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Comparative Study
. 2018 Nov;12(11):2807-2810.
doi: 10.1038/s41396-018-0221-y. Epub 2018 Jul 16.

Insights Into Global Planktonic Diatom Diversity: The Importance of Comparisons Between Phylogenetically Equivalent Units That Account for Time

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Free PMC article
Comparative Study

Insights Into Global Planktonic Diatom Diversity: The Importance of Comparisons Between Phylogenetically Equivalent Units That Account for Time

Teofil Nakov et al. ISME J. .
Free PMC article

Abstract

Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively lower Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a metabarcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some have had more time to diversify than others. However, species richness was largely independent of genus age, suggesting that disparities in species richness among genera were better explained by variation in rates of speciation and extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Age and estimated taxon richness of the 20 most abundant marine planktonic diatom genera identified by the Tara Oceans metabarcode project [3]. Crown ages and uncertainty (grey bars) in million years ago (Mya) were estimated from 1000 bootstrap phylogenies [11]. a Taxon richness was estimated from the number of OTU swarms in the Tara Oceans dataset (b) and the number of accepted species names in DiatomBase [14] (c). Black curves in b, c delimit 95% confidence intervals of expected richness given the crown age of a clade, empirical extinction fraction, and diatom-wide estimate of the net diversification rate (see [11] for details). Blue and green bars in c show the difference in species richness as measured by OTU swarms b and DiatomBase names c. Blue bars show which genera have fewer OTUs than DiatomBase names, suggesting that the number of OTUs might underestimate species richness, whereas green bars show which genera might have more species than described by traditional taxonomy
Fig. 2
Fig. 2
The genus Thalassiosira encompasses at least ten marine (white circles) and four freshwater (black squares) planktonic diatom genera (including Thalassiosira) that range from 4–63 My in age. Topology and divergence times are based on Nakov et al. [11]

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