An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid

Barrett, Craig F.; Freudenstein, John V.

doi:10.1111/j.1365-294x.2011.05124.x

Cited by 77 publications

(86 citation statements)

References 78 publications

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“…Lineages can be treated as species hypotheses based on taxon-specific divergence thresholds, but hypothesis tests are necessary to justify taxonomic consideration of lineages as species. Recent work supports the value of identifying candidate species based on the concordance of mtDNA lineage divergence with nuclear gene genealogies, and characters drawn from morphology, ecology, reproduction or behavior (Blanquer and Uriz, 2008; Bucklin and Frost, 2009; Cardosa et al, 2009; Halt et al, 2009; Naughton and O”Hara, 2009; Vieites et al, 2009; Barrett and Freudenstein, 2011). However, DNA barcoding has yet to bridge the gap with alpha taxonomy for marine invertebrates, despite adoption by large-scale marine biodiversity inventories (e.g.…”

Section: Introductionmentioning

confidence: 85%

Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

Krug

Vendetti

Rodriguez

et al. 2013

Molecular Phylogenetics and Evolution

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DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed “species” each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The “circumtropical” Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The “monotypic” and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated.

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Section: Introductionmentioning

confidence: 85%

Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

Krug

Vendetti

Rodriguez

et al. 2013

Molecular Phylogenetics and Evolution

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show abstract

“…However, it is a mistake to characterize the entire field as adopting the GLC or to assume that the GLC is a prerequisite for species delimitation (e.g. Rosell et al 2010;Barrett & Freudenstein 2011;Duminil et al 2012). However, it is good practice to define some species concept when reporting investigation that includes a substantial species delimitation component, if only because this articulation enforces the need for a clear argument regarding the criteria used to recognize species.…”

Section: Box 3 Species Concepts and Species Delimitationmentioning

confidence: 99%

“…This pairing of a species discovery method with BPP has been followed by a number of authors (e.g. Barrett & Freudenstein 2011;Setiadi et al 2011). A particularly useful approach may be the pairing of discovery methods that model the species tree to identify putative lineages.…”

Section: Strategies For Complex Empirical Investigationsmentioning

confidence: 99%

How to fail at species delimitation

et al. 2013

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Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages.

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“…Coalescence-based, multi-locus species delimitation methods are rapidly gaining popularity in studies on closely related species that are difficult to distinguish based on phenotypic features, and have been applied in various eukaryotic groups including animals (Carstens & Dewey, 2010;Leaché & Fujita, 2010;Yang & Rannala, 2010;Camargo et al, 2012), fungi (Leavitt et al, 2011) and land plants (Barrett & Freudenstein, 2011). Also in algae, phylogenetic and population genetic approaches have been combined to study boundaries between closely related species and assess confounding factors such as incomplete lineage sorting, trans-species polymorphism, hybridization and introgression.…”

Section: Multi-locus Species Delimitationmentioning

confidence: 99%

DNA-based species delimitation in algae

Leliaert

Verbruggen

Vanormelingen

et al. 2014

European Journal of Phycology

311

285

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Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming the standard for delimiting species and testing their traditional boundaries. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation. We review these recent developments in DNA-based species delimitation methods, and discuss how they have changed and continue to change our understanding of algal species boundaries. Although single-locus approaches have proven effective for a first rapid and large-scale assessment of species diversity, species delimitation based on single gene trees falls short due to gene tree-species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization and introgression. Data from unlinked loci and multi-species coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors. Several of these methods also provide statistical support regarding species boundaries, which is important because speciation is a process and therefore uncertainty about precise species boundaries is inevitable in recently diverged lineages.

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An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid

Cited by 77 publications

References 78 publications

Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

How to fail at species delimitation

DNA-based species delimitation in algae

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