Skip to main content
Log in

Guidelines for DNA taxonomy, with a focus on the meiofauna

Marine Biodiversity Aims and scope Submit manuscript

Abstract

Describing biological diversity is a challenging endeavour, especially for the small, cryptic animals that make up the meiofauna. The field of DNA taxonomy, i.e., the use of DNA to delineate species boundaries, is rapidly growing and changing; herein we review the recent advances in the acquisition of DNA sequence data and the analytical tools for DNA-based species delimitation, with a focus on applications to the meiofauna. After providing general guidelines on the data collection and analysis steps (sampling design, sequencing, phasing of nuclear markers, and sequence alignment), we explain the rationale and usage of several widely used or promising methods developed for delineating species from single-locus data sets (distance-based DNA barcoding, automated barcode gap discovery, K/θ, generalized mixed Yule–coalescent models, Poisson tree process model, and haplowebs). As it is increasingly recognised that several loci are required to delineate species accurately, we then briefly outline multilocus species delimitation approaches (Structure, Structurama, Bayesian phylogenetics & phylogeography, SpedeSTEM, O’Meara’s heuristic search, and several newly published Bayesian approaches based on the multispecies coalescent).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Adjeroud M, Guérécheau A, Vidal-Dupiol J et al (2014) Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system. Mar Biol 161:531–541

    Article  Google Scholar 

  • Adolfsson S, Michalakis Y, Paczesniak D et al (2010) Evaluation of elevated ploidy and asexual reproduction as alternative explanations for geographic parthenogenesis in Eucypris virens ostracods. Evolution 64:986–997

    Article  CAS  PubMed  Google Scholar 

  • Avise JC, Arnold J, Ball RM et al (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489–522

    Article  Google Scholar 

  • Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    Article  CAS  PubMed  Google Scholar 

  • Baretta-Bekker JG, Duursma EK, Kuipers BR (eds) (1998) Encyclopedia of marine sciences. Springer, Berlin, pp 1–357

    Book  Google Scholar 

  • Bell DA, DeMarini DM (1991) Excessive cycling converts PCR products to random-length higher molecular weight fragments. Nucleic Acids Res 19:5079

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bellati A, Carranza S, Garcia-Porta J, Fasola M, Sindaco R (2015) Cryptic diversity within the Anatololacerta species complex (Squamata: Lacertidae) in the Anatolian Peninsula: evidence from a multi-locus approach. Mol Phylogenet Evol 82:219–233

    Article  PubMed  Google Scholar 

  • Benson DA, Cavanaugh M, Clark K et al (2013) GenBank. Nucleic Acids Res 41:D36–D42

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bergsten J, Bilton DT, Fujisawa T et al (2012) The effect of geographical scale of sampling on DNA barcoding. Syst Biol 61:851–869

    Article  PubMed Central  PubMed  Google Scholar 

  • Bik HM, Sung W, De Ley P et al (2012) Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol Ecol 21:1048–1059

    Article  PubMed Central  PubMed  Google Scholar 

  • Birky CW (2013) Species detection and identification in sexual organisms using population genetic theory and DNA sequences. PLoS One 8:e52544

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Birky CW, Wolf C, Maughan H et al (2005) Speciation and selection without sex. Hydrobiologia 546:29–45

    Article  CAS  Google Scholar 

  • Birky CW, Adams J, Gemmel M, Perry J (2010) Using population genetic theory and DNA sequences for species detection and identification in asexual organisms. PLoS One 5:e10609

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Birky CW, Ricci C, Melone G, Fontaneto D (2011) Integrating DNA and morphological taxonomy to describe diversity in poorly studied microscopic animals: new species of the genus Abrochtha Bryce, 1910 (Rotifera: Bdelloidea: Philodinavidae). Zool J Linn Soc 161:723–734

    Article  Google Scholar 

  • Blanco-Bercial L, Cornils A, Copley N, Bucklin A (2014) DNA barcoding of marine copepods: assessment of analytical approaches to species identification. PLoS Curr Tree Life 6:ecurrents.tol.cdf8b74881f87e3b01d56b43

  • Blin N, Stafford DW (1976) A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res 3:2303–2308

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bode SNS, Adolfsson S, Lamatsch DK et al (2010) Exceptional cryptic diversity and multiple origins of parthenogenesis in a freshwater ostracod. Mol Phylogenet Evol 54:542–552

