Buss, D. L. | bioRxiv Science

bioRxiv2025

2000-year fish bone record reveals transition to commercial fisheries during climatic change

Animal bones from archaeological contexts can reveal the interplay between past environments and human societies. Resource acquisition shaped many aspects of past societies and influenced the development of trade networks and migration. Fish have been a cornerstone of human subsistence for millennia, yet the rise of commercial fishing and trade was complex. Here, we synthesised a database of [~]1.9 million zooarchaeological fish records spanning 2000 years across Europe. Using machine-learning of catch compositions alongside fish thermal tolerances, we show that fisheries became less local over time, with homogenisation coinciding with Little Ice Age-associated cooling, a period of documented resource scarcity, concurring with growing trade. Moreover, increased proportions of marine taxa and more specialist marine fisheries were observed in the preceding Medieval Climate Anomaly, to sustain concurrent urban and population growth. Enhanced use of marine protein buffered food insecurity, whilst signalling the transition from localised to trans-regional trade networks.

ecology↗

bioRxiv2023

A standard protocol to report discrete stage-structured demographic information

O_LIStage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology, and conservation science. Accordingly, MPMs now exist for over 3,000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. C_LIO_LIHere, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. C_LIO_LIOver 80% of surveyed researchers (n=60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility, and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardized protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare, and Zenodo. C_LIO_LICombining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology, and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility. C_LI

ecology↗