Molecular systematic and species identification (DNA barcoding)

Type: 
Master Thesis subject (30 ECTS)
programme: 
EMBC+
Even though morphology has been the foundation of taxonomy for centuries, it has often failed to delineate species boundaries, especially in the case of overlapping and variable phenotypes. Molecular genetics provide tools to overcome this problem and the additional incorporation of ecological data leads to an integrative taxonomy approach for a more precise analysis of biodiversity. In cases where morphological characters are not diagnostic (e.g. sibling species) or such characters are lost (e.g. fragments of a specimen), molecular genetic methods are virtually the only way for species identification. Additionally, many marine organisms and especially their diverse developmental stages, such as (1) eggs and larvae of fishes and invertebrates, (2) zoo- and phytoplankton, and (3) benthic invertebrates, are cumbersome and difficult to identify by morphological characters. Classical microscopy methods are time-consuming and require a high degree of taxonomic expertise, which is currently falling short. The “gold standard” in molecular genetic identification are DNA sequences. The consortium for the barcoding of life (CBOL) established a fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) as the standard for the identification of metazoans, which are deposited in the barcoding of life data base (www.barcodinglife.org) and GeneBank. Identification can be done by sequencing the required marker with universal primers and re-constructing a phylogenetic tree. A possible thesis topic is the molecular systematics of European flatfishes based on mitochondrial DNA sequences (COI, cyt b, 16S). Theses sequences are already available and therefore the thesis will not include molecular genetic work in the laboratory. More information about DNA barcoding and molecular systematic can be obtained from the following publications, which can be requested from me: Ardura A, Morote E, Kochzius M, Garcia-Vazquez E (2016) Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes. PeerJ 4:e2438; DOI 10.7717/peerj.2438 Dohna TA, Kochzius M (2015) Obstacles to molecular species identification in sea anemones (Hexacorallia: Actiniaria) with COI, a COI intron, and ITS II. Marine Biodiversity, DOI 10.1007/s12526-015-0329-5 Chitipothu S, Cariani A, Bertasi F,
Stagioni M, Kochzius M, Blohm D,
Tinti T, Landi M (2014) Invertebrate DNA chip: opportunities and challenges in the
development and application of microarrays for marine
biodiversity studies. In: Rogers JV (ed) Microarrays: principles, applications and technologies. Genetics - research and issues. Nova Science Publishers, Inc., pp 101-134 Laakmann S, Auel H, Kochzius M (2012) Evolution in the deep sea: biological traits, ecology and phylogenetics of pelagic copepods. Molecular Phylogenetics and Evolution 65: 535–546 Kochzius M, Seidel C, Antoniou A, Botla SK, Campo D, Cariani A, Garcia Vazquez E, Hauschild J, Hervet C, Hjörleifsdottir S, Hreggvidsson G, Kappel K, Landi M, Magoulas A, Marteinsson V, Nölte M, Planes P, Tinti T, Turan C, Venugopal MN, Weber H, Blohm D (2010) Identifying fishes through DNA barcodes and microarrays. PLoS ONE 5(9): e12620. doi:10.1371/journal.pone.0012620 Kochzius M (2009) Trend in fishery genetics. In: Beamish R, Rothschild B (eds) The Future of Fishery Science in North America. Fish & Fisheries Series, Springer Science + Business Media B.V., pp 453-493 Richter C, Roa-Quiaoit HA, Jantzen C, Zibdeh M, Kochzius M (2008) Collapse of a new living species of giant clam in the Red Sea. Current Biology 18: 1349-1354 Froukh T, Kochzius M (2008) Species boundaries and evolutionary lineages in the blue green damselfishes Chromis viridis and C. atripectoralis (Pomacentridae). Journal of Fish Biology 72: 451-457 Kochzius M, Söller R, Khalaf MA, Blohm D (2003) Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 28: 396-403
Number of students: 
1
academic year: 
2016-2017
2017-2018
Contact person email: 
contact person first name: 
Marc
contact person last name: 
Kochzius
Institutes Involved: 
Reference Number: RP-48241