    Article  CAS  PubMed  Google Scholar 

  • Bouckaert R, Heled J, Kühnert D et al (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Brandão SN, Sauer J, Schön I (2010) Circumantarctic distribution in Southern Ocean benthos? A genetic test using the genus Macroscapha (Crustacea, Ostracoda) as a model. Mol Phylogenet Evol 55:1055–1069

    Article  PubMed  Google Scholar 

  • Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Waddell PJ (1993) Partitioning and combining data in phylogenetic analysis. Syst Biol 42:384–397

    Article  Google Scholar 

  • Butlin R, Bridle J, Schluter D (eds) (2009) Speciation and patterns of diversity. Cambridge University Press, Cambridge, pp 1–346

    Book  Google Scholar 

  • Calvignac S, Konecny L, Malard F, Douady CJ (2011) Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts). Mitochondrion 11:246–254

    Article  CAS  PubMed  Google Scholar 

  • Camargo A, Morando M, Avila LJ, Sites JW (2012) Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution 66:2834–2849

    Article  PubMed  Google Scholar 

  • Carson H (1957) The species as a field for recombination. In: Mayr E (ed) The species problem. American Association for the Advancement of Science, Washington, pp 23–38

    Google Scholar 

  • Carstens BC, Pelletier TA, Reid NM, Satler JD (2013) How to fail at species delimitation. Mol Ecol 22:4369–4383

    Article  PubMed  Google Scholar 

  • Casiraghi M, Labra M, Ferri E et al (2010) DNA barcoding: a six-question tour to improve users’ awareness about the method. Brief Bioinform 11:440–453

    Article  CAS  PubMed  Google Scholar 

  • Cassens I, Mardulyn P, Milinkovitch M (2005) Evaluating intraspecific “network” construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach? Syst Biol 54:363–372

    Article  PubMed  Google Scholar 

  • Clark AG (1990) Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 7:111–122

    CAS  PubMed  Google Scholar 

  • Collins RA, Cruickshank RH (2012) The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–975

    PubMed  Google Scholar 

  • Collins RA, Cruickshank RH (2014) Known knowns, known unknowns, unknown unknowns and unknown knowns in DNA barcoding: a comment on Dowton et al. Syst Biol 63:1005–1009

    Article  PubMed  Google Scholar 

  • Cornils A, Held C (2014) Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida). Front Zool 11:1–17

    Article  CAS  Google Scholar 

  • Creer S, Fonseca VG, Porazinska DL et al (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol Ecol 19:4–20

    Article  PubMed  Google Scholar 

  • Curini-Galletti M, Artois TJ, Delogu V et al (2012) Patterns of diversity in soft-bodied meiofauna: dispersal ability and body size matter. PLoS One 7:e33801

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Davey JL, Blaxter ML (2010) RADseq: next-generation population genetics. Brief Funct Genomics 9:416–423

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • de Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879–886

  • Deiner K, Walser J-C, Mächler E, Altermatt F (2015) Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol Conserv 183:53–63

    Article  Google Scholar 

  • Dellicour S, Flot J-F (2015) Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC. Syst Biol

  • Dover G (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117

    Article  CAS  PubMed  Google Scholar 

  • Dowton M, Meiklejohn K, Cameron SL, Wallman J (2014) A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. Syst Biol 63:639–644

    Article  PubMed  Google Scholar 

  • Doyle JJ (1995) The irrelevance of allele tree topologies for species delimitation, and a non-topological alternative. Syst Bot 20:574–588

    Article  Google Scholar 

  • Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ence DD, Carstens BC (2011) SpedeSTEM: a rapid and accurate method for species delimitation. Mol Ecol Resour 11:473–480

    Article  PubMed  Google Scholar 

  • Esselstyn JA, Evans BJ, Sedlock JL, Anwarali Khan FA, Heaney LR (2012) Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats. Proc R Soc Lond B 279:3678–3686

  • Estoup A, Largiadèr CR, Perrot E, Chourrout D (1996) Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Mol Mar Biol Biotech 5:295–298

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Ezard THG, Fujisawa T, Barraclough TG (2009) splits: SPecies’ LImits by Threshold Statistics. http://R-Forge.R-project.org/projects/splits/

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    PubMed Central  CAS  PubMed  Google Scholar 

  • Flot J-F (2007) CHAMPURU 1.0: a computer software for unravelling mixtures of two DNA sequences of unequal lengths. Mol Ecol Notes 7:974–977

