Selective Preservation of Past Life: Which Ecological Signals Survive in the Fossil Record?

This repository contains the computational materials associated with the manuscript Selective Preservation of Past Life: Which Ecological Signals Survive in the Fossil Record?, submitted to Ecography. The study uses present-day mammalian biodiversity as a reference to evaluate how simulated fossil-record incompleteness alters the representation of different biodiversity properties. Five sequential filters account for sediment availability, geographical range size, adult body mass, fossil-site distribution and taxonomic sampling. Three species-retention scenarios (25%, 50% and 75%) are evaluated. The analyses examine changes in mammalian species richness across five Köppen–Geiger climatic biomes and geographical regions, richness patterns across temperature–precipitation space, functional trait probability distributions based on maximum longevity and litter size, and the relative representation of five mammalian orders: Carnivora, Rodentia, Cetartiodactyla, Primates and Chiroptera. The computational workflow was developed in R and is organized into scripts for data preparation, sequential filtering, biodiversity analyses and figure generation. The analyses use mammalian distribution information from the IUCN Red List, taxonomic and trait information from COMBINE, climatic variables from WorldClim 2.1, sediment information from the Global Unconsolidated Sediments Map and fossil occurrence records from the Paleobiology Database. The simulations evaluate three retention scenarios using a fixed random seed (288), with one stochastic realization per scenario. The resulting analyses describe changes across sequential filtering stages rather than independent effects of individual preservation processes. The materials are provided for scientific evaluation and reproducibility. Access to original third-party datasets remains subject to the licensing and redistribution conditions established by their respective providers.