The use of partialcox1,rbcL and LSU rDNA sequences for phylogenetics and species identification within theNitzschia paleaspecies complex (Bacillariophyceae)

Abstract

Cox1 has been suggested as a barcode marker for diatoms but it has not been tested intensively in any group of closely related species outside Sellaphora. We evaluated the use of cox1, LSU and rbcL for phylogeny and identification in the taxonomically problematic but ecologically important freshwater diatom Nitzschia palea, for which LSU rDNA sequences, mating and morphological data had already been published, and for which DNA and/or clonal isolates were still available; some new isolates were added. The previous and new information concur in suggesting that N. palea is a complex of several or many species. Where cox1 sequences could be obtained, they were more variable than LSU and rbcL and discriminated between lineages that differed in their morphologies, mating compatibilities, LSU sequences or rbcL sequences. Repeated failures for some strains to recover cox1 sequences from DNA that yielded LSU and rbcL suggest that cox1 will be impractical as a universal barcode marker in diatoms until better primers are designed. LSU and rbcL, though less variable than cox1, can be sequenced reliably in N. palea and, together, seem to show sufficient discrimination to be worth further consideration for species recognition.

Molecular species discovery in the diatom Sellaphora and its congruence with mating trials.

“…While it is possible to correctly identify strains using mean values for one or a few morphological characters when only two to three species are present, adding more species prevents separation of all species and causes variation to be clinal, as is shown here for pole width and stria density. This is also exemplified in the Nitzschia palea species complex (Trobajo et al 2009(Trobajo et al , 2010, where both stria density and valve width vary more or less continuously, despite the presence of genetic discontinuities revealed by sequence analysis and mating data. Another complicating factor is the gradual change in valve morphology with decreasing cell size, the nature of which may differ between species.…”

Microbial mats as shelter microhabitat for amphipods in an intermittent karstic spring

“…palea is a pennate diatom with the nitzschioid eccentically positioned raphe within a keel supported by fibulae (Spaulding and Edlund, 2008), lanceolate valves, barely visible striae with parallel sides and poles terminating with subcapitate apices (Kociolek et al, 2011). It is a benthic diatom with wide geographical distribution in freshwater lentic and lotic habitats (Trobajo et al, 2010). N. palea is a taxonomically problematic species encompassing a multitude of cryptic and pseudocryptic species into a N. palea complex (Trobajo et al, 2009).…”

A floristic survey of marine tube-forming diatoms reveals unexpected diversity and extensive co-habitation among genetic lines of theBerkeleya rutilanscomplex (Bacillariophyceae)

“…The most common markers are: the 5′ end of the cytochrome c oxidase I gene, COI-5P (Evans et al, 2007); the nuclear small subunit ribosomal DNA, SSU (Moniz & Kaczmarska, 2009;Zimmerman et al, 2011); the universal plastid amplicon, UPA (Sherwood & Presting, 2007;Hamsher et al, 2011); the large subunit of RUBISCO, rbcL (Evans et al, 2007(Evans et al, , 2008Trobajo et al, 2010;Hamsher et al, 2011); the LSU D2/D3 Hamsher et al, 2011); and the internal transcribed spacers of rDNA (ITS) (Behnke et al, 2004;Amato et al, 2007;Moniz & Kaczmarska, 2009. The SSU and UPA markers have broad applicability across protistan taxa and can be easily used in environmental surveys (Godhe et al, 2008;Sherwood et al, 2008), but cannot distinguish between closely related species and therefore are not the best markers for uncovering diatom diversity (Moniz & Kaczmarska, 2009;Hamsher et al, 2011;Zimmerman et al, 2011).…”

“…In other cases this diversity is cryptic and no morphological characters have been identified to distinguish between genetic species groups (e.g. in Cyclotella and Nitzschia: Beszteri et al, 2005;Trobajo et al, 2009Trobajo et al, , 2010.…”