    Article  CAS  Google Scholar 

  • Flot J-F (2010a) Vers une taxonomie moléculaire des amphipodes du genre Niphargus: exemples d’utilisation de séquences d’ADN pour l’identification des espèces. Bull Soc Sci Nat Ouest Fr 32:62–68

  • Flot J-F (2010b) SeqPHASE: a web tool for interconverting phase input/output files and fasta sequence alignments. Mol Ecol Resour 10:162–166

    Article  CAS  PubMed  Google Scholar 

  • Flot J-F, Tillier S (2007) The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: the putative D-loop and a novel ORF of unknown function. Gene 401:80–87

    Article  CAS  PubMed  Google Scholar 

  • Flot J-F, Tillier A, Samadi S, Tillier S (2006) Phase determination from direct sequencing of length-variable DNA regions. Mol Ecol Notes 6:627–630

    Article  CAS  Google Scholar 

  • Flot J-F, Magalon H, Cruaud C et al (2008) Patterns of genetic structure among Hawaiian corals of the genus Pocillopora yield clusters of individuals that are compatible with morphology. C R Biol 331:239–247

    Article  PubMed  Google Scholar 

  • Flot J-F, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle’s “field for recombination” approach and its application to the coral genus Pocillopora in Clipperton. BMC Evol Biol 10:372

    Article  PubMed Central  PubMed  Google Scholar 

  • Flot J-F, Blanchot J, Charpy L et al (2011) Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecol 11:22

    Article  PubMed Central  PubMed  Google Scholar 

  • Flot J-F, Dahl M, André C (2013) Lophelia pertusa corals from the Ionian and Barents seas share identical nuclear ITS2 and near-identical mitochondrial genome sequences. BMC Res Notes 6:144

    Article  PubMed Central  PubMed  Google Scholar 

  • Flot J-F, Bauermeister J, Brad T et al (2014) Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania. Mol Ecol 23:1405–1417

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Folmer O, Black M, Hoeh W et al (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299

    CAS  PubMed  Google Scholar 

  • Fonseca VG, Carvalho GR, Sung W et al (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun 1:98

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Fonseca VG, Carvalho GR, Nichols B et al (2014) Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Glob Ecol Biogeogr 23:1293–1302

    Article  Google Scholar 

  • Fontaneto D (2014) Molecular phylogenies as a tool to understand diversity in rotifers. Int Rev Hydrobiol 99:178–187

    Article  CAS  Google Scholar 

  • Fontaneto D, Herniou EA, Boschetti C et al (2007) Independently evolving species in asexual bdelloid rotifers. PLoS Biol 5:e87

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Fontaneto D, Kaya M, Herniou EA, Barraclough TG (2009) Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy. Mol Phylogenet Evol 53:182–189

    Article  CAS  PubMed  Google Scholar 

  • Fontaneto D, Iakovenko N, Eyres I et al (2011) Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach. Hydrobiologia 662:27–33

    Article  CAS  Google Scholar 

  • Fourment M, Gibbs M (2006) PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. BMC Evol Biol 6:1

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Freeman JL, Perry GH, Feuk L et al (2006) Copy number variation: new insights in genome diversity. Genome Res 16:949–961

    Article  CAS  PubMed  Google Scholar 

  • Fujisawa T, Barraclough TG (2013) Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: a revised method and evaluation on simulated datasets. Syst Biol 62:707–724

    Article  PubMed Central  PubMed  Google Scholar 

  • Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C (2012) Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol Evol 27:480–488

    Article  PubMed  Google Scholar 

  • Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397–423

    Article  Google Scholar 

  • Garza JC, Freimer NB (1996) Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Res 6:211–217

    Article  CAS  PubMed  Google Scholar 

  • Garza JC, Slatkin M, Freimer NB (1995) Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol Biol Evol 12:594–603

    CAS  PubMed  Google Scholar 

  • Gaston KJ, Blackburn TM (2000) Pattern and process in macroecology. Blackwell Publishing, Oxford, pp 1–377

    Book  Google Scholar 

  • Giere O (2009) Meiobenthology the microscopic motile fauna of aquatic sediments. 1–527

  • Gollner S, Fontaneto D, Arbizu PM (2011) Molecular taxonomy confirms morphological classification of deep-sea hydrothermal vent copepods (Dirivultidae) and suggests broad physiological tolerance of species and frequent dispersal along ridges. Mar Biol 158:221–231

