Genome-Wide analysis of Marsupial Retroposons: Phylogenetic markers for reconstructing their Evolution
Final Report Abstract
Mammalian genomes do not only contain genes, but in addition contain genetic sequences called transposable elements. Transposable elements propagate in the genome via either a copy-and-paste or cut-and-paste mechanism. Retrotransposons utilize the copy-and-paste approach and make up almost 40% of the human genome. Most of the retrotransposon insertions are silent DNA fossils that inserted in the distant past. Only a small fraction of the retrotransposons in a genome, the ‘source elements’, is capable of producing new copies. It was discovered in the Tasmanian devil genome, a carnivorous marsupial threatened by extinction by a contagious cancer, that active source elements are missing. So far the absence of active source elements has only been recorded in a group of South American rodents, the megabats and the thirteen-lined squirrel. The finding that the Tasmanian devil genome might lack active source elements was highly unexpected and triggered further investigations into the genome of this endangered species. Retrotransposons can be used as markers to determine relationships among species, as newly inserted copies are passed on through the generations and can persist in the genome for millions of years. This has been utilized to resolve the relationships among the living marsupials. Modern marsupials are found in South America and Australia and are divided into seven major groups (orders). The retrotransposon approach could finally settle an almost thirty-year long debate regarding the phylogenetic position of the South American order Microbiotheria. Using retrotransposable elements, Microbiotheria was placed as the sistergroup to all living Australian marsupials. This discovery gathered considerable interest from the public after the findings was reported in various media, including the BBC, LA times and Science News among others. Further retrotransposon studies have been able to resolve the relationships among the four Australian marsupial orders, and in particular the position of the marsupial mole. The marsupial mole is a classic case of convergent evolution in which distantly related organisms (placental and marsupial mammals in this case) have independently acquired similar traits due to adaptation to similar environments. These adaptations have confounded attempts to resolve its true phylogenetic position among other marsupials. The results of the retrotransposon studies suggest that there is no clear relationship among the four Australian marsupial orders. Rather, we observe a patchwork of phylogenetic signals that result from the extremely rapid speciation events that took place 66 million years ago. Similarly, work on phylogenetically informative retrotransposon insertions show that the much younger radiation of Australian kangaroos is currently experiencing the same phenomenon, where the phylogenetic signal can become corrupted due to rapid speciation processes and hybridization among species. Retrotransposable elements are an excellent tool for resolving relationships among marsupials and have resolved many long-standing issues in phylogenetics. In addition, investigation of the transposable elements in the marsupial genome can offer insights into the evolution of the mammalian genome.
Publications
- (2010) Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS Biology. 8(7):e1000436
Nilsson, MA, Churakov, G, Sommer, M, Tran, V, Brosius, J, Schmitz, J
- (2012) Expansion of CORE-SINEs in the genome of the Tasmanian devil. BMC Genomics. 13(1):172
Nilsson, MA, Janke, A, Murchison, E, Ning, Z, Hallström, BM.
(See online at https://doi.org/10.1186/1471-2164-13-172) - Disentangling the relationship of the Australian marsupial orders using retrotransposon and evolutionary network analyses. Genome Biology and Evolution, Volume 7, Issue 4, 1 April 2015, Pages 985–992
Gallus, S, Janke, A, Kumar, V, Nilsson, MA
(See online at https://doi.org/10.1093/gbe/evv052) - Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Molecular Biology and Evolution, Volume 32, Issue 5, 1 May 2015, Pages 1268–1283
Gallus, S, Hallström, BM, Kumar, V, Dodt, WG, Janke, A, Schumann, GG, Nilsson, MA
(See online at https://doi.org/10.1093/molbev/msv017)
