Phylogenetics Summer Course 2014

Current State of Registrations:

What?: Week-long, intensive phylogenetics course covering all aspects of modern molecular phylogenetics and phylogenomics.

Where?: Department of Biology, National University of Ireland Maynooth.  This is approximately 40 minutes from Dublin Airport (Aer Lingus, British Airways, Ryanair, American Airlines, Lufthansa, Air France, etc.) ,  25km from the centre of Dublin, Ireland.

[symple_googlemap title=”NUI Maynooth” location=”National University of Ireland Maynooth” zoom=”10″ height=250]

When?: Sunday August 31st – Friday September 5th (inclusive), 2014.

Who is it for?: This course starts with the basics of phylogenetic reconstruction and deals with all the major methods and all kinds of data from genes to genomes.  Therefore, it is particularly suited to researchers that have a keen interest in phylogenetic reconstruction but have little or no practical experience or theoretical background (ideally suited to new Masters/PhD students/post-docs, but also investigators moving into this area of research).  We welcome organismal phylogeneticists or genome scientists who are trying to make sense of the evolutionary history of any kind of gene or genome.

Course structure: Every day will begin with formal lectures covering all parts of phylogenetic reconstruction.  The afternoons will be taken up with practicals.  In addition, the course will have specific lectures that demonstrate “use cases” for phylogenetics, with examples from prokaryotes, animals, plants, protozoans and fungi.

Student involvement:  All students are expected to give a five minute presentation of their research agenda.  This will happen towards the beginning of the week, in order to encourage discussions during the course.

Course fee: €750.  This includes a welcome reception on Sunday August 31st, all coffee breaks and all lunches during the week and the course dinner on Thursday evening. It does not include accommodation.

Accommodation: If you are accepted on the course, we will make several recommendations for inexpensive (~€27 – €70 per night) or more luxurious accommodation (~€100-€250 per night).  You must organise and pay for your own accommodation.

Application process: Send an email to with your CV and a one-paragraph document stating why this course is useful for you. Please state your familiarity with unix/bioinformatics – are you an absolute beginner? proficient? expert?  We will accept applications until the course is full.  Places will be offered in a first-come, first-served basis and if you are considered to be an appropriate candidate, you will receive your acceptance email within two days of applying.

Note 1: All students will be presented with a certificate of completion for this course and it can be used as part of post-graduate studies.

Note 2: We have found it better if students bring their own laptops.  Please let us know if this is a problem for you and we will supply a laptop.
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Teaching staff:

[symple_tab title=”Professor James McInerney”]

[symple_testimonial by=”Professor James O. McInerney”]

Work in Professor McInerney’s lab is focussed on gene and genome evolution, with the emphasis at the moment on horizontal gene transfer in prokaryotes and mobile genetic elements, the origin of the Eukaryotic cell and gene family evolution in eukaryotes.

Prof. McInerney was one of the founding directors of the Irish Centre for High End Computing. He is an Associate Editor of Molecular Biology and Evolution, Biology Direct, Journal of Experimental Zoology and is currently serving as the secretary for the Society for Molecular Biology and Evolution.

Sample publications:
Alvarez-Ponce, D., Lopez, P., Bapteste, E. and McInerney, J.O. (2013). Gene similarity networks provide tools for understanding eukaryote origins and evolution. Proceedings of the National Academy of Sciences USA 110(17):E1594-1603. doi: 10.1073/pnas.1211371110.

Nelson-Sathi, S., Dagan, T., Landan, G., Janssen, A., Steel, M., McInerney, J. O., Deppenmeier, U., and Martin, W.F. (2012). Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proceedings of the National Academy of Sciences USA 109 (50) 20537-20542, doi: 10.1073/pnas.1209119109.

Bapteste, E., Bouchard F., Baquero F., McInerney J.O., Lopez P. and Burian R.M. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proceedings of the National Academy of Sciences USA 109:45 18266-18272, doi:10.1073/pnas.1206541109.

Feuda, R., Hamilton, S.C., McInerney, J.O. and Pisani, D. (2012) Metazoan opsin evolution reveals a simple route to animal vision. Proceedings of the National Academy of Sciences USA 109:46 18868-18872, doi: 10.1073/pnas.1204609109.

Cotton, J.A., and McInerney, J.O. (2010) Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proceedings of the National Academy of Sciences USA 107:40 17252-17255.

McInerney, J.O. and Pisani, D (2007) Genetics: Paradigm for Life. Science 318:1390-1391.

Kinsella, R.J., Fitzpatrick, D.A., Creevey, C.J. and McInerney J.O. (2003). Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution and gene duplication. Proceedings of the National Academy of Sciences USA, 100, 10320-10325.

McInerney, J.O. (1998). Replicational and Transcriptional Selection on Codon Usage in Borrelia burgdorferi. Proceedings of the National Academy of Sciences USA: 95 10698-10703.