    Article  Google Scholar 

  • Grummer JA, Bryson RW, Reeder TW (2014) Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Syst Biol 63:119–133

    Article  PubMed  Google Scholar 

  • Hare MP, Palumbi SR (1999) The accuracy of heterozygous base calling from diploid sequence and resolution of haplotypes using allele-specific sequencing. Mol Ecol 8:1750–1752

    Article  CAS  PubMed  Google Scholar 

  • Hausdorf B, Hennig C (2010) Species delimitation using dominant and codominant multilocus markers. Syst Biol 59:491–503

    Article  CAS  PubMed  Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321

    Article  CAS  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:e312

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Heled J, Drummond AJ (2010) Bayesian inference of species trees from multilocus data. Mol Biol Evol 27:570–580

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hellberg ME (2006) No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol Biol 6:24

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Hey J (2009) On the arbitrary identification of real species. In: Butlin RK, Bridle J, Schluter D (eds) Speciat. Patterns divers. Cambridge University Press, Cambridge, pp 15–28

    Chapter  Google Scholar 

  • Hillis DM, Moritz C, Porter CA, Baker RJ (1991) Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 251:308–310

    Article  CAS  PubMed  Google Scholar 

  • Hodges E, Xuan Z, Balija V et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39:1522–1527

    Article  CAS  PubMed  Google Scholar 

  • Huang D, Meier R, Todd PA, Chou LM (2008) Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding. J Mol Evol 66:167–174

    Article  CAS  PubMed  Google Scholar 

  • Huelsenbeck JP, Andolfatto P (2007) Inference of population structure under a Dirichlet process model. Genetics 175:1787–1802

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Huelsenbeck JP, Andolfatto P, Huelsenbeck ET (2011) Structurama: Bayesian inference of population structure. Evol Bioinforma 2011:55–59

    Article  Google Scholar 

  • Iakovenko NS, Kašparová E, Plewka M, Janko K (2013) Otostephanos (Rotifera, Bdelloidea, Habrotrochidae) with the description of two new species. Syst Biodivers 11:477–494

    Article  Google Scholar 

  • Jones M, Ghoorah A, Blaxter M (2011) jMOTU and taxonerator: turning DNA barcode sequences into annotated operational taxonomic units. PLoS ONE 6(4):e19259

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jones G, Aydin Z, Oxelman B (2014) DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics. doi:10.1093/bioinformatics/btu770

  • Jörger KM, Norenburg JL, Wilson NG, Schrödl M (2012) Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs. BMC Evol Biol 12:245

    Article  PubMed Central  PubMed  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic, New York, pp 21–132

    Chapter  Google Scholar 

  • Kånneby T, Todaro MA, Jondelius U (2012) A phylogenetic approach to species delimitation in freshwater Gastrotricha from Sweden. Hydrobiologia 683:185–202

    Article  CAS  Google Scholar 

  • Katoh K, Asimenos G, Toh H (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537:39–64

    Article  CAS  PubMed  Google Scholar 

  • Kekkonen M, Hebert PDN (2014) DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Mol Ecol Resour 14:706–715

    Article  PubMed Central  PubMed  Google Scholar 

  • Kieneke A, Martínez Arbizu PM, Fontaneto D (2012) Spatially structured populations with a low level of cryptic diversity in European marine Gastrotricha. Mol Ecol 21:1239–1254

    Article  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kircher M, Kelso J (2010) High-throughput DNA sequencing – concepts and limitations. Bioessays 32:524–536

  • Knauth S, Schmidt H, Tippkötter R (2013) Comparison of commercial kits for the extraction of DNA from paddy soils. Lett Appl Microbiol 56:222–228

    Article  CAS  PubMed  Google Scholar 

  • Kornobis E, Pálsson S (2013) The ITS region of groundwater amphipods: length, secondary structure and phylogenetic information content in Crangonyctoids and Niphargids. J Zool Syst Evol Res 51:19–28

    Article  Google Scholar 

  • Koufopanou V, Burt A, Taylor JW (1997) Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc Natl Acad Sci U S A 94:5478–5482

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kubatko LS, Carstens BC, Knowles LL (2009) STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971–973

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Leaché AD, Fujita MK, Minin V, Bouckaert RR (2014) Species delimitation using genome-wide SNP data. Syst Biol 63:534–542

