DOI: 10.5061/dryad.wstqjq2wj
title: Data from: The interaction between the Linnean and Darwinian shortfalls affects our understanding of the evolutionary dynamics driving diversity patterns of New World coralsnakes

description: Aim: In this study, we sought to understand how the Linnean shortfall
 (i.e., the lack of knowledge about species taxonomy) interacts with the
 Darwinian shortfall (i.e., the lack of knowledge about phylogenetic
 relationships among species), which potentially jeopardizes geographical
 patterns in estimates of speciation rates. Location: New World Taxon:
 Coralsnakes (Serpentes: Elapidae) Methods: We created an index of
 taxonomic uncertainty (ITU) that measures the likelihood of current
 species being split after undergoing future taxonomic revisions. The ITU
 was used in simulations where species with higher taxonomic uncertainty
 had a higher likelihood of having their phylogenetic branches split,
 generating new hypothetical species along their geographic ranges. We
 estimated the speciation rates before and after the split of taxonomically
 uncertain species. Results: We found that a high number of coralsnake
 species display substantial taxonomic uncertainty, positively correlated
 with the latitude of the species' geographical range centroid. The
 estimated speciation rates based on currently available data have a weak
 relationship with latitude. However, after incorporating taxonomic
 uncertainty into the phylogeny, we detect a higher positive correlation
 between speciation rate and latitude. Main conclusions: The observed
 change in speciation rates following the incorporation of taxonomic
 uncertainty highlights how such uncertainty can undermine the empirical
 evaluation of geographical patterns in speciation rates, revealing an
 interaction between the latitudinal taxonomic gradient and the latitudinal
 diversity gradient. Given that taxonomic changes can alter the number of
 species recognized as valid over time, our study highlights the need to
 incorporate taxonomic uncertainty into macroecological and
 macroevolutionary studies, enhancing the robustness of patterns inferred
 from these data. --
description: Data List of accepted species and their
 description years: New World coralsnake accepted species and description
 years were obtained from Silva Jr. et al. (2021a).
 Maximum body size: The maximum body size was obtained from
 Feldman et al. (2015), Silva Jr. et al. (2021b), and the specialized
 literature. Number of synonyms: The number of synonyms
 was obtained from the Reptile Database (Uetz et al., 2022) and Silva Jr.
 et al. (2021b). Published papers: The number of
 published papers for each species was obtained from searches in Web of
 Science and Scopus using the accepted species name and its
 synonyms. Taxonomic uncertainty: We distributed a
 questionnaire to taxonomists specializing in coralsnakes and asked them
 what the likelihood was of each species undergoing a splitting.
 Taxonomists could answer with “very unlikely,” “unlikely,” “likely,” or
 “very likely.” We assigned a value range from 1 (very unlikely) to 4 (very
 likely) and obtained the average of the taxonomists’ answers for each
 species. Macroecological variables: Occurrence records
 were gathered from the Global Biodiversity Information Facility (GBIF,
 https://www.gbif.org/), scientific literature, and vouchers from museums and biological collections. Records retrieved from GBIF underwent a cleaning process. We calculated the number of occurrence records for each species. We used the occurrence records to generate the geographic range for each species using minimum convex polygons and calculated the range size in square kilometers. We also obtained the centroid for each species. Phylogenetic tree: The phylogeny was obtained from Tonini et al. (2016). Species in Tonini’s phylogeny that were not considered valid by our list of accepted species were removed, and accepted species not present in Tonini’s phylogeny were included based on taxonomy. We explored uncertainty in branch lengths by obtaining one thousand phylogenetic trees. Data analysis We calculated the speciation rate using the DR statistic proposed by Jetz et al. (2012) for each species. We performed a Phylogenetic Generalized Least Squares (PGLS) where the eight variables mentioned above (year of description, number of occurrence records, number of papers, DR, number of synonyms, latitude of the centroid, body size, and range size) were used to model the taxonomists’ responses. The estimated values of the model were scaled to vary between 0 and 1 and were used as our Index of Taxonomic Uncertainty (ITU). Values closer to 1 indicate high taxonomic uncertainty (i.e., high likelihood of species splitting), while values closer to 0 indicate low taxonomic uncertainty (i.e., low likelihood of species splitting). ITU was used in simulations where species with high ITU had a higher likelihood of undergoing splitting, generating new sister species in phylogenetic trees. For each of the 1,000 phylogenetic trees, 100 new phylogenies were generated. To estimate the effect of latitude on speciation patterns, we performed two PGLS models. The first model considered the DR statistic as a function of latitude (formula: DR ~ latitude), while the second model incorporated a quadratic term to account for non-linear trends in speciation patterns (formula: DR ~ latitude + latitude²).
