Preprints
Filtering by Subject: Evolution
Toxin resistance mechanisms span biological scales in the Royal Ground Snake (Colubridae: Erythrolamprus reginae)
Published: 2025-06-13
Subjects: Animal Sciences, Behavior and Ethology, Biology, Cellular and Molecular Physiology, Comparative and Evolutionary Physiology, Ecology and Evolutionary Biology, Evolution, Genomics, Integrative Biology, Life Sciences, Molecular Biology, Neuroscience and Neurobiology, Physiology, Systems and Integrative Physiology Life Sciences, Systems Biology, Zoology
Exposure to multiple toxic compounds imposes diverse selective pressures, potentially leading to a toxin-resistant phenotype that operates across biological levels. There are several known toxin resistance mechanisms–such as behavioral avoidance, metabolic detoxification, and target-site insensitivity. However, most studies have been conducted with exposure to a single toxin or have focused on [...]
Seabird range contraction and dispersal under climate change
Published: 2025-06-03
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Many marine ectotherms have historically adapted to local climate change by evolving smaller body sizes, reducing their energy demands in warmer waters but limiting their dispersal and speciation rate. Whether endothermic marine species respond similarly remains unclear, as temperature minimally affects their size diversity, and the drivers of their dispersal and speciation are poorly understood. [...]
Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions
Published: 2025-06-03
Subjects: Evolution, Genetics and Genomics, Life Sciences
Genes that don't have identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been found in many other species. This has fostered a whole field of research aiming at tracing back their evolutionary origin and functional significance. Orphan genes represent an [...]
Cellular Innovations and Diversity in the Lepidopteran Compound Eye
Published: 2025-05-28
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Entomology, Evolution, Life Sciences, Molecular Genetics
Lepidoptera, having co-diversified with flowering plants and adapted to various diel niches, present a remarkable system for studying compound eye cell type diversity. Here we synthesize the latest research regarding lepidopteran eye evolution across different timescales, from species-level variation to family-level changes, and mechanistic levels, from broad anatomical variation to molecular [...]
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-06
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed tree topology, it would be natural to use IQ-TREE to obtain the tree. However, it is currently not possible to integrate these tools seamlessly, as MCMCTree [...]
Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation
Published: 2025-05-06
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on radically different datatypes (e.g., discrete and morphometric) and methods (phylodynamic vs comparative methods). Here, we ask whether these competing approaches [...]
“A history of the world imperfectly kept”: Will we ever know how biodiversity has changed over deep time?
Published: 2025-05-03
Subjects: Biodiversity, Evolution, Paleobiology
The fossil record is our only direct source of evidence for how life on Earth has waxed and waned over its long history. However, the fossil record is also incomplete and biased in many ways, after passing through biological, geological, and socio-economic filters. This means that we only possess snapshots of information, relating to specific places and times in Earth history, from which to try [...]
Mechanistic and Phylogenetic Perspectives on Pregnancy Sickness
Published: 2025-04-14
Subjects: Behavior and Ethology, Comparative and Evolutionary Physiology, Endocrinology, Evolution, Maternal and Child Health
Evolutionary biologists have long been fascinated by the peculiar trait of pregnancy sickness, the syndrome experienced by two-thirds of pregnant individuals which includes nausea and vomiting of pregnancy and, in 2% of cases, progresses to a pathological extreme known as hyperemesis gravidarum. With the recent discovery of the placental hormone GDF15 as the main causal factor in pregnancy [...]
Deep-learning technology provides insights into the morphological evolution of birds
Published: 2025-04-09
Subjects: Biodiversity, Bioinformatics, Computational Engineering, Evolution, Life Sciences, Ornithology, Research Methods in Life Sciences
The evolution of biological morphology is critical for understanding the diversity of the natural world, yet traditional analyses often involve subjective biases in the selection and coding of morphological traits. This study employs deep learning techniques, utilizing a pretrained ResNet34 model capable of recognizing over 10,000 bird species, to explore avian morphological evolution. We [...]
Plant genomic variation and its implications for proposed EU NGT legislation
Published: 2025-04-09
Subjects: Biotechnology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics, Plant Breeding and Genetics Life Sciences, Plant Sciences
The European Commission proposal for New Genomic Techniques (NGTs) of July 2023 specifies that NGT1 plants, which are considered equivalent to conventional plants, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be of any size and number. Here, we examine the proposed 20/20 NGT1 limit against the background of the [...]
The molecular evolutionary basis of species formation revisited
Published: 2025-04-09
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences
How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers leads to the origin of new species was proposed nearly 90 years ago. However, empirical evidence for the genetic mechanisms that cause reproductive barriers took many decades to accumulate. In 2010, Presgraves presented a comprehensive review of the [...]
Ecological harshness mediates reproductive trade-offs in a great tit population
Published: 2025-04-06
Subjects: Ecology and Evolutionary Biology, Evolution, Population Biology
Lack’s seminal work on bird clutch sizes has spurred expansive research on reproductive trade-offs, especially focusing on offspring quantity–quality trade-offs and the potential fitness consequences for the parents. The environment is a critical driver of the expression of individual reproductive traits, influencing them through plastic responses. However, the plasticity of reproductive [...]
Variability, drivers, and utility of genetic diversity-area relationships in terrestrial vertebrates
Published: 2025-04-03
Subjects: Biodiversity, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Life Sciences
Maintaining genetic diversity within and among populations is critical for conservation and a prominent goal of the Kunming-Montreal Global Biodiversity Framework. However, direct estimates of genetic diversity are unavailable for most species, and time and resources are insufficient to fill these substantial data gaps and meet conservation target timelines. Robust, proxy-based predictions of [...]
Evolution under fluctuating conditions and exposure to heatwaves in the seed beetle, Callosobruchus maculatus
Published: 2025-03-24
Subjects: Evolution
Heatwaves, temporary periods of elevated temperatures, are increasing both in magnitude and in frequency and have been shown to have devastating negative effects on a wide range of taxa. However, to date, most studies investigating the impacts of heatwaves have either focus on populations that have evolved under constant conditions prior to assaying or, more importantly, only investigated the [...]
Quantifying macro-evolutionary patterns of trait mean and variance with phylogenetic location-scale models
Published: 2025-03-24
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences
Understanding how both the mean (location) and variance (scale) of traits differ among species and lineages is fundamental to unveiling macroevolutionary patterns. Yet, traditional phylogenetic comparative methods primarily focus on modelling mean trait values, often overlooking variability and heteroscedasticity that can provide critical insights into evolutionary dynamics. Here, we introduce [...]