  • Leasi F, Norenburg JL (2014) The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea. PLoS One 9:e104385

    Article  PubMed Central  PubMed  Google Scholar 

  • Leasi F, Tang CQ, De Smet WH, Fontaneto D (2013) Cryptic diversity with wide salinity tolerance in the putative euryhaline Testudinella clypeata (Rotifera, Monogononta). Zool J Linn Soc 168:17–28

    Article  Google Scholar 

  • Lefébure T, Douady CJ, Gouy M, Gibert J (2006) Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Mol Phylogenet Evol 40:435–447

    Article  PubMed  CAS  Google Scholar 

  • Li X (2012) Molecular and evolutionary insights into sexual marine mammals and asexual bdelloid rotifers. PhD thesis: University of Namur 1–181

  • Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079

  • Lim GS, Balke M, Meier R (2012) Determining species boundaries in a world full of rarity: singletons, species delimitation methods. Syst Biol 61:165–169

    Article  PubMed  Google Scholar 

  • Liu L, Pearl DK, Brumfield RT, Edwards SV (2008) Estimating species trees using multiple-allele DNA sequence data. Evolution 62:2080–2091

  • Lohse K (2009) Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006). Syst Biol 58:439–442

    Article  PubMed  Google Scholar 

  • Lorion J, Buge B, Cruaud C, Samadi S (2010) New insights into diversity and evolution of deep-sea Mytilidae (Mollusca: Bivalvia). Mol Phylogenet Evol 57:71–83

    Article  PubMed  Google Scholar 

  • Maddison WP, Maddison DR (2014) Mesquite: a modular system for evolutionary analysis. Version 3.01 http://mesquiteproject.org

  • Magurran AE, Henderson PA (2003) Explaining the excess of rare species in natural species abundance distributions. Nature 422:714–716

    Article  CAS  PubMed  Google Scholar 

  • Malekzadeh-Viayeh R, Pak-Tarmani R, Rostamkhani N, Fontaneto D (2014) Diversity of the rotifer Brachionus plicatilis species complex (Rotifera: Monogononta) in Iran through integrative taxonomy. Zool J Linn Soc 170:233–244

    Article  Google Scholar 

  • Marrone F, Brutto S, Lo AM (2010) Molecular evidence for the presence of cryptic evolutionary lineages in the freshwater copepod genus Hemidiaptomus G.O. Sars, 1903 (Calanoida, Diaptomidae). Hydrobiologia 644:115–125

    Article  CAS  Google Scholar 

  • Marrone F, Lo Brutto S, Hundsdoerfer AK, Arculeo M (2013) Overlooked cryptic endemism in copepods: systematics and natural history of the calanoid subgenus Occidodiaptomus Borutzky 1991 (Copepoda, Calanoida, Diaptomidae). Mol Phylogenet Evol 66:190–202

    Article  PubMed  Google Scholar 

  • Martens K, Halse S, Schön I (2012) Nine new species of Bennelongia De Deckker & McKenzie, 1981 (Crustacea, Ostracoda) from Western Australia, with the description of a new subfamily. Eur J Taxon 8:1–56

    Google Scholar 

  • Martens K, Halse S, Schön I (2013) On the Bennelongia barangaroo lineage (Crustacea, Ostracoda) in Western Australia, with the description of seven new species. Eur J Taxon 66:1–59

    Google Scholar 

  • Mayr E (1982) The growth of biological thought diversity, evolution and inheritance. Belknap Press of Harvard University Press, Cambridge, pp 1–974

    Google Scholar 

  • McCormack JE, Hird SM, Zellmer AJ et al (2013) Applications of next-generation sequencing to phylogeography and phylogenetics. Mol Phylogenet Evol 66:526–538

    Article  CAS  PubMed  Google Scholar 

  • Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3:267–278

    Article  CAS  PubMed  Google Scholar 

  • Meyer-Wachsmuth I, Curini-Galletti M, Jondelius U (2014) Hyper-cryptic marine meiofauna: species complexes in Nemertodermatida. PLoS One 9:e107688

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Miller JT, Spooner DM (1999) Collapse of species boundaries in the wild potato Solanum brevicaule complex (Solanaceae, S. sect. Petota): molecular data. Plant Syst Evol 214:103–130

    Article  Google Scholar 

  • Monaghan MT, Wild R, Elliot M et al (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Syst Biol 58:298–311

