Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates

Most described species have not been explicitly included in phylogenetic trees—a problem named the Darwinian shortfall—due to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group where at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully-sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Therefore, future efforts shou..., (a)   Phylogenetic assessment and species-level covariates
We firstly identified which tetrapod species had their evolutionary relationships imputed in fully-sampled phylogenies available for the group (1–5), thus creating a binary response variable for 33,281 species included in such phylogenies. We excluded 228 marine species (according to the International Union for Conservation of Nature — IUCN), keeping only terrestrial vertebrates (n = 33,053) in subsequent analyses. We then selected eight putative predictors to investigate how species’ biology, geography and biodiversity appeal, and socioeconomic-related factors affect the probability of species being imputed on phylogenies. Many predictors used here comes from the TetrapodTraits, a recent database for the world’s tetrapod including standardised species-level attributes (6). Below, we outline the attributes used as predictors, along with brief explanations of how they were computed.
The year of species description was based on th..., , # README: Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates

[https://doi.org/10.5061/dryad.wdbrv15ww](https://doi.org/10.5061/dryad.wdbrv15ww)

There are five main documents associated with this paper:

(*1*) our raw data (**AdditionalVars.csv**); (*2*) marine taxa as per the IUCN (**marine_spp_IUCN.csv**); (*3*) phylogenetic trees for amphibians, birds, mammals, and reptiles stored in a zip file (**phylo_trees.zip**); (*4*) outputs from phylogenetic autocorrelation analyses (**phylocorr_outs.zip**); and (*5*) the R code (**Rcode_DarwinianShortfalls.R**).

## Description of the data and file structure

(*1*) **AdditionalVars.csv**; contains 3 columns, each one explained below:

* Scientific.Name: scientific name of each species included in the most fully-sampled phylogenies for tetrapods.

- sequenced: Informs if there is any genetic data available for each species (data obtained from Smid 2022; DOI: 10.1111/jbi.14491)

* GBIF_occ: Total number of pr...