Global patterns of taxonomic uncertainty and its impacts on biodiversity research
Creators: name: Guedes, Jhonny J. M.
name: Moura, Mario R.
name: Jardim, Lucas
name: Diniz-Filho, José Alexandre F.
Publisher: name: Zenodo
Year: 2025
Subjects: Beta taxonomy
description trends
Diversification rates
Macroecology
synonymy
Systematics
taxonomic uncertainty
terrestrial vertebrates

description: Over two million species have been named so far, but many will be invalidated due to redundant descriptions. Undetected invalid species (i.e., synonyms) can impair inferences we make in biodiversity research and hamper the implementation of effective conservation strategies. However, the processes leading to the accumulation of invalid names remain largely unknown. Using multi-model inferences, we investigated the patterns and potential drivers of species- and assemblage-level variation in synonym counts across terrestrial vertebrates globally. We also explored how taxonomic uncertainty (i.e., instability in species identities) can affect latitudinal variation of diversification rates. The average number of synonyms was higher for species described earlier, better represented in scientific collections, with larger geographic ranges, occurring in temperate regions, and in areas of high biodiversity attention. In assemblage-level models, a higher average number of synonyms was associated with temperate regions harbouring more early-described species. Areas of high endemism richness showed fewer synonyms across amphibians and reptiles but had an inverse effect for birds and mammals. Other predictor-response relationships varied across taxonomic groups, biogeographical realm, and spatial grain. Assuming that more synonyms indicate more stable species that have been thoroughly studied and reviewed, high synonym numbers in temperate species and assemblages support claims of a potential latitudinal taxonomy gradient, where geographic variation in taxonomic practice could hinder the proper recognition of tropical species. We show that the accumulation of invalid names is not random and discuss how invalid hidden names can affect biodiversity inferences. A potential approach to address this problem would be developing a taxonomic uncertainty metric that could be incorporated into models (i.e., as weights to account for varying degrees of uncertainty during the fitting process). Our study provides an initial approximation and highlights the often-neglected issue of uncertainty and instability in species identities from a macroecological perspective.
description: Funding provided by: Coordenação de Aperfeicoamento de Pessoal de Nível SuperiorROR ID: https://ror.org/00x0ma614Award Number: 88887.478942/2020-00
Funding provided by: National Council for Scientific and Technological DevelopmentROR ID: https://ror.org/03swz6y49Award Number: 465610/2014-5
Funding provided by: São Paulo Research FoundationROR ID: https://ror.org/02ddkpn78Award Number: 2021/11840-6 and 2022/12231-6
Funding provided by: Fundação de Apoio a Pesquisa do Estado de GoiásROR ID: https://ror.org/00w8cq239Award Number: 201810267000023
description: Synonym Data

We extracted the number of synonyms per species from the Catalogue of Life (CoL) Checklist (https://www.checklistbank.org/dataset/286246/download; Bánki et al., 2024) on 20 Feb 2024. The taxonomic backbone of the CoL for amphibians, birds, and mammals was based on the Integrated Taxonomic Information System (ITIS; https://itis.gov/), while data for reptiles were from the Reptile Database (http://www.reptile-database.org; Uetz and Hošek, 2021). The CoL dataset included columns for rank and status, with the former informing if a scientific name represented, for example, a species or subspecies, and the latter indicating whether names were accepted, ambiguous, or unique synonyms. Using these columns, we filtered our dataset to include only accepted (i.e., valid) species and unique synonyms (i.e., invalid names). Consequently, currently valid subspecies were not analysed, as they are classified neither as full species nor as synonyms. However, we conducted a sensitivity analysis for cross-species models, treating valid subspecies as synonyms to assess the robustness of our main conclusions amid significant taxonomic changes. 

Taxonomic Data

We followed the taxonomy employed in fully-sampled phylogenies available for amphibians (Jetz and Pyron, 2018), turtles and crocodiles (Colston et al., 2020), squamates (Tonini et al., 2016), birds (Jetz et al., 2012), and mammals (Upham, Esselstyn and Jetz, 2019) to incorporate species' phylogenetic relationship into analyses and to take advantage of a recently available trait database for the world's tetrapods (Moura et al., 2024). While the taxonomies we followed included mostly species described before 2016, we highlight that taxa described after that may not have been targeted by revisionary work that could lead to the accumulation of synonyms.