description: --- ##### This repository contains all data, scripts, and functions
 related to the manuscript titled *'The interaction between the
 Linnean and Darwinian shortfalls affects our understanding of the
 evolutionary dynamics driving diversity patterns of New World
 coralsnakes*' published in the *Journal of Biogeography.* **R
 scripts:** contains all R scripts used to run analyses and generate
 figures for the results of these analyses. **(1) ITU.R:** R script used to
 perform PGL regression, where eight macroecological and taxonomic
 variables were used to model taxonomists’ responses. **(2) Maps.R:** R
 script used to generate Figure 2. **(3)
 Script_micurus_tese_novo_26_02_2024_10_22.R:** R script used to perform
 the simulations in which species with a higher ITU had a higher likelihood
 of having their branches split in the phylogenetic trees. **(4)
 Simulation_analysis.R:** R script used to analyze the results of
 simulations and to generate Figure 3. **(5) Creating_metadata.R: **R
 script for creating metadata for the output of simulations.  **Raw data:
 contains the raw data used to create the Index of Taxonomic Uncertainty,
 perform the simulations, and generate the figures.** **(1)
 Coralsnakes_data_ITU.xlsx: data used to perform PGLS regression analysis
 and to generate the index of taxonomic uncertainty (ITU).** **Species:**
 list of the 85 New World coralsnake species **Description date:** date of
 description of each New World coral snake species multiplied by -1. The
 date of description refers to the date on which the species was first
 described. **Latitude:** latitude of the centroid of each New World
 coralsnake species in decimal degrees taken as the midpoint of the
 geographic range. **Longitude:** longitude of the centroid of each New
 World coralsnake species in decimal degrees taken as the midpoint of the
 geographic range. **Range size:** geographic range size of each New World
 coralsnake species in square kilometers calculated from minimum convex
 polygons. **Synonyms:** number of synonyms for each New World coralsnake
 species. **Papers:** number of scientific papers for each New World
 coralsnake species in which the species is the focal taxon. **Records:**
 number of occurrence records retrieved from GBIF, scientific papers, and
 natural history museums for each New World coralsnake species. **DR:** the
 estimated DR statistic for each New World coralsnake species. **Body
 size:** total body length of each New World coralsnake species (from snout
 to tail tip) in millimeters. **Splitting:** average response of
 taxonomists regarding the likelihood of an accepted New World coralsnake
 species being split after undergoing a taxonomic revision. **(2)
 data_maps.xlsx: data used to generate Figure 2** **Species:** list of the
 85 New World coralsnake species. **Latitude:** latitude of the centroid of
 each New World coralsnake species in decimal degrees. **Longitude:**
 longitude of the centroid of each New World coralsnake species in decimal
 degrees. **ITU:** Index of Taxonomic Uncertainty for the 85 New World
 coralsnakes based on taxonomists’ responses modeled for macroecological
 and taxonomic variables. It measures the likelihood of an accepted
 coralsnake species being split into two or more species after undergoing a
 taxonomic revision. **ITU_intervals:** ITU classified in intervals of 0.2.
 **DR:** the DR statistic estimated for each New World coralsnake species.
 **DR_intervals:** DR statistic classified in intervals of 0.2. **(3)
 Vetor.xlsx: contains data used to perform simulations** **Species:** list
 of the 85 New World coralsnake species **ITU:** Index of Taxonomic
 Uncertainty for the 85 New World coralsnakes based on taxonomists’
 responses modeled for macroecological and taxonomic variables. It measures
 the likelihood of an accepted coral snakespecies being split into two or
 more species after undergoing a taxonomic revision. **LatMin:** minimum
 latitude of the geographic range for each New World coralsnake species.
