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Journal ArticleDOI

Integrative taxonomy, or iterative taxonomy?

TLDR
The term ‘iterative taxonomy’ is proposed for current practice that treats species boundaries as hypotheses to be tested with new evidence, and a search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses.
Abstract
The recently introduced term ‘integrative taxonomy’ refers to taxonomy that integrates all available data sources to frame species limits. We survey current taxonomic methods available to delimit species that integrate a variety of data, including molecular and morphological characters. A literature review of empirical studies using the term ‘integrative taxonomy’ assessed the kinds of data being used to frame species limits, and methods of integration. Almost all studies are qualitative and comparative – we are a long way from a repeatable, quantitative method of truly ‘integrative taxonomy’. The usual methods for integrating data in phylogenetic and population genetic paradigms are not appropriate for integrative taxonomy, either because of the diverse range of data used or because of the special challenges that arise when working at the species/population boundary. We identify two challenges that, if met, will facilitate the development of a more complete toolkit and a more robust research programme in integrative taxonomy using species tree approaches. We propose the term ‘iterative taxonomy’ for current practice that treats species boundaries as hypotheses to be tested with new evidence. A search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses. We identify two recent empirical examples that use the process of iterative taxonomy.

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Citations
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Journal ArticleDOI

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

TL;DR: Automatic Barcode Gap Discovery is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.
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Coalescent-based species delimitation in an integrative taxonomy

TL;DR: Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.
Journal ArticleDOI

Cryptic species as a window into the paradigm shift of the species concept

TL;DR: It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.
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Multi‐locus species delimitation in closely related animals and fungi: one marker is not enough

TL;DR: In this paper, the authors conducted a broadly comparative literature review addressing the efficacy of molecular markers for delimiting closely related species over a broad taxonomic range and found no relationship between increased sampling of intraspecific variability and delimitation success.
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Large-scale species delimitation method for hyperdiverse groups.

TL;DR: The formalized strategy applied here outlines an effective and reproducible protocol for large‐scale species delimitation of hyperdiverse groups and identified 27 novel species hypotheses not linked to available species names in the literature.
References
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Journal ArticleDOI

Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species

TL;DR: It is indicated that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria and constraints on intraspecific mitochondrial DNA divergence arising through selective sweeps mediated via interactions with the nuclear genome.
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Species Concepts and Species Delimitation

TL;DR: A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence relevant to assessing lineage separation.
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Gene Trees in Species Trees

TL;DR: When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny, and discord can arise from horizontal transfer, lineage sorting, and gene duplication and ex- tinction.
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Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

TL;DR: This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized.
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Gene tree discordance, phylogenetic inference and the multispecies coalescent

TL;DR: The complexities of genealogical discordance are discussed and the issues that new methods for multilocus species tree inference will need to address are reviewed to account successfully for naturally occurring genomic variability in evolutionary histories.
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