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Table 1 Work areas for the scientific and technical development of integrative taxonomy

From: The integrative future of taxonomy

Improving taxonomic work protocols Development of pragmatic operational protocols to discovering and describing species (Figure 2d). There is an inevitable trade-off between using complex integrative approaches for delimiting species that may provide stable names, and the need to accelerate the pace of taxonomic descriptions [92]. Indeed, of the many empirical methods available for species delimitation [22, 25], most require extensive sampling, absence of missing data, and/or complete species-level molecular phylogenetic trees. Clearly, for most areas and groups of diverse organisms of the world, data at hand will be insufficient for in-depth studies of evolutionary separation of lineages.
Refinement of probabilistic procedures to evaluate character congruence New methods should be able to deal with the heterogeneity of the evolutionary process, with situations of character incongruence, and to include fixed characters states as well as states distributed in different frequencies across populations. In this sense population geneticists have efficient tools to estimate if combinations of alleles occur more frequently than expected randomly -a situation termed linkage disequilibrium [99]- and this method can be applied to discover cryptic sympatric species [e.g., [100]]. Also, phylogeneticists have developed approaches as CONCATERPILLAR [101], which take into account different evolutionary rates of different loci and allow identification of those that should be analyzed independently or concatenated. Extending such approaches to non-molecular characters could result in more rigorous protocols of integrative taxonomy.
Development of modular software for species delimitation, description and publishing. Besides including phylogenetic and population genetics modules, as in Mesquite [102], such software should include modules for statistical analysis of morphological data, should be able to extract character information from bi- and tri-dimensional imagery [103] and from sequence data (such as pure and private diagnostic nucleotide substitutions, e.g. [49]), and should also incorporate packages for ecological and geographical modeling and mapping, as well as for bioacoustics. It could also implement a package for building standardized species descriptions that could be directly submitted for peer-review to major taxonomic journals at the same time that supporting data are automatically sent to biodiversity databases (e.g. GBIF, Species2000, Zoobank, GenBank, CBOL, MorphoBank); hyperlinked species descriptions represent an advance in this sense [13].
Automated identification of candidate species Development of methods for automatically identifying, naming, documenting and cataloguing candidate species through the combination of DNA barcoding and digital image processing [12, 103]. These approaches could be especially helpful for the preliminary screening of hyperdiverse groups such as small arthropods and nematodes, or for geographical areas facing imminent habitat destruction (and therefore in need of rapid inventories of species diversity and conservation priorities).
Application of genomic analyses to taxonomy (GenoTaxonomy). Population genomics aims to identify regions of the genome with greater differentiation than expected from the average across many loci affected by reduced gene flow due to reproductive isolation or local adaptation [104]. The automatic identification of those regions, to be used as diagnostic characters, might be the key to substantially accelerate species discovery, especially if applicable through modular taxonomic software. Given the enormous expected increases of genomic data [105] such approaches will soon become applicable.