Data from: Avoiding impacts of phylogenetic tip-state-errors on dispersal and extirpation rates in alpine plant biogeography

Aim: Many biogeographic analyses require some form of automated state
assignment to tips of phylogenetic trees, reflecting a species presence or
absence in a particular area, e.g., a biome. As datasets get exponentially
larger, such procedures may increasingly induce errors (here called
tip-state-error), but the specific algorithmic cause and consequence on
downstream estimation of dispersal and extinction rates remains poorly
known. We aim to improve automated tip-scoring methods in the context of
the alpine biome by leveraging elevation information. We document the
profound effect of tip-state-errors on Dispersal-Extirpation-Cladogenesis
(DEC) models. Location: The European Alpine Arc. Taxon: 3’317 vascular
plant species, emphasizing six focal clades: Campanula, Carex, Festuca,
Ranunculus, Saxifraga, and Viola. Methods: We use GBIF data to classify
whether species occur above the upper climatic treeline using a newly
developed algorithm ElevDistr or a gridded landscape model of thermal
belts, under various filtering thresholds. We compared classification
performance using the Flora Alpina as validation data. To determine if
tip-state-error biases the dispersal and extirpation rate estimation, we
fit DEC models for selected clades using tip-states from different
classification models. Results: ElevDistr is less error prone than other
approaches. Filtering thresholds lower the false positive rate but
increase the false negative rate. Inflated false positive rates bias the
dispersal rate estimation upward, while inflated false negative rates lead
to upward bias in extirpation rate estimation. Main conclusions: Even
moderate tip-state-error may lead to profound systematic bias in dispersal
and extinction rate estimation if an unbalanced ratio between false
positive and false negative rates occurs. Therefore, careful validation is
imperative, though ElevDistr alleviates this problem in the context of the
alpine environment. Overall, our results document contrasting rates of
alpine biome shifts across the studied genera and have major implications
for studies addressing the likelihood of niche evolution versus geographic
dispersal.