    Article  CAS  PubMed  Google Scholar 

  • Montero-Pau J, Gómez A, Muñoz J (2008) Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs. Limnol Oceanogr Methods 6:218–222

    Article  CAS  Google Scholar 

  • Moore WS (1995) Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49:718–726

    Article  Google Scholar 

  • Morgan MJ, Bass D, Bik HM et al (2014) A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proc R Soc Lond B 281:20133076

    Article  CAS  Google Scholar 

  • O’Meara BC (2010) New heuristic methods for joint species delimitation and species tree inference. Syst Biol 59:59–73

    Article  PubMed  Google Scholar 

  • Obertegger U, Fontaneto D, Flaim G (2012) Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera, Monogononta) in mountain lakes. Freshw Biol 57:1545–1553

    Article  Google Scholar 

  • Obertegger U, Flaim G, Fontaneto D (2014) Cryptic diversity within the rotifer Polyarthra dolichoptera along an altitudinal gradient. Freshw Biol 59:2413–2427

    Article  Google Scholar 

  • Padial JM, Miralles A, De la Riva I, Vences M (2010) The integrative future of taxonomy. Front Zool 7:16

    Article  PubMed Central  PubMed  Google Scholar 

  • Palumbi S, Baker C (1994) Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol Biol Evol 11:426–435

    CAS  PubMed  Google Scholar 

  • Pante E, Puillandre N, Viricel A et al. (2015) Species are hypotheses: avoid connectivity assessments based on pillars of sand. Mol Ecol 24:525–544

  • Papadopoulou A, Bergsten J, Fujisawa T et al (2008) Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters. Philos Trans R Soc Lond B Biol Sci 363:2987–2996

    Article  PubMed Central  PubMed  Google Scholar 

  • Pons J, Barraclough TG, Gomez-Zurita J et al (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609

    Article  PubMed  Google Scholar 

  • Pont-Kingdon GA, Okada NA, Macfarlane JL et al (1995) A coral mitochondrial mutS gene. Nature 375:109–111

    Article  CAS  PubMed  Google Scholar 

  • Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256

    Article  CAS  PubMed  Google Scholar 

  • Posada D, Crandall KA (2001) Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol 16:37–45

    Article  PubMed  Google Scholar 

  • Powell JR (2012) Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data. Methods Ecol Evol 3:1–11

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • Prosser SWJ, Martínez-Arce A, Elías-Gutiérrez M (2013) A new set of primers for COI amplification from freshwater microcrustaceans. Mol Ecol Resour 13:1151–1155

    CAS  PubMed  Google Scholar 

  • Puillandre N, Lambert A, Brouillet S, Achaz G (2012a) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol 21:1864–1877

    Article  CAS  PubMed  Google Scholar 

  • Puillandre N, Modica MV, Zhang Y et al (2012b) Large-scale species delimitation method for hyperdiverse groups. Mol Ecol 21:2671–2691

    Article  CAS  PubMed  Google Scholar 

  • Rameckers J, Hummel S, Herrmann B (1997) How many cycles does a PCR need? Determinations of cycle numbers depending on the number of targets and the reaction efficiency factor. Naturwissenschaften 84:259–262

    Article  CAS  PubMed  Google Scholar 

  • Rannala B, Yang Z (2013) Improved reversible jump algorithms for Bayesian species delimitation. Genetics 194:245–253

    Article  PubMed Central  PubMed  Google Scholar 

  • Rasmussen RS, Morrissey MT, Hebert PDN (2009) DNA barcoding of commercially important salmon and trout species (Oncorhynchus and Salmo) from North America. J Agric Food Chem 57:8379–8385

    Article  CAS  PubMed  Google Scholar 

  • Ratnasingham S, Hebert PDN (2007) BOLD: The barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7:355–364

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 8:e66213

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rees HC, Maddison BC, Middleditch DJ, Patmore JRM, Gough KC (2014) The detection of aquatic animal species using environmental DNA – a review of eDNA as a survey tool in ecology. J Appl Ecol 51:1450–1459

    Article  CAS  Google Scholar 

  • Reid NM, Carstens BC (2012) Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol 12:196

    Article  PubMed Central  PubMed  Google Scholar 

  • Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081–1084

    Article  CAS  PubMed  Google Scholar 

  • Rodman JE, Cody JH (2003) The taxonomic impediment overcome: NSF’s Partnerships for Enhancing Expertise in Taxonomy (PEET) as a model. Syst Biol 52:428–435

