title: An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding.
abstract: Molecular surveys of meiofaunal diversity face some interesting methodological challenges when it comes to interstitial nematodes from soils and sediments. Morphology-based surveys are greatly limited in processing speed, while barcoding approaches for nematodes are hampered by difficulties of matching sequence data with traditional taxonomy. Intermediate technology is needed to bridge the gap between both approaches. An example of such technology is video capture and editing microscopy, which consists of the recording of taxonomically informative multifocal series of microscopy images as digital video clips. The integration of multifocal imaging with sequence analysis of the D2D3 region of large subunit (LSU) rDNA is illustrated here in the context of a combined morphological and barcode sequencing survey of marine nematodes from Baja California and California. The resulting video clips and sequence data are made available online in the database NemATOL (http://nematol.unh.edu/). Analyses of 37 barcoded nematodes suggest that these represent at least 32 species, none of which matches available D2D3 sequences in public databases. The recorded multifocal vouchers allowed us to identify most specimens to genus, and will be used to match specimens with subsequent species identifications and descriptions of preserved specimens. Like molecular barcodes, multifocal voucher archives are part of a wider effort at structuring and changing the process of biodiversity discovery. We argue that data-rich surveys and phylogenetic tools for analysis of barcode sequences are an essential component of the exploration of phyla with a high fraction of undiscovered species. Our methods are also directly applicable to other meiofauna such as for example gastrotrichs and tardigrades.
authors.affiliation: Department of Nematology, University of California, Riverside, CA 92521, USA. paul.deley@ucr.edu
authors.forename: Paul
authors.initials: P
authors.lastname: De Ley
authors.forename: Irma Tandingan
authors.initials: IT
authors.lastname: De Ley
authors.forename: Krystalynne
authors.initials: K
authors.lastname: Morris
authors.forename: Eyualem
authors.initials: E
authors.lastname: Abebe
authors.forename: Manuel
authors.initials: M
authors.lastname: Mundo-Ocampo
authors.forename: Melissa
authors.initials: M
authors.lastname: Yoder
authors.forename: Joseph
authors.initials: J
authors.lastname: Heras
authors.forename: Dora
authors.initials: D
authors.lastname: Waumann
authors.forename: Axayácatl
authors.initials: A
authors.lastname: Rocha-Olivares
authors.forename: A H
authors.initials: AH
authors.lastname: Jay Burr
authors.forename: James G
authors.initials: JG
authors.lastname: Baldwin
authors.forename: W Kelley
authors.initials: WK
authors.lastname: Thomas
mesh_terms: D000818:Animals; D001483:Base Sequence; D044822:Biodiversity; D002140:California; D016000:Cluster Analysis; D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D017931:DNA Primers; D001330:Electronic Data Processing / Q000379:methods*; D008800:Mexico; D018715:Microscopy, Video / Q000379:methods; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D009348:Nematoda / Q000033:anatomy & histology* / Q000235:genetics*; D010802:Phylogeny; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D012339:RNA, Ribosomal, 28S; D004247:DNA