Preprints
Filtering by Subject: Evolution
Complete de novo assembly of Wolbachia endosymbiont of contemporary Drosophila simulans using long-read genome sequencing.
Published: 2025-10-09
Subjects: Evolution, Genomics
We present a contemporary high-quality, complete de novo assembly of Wolbachia pipientis (wRi Merrill 23, CP199298), an alphaproteobacterial endosymbiont of Drosophila simulans. This assembly was generated using long read sequencing of wRi-infected D. simulans embryos collected from the Merrill College at the University of California, Santa Cruz in October 2023.
What fraction of the genomic basis of local adaptation are we missing?
Published: 2025-10-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences
How will species adapt to changing environments? To what extent does adaptation to previous conditions maintain the variation needed to adapt to future conditions? To answer these kinds of questions, we need to identify locally adaptive alleles and quantify their effects. Theory shows that the architecture of adaptation can depend upon the nature of mutation and on how ecology shapes the [...]
PyTLidar: A Python Package for Tree QSM Modeling from Terrestrial Lidar Data
Published: 2025-09-17
Subjects: Computer Sciences, Evolution, Other Forestry and Forest Sciences
PyTLidar is an open-source Python package that reconstructs 3D tree Quantitative Structure Models (QSM) from Terrestrial Lidar Scanning (TLS) data, providing a user-friendly tool that improves and expands upon the MATLAB-based TreeQSM method. QSMs are used to automate detection and calculation of various topological and volumetric measurements that would normally take great effort to gather in [...]
A standardised framework for classifying estimates of reproductive isolation across the Tree of Life
Published: 2025-09-10
Subjects: Evolution
Understanding reproductive isolation (RI) between lineages is a central goal of speciation research. While the strength of RI has been estimated across a broad range of taxa, synthesising these data remains challenging, partially because we lack a common language for classifying and reporting RI estimates. Here, we present the Reproductive Isolation Ontology (RIO), a structured framework designed [...]
Lateralisation shapes spatial learning in lizards
Published: 2025-08-31
Subjects: Behavior and Ethology, Biology, Evolution, Other Ecology and Evolutionary Biology
Spatial memory is fundamental cognitive process that allows animals to navigate and interact with their environment effectively. While extensively studied in mammals and birds, the mechanisms underlying spatial cognition in reptiles remain less understood. In this study, we investigated spatial learning and the potential influence of behavioural lateralisation in the common wall lizard (Podarcis [...]
Frequent shifts in pollination strategy are decoupled from diversification in the terrestrial orchids
Published: 2025-08-27
Subjects: Biodiversity, Bioinformatics, Biology, Botany, Ecology and Evolutionary Biology, Evolution, Life Sciences, Plant Sciences
Pollinator attraction strategies are central to orchid reproductive biology and have long been hypothesised to accelerate speciation rates, particularly through specialised coevolutionary interactions. However, most macroevolutionary evidence comes from studies of individual genera or tribes, leaving broad-scale patterns unresolved. Here, we reconstruct the evolution of pollination strategy in [...]
Fast evolving flowers drive cactus diversification
Published: 2025-08-22
Subjects: Biodiversity, Bioinformatics, Botany, Ecology and Evolutionary Biology, Evolution, Life Sciences
The rise of biodiversity is shaped by variation in diversification rates. Across the Tree of Life, numerous forces are thought to influence these rates, including the evolution of adaptive traits, climate change, and interactions with other organisms. In the flowering plants, a longstanding hypothesis favoured by Darwin suggests that floral evolution is a driving force for plant diversity. [...]
Changes in pollen production, pollen heteromorphism and ovule production with increased selfing in Viola arvensis
Published: 2025-08-21
Subjects: Ecology and Evolutionary Biology, Evolution, Plant Biology, Population Biology
Predictive Evolutionary Genomics: Principles, Validation, and Practice
Published: 2025-08-11
Subjects: Agriculture, Biodiversity, Ecology and Evolutionary Biology, Evolution, Genomics, Life Sciences, Plant Sciences, Population Biology
Contemporary evolution occurs on observable timescales, enabling prospective evolutionary forecasting with quantitative frameworks rather than only retrospective inference. We propose a unified probabilistic framework that integrates three approaches linked to detectability windows through time. Trait-based models use multivariate quantitative-genetic equations to project correlated phenotypic [...]
Latitudinal genetic diversity gradients steepen toward the poles
Published: 2025-07-22
Subjects: Evolution, Genetics, Population Biology
Latitudinal biodiversity gradients are among the best-described biogeographic patterns. However, there is little agreement on whether genetic diversity, the most fundamental level of biodiversity, is also latitudinally distributed. The confusion about the distribution of genetic diversity at biogeographic scales stems in part from the fact that genetic diversity gradients have been described for [...]
Habitat availability, Jurassic and Cretaceous origins of the deep-bodied shark morphotype, and the rise of pelagic sharks
Published: 2025-07-18
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Macroevolutionary trends in morphology fundamentally shape our understanding of marine ecosystems through deep time. Sharks (Elasmobranchii: Selachii) have been suggested to broadly exhibit two discrete body forms: one ‘shallow-bodied’ form associated with slow-moving benthic species, and a ‘deep-bodied’ form typified by highly active pelagic taxa. Until now, the validity or evolution of these [...]
A systems-modelling approach to predict biological responses to extreme heat
Published: 2025-07-16
Subjects: Animal Sciences, Comparative and Evolutionary Physiology, Evolution, Integrative Biology, Other Ecology and Evolutionary Biology, Systems and Integrative Physiology Life Sciences, Systems Biology
Anthropogenic climate change is leading to more frequent and extreme heat waves. These short-term but large-scale events are radically re-shaping interactions among organisms – impacting biodiversity, community composition and ecosystem services crucial to natural systems and food security. Predicting heat wave impacts on interacting species requires an understanding of the processes driving [...]
Allometry and shared ancestry, rather than ecology, shapes the evolution of 3D eye size in temperate butterflies
Published: 2025-06-24
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences, Other Ecology and Evolutionary Biology
Sensory traits shape animal lifestyles due to the central role they play in retrieving and processing environmental information. However, being some of the most energetically expensive tissues to build and maintain, ecological demands often modulate investment in these organs. Evidence that ecology shapes the evolution of sensory traits is plenty but is heavily biased towards vertebrates and has [...]
Female driven reduction of sexual dimorphism in hominins
Published: 2025-06-21
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Sexual dimorphism is a key indicator of social structure and selective pressures in primate evolution, yet its evolutionary drivers in hominins remain contentious. Here, we combine cutting edge dimorphism estimation methods, with Bayesian phylogenetic comparative analyses to disentangle the sex-specific contributions and evolutionary dynamics underlying changes in body mass and canine size across [...]
From vocal homophily to vocal repertoire flexibility: Unravelling the socioecological drivers of language evolution
Published: 2025-06-16
Subjects: Animal Studies, Anthropology, Behavior and Ethology, Evolution
Since diverging from the last common ancestor with bonobos and chimpanzees, the communication system of the hominin lineage underwent a radical transformation. Vocal production learning - the ability to produce novel vocalizations based on experience - is the necessary pre-condition for changing an ape-like communication system into one that is infinitely flexible, extensively learned, and [...]