a considerable fraction retains intact open reading frames under purifying selection. We establish a two-stage model in which a conserved formation bias toward highly expressed housekeeping genes is followed by lineage-specific selective filtering that shapes distinct functional repertoires. Testing this model, we show that the mammalian X chromosome exports retrocopies to autosomes at significantly elevated rates enriched for functionally constrained copies, establishing meiotic sex chromosome inactivation as the selective driver. Furthermore, tumor suppressor gene retrocopies accumulate preferentially over oncogene retrocopies in large-bodied and long-lived mammalian lineages, identifying retrocopy-mediated tumor suppressor dosage expansion as a previously unrecognized genomic correlate of Petos paradox. Beyond cancer-related dynamics, retrocopy abundance itself correlates with key mammalian life-history traits, including brain mass, generation length, and reproductive timing, which suggests that retrocopy turnover is broadly coupled to organismal pace-of-life. These findings recast retrocopies as a major axis of vertebrate genome evolution and provide a comprehensive resource for studying gene duplicate innovation.

genomics↗

bioRxiv2025

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

Saccharomycotina yeasts are a highly diverse and widely distributed subphylum of ascomycete fungi that exhibit diversity in their asexual growth morphologies; the human commensal yeast Candida albicans exhibits both unicellular and filamentous growth, whereas the bakers yeast Saccharomyces cerevisiae grows unicellularly by budding. Filamentous growth (and the production of hyphae) can comprise linear and branched budding cells that do not undergo cell separation, termed pseudohyphae, or of tubular filaments with septa that perforate allowing movement of organelles, termed true hyphae. We integrated phenotypic, genomic, metabolic, and isolation environment data from 1,154 strains from 1,051 Saccharomycotina species to examine the variation and evolutionary history of filamentation across Saccharomycotina and determine the extent to which genes, metabolic traits, and environments can predict filamentation types. We found that 63.37% of strains can form filaments; 6.56% can form true hyphae, 42.40% can form pseudohyphae, and 14.39% can form both true hyphae and pseudohyphae. We found that the distributions of species that can produce true hyphae or that can filament were more strongly correlated with the yeast phylogeny than the distribution of species with pseudohyphae. Ancestral state reconstruction suggested that the ability to form true hyphae and/or pseudohyphae evolved several times in yeast evolution. We infer that most yeast ancestors likely produced pseudohyphae or lacked filaments, while the Saccharomycotina last common ancestor likely produced pseudohyphae but not true hyphae. Machine learning models trained on genomic and metabolic features predicted filament morphologies with about 70% accuracy. Connecting the evolution of Saccharomycotina morphologies to their genomic, metabolic, and ecological characteristics will enrich our understanding of the evolution of the diversity of lifestyles observed in this lineage.

evolutionary biology↗

bioRxiv2024

Gestation length drives brain size and litter size variation in eutherian mammals

The length of gestation in eutherian mammals, which is key to their reproductive success, is closely connected to other life history traits and with body mass and brain mass, but causal relationships between these variables are unclear. Here, we used an integrative analytical framework to evaluate the evolutionary relationships between gestation length and eight other traits on a dataset of 3,258 eutherian mammals and infer causality. We identify variation in generation length and litter size as the primary predictors of eutherian gestation length variation, whereas additional traits, such as brain mass, significantly predict gestation length only in specific mammalian orders. Using a structural equation modeling approach known as phylogenetic path analysis to infer causality, we find that gestation length variation positively influences brain mass variation and negatively influences litter size variation. Furthermore, body mass causally influences gestation length variation only in certain orders. Consistent with these causal inferences, examination of trait-trait coevolution reinforces that gestation length is strongly positively associated with brain mass, strongly negatively associated with litter size, and only moderately correlated with body mass. These findings reveal how gestation length directly and indirectly influences, and is influenced by, other key eutherian traits. Our study establishes a robust framework for identifying causal relationships within suites of correlated and co-evolving traits.

evolutionary biology↗

bioRxiv2023

The evolution of gestation length in eutherian mammals

Gestation length, or the duration of pregnancy, is a critical component of mammalian reproductive biology1. Eutherian mammals exhibit striking variation in their gestation lengths2-5, which has traditionally been linked to and allometrically scales with variation in other life history traits, including body mass and lifespan5-8. How the phenotypic landscape of gestation length variation, including its associations with body mass and lifespan variation, changed over mammalian evolution remains unknown. Phylogeny-informed analyses of 845 representative extant eutherian mammals showed that gestation length variation substantially differed in both whether and how strongly it was associated with body mass and lifespan across mammalian clades. For example, gestation length variation in Chiroptera and Cetacea was not associated with lifespan or body mass but was strongly associated only with body mass in Carnivora. We also identified 52 adaptive shifts in gestation length variation across the mammal phylogeny and 14 adaptive shifts when considering all three life history traits; the placements of six adaptive shifts are common in the two analyses. Notably, two of these shifts occurred at the roots of Cetacea and Pinnipedia, respectively, coinciding with the transition of these clades to the marine environment. The varying dynamics of the phenotypic landscape of gestation length, coupled with the varying patterns of associations between gestation length and two other major life history traits, raise the hypothesis that evolutionary constraints on gestation length have varied substantially across mammalian phylogeny. This variation in constraints implies that the genetic architecture of gestation length differs between mammal clades.

evolutionary biology↗

bioRxiv2020

Building a high-quality reference genome assembly for the the eastern Mediterranean Sea invasive sprinter Lagocephalus sceleratus (Tetraodontiformes, Tetraodontidae)

The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. However, the genomic resources and especially reference assemblies are sparse for the members of the family. In this study, we focus on the silver-cheeked toadfish (Lagocephalus sceleratus) a well-known invasive sprinter that has invaded and spread throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal within a decade. We sequenced the genome of L. sceleratus using a single MinION flow cell for the main assembly, and Illumina reads for polishing the assembly. The resulted assembly consisted of 241 contigs (N50 = 11,3 Mb) with a total size of 360 Mb and yielded 98% BUSCO completeness. The high-quality genome assembly built here is expected to set the ground for future studies on this focal species invasive biology.

genomics↗