| Title | The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna |
| Abstract | 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. |
| Source | Proceedings of the National Academy of Sciences of the United States of America (Online) 109 (40), pp. 16208–16212 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America (Online) |
| Editor | National Academy of Sciences, Washington, DC, Stati Uniti d'America |
| Year | 2012 |
| Type | Articolo in rivista |
| DOI | 10.1073/pnas.1209160109 |
| Authors | Tang, Cuong ;Leasi, Francesca ;Obertegger, Ulrike ;Kieneke, Alexander ;Barraclough, Timothy ;Fontaneto, Diego |
| Text | 223058 2012 10.1073/pnas.1209160109 The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna Tang, Cuong ;Leasi, Francesca ;Obertegger, Ulrike ;Kieneke, Alexander ;Barraclough, Timothy ;Fontaneto, Diego Department of Life Sciences, Imperial College London, Ascot, Berkshire SL5 7PY, United Kingdom ;Department of Biodiversity, Earth and Environmental Science, Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103 ;Sustainable Agro Ecosystems and Bioresources Department, Edmund Mach Foundation, Agricultural Institute at San Michele all Adige Research and Innovation Centre, 38010 San Michele all Adige, Italy ;Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, 26382 Wilhelmshaven, Germany ;CNR ISE, Pallanza Verbania 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. 109 http //www.pnas.org/content/109/40/16208.full Articolo in rivista National Academy of Sciences 1091 6490 Proceedings of the National Academy of Sciences of the United States of America Online Proceedings of the National Academy of Sciences of the United States of America Online Proc. Natl. Acad. Sci. U.S. Am. Online Proceedings of the National Academy of Sciences of the United States of America Online PNAS online Online PNAS Online diego.fontaneto FONTANETO DIEGO TA.P04.016.004 Ecologia teorica e applicata degli ecosistemi acquatici |
