Phylogenetics in Practice

Insight into the evolutionary past of organisms has profound consequences for many areas affecting our daily life, including drug development, food production, agriculture, and biodiversity conservation to name but a few.
Examples of applications where our new algorithms and methodologies have shed light include the evolutionary past of yeast [1] (which is of use in classifying yeast which cause food spoilage), the origin of the evolutionary phenomenon of polyploidy [2] (which is very common in plants, including crops such as wheat), understanding the genetic diversity and dispersal of plants [3], reconstructing/understanding the evolution of viruses such as Hepatitis and SARS [4], and shedding light in the evolutionary relationships between over 500 different wheat varieties [5] some of which are part of the GEDIFLUX EU Framework V project.
 

References

  1. Wu, Q., James, S., Roberts, I., Moulton, V., Huber,K.T., Exploring contradictory phylogenetic relationships in yeast, FEMS Yeast Research.
  2. Brysting, A., Oxelman, B., Huber,K.T., Moulton,V., Brochmann,C., Untangling complex histories of genome mergings in high polyploids, Systematic Biology, 56, 2007, 467-476.
  3. Winkworth, R., Bryant, D., Lockhart, P., Havell, D., Moulton, V., Biogeographic interpretation of split graphs: Least squares optimization of edge lengths Systematic Biology, 54, 2005, 56-65.
  4. Magiorkinis, G., Magiorkinis, E., Paraskevis, D., Vandamme, A.M., Van Ranst, M., Moulton, V., Hatzakiu, A., Phylogenetic analysis of the full-length SARS-CoV sequences: Evidence for phylogenetic discordance in three genomic regions Journal of Medical Virology, 74(3), 2004, 369-372.
  5. Kettleborough, G., Dicks, J., Roberts, I.N., Huber, K.T. Reconstructing (Super)trees from data sets with missing distances: Not all is lost, Molecular Biology and Evolution 36(6), 2015, 1628-1642.