Thesis supervisor: Imre Derényi
Location of studies (in Hungarian): ELTE Faculty of Science Department of Biological Physics / ELTE-TTK Biológiai Fizika Tsz. Abbreviation of location of studies: ELTE
Description of the research topic:
"50 years ago this year Emil Zukerkandl and Linus Pauling published the first evolutionary tree based on molecular sequences(Zukerkandl 1965). Since then, coupled with a spectacular increase in the speed, and decrease in the cost of DNA sequencing, the rapidly growing field of molecular evolution has revealed the existence of the three domains of life and demonstrated that 1-4% of the DNA of humans of non-African origin is Neanderthal-derived. The science of molecular evolution, it has been said, is in its golden age. In order to fulfil its promise, however, the dawning era of genomics has to step beyond data collection towards developing and applying methods that synthesise large data sets with theoretical models of evolution.
Horizontal gene transfer (HGT), the acquisition of genes from other species, is a major evolutionary force. It allows unicellular organisms to evolve rapidly not only by mutation and rapid multiplication, but also by external acquisition of genetic innovations. From a phylogenetic perspective, however, its success as an adaptive process has made the reconstruction of the history of life an intricate puzzle. A widespread view holds that a tree-like view of relationships among species is incompatible with the actual abundance of HGT. However, we have recently shown that instead of being considered a nuisance, HGT events can be informative (Abby 2010, Szöllősi 2012). Removing the effect of HGT in phylogenies simply discards pieces of the puzzle and ignores a majority of gene histories.
In the proposed research the PhD student will be expected to apply and further develop phylogenetic models of HGT that explicitly explain differences between the species and gene trees using transfer events (Szöllősi 2012, 2013a, 2013b & 2015). She will use these methods to reconstruct HGT events based on genome-scale data with aim of extracting novel information from these “molecular fossils”. She will have a choice of several open topics that can be adressed using the results, which include:
1. Using HGT abundance as a measure of ancient biodiversity. As first pointed out by Maddison (Maddison 1997) and later elaborated by Gogarten et al. (Fournier 2009), the overwhelming majority of transfer events have occurred from species that are today extinct (Szöllősi 2013a and Fig.3B). We will use reconstructed HGT events to infer ancestral biodiversity and correlate it with the geological and fossil records.
2. Using highways of HGT to learn about ancient microbial communities. Ancient microbial communities have conditioned HGT frequencies. Indeed, two species can only exchange genes if they are in close contact. As a consequence, gene transfer frequencies between two species can be seen as a measure of ecological co-occurrence. We will use estimates of HGT frequencies between branches of the prokaryotic tree of life to produce hypotheses about the spatial proximity between ancient organisms. This will be combined with ongoing work on using information on ancient environments from metabolic networks reconstructed from ancestral gene contents.
3. Interpreting HGT events using system-level phenotypes. The majority of HGT events are believed to be adaptive, i.e., correspond to the acquisition of genes that offer a selective advantage to the recipient organism. Understanding the determinants of successful HGT, however requires system-level models of ancient organisms. We will use reconstructed ancestral metabolic networks and correlation with ancient environments to investigate the causes and effects of HGT events.
References:
Abby, Tannier Gouy, Daubin (2012) PNAS 109(13):4962-7. Lateral gene transfer as a support for the tree of life.
Fournier, Gogarten (2009) Philos Trans R Soc Lond B Biol Sci. 364(1527):2229-39. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life.
Maddison (1997) Syst Biol. 46 (3): 523-536. Gene trees in Species trees.
transfer reconstructs the pattern and relative timing of speciations.
Szöllősi, Tannier, Lartilot, Daubin (2013a) Syst Biol. 62(3):386-97. Lateral gene transfer from the dead.
Szöllősi, Rosikiewicz, Boussau, Tannier, Daubin (2013b) Efficient exploration of the space of reconciled gene trees.
Szöllősi, Tannier, Daubin, Boussau (2015) Syst Biol. syu048. The Inference of Gene Trees with Species Trees.
Zukerkandl, Pauling (1965) J Theor Biol. 8(2):357-66. Molecules as documents of evolutionary history.
"
Required language skills: angol Further requirements: Programming skills and a strong knowledge of mathematics.
Number of students who can be accepted: 1
Deadline for application: 2015-05-29
2024. IV. 17. ODT ülés Az ODT következő ülésére 2024. június 14-én, pénteken 10.00 órakor kerül sor a Semmelweis Egyetem Szenátusi termében (Bp. Üllői út 26. I. emelet).
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