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

被引:255
作者
Tang, Cuong Q. [1 ]
Leasi, Francesca [1 ,2 ]
Obertegger, Ulrike [3 ]
Kieneke, Alexander [4 ]
Barraclough, Timothy G. [1 ]
Fontaneto, Diego [1 ,5 ]
机构
[1] Univ London Imperial Coll Sci Technol & Med, Dept Life Sci, Ascot SL5 7PY, Berks, England
[2] Drexel Univ, Acad Nat Sci, Dept Biodivers Earth & Environm Sci, Philadelphia, PA 19103 USA
[3] Edmund Mach Fdn, Inst Agr, San Michele AllAdige Res & Innovat Ctr, Sustainable Agroecosyst & Bioresources Dept, I-38010 San Michele All Adige, Italy
[4] Senckenberg Meer Wilhelmshaven, German Ctr Marine Biodivers Res, D-26382 Wilhelmshaven, Germany
[5] CNR, Inst Ecosyst Study, I-28922 Verbania, Italy
基金
英国生物技术与生命科学研究理事会; 英国自然环境研究理事会;
关键词
DNA barcodes; species delimitation; microinvertebrates; environmental DNA; ENVIRONMENTAL DNA; BIOGEOGRAPHIC PATTERNS; SPECIES DELIMITATION; CRYPTIC SPECIATION; TAXONOMY; COMPLEX; ROTIFERA; BARCODE;
D O I
10.1073/pnas.1209160109
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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 small-subunit 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.
引用
收藏
页码:16208 / 16212
页数:5
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