weatherxbiodiversity-projection

Initial release

Canonical replication of Soroye et al. 2020 (Climate change contributes to widespread declines among bumble bees across continents, 10.1126/science.aax8591) for **Iberian *Bombus***, with a future projection under DestinE Climate DT SSP3-7.0.

Two tiers.

• Tier 1 — historical fit. Replicates Soroye's GLMM on Iberian Bombus using Soroye's bundled CRU TS 3.24.01 climate inputs (Figshare deposit) and own-issued GBIF Iberian Bombus download DOIs. Run twice: once on the original CEA grid (~100 km), once on HEALPix nside=64 (~92 km).
• Tier 2 — future projection. Applies the fitted GLMM to DestinE Climate DT SSP3-7.0 (IFS-NEMO standard, native HEALPix nside=128) for the 2020–2029 and 2030–2039 horizons via polytope on LUMI. Tier 2 only runs on the DestinE Jupyter platform; Tier 1 runs anywhere.

Headline result — Tier 1

The GLMM coefficient on standardised TEI_delta is positive, large, and credible at both spatial substrates:

• CEA (~100 km cells): +0.479 (replicates Soroye's published value within ±5%).
• HEALPix nside=64 (~92 km cells): +0.454, 95% HDI [+0.130, +0.751].

Both within ±30 percent of each other; same sign and order of magnitude as the original. Soroye's central biological claim — that thermal-niche exceedance increases extirpation probability — replicates on Iberian Bombus at two independent pixelisations. A higher-resolution sibling study at HEALPix nside=128 finds +0.347, HDI [+0.139, +0.533] — confirming substrate-robustness across three independent pixelisations.

Headline result — Tier 2

Under SSP3-7.0 at 2030–2039, mean future TEI rises from ~0.43 (historical) to ~0.45–0.50, a systematic drift toward each species' upper thermal niche edge. None of the studied Iberian Bombus species hits TEI > 1 (Soroye's actual extirpation threshold) at any currently-occupied cell over the next 15 years — the extirpation event is a longer-timescale phenomenon, with 2030–2039 being the early-warning period.

The substrate-stable per-species ranking (filtered to species with at least 10 occupied cells per substrate, using main-effects-only η at projection time):

• Highest-risk: B. humilis, B. muscorum, B. ruderarius — short-tongued grassland specialists already documented in decline elsewhere in Europe.
• Lowest-risk: B. terrestris, B. pascuorum, B. pratorum — dominant Western Palearctic generalists.

The substrate-stable Iberian projection independently identifies the same European high-risk species the long-term monitoring data flag.

Caveat — small-N species

Per-species ranking under SSP3-7.0 is grid-coupled at the projection step for species observed in fewer than ~10 historical Iberian cells (18 of 31 species in the study, including the narrowly-distributed Pyrenean specialists B. pyrenaeus, B. mucidus, B. mendax, B. wurflenii, B. monticola). The mechanism, validated and refuted hypotheses, and recommended reporting protocol are documented in the methodological sibling weatherxbiodiversity-substrate-sensitivity.

Reproducibility

git clone https://github.com/annefou/weatherxbiodiversity-projection.git
cd weatherxbiodiversity-projection
mamba env create -f environment.yml
mamba activate weatherxbiodiversity-projection
snakemake --cores 1            # Tier 1 (CEA + HEALPix)
snakemake --cores 1 tier2      # Tier 2 (DestinE) — needs DestinE credentials

Or with Docker (Tier 1 only): docker run --rm ghcr.io/annefou/weatherxbiodiversity-projection:latest.

Data sources

• Climate (Tier 1 fit + niche limits): CRU TS 3.24.01 from Soroye's Figshare deposit (kept identical to original).
• Occurrences: GBIF, own-issued download DOIs for Iberian Bombus.
• Climate (Tier 2 projection): DestinE Climate DT SSP3-7.0, IFS-NEMO standard, native HEALPix nside=128 via polytope on LUMI.

Companions

• weatherxbiodiversity-projection-nside128 — substrate extension with full GLMM refit at HEALPix nside=128.
• weatherxbiodiversity-substrate-sensitivity — methodological diagnostic that combines both single-substrate replications.

The Jupyter Book is at https://annefou.github.io/weatherxbiodiversity-projection/.