[symple_tab title=”Dr. Mary O’Connell”]
[symple_testimonial by=”Dr. Mary O’Connell”]

Dr. O’Connell is principal Investigator of the Bioinformatics and Molecular Evolution group at the School of Biotechnology, Dublin City University.  She is an evolutionary genomicist and her research fits into four main themes – evolution of the immune system, tetrapod molecular synapomorphies, adaptation in proteins, and evolutionary theory.

She has worked on the role of positive selection in molecular evolution and the assessment of rate heterogeneity in protein coding regions of mammal, bird and amphibian genomes. Additionally, she has worked on the evolution of genomic imprinting in mammals and plants from an analytical and quantitative perspective. She continues to expand her interests in both the analytical/empirical analyses of genomic data from a molecular evolutionary perspective and also in the theoretical underpinnings and modelling of evolutionary processes.

Sample publications:

McInerney, J.O., O’Connell, M.J., and Pisani, D. (2014) The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology 12(6):449-455.

Liu S., Lorenzen E.D., Fumagalli M., Li B., Harris K., Xiong Z., Zhou L., Korneliussen T.S., Somel M., Babbitt C., Wray G., Li J., He W., Wang Z., Fu W., Xiang X., Morgan C.C., Doherty A., O’Connell M.J., McInerney J.O., Born E.W., Dalén L., Dietz R., Orlando L., Sonne C., Zhang G., Nielsen R., Willerslev E., Wang J. (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157 (4):785–794.

Morgan CC, McCartney AM, Donoghue MTA, Loughran NB, Spillane C, Teeling EC and O’Connell MJ* (2013) Molecular adaptation of telomere assciated genes in mammals. BMC Evolutionary Biology. 13:251. doiL10.1186/1471-2148-13-251

Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO and O’Connell MJ* (2013) Heterogeneous models place the root of the placental mammal phylogeny. Molecular Biology and Evolution. doi: 10.1093/molbev/mst11

Dmitriev P, Barat A, Polesskaya A, O’Connell MJ, Robert T, Dessen T, Walsh TA, Lazar V, Turki A, Carnac G, Laoudj-Chenivesse D, Lipinski M and Vassetzky YS. (2013) Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes. BMC Genomics 14:265. doi:10.1186/1471-2164-14-265

Shakya K, O’Connell MJ and Ruskin HJ (2012) The Landscape for Epigenetic/Epigenomic Biomedical Resources. Epigenetics 7(9):982-6.

Morgan CC, Shakya K, Webb AE, Walsh TA, Lynch M, Loscher CE, Ruskin HJ and O’Connell MJ* (2012) Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. BMC Evolutionary Biology 12:114 doi:10.1186/1471-2148-12-114.

Loughran NB, McCormick-Hill S, Hinde S, Leidal KG, Bloomberg S, Loughran ST, O’Connor B, Fagan C, Nauseef WM* and O’Connell MJ* (2012) Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase. Molecular Biology and Evolution 29 (8): 2039-2046.

[symple_tab title=”Dr. David Fitzpatrick”]

[symple_testimonial by=”Dr. David Fitzpatrick”]

Dr. Fitzpatrick’s laboratory focuses on the evolution of unicellular microorganisms paying special attention to fungal species. They use comparative genomics, phylogenomics, phylogenetics and synteny based tools to elucidate fungal gene and genome evolution. We are currently using comparative genomics to perform an analysis of yeast species, both pathogenic and non-pathogenic, to identify species-specific metabolic pathways and lineage-specific loss or gain of metabolic genes.

The presence or absence of particular pathways or pathway components can be correlated with pathogenesis and species-specific virulence characteristics, which can lead to the development of novel therapeutic strategies. We are also investigating the frequency of horizontal gene transfer within the Candida genus. Acquired genetic material from an external source can lead to increased virulence and can provide novel antifungal drug targets. We are also interested in sequencing and annotating medically / biotechnological important fungal strains.

Sample publications:

Haggerty, L.S., Jachiet, P.A.,  Hanage, W.P., Fitzpatrick, D., Lopez, P., O’Connell, M.J., Pisani, D., Wilkinson, M., Bapteste, E., and McInerney, J.O., (2014) A pluralistic account of homology: adapting the models to the data. Molecular Biology and Evolution 31 (3): 501-516.

Sharma, V., He, C., Sacca-Schaeffer, J., Brzozowski, E., Martin-Herranz, D.E., Mendelowitz, Z., Fitzpatrick, D.A., O’Halloran, D.A., (2013) Insight into the family of Na+/Ca2+ exchangers of Caenorhabditis elegans. Genetics 195 (2) 611-619.

Collins, C., Keane, T.M., Turner, D.J., O’Keeffe, G., Fitzpatrick, D.A., and Doyle, S. (2013) Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System. Journal of Proteome Research 12:6 2552-2570.

Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Burglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Soon Heng Tan C, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus B. (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biology 14(2):R11

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 459(7247):657-662.




