TU BRAUNSCHWEIG

Topic P: Patterns of aquatic endemism and biodiversity on the Tibetan Plateau detected by modern and ancient DNA

Complementary Chinese topic: Effects of microbial activities on modern DNA

Research objectives

While our work will include classical microscopic and macroscopic analysis of biological communities, we will heavily focus on applying molecular metabarcoding approaches to obtain integrative species inventories for the ecosystems studied, and track population dynamics back in time by analysis of paleoenvironmental DNA. For the first phase of TransTiP, we will concentrate on invertebrates as ostracods and chironomids, because these groups contain endemic and undescribed species (e.g. Makarchenko and Kobayashi, 1997; Wang, 2000; Yu et al., 2009), and the parallel analysis using classical microfossil techniques (W2 + P1) will allow to cross-evaluate success and results of DNA extraction + metabarcoding. During fieldwork, the postdoctoral researcher will collect living larval + adult specimen in the Nam Co catchment. These will be determined, sorted and used for DNA metabarcoding on Illumina platforms, following and adapting approaches established in the applicant’s laboratories (Vences et al., 2016). DNA sequences obtained will be used to extend existing genetic libraries, catch modern haplotype diversity, build regional phylogenetic trees and detect the origin of species endemic on the TP. Sequencing will be carried out in the genome center of the Helmholtz Institute for Infection Research, Braunschweig (regularly collaborating with the Vences lab). Potentially new taxa will be described in cooperation with leading taxonomic experts for the organism groups (E. Makarchenko for chironomids, P. Frenzel for ostracods). Sediment sampling and paleoenvironmental DNA extraction will follow protocols specifically designed for extraction from ancient sediments to avoid contamination with modern material (e.g. Anderson-Carpenter et al., 2011, Rawlence et al., 2014), and analysis take place at the fossil DNA laboratory of the M. Hofreiter (Potsdam University). Analysis on short cores will complement classical microfossil approaches and focus on changes in haplotype diversity that cannot be detected otherwise. Based on our expertise with metabarcoding and eDNA analyses we are fully convinced that metabarcoding of extant organisms will be successful and generate a large set of highly relevant data, leading to a very efficient and objective high-throughput inventory of current freshwater diversity in the study system. In contrast, we are aware that metabarcoding of ancient DNA is challenging and will require solving numerous practical problems. By collaborating with the Hofreiter lab (specialized in ancient DNA) we are however optimistic to overcome these challenges and thereby provide pioneering studies in the molecular ecology of ancient freshwater communities. 

Sino-German complementarity of research

For terrestrial tissue, highest depletion rates of DNA seem to occur during decomposition in the terrestrial environment, and strongly decelerated DNA degradation is observed after embedding in lake sediments (Andersen-Carpenter et al., 2011). For tissue of aquatic organisms, factors influencing the preservation or loss of DNA are largely unknown. Our Chinese colleagues will use their expertise in the analysis of microbial communities and microbial DNA in lake water, sediment and ice cores on the TP (e.g. Huang et al., 2014; Liu et al., 2016) to access microbial diversity and rates of microbial activity in aquatic environments of the Nam Co catchment. Microbial community structure and activity will be compared against amount and diversity of (paleo-) environmental DNA extracted from sediments (P2), to access potential connections between DNA preservation and microbial activity. This shall contribute to develop more precise site selection criteria for paleoenvironmental DNA studies and enhance the predictability of success when applying the paleoenvironmental DNA approach.

Mentors: Prof. Dr. Miguel Vences, TU Braunschweig
Prof. Dr. Antje Schwalb, TU Braunschweig
Prof. Dr. Liu Yongqin, ITP

 

»References

Makarchenko, E., Kobayashi, T., 2007. Diamesa amanoi sp. n., a new species of Diamesinae (Diptera, Chironomidae) from Nepal, with notes on taxonomy and distribution of some Diamesa Meigen. Medical Entomology and Zoology 48, 45-48.

Wang, X. H., 2000. A revised checklist of Chironomidae from China (Diptera). In: Hoffrichter, O. (Ed.): Late 20th Century Research on Chironomidae. An Anthology from the 13th International Symposium on Chironomidae. Shaker, Aachen, 629-652.

Yu, N., Zhao, Q., Li, E., Chen, S., Chen L., 2009. An updated and annotated checklist of recent nonmarine ostracods from China. Zootaxa 2067, 29-50.

Vences, M., Lyra, M.L., Perl, R.G.B., Bletz, M.C., Stankovic, D., Lopes, C.M., Jarek, M., Bhuju, S., Geffers, R., Haddad, C.F.B., Steinfartz, S., 2016. Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene. Conservation Genetics Resources 8, 323-327.

Anderson-Carpenter, L. McLachlan, J., Jackson, S. T., Kuch, M., Lumibao, C. Y., Poinar, H. N., 2011. Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics. BMC Evolutionary Biology 11:30.

Rawlence, N.J., Lowe, D.J., Wood, J.R., Young, J.M., Churchman, G.J., Huang, Y.-T., Cooper, A., 2014. Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects. Journal of Quaternary Science 29, 610-626.

Huang, S., Liu, Y., Hu, A., Liu, X., Chen, F., Yao, T., Jiao, N., 2014. Genetic diversity of picocyanobacteria in Tibetan lakes: assessing the endemic and universal distributions. Applied Environment Microbiology 80 (24), 7640-7650.

Liu, Y., Priscu, J.C., Yaou, T., Vick-Majors, T., Xu, B., Jiao, N., Santibáñez, P., Huang, S., Wang, N., Greenwood, M., Michaud, A.B., Kang, S., Wang, J., Gao, Q., Yang, Y., 2016. Bacterial responses to environmental change in the Tibetan Plateau over the past half century. Environmental Microbiology 18, 1930-1941.


  aktualisiert am 29.08.2017
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