We merged the information from the CoL with data from the TetrapodTraits using fuzzy logic to check for and fix mismatches in species names between datasets due to spelling errors. For such, we used the fuzzyjoin package (Robinson, 2020) in software R version 4.3.1 (R Core Team, 2023). Checks were initially performed between valid species names in both datasets, then between valid species in TetrapodTraits with unique synonyms (i.e., names that can be tracked back to a single valid species) in the CoL database. After merging operations, we found synonym information for 31,175 (93.7%) species in TetrapodTraits. Our dataset initially included 33,281 species: 7,238 amphibians, 9,993 birds, 5,911 mammals, and 10,139 reptiles. However, we removed 228 marine species (as per the International Union for Conservation of Nature — IUCN) and focused solely on terrestrial vertebrates (n = 33,049). 

Species-level Covariates

Attributes related to species biology included body size and habitat use. For body size, we used body mass data for birds, mammals, and reptiles, which had on average a data coverage exceeding 95% (n = 24,758 out of 25,811 species), and body length for amphibians, which covered 97.9% (n = 7,083) of species. Habitat use data were obtained for 31,497 species (95.3%), being converted into a continuous metric of verticality (Oliveira and Scheffers, 2019), with species scored as: 0 = strictly fossorial, 0.25 = fossorial and aquatic/ terrestrial , 0.5 = aquatic, or terrestrial, or aquatic/ terrestrial, or fossorial/ terrestrial/ arboreal, or fossorial/ terrestrial / aquatic/ arboreal, 0.75 = terrestrial and arboreal, or aquatic and arboreal, or terrestrial and aquatic/ arboreal, or terrestrial and aerial, or terrestrial and arboreal/ aerial, and 1 = strictly arboreal or aerial. Sources on body size and microhabitat are available in Moura et al. (2024).

Attributes related to taxonomic practice included year of description, taxonomic activity, and knowledge of species' evolutionary relationships. Species' description years were based on the original publication date and was available for all but one species (the squamate Indotyphlops pushpakumara, a nomen nudum included in Tonini's phylogeny; Tonini et al., 2016). To inform taxonomic activity per species, we selected all taxa described within the same family and year, and then tallied the total number of unique taxonomists. Because the per-family number of taxonomists is expected to increase with family richness, we divided the number of taxonomists by the number of species described per year in a given family (Moura and Jetz, 2021). We acknowledge that many authors contributing to species descriptions are not necessarily taxonomists, with recent rise in authorship reflecting changes in taxonomic practice rather than an increase in taxonomic capacity (Boero, 2001; Rodrigues et al., 2010; Bebber et al., 2014). Despite this potential bias, the number of authors remains a useful proxy for taxonomic activity in beta taxonomic studies, highlighting the growing collaboration between taxonomists and researchers from various fields (Grieneisen et al., 2014; Poulin and Presswell, 2016). Lastly, we used a binary variable to identify tetrapod species with evolutionary relationships imputed (0 = not imputed, 1 = imputed) in fully-sampled phylogenies (Jetz et al., 2012; Tonini et al., 2016; Jetz and Pyron, 2018; Upham, Esselstyn and Jetz, 2019; Colston et al., 2020).

Some predictors analysed here were extracted from Moura et al. (2024) and represent within-range attributes derived from spatial intersections between expert-based range maps for amphibians (Jetz, McPherson and Guralnick, 2012; IUCN, 2021; Moura et al., 2024), birds (Jetz et al., 2012; Jetz, McPherson and Guralnick, 2012), mammals (Jetz, McPherson and Guralnick, 2012; IUCN, 2021; Marsh et al., 2022) and reptiles (Roll et al., 2017; Colston et al., 2020; IUCN, 2021), environmental, and socioeconomic layers using Lambert's cylindrical equal-area grid of 110×110 km. This spatial resolution has been suggested to minimises comission errors related to the use of expert range maps (Hurlbert and Jetz, 2007). We used the following spatially based attributes: (i) range size, computed as the number of 110×110 km grid cells overlapped by the species' range, (ii) latitude, based on the centroid of each species' range map, (iii) elevation, as the average within-range elevation, and (iv) on-ground accessibility, measured as the average within-range time to travel to cities with more than 50,000 inhabitants (ETA50k). These four attributes were available for 33,037 (99.6 %) species.