Programme – tentative and subject to change

[spoiler show=”Show Full Timetable”]Day 1 (Sunday August 31st, 2014)  ”Meet and Greet”

Meeting with students.(8:00PM) “Welcome introductions and refreshments”


Day 2 (Monday September 1st, 2014) “Setting the scene”

Lecture I (9.00 – 10.30): James McInerney – “Introduction to Gene and Genome Evolution”

Coffee break (10.30 – 10.45) (Provided by the course)

Student introductions and presentations I (10.45 – 12.30)

Lunch (12.30-1.30) (Provided by the course)

Student introductions and presentations II ( 1.30 – 3:00)

Coffee Break (3.00 – 3.15) (Provided by the course)

Practical session I (3.15 – 5.00): David Fitzpatrick (leading demonstrator) – “Unix pipelining and the automation of analyses in comparative genomics and phylogenomics I”

Seminar I (5.00 – 5.45): Mary O’Connell – “Phylogenomics and the Evolution of Function”


Day 3 (Tuesday September 2nd, 2014) “Theory and Practice”

Lecture II (9.00 – 10.30): James McInerney – “Maximum Parsimony, Evolutionary Distances & Molecular Clocks I”

Coffee break (10.30 – 10.45) (Provided by the course)

Lecture III (10.45 – 12.30) James McInerney – “Maximum Parsimony, Evolutionary Distances & Molecular Clocks II”

Lunch (12.30-1.30) (Provided by the course)

Practical session II ( 1.30 – 3:00): David Fitzpatrick (leading demonstrator) – “Multiple sequence alignment”

Coffee Break (3.00 – 3.15) (Provided by the course)

Practical session III (3:15-5:00): Mary O’Connell (leading demonstrator) – “Parsimony and Distance analyses”

Seminar II (5.00 -5.45): James McInerney – “Evolutionary Analyses of Eukaryote Origins.


Day 4 (Wednesday September 3rd, 2014) “Single gene analyses”

Lecture IV (9.00 – 10.30): Mary O’Connell – “Searching tree space and determining support”

Coffee break (10.30 – 10.45) (Provided by the course)

Lecture V (10.45 – 12.30): James McInerney – “Introduction to Maximum Likelihood and Bayesian Analyses”

Lunch (12.30 – 1.30) (Provided by the course)

Practical session IV (1.30 – 3.00): Mary O’Connell (leading demonstrator) – “Model selection using Maximum Likelihood”

Coffee Break (3.00 – 3.15) (Provided by the course)

Practical session V (3.15 – 5.00):  James McInerney  (leading demonstrator) – “PAUP & RAxML Maximum Likelihood”

Seminar III (5.00-5.45): David Fitzpatrick “Fungal Phylogenomic Analyses”


Day 5 (Thursday September 4th, 2014) “Using Phylogenies”

Lecture VI (9.00 – 10.30): David Fitzpatrick – “Troubleshooting phylogenomics”

Coffee Break (10:30 – 10:45) (Provided by the course)

Lecture VII (10.45 – 12.30): Mary O’Connell – “Codon-based models of evolution”

Lunch (12.30 1.30) (Provided by the course)

Practical session VI (1.30 – 3.00): James McInerney (leading demonstrator) – “MrBayes & Phylobayes – Bayesian phylogenomics”

Coffee break (3.00-3.15) (Provided by the course)

Practical session VII (3.15 – 5.00): Mary O’Connell (leading demonstrator) – “Codon Models using PAML”

7:00: Conference Dinner


Day 6 (Friday September 5th, 2014) “Scaling up to genomes”

Lecture VIII (9.00 – 10.30): David Fitzpatrick –  “large-scale phylogenomic tools”

Coffee Break (10.30 – 10.45) (Provided by the course)

Practical session VIII (10.45 – 12.30): Mary O’Connell (leading demonstrator) – “Unix pipelining and the automation of analyses in comparative genomics and phylogenomics II”

Lunch (12.30 – 1.30) (Provided by the course)

Practical session IX (1.30 – 3.00): Student Data Analysis (all teachers and demonstrators)

Coffee Break (3.00 – 3.15) (Provided by the course)

Practical session X (3.15 – 5.00): Student Data Analysis (all teachers and demonstrators)


Course ends


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Software Programs we will use:


Clustal Omega








Learning Outcomes:

1. Basic understanding of Unix-like operating systems.

2. Understanding of the questions that can be answered using phylogenetic reconstruction

3. You will know how alignments are constructed.

4. You will know how Maximum Parsimony, Distance Matrix, Maximum Likelihood and Bayesian methods work.

5. You will know how to test for signal in your data.

6. You will know how to analyse your phylogenetic hypotheses for robustness.

7. You will know how to use phylogenies in order to detect selective constraints on protein-coding sequences.

8. You will know how to test phylogenetic models.

9. You will see how phylogenetics can be extended to phylogenomics.

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If you have questions, you can contact us here:


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