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Aim To review published evidence regarding the factors that influence the geographic variation in diversity of soil organisms at different spatial scales. Location Global.Methods A search of the relevant literature was conducted using the Web of Science and the author's personal scientific database as the major sources. Special attention was paid to include seminal studies, highly cited papers and/or studies highlighting novel results.Results Despite their significant contribution to global biodiversity, our taxonomic knowledge of soil biota is still poor compared with that of most aboveground organisms. This is particularly evident for small-bodied taxa. Global patterns of soil biodiversity distribution have been poorly documented and are thought to differ significantly from what is reported above-ground. Based on existing data, it appears that microorganisms do not respond to large-scale environmental gradients in the same way as metazoans. Whereas soil microflora seem to be mainly represented by cosmopolitan species, soil animals respond to altitudinal, latitudinal or area gradients in the same way as described for above-ground organisms. At local scales, there is less evidence that local factors regulate above-and below-ground communities in the same way. Except for a few taxa, the humpbacked response to stress and disturbance gradients doesn't seem to apply underground. Soil communities thus appear weakly structured by competition, although competitive constraints may account for assembly rules within specific taxa. The main factor constraining local soil biodiversity is the compact and heterogeneous nature of soils, which provides unrivalled potential for niche partitioning, thus allowing high levels of local biodiversity. This heterogeneity is increased by the impact of ecosystem engineers that generate resource patchiness at a range of spatio-temporal scales.

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The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.