Project groups

L-2.3 | BIOINFORMATIC TOOLS FOR STUDYING LONG-SCALE CHANGES IN BIODIVERSITY (PHYLOGENY) AND THEIR CORRELATION WITH ENVIRONMENTAL CHANGES

Project leader:
Prof. Dr. Axel Janke

Phylogenetic analyses have shown that radiations of mammals and other vertebrates can be correlated to environmental changes. A famous example is the radiation of mammals after the K/T boundary at 65 million years ago, when dinosaurs became extinct. But there are numerous other significant events in Earth's history at 100, 35 and 2.5 million years ago that may have influenced mammalian evolution. (see figure).

D1.2This is a phylogenomic tree based on 3 million DNA characters from protein coding genes. It showa estimated times of mammalian divergences (Hallström and Janke 2008). The orange and blue lines mark significant changes in the environment at 100, 65, 35 and 2.5 million years ago. We are studying if these events left signatures in the mammalian genomes.


Mammals are an ideal group for such studies, because some 35 species in this group have had their whole genomes sequenced. These sequences can be studied to find genomic signatures that might have been triggered by these changes. Mammalian studies also profit from advances in biomedical genomics, because tools and methods that are developed for human genetics can often be directly applied to the genomes of other mammals.

One of our approaches is to compare mammalian genomes (comparative genomics), reconstruct ancestral character states, analyze and date their changes. Using this temporal information we attempt to correlate it to historic events. For example, when one consistently detects faster evolutionary rates across different lineages and for different climatic events, one may postulate a causal connection. This will teach us a lot about if and how evolutionary processes shape the genome, and consequently the organism. This knowledge equips us to better understand how climate or environmental changes could affect the biodiversity of the planet.

These analyses depend on bioinformatic tools, which we develop or adapt to our questions in order to analyze the tremendous amount of data from the increasingly numerous mammalian genome sequences. When necessary we will produce new sequence data for hypothesis testing and complementing existing data. 

Team

Dr. Maria Nilsson-Janke, Researcher
Dr. Yichen Zheng, Researcher
Dr. Vikas Kumar, Scientific Assistant
Fritjof Lammers, Ph.D. student
Sven Winter, Ph.D. student

Publications

Bock, F., Fennessy, J., Bidon, T., Tutchings, A., Marais, A., Deacon, F. & A. Janke (2014): : Mitochondrial sequences reveal a clear separation between Angolan and South African giraffe along a cryptic rift valley. - BMC Evolutionary Biology 2014, 14:219

Edwards, S.V., Xi, Z., Janke, A., Faircloth, B.C., McCormack, J.E., Glenn, T.C., Zhong, B., Wu, S., Lemmon, E.M., Lemmon, A.R., Leaché, A.D., Liu, L. & C.C. Davis (2015) : Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics. - Molecular Phylogenetics and Evolution 94 A: 447–462

Fennessy, J., Bock, F., Tutchings, A., Brenneman, R. & A. Janke (2013) : Mitochondrial DNA analyses show that Zambia's South Luangwa Valley giraffe (Giraffa camelopardalis thornicrofti) are genetically isolated. - African Journal of Ecology 51: 635–640.

Gallus S., Lammers F. & M. Nilsson Janke (2016) : When Genomics is not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials. - Genome Biology and Evolution

Gallus, S., Hallström, B. M., Kumar, V., Dodt, W. G., Janke, A, Schumann, G. G. & M. Nilsson Janke (2015) : Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. - Molecular Biology and Evolution (early Access)

Gallus, S., Janke, A., Kumar, V & M.A. Nilsson (2015) : Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses. - Genome Biology and Evolution  

Gallus, S., Kumar, V., Bertelsen, M.F., Janke, A. & M.A. Nilsson (2015) : Survey sequencing of the Java Mouse Deer (Tragulus javanicus) and Lesser kudu (Tragelaphus imberbis) genomes revealed differential expansion of RTE elements in Ruminantia. Gene Vol 571 (2) 271 - 278

Hallström, B.M. & A. Janke (2010) : Mammalian evolution may not be strictly bifurcating. - Molecular Biology and Evolution, 27 (12): 2804-2816. doi: 10.1093/molbev/msq166 .

Hallström, B.M., Schneider, A., Zoller, S. & A. Janke (2011) : A genomic approach to examine the complex evolution of laurasiatherian mammals. - PLoS ONE 6:e28199.

Janke, A. (2010) : The Rise of Amphibians: 365 Million Years of Evolution. - Systematic Biology 59(4): 488-490.

Khan, A.A., Janke, A., Shimokawa, T. & H. Zhang (2011) : Phylogenetic analysis of kindlins suggests subfunctionalization of an ancestral unduplicated kindlin into three paralogs in vertebrates. -  Evolutionary Bioinformatics online 7:7-19. [0]

Kumar, V., Kutschera, V.E., Nilsson, M.A. & A. Janke (2015) : Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes. - BMC Genomics (2015) 16:585

Kumar, V., Hallström, B.M. & A. Janke (2013) : Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires. - PLoS ONE 8(4): e60019.

M. Nilsson Janke (2015) : The devil is in the details: transposable element analysis of the Tasmanian devil genome. - Mobile Genetic Elements

Nilsson M.A., Härlid A., Kullberg M. & A. Janke (2010) : The impact of fossil calibrations, codon positions and relaxed clocks on the divergence time estimates of the native Australian rodents (Conilurini). - Gene 455(1-2): 22-31.

Nilsson, M.A., Klassert, D., Bertelsen, M.F., Hallström, B.M. & A. Janke (2012) : Activity of Ancient RTE Retroposons during the Evolution of Cows, Spiral-Horned Antelopes, and Nilgais (Bovinae). - Molecular Biology and Evolution 29 (10): 2885-2888.

Nilsson, M.A., Janke, A., Murchison, E.P., Ning, Z. & B.M. Hallström (2012) : Expansion of CORE-SINEs in the genome of the Tasmanian devil. - BMC Genomics. 2012 May 6; 13(1): 172.

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