Preprints
Filtering by Subject: Ecology and Evolutionary Biology
Mitochondrial genome evolution: the influence of partitioning, calibration, and gene heterogeneity on pleurodontan substitution rates
Published: 2025-09-15
Subjects: Ecology and Evolutionary Biology, Genetics and Genomics, Molecular Genetics
Substitution rate estimates are a key source of information in modern evolutionary biology, underpinning divergence time inference and other evolutionary analyses. Mitochondrial DNA nucleotide substitution rates, in particular, are commonly used for these purposes. However, these rates are typically derived from a small set of genes, closely related species, or from a limited number of model [...]
Ecosystem dynamics in dry heathlands: spatial and temporal effects of environmental drivers on the vegetation
Published: 2025-09-11
Subjects: Ecology and Evolutionary Biology, Life Sciences
To understand and estimate the effects of environmental drivers on temperate dry heathland vegetation, pin-point cover data from 102 Danish sites sampled during a 16-year period was regressed onto selected environmental variables. The effects of nitrogen deposition, soil pH, soil C-N ratio, soil type, precipitation and grazing on the heathland vegetation was modelled in a spatio-temporal [...]
squidSim: a flexible R package for structured and reproducible simulations in Ecology and Evolutionary Biology
Published: 2025-09-10
Subjects: Ecology and Evolutionary Biology, Statistical Methodology
1. Complex statistical methodology now allows a growing array of questions to be addressed in ecology and evolutionary biology. However, the particular question being addressed or the complex nature of the data collected often raise issues with how statistical models perform and potentially limit inference. Simulations provide a powerful approach to help empiricists understand the assumptions, [...]
Natural developmental temperatures of ectotherms: A systematic map and comparative analysis
Published: 2025-09-10
Subjects: Ecology and Evolutionary Biology, Life Sciences
In ectothermic animals, physiological processes are highly sensitive to environmental temperatures. Developmental temperatures, in particular, have large and long-lasting impacts on ectotherm phenotypes. However, most phenotypic responses are studied in the laboratory, and may not accurately reflect ecological impacts in natural environments. In this study, we provide the first synthesis of [...]
Mapping the landscape of live baitfish regulations for aquatic invasive species prevention in the United States
Published: 2025-09-10
Subjects: Aquaculture and Fisheries Life Sciences, Biodiversity, Ecology and Evolutionary Biology, Environmental Policy, Marine Biology, Public Policy
Aquatic invasive species (AIS) pose a significant risk to global ecosystems, economies, and societies. In the United States, the live baitfish trade is a major pathway for their spread. While the presence of invasive species and pathogens in this trade has been documented, a comprehensive, nationwide analysis of the regulations governing live baitfish has been lacking. This study fills that gap [...]
Fossils for Future: the billion-dollar case for paleontology’s digital infrastructure
Published: 2025-09-10
Subjects: Arts and Humanities, Bioinformatics, Earth Sciences, Ecology and Evolutionary Biology, Life Sciences, Other Arts and Humanities, Physical Sciences and Mathematics
The digital revolution has transformed paleontology through the development of open-access, community-driven databases that underpin some of the most impactful research in biodiversity, climate change, and extinction dynamics. These systems safeguard high-effort, volunteered data and have revealed major macroevolutionary patterns, including mass extinctions. However, of 118 paleontological and [...]
Interaction Matrices as Unifying Tools for Navigating Ecological Complexity
Published: 2025-09-04
Subjects: Ecology and Evolutionary Biology, Life Sciences
Interaction matrices summarise pairwise species impacts within ecological communities into an analytically tractable format and have been central to advancing our understanding of ecosystem dynamics. However, despite their ubiquity, they have faced constant, recurring, criticism for oversimplifying ecological complexity. While suggested extensions address specific shortcomings, they often come [...]
Revealing the unknown world of the endangered Lear's macaw using GPS-tracking data: identification of critical habitats for conservation
Published: 2025-08-31
Subjects: Biology, Ecology and Evolutionary Biology
Understanding space use and home range is essential for the conservation planning of threatened species as it helps to assess the suitability, extent, and placement of conservation areas that are imperative for species survival and protection. The Endangered Lear’s macaw (Anodorhynchus leari), a highly mobile frugivore, feeding specialist and endemic to Brazil’s Caatinga dry forest, faces ongoing [...]
High-resolution range mapping of mycorrhizal fungal species reveals systematic biases in their protection
Published: 2025-08-31
Subjects: Ecology and Evolutionary Biology, Environmental Studies
Mycorrhizal fungi are essential to ecosystem functioning but have been overlooked in conservation agendas due to data limitations and a historical focus on plants and animals. We present the first global, species-level assessment of the area-based conservation of mycorrhizal fungi. Using 16.5 million site-by-taxon presence–absence records, we created high-resolution range maps for 189 arbuscular [...]
Frequent shifts in pollination strategy are decoupled from diversification in the terrestrial orchids
Published: 2025-08-28
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 [...]
Modelling complex habitat use for threatened bat species decision-making in landscapes with competing priorities
Published: 2025-08-27
Subjects: Animal Sciences, Biodiversity, Desert Ecology, Ecology and Evolutionary Biology, Environmental Studies, Life Sciences, Zoology
Species distribution models (SDMs) provide valuable information to aid conservation decisions, particularly in landscapes where economic and biodiversity priorities compete. Generating SDMs for species that rely on discrete habitat types for different activities (e.g. roosting or foraging) can be challenging, and result in outputs that are not appropriately tailored for end use. We collated [...]
Long-read sequencing for biodiversity analyses - a comprehensive guide
Published: 2025-08-26
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Environmental Monitoring, Genetics and Genomics, Life Sciences
DNA-based monitoring of biodiversity has revolutionised our ability to describe communities and rapidly assess anthropogenic impacts on biodiversity. Currently established molecular methods for biomonitoring rely heavily on classic metabarcoding utilising short reads, mostly through Illumina data. However, increasingly more studies use long-read sequencing technologies, such as Oxford Nanopore [...]
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. [...]
Herbarium specimens reveal long-term decline in pollination services since in the 1970s
Published: 2025-08-22
Subjects: Biodiversity, Botany, Ecology and Evolutionary Biology, Environmental Monitoring, Natural Resources and Conservation, Other Ecology and Evolutionary Biology, Plant Biology, Plant Sciences
Anthropogenic change has resulted in pollinator decline and altered plant-pollinator interactions. This may drive widespread declines in pollination and reproductive success of plants, yet few datasets allow us to track changes in pollination services over time. Herbaria provide a unique opportunity to assess pollination services across broad spatial and temporal scales, and the associated [...]
Sydney Phylogenetics Workshop: Lessons from the past 15 years
Published: 2025-08-22
Subjects: Ecology and Evolutionary Biology
Phylogenetic analysis forms an important component of research in the life sciences, enabling the study of evolutionary relationships, timescales, patterns, and processes. Phylogenetic trees are used in a wide variety of research fields, including molecular ecology, taxonomy and systematics, conservation genetics, and microbiology. Accordingly, there is a strong demand for accessible training in [...]