Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy

Fontaneto, Diego; Kaya, Murat; Herniou, Elisabeth A.; Barraclough, Timothy G.

doi:10.1016/j.ympev.2009.04.011

Cited by 170 publications

(141 citation statements)

References 52 publications

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“…Previous analyses had shown that COI provided more than 15 species in the complex (e.g. Fontaneto et al, 2009;Malekzadeh-Viayeh et al, 2014). Yet, both COI and ITS1 provide congruent monophyletic lineages, at least for the 14 species with both markers available.…”

Section: Support For Species Identitymentioning

confidence: 99%

“…Phylum Rotifera is one of several phyla with a high level of cryptic diversity (Fontaneto et al, 2009;García-Morales & Elías-Gutiérrez, 2013;Gabaldón et al, 2016). Cryptic diversity is expected in rotifers, due to the small size of these animals, the paucity of taxonomically relevant morphological features, and the scarcity of rotifer taxonomists (Wallace et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

et al. 2016

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Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size).

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Section: Support For Species Identitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

et al. 2016

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“…Fontaneto et al, 2009;García-Morales and Elías-Gutiér-rez, 2013;Leasi et al, 2013). Considering this, we feel that the time has come to re-evaluate available literature records of Thai Rotifera, to serve as a basis for future work utilising the new techniques that are increasingly becoming available.…”

Section: Introductionmentioning

confidence: 99%

A checklist of the freshwater rotifer fauna of Thailand (Rotifera, Monogononta, Bdelloidea)

2013

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“…Meiofaunal organisms (defined as animals that can pass through a 500-μm mesh) cannot be reliably treated using traditional taxonomic methods because of their size (<2 mm), morphological homogeneity (12), noninformative species descriptions (13), and lack of expert taxonomists (14). It is therefore expected that morphospecies will underestimate the true diversity of these organisms (12).…”

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confidence: 99%

“…It is therefore expected that morphospecies will underestimate the true diversity of these organisms (12). The use of eDNA surveys can potentially make species delimitation more efficient and cost-effective (3).…”

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The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

Tang

Leasi

Obertegger

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding smallsubunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.DNA barcodes | species delimitation | microinvertebrates | environmental DNA

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Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy

Cited by 170 publications

References 52 publications

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

A checklist of the freshwater rotifer fauna of Thailand (Rotifera, Monogononta, Bdelloidea)

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

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