Project groups

L-3.1 | BENTHOS BARCODING (2008-2011)

Project leader:
Prof. Dr. Markus Pfenninger

Fast and accurate species identification is the essential part of biodiversity research and at the same time its major bottleneck. Traditional morphological identification of species is time consuming, cannot differentiate between cryptic species, enlighten phenotypic plasticity within one species and strongly depends on experts. Furthermore, a disadvantage of morphological keys is their restriction to particular life stages or sex. Additionally, environmental samples frequently contain small fragments of organisms which mostly cannot be identified by morphological criteria. At last, sample conservation with ethanol can lead to deformation of specimens which also hinders morphological identification.
We will develop an automated identification technique based on DNA barcoding to identify species composition of freshwater benthos. At first a reference library will be established containing the COI mtDNA sequences of organisms. As a first step of, we will create DNA barcodes for benthos species from streams of low mountain ranges including about 500 taxa. This species have been morphologically identified by experts beforehand.
The next step will be to unravel the species composition of a mixed environmental sample of macrozoobenthos via next generation sequencing (NGS) using the Genome Sequencer FLX (Roche, Basel). Sequencing mixed species eliminates the time consuming step of sorting individuals out of environmental samples.

 

Publications

Jansen, M., Bloch, R., Schulze, A. & M. Pfenninger (2011) : Integrative inventory of Bolivia’s lowland anurans reveals hidden diversity. - Zoologica Scripta 40, 567-583.

Jansen, M. & G. Köhler : Reptilia, Squamata, Amphisbaenidae, Amphisbaena cegei Montero, 1997, and Reptilia, Squamata, Teidae, Tupinambis rufescens (Günther, 1871): vertical range extension. CheckList 6(4):503-504.

Pérez-Losada, M., Bloch. R., Breinholt, J.W., Pfenninger, M. & J. Domínguez (2012) : Taxonomic assessment of Lumbricidae (Oligochaeta) earthworm genera using DNA barcodes. - European Journal of Soil Biology 48: 41-47.

Römbke, J., Aira, M., Backeljau, T., Breugelmans, K., Dominguez, J., Funke, E., Graf, N., Hajibabaei, M., Perez-Losada, M., Porto, P.G., Schmelz, R.M., Vierna, J., Vizcaino, A & M. Pfenninger (2015) : DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories. Applied Soil Ecology

Schulze, A. & M. Jansen : A tadpole of Trachycephalus venulosus (Anura: Hylidae) as prey for a fishing spider (Araneae: Pisauridae) in the Bolivian Chiquitano Dry Forest. Herpetology Notes 3: 297-298.

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