To evaluate endemism richness, we used the spatial intersections of species' range maps across the 110×110 km grid cells (available in Moura et al., 2024) to compute the sum of the inverse range sizes of all species per taxonomic class within a grid cell (Kier and Barthlott, 2001), which we then used to calculate the median value for each species based on the grid cells they occupy. Endemism richness was available for 33,898 (96 %) species. We obtained the number of preserved specimens deposited in biological collections per species based on the Global Biodiversity Information Facility (GBIF) database — data available for 32,985 (99.8%) species. Specifically, we used the function occ_count in the rgbif R package (Chamberlain et al., 2023), creating search queries with valid species names plus their unique synonyms and setting the basisOfRecord argument to preserved specimens. After excluding species with missing data in the response or predictor variables, our final dataset had a total of 28,802 terrestrial vertebrates: 6,440 amphibians, 9,183 birds, 4,158 mammals, and 9,021 reptiles.

 

Assemblage-level Covariates

For assemblage-level analyses, we modelled the average number of synonyms per grid cell for each taxonomic class separately across three spatial grains (110, 220, and 440 km). As predictors, we used latitude, as well as median values per grid cell for elevation (Amatulli et al., 2018), ETA50K (Nelson et al., 2019), endemism richness, and year of description. For the number of preserved specimens per assemblage, we downloaded all data on preserved tetrapod species available on GBIF (GBIF.org, 2024) on 03 Apr 2024, selecting only records with available coordinates and not flagged as suspicious (potentially erroneous) by GBIF. In total, we downloaded 12,485,651 records; however, after data cleaning procedures (i.e., removing duplicate records), the number of observations was reduced to 6,288,920.

We computed three additional predictors for the assemblage-level analyses: species richness, representing the number of species whose range intersected each grid cell;  median per capita gross domestic product at 5 arc-min resolution, weighted by the country area covering each grid cell (Kummu, Taka and Guillaume, 2018), which represents a proxy for financial resources potentially available for biodiversity research; and the number of biodiversity institutions — i.e., herbaria, museums, and universities — per grid cell, based on the dataset available in the R package CoordinateCleaner (Zizka et al., 2019).

Determinants of Synonym Count Variation 

We modelled synonym counts per species (cross-species analyses) and the average number of synonyms (i.e., total number of synonyms divided by the total number of species) per grid cell (assemblage-level analyses) separately for amphibians, reptiles, birds, and mammals. Our two response variables were modelled as a function of biological, geographical, taxonomical, and socioeconomic-related factors (see Figure 1).

In the cross-species analyses, we modelled synonym counts through generalised linear models (GLMs) using a negative binomial distribution to account for overdispersion (Lindén and Mäntyniemi, 2011; Stoklosa, Blakey and Hui, 2022). We assessed whether phylogenetic regression models were necessary by examining the phylogenetic autocorrelation of GLM residuals, constructing Moran's I correlograms with coefficients calculated at 14 distance classes (Revell, 2010). For this, we used the most recent phylogenies available for major tetrapod groups: amphibians (Jetz and Pyron, 2018), turtles and crocodiles (Colston et al., 2020), squamates (Tonini et al., 2016), birds (Jetz et al., 2012), and mammals (Upham, Esselstyn and Jetz, 2019). We selected 50 fully sampled phylogenies, computing Moran's I correlations for each tree and then averaging the results (except for global models, where due to computation constraints, we limited calculations to five trees). For reptiles, we first combined Tonini's et al. and Colston's et al. phylogenies using the R function tree.merger in the package RRphylo v. 2.7.0 (Castiglione, Serio, et al., 2022), which preserves branch length information in the combined trees (Castiglione, Melchionna, et al., 2022). We inspected model residuals using the R package DHARMa v. 0.4.6 (Hartig, 2022) and assessed model fit by calculating Nagelkerke's pseudo-R2 with the R package performance v. 0.10.2 (Lüdecke et al., 2021). Analyses of phylogenetic autocorrelation were performed using the R packages phylobase (Bolker et al., 2020) and phylosignal (Keck et al., 2016).

