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Abstract Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We presentBeeBDC, a newRpackage, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducibleBeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and, we added record-level flags for a series of potential quality issues. These data are provided in two formats, “cleaned” and “flagged-but-uncleaned”. TheBeeBDCpackage with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducibleRworkflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.
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This content will become publicly available on November 1, 2026
ppgm: an R package for integrating neontological, palaeontological, and climate data in a phylogenetic comparative framework
Abstract Understanding how changes in climate affect habitat availability for species through time is critical for macroevolutionary, ecological, and conservation research. When combined with palaeoclimate reconstructions, the fossil record provides insights into how species' geographic distributions have responded to past climate shifts, including under non‐analogous climate conditions. Palaeophylogeographic models (PPGMs) offer a framework to integrate modern and palaeontological data into phylogenetic comparative analyses of species climate tolerances. TheppgmR package is an implementation of PPGMs, which estimates species climate envelopes, reconstructs ancestral climatic tolerances across phylogenies, and projects these onto palaeoclimatic maps to identify climatically available regions through time. The package also supports direct inclusion of fossil occurrences with associated palaeoclimatic data, allowing a reconstruction of past trends of species climate tolerances projected into palaeoclimatic maps to pinpoint the locations of climate availability through time according to the fossil record. We demonstrate the broad applicability ofppgmthrough detailed case studies, showing its potential for addressing research questions in macroevolutionary and conservation palaeobiology research. Theppgmpackage complements existing R packages by allowing researchers to use analytical techniques on large integrated datasets and facilitates reproducible analyses of species climate niches over deep and shallow time.
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- PAR ID:
- 10682278
- Publisher / Repository:
- John Wiley & Sons
- Date Published:
- Journal Name:
- Palaeontology
- Volume:
- 68
- Issue:
- 6
- ISSN:
- 0031-0239
- Subject(s) / Keyword(s):
- palaeobiogeography, palaeoclimatic reconstruction, climate niche, fossil data integration, phylogenetic comparative methods, R package.
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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