    PubMed  Google Scholar 

  • Ross HA (2014) The incidence of species-level paraphyly in animals: a re-assessment. Mol Phylogenet Evol 76:10–17

    Article  PubMed  Google Scholar 

  • Rossberg AG, Rogers T, McKane AJ (2013) Are there species smaller than 1 mm? Proc R Soc Lond B 280:20131248

    Article  Google Scholar 

  • Rossberg AG, Rogers T, Mckane AJ (2014) Current noise-removal methods can create false signals in ecogenomic data. Proc R Soc Lond B 281:20140191

    Article  Google Scholar 

  • Roux KH (2009) Optimization and troubleshooting in PCR. Cold Spring Harb Protoc

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    CAS  PubMed  Google Scholar 

  • R Core Team (2014) R: A language and environment for statistical computing. R Core Team. R Foundation for Statistical Computing, Vienna

    Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

    Article  CAS  PubMed  Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463–5467

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schlick-Steiner BC, Steiner FM, Seifert B et al (2010) Integrative taxonomy: a multisource approach to exploring biodiversity. Annu Rev Entomol 55:421–438

    Article  CAS  PubMed  Google Scholar 

  • Schmidt BR, Kéry M, Ursenbacher S et al (2013) Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods Ecol Evol 4:646–653

    Article  Google Scholar 

  • Schmidt-Roach S, Miller KJ, Lundgren P, Andreakis N (2014) With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics. Zool J Linn Soc 170:1–33

    Article  Google Scholar 

  • Schön I, Pinto RL, Halse S et al (2012) Cryptic species in putative ancient asexual Darwinulids (Crustacea, Ostracoda). PLoS One 7:e39844

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Shearer TL, Coffroth MA (2008) Barcoding corals: limited by interspecific divergence, not intraspecific variation. Mol Ecol Resour 8:247–255

    Article  CAS  PubMed  Google Scholar 

  • Shearer TL, Van Oppen MJH, Romano SL, Wörheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11:2475–2487

    Article  CAS  PubMed  Google Scholar 

  • Shearn R, Koenders A, Halse S et al (2012) A review of Bennelongia De Deckker & Mckenzie, 1981 (Crustacea, Ostracoda) species from eastern Australia, with the description of three new species. Eur J Taxon 25:1–35

    Google Scholar 

  • Simpson GG (1951) The species concept. Evolution 5:285–298

    Article  Google Scholar 

  • Sites JW, Marshall JC (2003) Delimiting species: a Renaissance issue in systematic biology. Trends Ecol Evol 18:462–470

    Article  Google Scholar 

  • Sites JW, Marshall JC (2004) Operational criteria for delimiting species. Annu Rev Ecol Evol Syst 35:199–227

    Article  Google Scholar 

  • Sluys R, Solà E, Gritzalis K et al (2013) Integrative delineation of species of Mediterranean freshwater planarians (Platyhelminthes: Tricladida: Dugesiidae). Zool J Linn Soc 169:523–547

    Article  Google Scholar 

  • Sonet G, Jordaens K, Nagy ZT et al (2013) Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. Zookeys 365:329–335

    Article  PubMed  Google Scholar 

  • Song H, Buhay JE, Whiting MF, Crandall KA (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci U S A 105:13486–13491

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978–989

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Stucky BJ (2012) SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms. J Biomol Tech 23:90–93

    Article  PubMed Central  PubMed  Google Scholar 

  • Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E (2012) Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 21:2045–2050

    Article  CAS  PubMed  Google Scholar 

  • Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437–460

    PubMed Central  CAS  PubMed  Google Scholar 

  • Talavera G, Dinca V, Vila R (2013) Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods Ecol Evol 4:1101–1110

    Article  Google Scholar 

  • Tamura K, Stecher G, Peterson D et al (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tang CQ, Leasi F, Obertegger U et al (2012) The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proc Natl Acad Sci U S A 109:16208–16212

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tang CQ, Humphreys A, Fontaneto D, Barraclough TG (2014a) Effects of phylogenetic reconstruction method on the robustness of species delimitation using single locus data. Methods Ecol Evol 5:1086–1094

    Article  PubMed Central  PubMed  Google Scholar 

  • Tang CQ, Obertegger U, Fontaneto D, Barraclough TG (2014b) Sexual species are separated by larger genetic gaps than asexual species in rotifers. Evolution 68:2901–2916