In the assemblage-level analyses, we initially modelled the average number of synonyms per grid cell using non-spatial GLMs with a Gaussian error distribution and an identity link function. We then tested for spatial autocorrelation (SAC) in model residuals using Moran's I coefficients based on 14 distance classes (Dormann et al., 2007; Revell, 2010). Upon detecting SAC in the residuals of the non-spatial GLMs (Supplementary Fig. S1), we proceeded with spatial GLMs. To account for SAC, we first calculated 'residuals autocovariates' (RAC), which were then included as covariates in the spatial GLMs, similar to an error-type SAR model (Meyer et al., 2015). Specifically, we used the autocov_dist function in the R package spdep v. 1.2.7 (Bivand, 2022) to compute RACs based on the queen's contiguity neighbourhood structure (a list of neighbourhood cells for each grid cell) and the residuals from the non-spatial model (see the R-code for details). After fitting the spatial models, we re-evaluated SAC in the residuals, which showed a substantial reduction compared to the non-spatial models (Supplementary Fig. S2). We inspected model residuals using the package DHARMa and assessed model fit through the coefficient of determination R2 statistic.

Continuous predictors were log10-transformed if their skewness or kurtosis fell outside the range of -2 to +2 (George and Mallery, 2010), and then centred and scaled (z-transformed) to allow direct comparisons of effect sizes. We checked for multicollinearity among predictors using Variation Inflation Factors (VIFs), where strong multicollinearity is usually attributed to VIFs > 10, suggesting that variables should be removed from the analysis (Kutner et al., 2005). As none of our continuous variables had VIFs > 5, all were retained for subsequent analyses (Supplementary Tables S1–2). We modelled synonym counts globally as well as separately for each biogeographic realm (Dinerstein et al., 2017), excluding Oceania due to its low sample size (Supplementary Table S3 ). Species whose ranges overlapped with realms by more than 70% were assigned to realm-scale models, which ensures that only species with a strong association to a specific realm are included in realm-specific analyses.

Influence of Synonym Counts on Diversification Rates

We explored the potential impacts of taxonomic uncertainty on eco-evolutionary research through an exercise based on latitudinal variation in recent speciation rates, measured by the diversification rate statistic (Jetz et al., 2012) using the R package picante v. 1.8.2 (Kembel et al., 2010). Initially, we identified cases where the estimated number of synonyms (Nest.) differed significantly from the observed number of synonyms (Nobs.) based on global cross-species models. Species with Nest. > Nobs. (negative residuals) were classified as needing to "gain" synonyms, leading to lumping events. Conversely, species with Nest. < Nobs. (positive residuals) were flagged as needing to "lose" synonyms, prompting splitting events by elevating synonyms to full species status.

In the lumping exercise, we collapsed branches of 10%, 15%, and 20% of species with the highest negative residual values, recomputing diversification rates for each proportion across 'new' phylogenies and calculating delta values based on current phylogenetic knowledge. This exercise involves removing the selected species from the phylogeny, mimicking their lumping with their respective sister species. In the splitting exercise, we selected 10%, 15%, and 20% of species with the highest positive residual values and added different proportions of synonyms (20%, 30%, and 40% of synonyms randomly chosen from the pool of synonyms among selected species) to the most recent phylogenies, thus reflecting distinct future scenarios of synonymisation rates. These synonyms were placed as a monophyletic clade within the current valid species to which they belong. If more than one synonym was added for the same species, the first synonym was placed at a position sampled by a uniform distribution of the valid species' branch length, and subsequent synonyms were placed randomly on sampled branches descending from the most recent common ancestor between the valid species and its synonyms. This procedure simulated the uncertainty about the phylogenetic relationships of synonyms. Again, we calculated delta values based on current phylogenetic knowledge. We performed an additional analysis in the splitting exercise, simulating under the Yule model to test its effect on branch lengths and the estimation of diversification rates, compared with a uniform distribution.

We bound species on phylogenies using the R packages phytools v. 1.2.0 (Revell, 2012) and ape v. 5.6.2 (Paradis and Schliep, 2019). Both lumping and splitting procedures were repeated for 100 trees. For each scenario, we computed the average species diversification rate across trees per taxonomic class and plotted these rates by latitude using the R package ggplot2 v. 3.4.0 (Wickham, 2016). This exercise allowed us to explore how speciation rates might be perceived under distinct scenarios of taxonomic knowledge.

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