The integrative future of taxonomy

Abstract

BackgroundTaxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species.ResultsIntegrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth.ConclusionsWe conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.

Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods

“…molecular, morphological, ecological, and behavioral) for taxonomy is expected to reduce subjectivity in delimiting taxa (Dayrat, 2005;Leaché et al, 2009;Padial et al, 2010;Schlick-Steiner et al, 2010;Yeates et al, 2011). However, in situations where cryptic species with indistinct morphological and ecological properties are present, integrative methods will not yield a clear result since different types of data may yield discordant conclusions (Fujita et al, 2012;Wiens and Penkrot, 2002).…”

Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus

“…These are necessarily subjective judgments. Lymbery et al (2015) suggested that an integrative or iterative approach (see Padial et al, 2010;Yeates et al, 2011), using molecular, ecological and morphological data together, might provide more objectivity, but unfortunately we know very little about the heritability of morphological and ecological traits in Echinococcus spp. The best 22 way to resolve this issue may be to use multilocus genotypic data in a coalescent-based approach to species delimitation (see section 7).…”

Molecular phylogenetics and biogeography of the Neotropical skink genus Mabuya Fitzinger (Squamata: Scincidae) with emphasis on Colombian populations

“…If the group was monophyletic we then looked for groups with 300 high clade support, i.e., parsimony and likelihood bootstrap sup-301 port P75% and Bayesian posterior probability P0.95, as uncon-302 firmed candidate species (Padial et al, 2010). We then checked 303 for minimal genetic divergences of 1.0% at 12S and 5% divergence 304 at Cytb.…”

“…We then checked 303 for minimal genetic divergences of 1.0% at 12S and 5% divergence 304 at Cytb. Although the specific levels of statistical support and levels 305 of genetic divergence are arbitrary, our goal was simply to flag 306 well-supported monophyletic clades with a notable genetic diver-307 gence as candidate species (Padial et al, 2010 (Carstens et al, 2013;Miralles and Vences, 2013 (Carstens et al,374 2013; Miralles and Vences, 2013 (Ree and Smith, 2008 we used four regions of high amphibian endemism (Duellman, Cytb data were available for 91% and 96% of samples, respectively. Table 2).…”