Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

Abstract

Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation-species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

“…Despite significant breakthroughs in our understanding of neutral processes (Zeng et al, 2015), a large and diverse collection of microbial genomes for comparison (National Center for Biotechnology Information-NCBI; Nordberg et al, 2014), a growing appreciation for integrative methods (Edwards and Knowles, 2014), and accepted impact of HGT, we currently lack a detailed understanding of how microbial diversity eventually leads to speciation. Additional consideration of the environmental parameters at the time the samples are taken, though often not feasible, would improve the understanding of contemporary forces of selection that are maintaining some of the metabolic differentiation between strains.…”

Genus Profundiconus Kuroda, 1956 (Gastropoda, Conoidea): Morphological and molecular studies, with the description of five new species from the Solomon Islands and New Caledonia

“…This could be due to either the lack of enough phylogenetic signal in the molecular marker at this taxonomic level, a rapid radiation event at the origin of the genus, or the extinction of different lineages during the evolutionary history of the group. This fact enhances the need for an integrative approach for species delimitation combining genetic, morphological and ecological data (Edwards & Knowles 2014;Carstens et al 2013), rather than relying on single locus genetic data only. …”

Different roads lead to Rome: Integrative taxonomic approaches lead to the discovery of two new lizard lineages in theLiolaemus montanusgroup (Squamata: Liolaemidae)

“…IT methods can be divided informally into two types of procedures: (1) step-by-step methods based on sequential analyses of independent data types, followed by a qualitative assessment of diversity in a hypothetico-deductive framework (Schlick-Steiner et al, 2010;Yeates et al, 2011;And ujar et al, 2014); and (2) model-based methods that simultaneously evaluate multiple data types, followed by delimitation of species based on a statistical or information criterion (Guillot et al, 2012;Edwards & Knowles, 2014;Sol ıs-Lemus et al, 2014). Both IT approaches can be used for the four focal areas of SDL: (1) validation of candidate species as evolutionary distinct lineages; (2) inferring species relationships; (3) detecting 'cryptic diversity'; and (4) individual specimen assignment to a species group (Edwards & Knowles, 2014;Leavitt, Moreau & Lumbsch, 2015).…”