 **LongMin:** minimum longitude of the geographic range for each New World
 coralsnake species. **LatMax:** maximum latitude of the geographic range
 for each New World coralsnake species. **LongMax:** maximum longitude of
 the geographic range for each New World coralsnake species. **LatC:**
 latitude of the centroid of each New World coralsnake species in decimal
 degrees. **LongC:** longitude of the centroid of each New World coralsnake
 species in decimal degrees. **(4) Micrurus.tree.tre: consensus
 phylogenetic tree used to perform PGLS regression** **(5):
 sunplin_Micrurus.txt: 1000 phylogenetic trees used in the simulations.**
 **Processed data: contains the output of the simulation.** **(1)
 Simulations_results.csv: results of simulations.**   **R2_lat_antes:**
 Adjusted R² for the linear model (formula: DR ~ latitude) before
 incorporating the Index of Taxonomic Uncertainty in the simulations and
 before splitting the species in the phylogeny. **lambda_lat_antes:** λ
 Page’s for the linear model (formula: DR ~ latitude) before incorporating
 the Index of Taxonomic Uncertainty in the simulations and before splitting
 the species in the phylogeny. **alpha_lat_antes:** α for the linear model
 (formula: DR ~ latitude) before incorporating the Index of Taxonomic
 Uncertainty in the simulations and before splitting the species in the
 phylogeny. **beta_lat_antes:** β for the linear model (formula: DR ~
 latitude) before incorporating the Index of Taxonomic Uncertainty in the
 simulations and before splitting the species in the phylogeny.
 **R2_quad_lat_antes**: Adjusted R² for the quadratic model (formula: DR ~
 latitude + latitude²) before incorporating the Index of Taxonomic
 Uncertainty in the simulations and before splitting the species in the
 phylogeny. **lambda_quad_lat_antes:** λ Page’s for the quadratic model
 (formula: DR ~ latitude + latitude²) before incorporating the Index of
 Taxonomic Uncertainty in the simulations and before splitting the species
 in the phylogeny. **alpha_quad_lat_antes:** α for the quadratic model
 (formula: DR ~ latitude + latitude²) before incorporating the Index of
 Taxonomic Uncertainty in the simulations and before splitting the species
 in the phylogeny. **beta1_quad_lat_antes:** β for the linear term of the
 quadratic model (formula: DR ~ latitude + latitude²) before incorporating
 the Index of Taxonomic Uncertainty in the simulations and before splitting
 the species in the phylogeny. **beta2_quad_lat_antes:** β for the
 quadratic term of the quadratic model (formula: DR ~ latitude + latitude²)
 before incorporating the Index of Taxonomic Uncertainty in the simulations
 and before splitting the species in the phylogeny. **R2_lat_depois:**
 Adjusted R² for the linear model (formula: DR ~ latitude) after
 incorporating the Index of Taxonomic Uncertainty in the simulations and
 after splitting the species in the phylogeny. **lambda_lat_depois:** λ
 Page’s for the linear model (formula: DR ~ latitude) after incorporating
 the Index of Taxonomic Uncertainty in the simulations and after splitting
 the species in the phylogeny. **alpha_lat_depois:** α for the linear model
 (formula: DR ~ latitude) after incorporating the Index of Taxonomic
 Uncertainty in the simulations and after splitting the species in the
 phylogeny. **beta_lat_depois:** β for the linear model (formula: DR ~
 latitude) after incorporating the Index of Taxonomic Uncertainty in the
 simulations and after splitting the species in the phylogeny.
 **R2_quad_lat_depois:** Adjusted R² for the quadratic model (formula: DR ~
 latitude + latitude²) after incorporating the Index of Taxonomic
 Uncertainty in the simulations and after splitting the species in the
 phylogeny. **lambda_quad_lat_depois:** λ Page’s for the quadratic model
 (formula: DR ~ latitude + latitude²) after incorporating the Index of
 Taxonomic Uncertainty in the simulations and after splitting the species
 in the phylogeny. **alpha_quad_lat_depois:** α for the quadratic model
 (formula: DR ~ latitude + latitude²) after incorporating the Index of
 Taxonomic Uncertainty in the simulations and after splitting the species
 in the phylogeny. **beta1_quad_lat_depois:** β for the linear term of the
 quadratic model (formula: DR ~ latitude + latitude²) after incorporating
 the Index of Taxonomic Uncertainty in the simulations and after splitting
 the species in the phylogeny. **beta2_quad_lat_depois:** β for the
 quadratic term of the quadratic model (formula: DR ~ latitude + latitude²)
 after incorporating the Index of Taxonomic Uncertainty in the simulations
 and after splitting the species in the phylogeny. **split:** the number of
 splits in each simulation. **index_run:** the number of runs. For each of
 the 1000 phylogenetic trees, 100 runs were performed. **index_tree:** the
 number of the phylogenetic tree. There are 1000 phylogenetic trees. #####
 Authors Lívia Estéfane Fernandes Frateles, Guilherme Rogie Gonçalves
 Tavares, Gabriel Nakamura, Nelson Jorge da Silva Jr., Levi Carina
 Terribile, José Alexandre F. Diniz-Filho