Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.

Highlights d Bees show a rare bimodal latitudinal gradient with highest richness at mid-latitudes d Xeric and temperate zones host higher richness than tropical areas d Plant productivity and richness are important drivers when forests are excluded d A global bee species richness reconstruction is presented for the first time

Spatial patterns of biodiversity are inextricably linked to their collection methods, yet no synthesis of bias patterns or their consequences exists. As such, views of organismal distribution and the ecosystems they make up may be incorrect, undermining countless ecological and evolutionary studies. Using 742 million records of 374 900 species, we explore the global patterns and impacts of biases related to taxonomy, accessibility, ecotype and data type across terrestrial and marine systems. Pervasive sampling and observation biases exist across animals, with only 6.74% of the globe sampled, and disproportionately poor tropical sampling. High elevations and deep seas are particularly unknown. Over 50% of records in most groups account for under 2% of species and citizen‐science only exacerbates biases. Additional data will be needed to overcome many of these biases, but we must increasingly value data publication to bridge this gap and better represent species' distributions from more distant and inaccessible areas, and provide the necessary basis for conservation and management.