    Article  PubMed Central  PubMed  Google Scholar 

  • Tautz D, Arctander P, Minelli A et al (2003) A plea for DNA taxonomy. Trends Ecol Evol 18:70–74

    Article  Google Scholar 

  • Tewhey R, Warner JB, Nakano M et al (2009) Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27:1025–1031

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Todd PA (2008) Morphological plasticity in scleractinian corals. Biol Rev 83:315–337

    Article  PubMed  Google Scholar 

  • Truett GE, Heeger P, Mynatt RL et al (2000) Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and Tris (HotSHOT). Biotechniques 29:52–54

    CAS  PubMed  Google Scholar 

  • Tulchinsky AY, Norenburg JL, Turbeville JM (2012) Phylogeography of the marine interstitial nemertean Ototyphlonemertes parmula (Nemertea, Hoplonemertea) reveals cryptic diversity and high dispersal potential. Mar Biol 159:661–674

    Article  Google Scholar 

  • Van Tassell CP, Smith TPL, Matukumalli LK et al (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247–252

    Article  PubMed  CAS  Google Scholar 

  • Velasco-Castrillón A, Page TJ, Gibson JAE, Stevens MI (2014) Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA. Biodiversity 15:130–142

    Article  Google Scholar 

  • Verovnik R, Sket B, Trontelj P (2005) The colonization of Europe by the freshwater crustacean Asellus aquaticus (Crustacea: Isopoda) proceeded from ancient refugia and was directed by habitat connectivity. Mol Ecol 14:4355–4369

    Article  CAS  PubMed  Google Scholar 

  • Vogler AP, Monaghan MT (2007) Recent advances in DNA taxonomy. J Zool Syst Evol Res 45:1–10

    Article  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Webb KE, Barnes DKA, Clark MS, Bowden DA (2006) DNA barcoding: a molecular tool to identify Antarctic marine larvae. Deep Sea Res II Top Stud Oceanogr 53:1053–1060

    Article  CAS  Google Scholar 

  • Wiemers M, Fiedler K (2007) Does the DNA barcoding gap exist?—a case study in blue butterflies (Lepidoptera: Lycaenidae). Front Zool 4:8

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Wiens JJ (2007) Species delimitation: new approaches for discovering diversity. Syst Biol 56:875–878

    Article  PubMed  Google Scholar 

  • Wiens JJ, Servedio MR (2000) Species delimitation in systematics: inferring diagnostic differences between species. Proc Biol Sci 267:631–636

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Williams S, Apte D, Ozawa T, Kaligis F, Nakano T (2011) Speciation and dispersal along continental coastlines and island arcs in the Indo‐West Pacific turbinid gastropod genus Lunella. Evolution 65:1752–1771

    Article  PubMed  Google Scholar 

  • Winship PR (1989) An improved method for directly sequencing PCR amplified material using dimethyl sulphoxide. Nucleic Acids Res 17:1266

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A 107:9264–9269

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yang Z, Rannala B (2014) Unguided species delimitation using DNA sequence data from multiple loci. Mol Biol Evol 31:3125–3135

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zeppilli D, Sarrazin J, Leduc D et al. (2015) Meiofauna as model organisms to assess global change in marine ecosystems. Mar Biodivers

  • Zhan A, MacIsaac HJ (2015) Rare biosphere exploration using high-throughput sequencing: research progress and perspectives. Conserv Genet

  • Zhang J, Kapli P, Pavlidis P, Stamatakis A (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29:2869–2876

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Daniela Zappilli for organising a workshop on meiofaunal studies in Brest and for inviting us to write this manuscript. We thank also Timothy G. Barraclough, William C. Birky Jr, Bryan Carstens, Simon Dellicour, Christophe Douady, Florian Malard, Nicolas Puillandre, Fabio Stoch, Ziheng Yang, and two anonymous reviewers for comments and suggestions. J.-F.F. is supported by the European Research Council (ERC-2012-AdG 322790).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Diego Fontaneto.

Additional information

Communicated by D. Zeppilli

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fontaneto, D., Flot, JF. & Tang, C.Q. Guidelines for DNA taxonomy, with a focus on the meiofauna. Mar Biodiv 45, 433–451 (2015). https://doi.org/10.1007/s12526-015-0319-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12526-015-0319-7

Keywords

Navigation