ANNUAL REPORT

October, 2009

Table of Contents

I. Executive Summary ...... 1-3

II. CGEB Membership (2009) ...... 4

III. Financial Status of the Centre ...... 5-6

IV. CGEB Governance ...... 7-8

V. Publications by CGEB Faculty and Trainees ...... 9-15

VI. CGEB Software Development ...... 16-18

VII. Invited Presentations from CGEB Faculty ...... 19-22

VIII. Collaborative Interactions between CGEB Members ...... 23

IX. Current External Research Grants and Funding...... 24-26

X. Honours/Awards/Distinctions ...... 27

XI. Supervision of Research Trainees ...... 28-30

XII. Contributions from CGEB Trainees ...... 31-35

XIII. Other Activities of the Centre A. CGEB Seminar Series ...... 36 B. CGEB Meeting Sponsorships ...... 36-37 C. CGEB Joint Lab Meetings ...... 37 D. CGEB Journal Club ...... 37

XIV. Future Directions...... 38-39

APPENDICES:

A. CGEB Governance Policy B. Letters to Faculty of Graduate Studies regarding “Policies and Procedures” governing postdoctoral trainees at Dalhousie University I. EXECUTIVE SUMMARY

Director: Dr. Andrew J. Roger Coordinator: Wanda Danilchuk (494-3569) Phone: 494-2620 Fax: 494-1355 Website: http://www.cgeb.dal.ca

The vast majority of biodiversity on Earth is microscopic and unicellular. These organisms play key roles in all known ecosystems and have done so since life first arose on the planet ~3.8 billion years ago. Microbes are the major primary producers in the ocean, they produce most of the oxygen we breathe, they are central players in nutrient cycling in terrestrial and aquatic habitats and are abundant commensals, symbionts and pathogens capable of causing disease in humans and other organisms. Yet despite their importance, until recently, very little was known about the ‘true’ diversity of unicellular organisms and their environmental impact beyond the few that were culturable in the laboratory. Research on microbial diversity and genomics in the last decade has revolutionized our understanding of the microbial world. It is now possible to isolate diverse unicellular organisms from the environment and characterize their genomes quickly and cheaply. Furthermore, meta-genomic technologies allow genomic surveys of whole microbial communities without the need for culturing at all. With the resulting exponential growth of genomic sequence databases and associated meta-data, development of computational and statistical methods for extraction of biologically meaningful information and hypothesis testing is becoming increasingly important. It is at this nexus of genomic, computational biological and evolutionary research that the internationally recognized researchers at the Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB) at Dalhousie University are making important advances.

CGEB encompasses ten researchers in the Faculty of Medicine [Andrew Roger, Ford Doolittle, Michael Gray, John Archibald, Claudio Slamovits], Faculty of Science [Joseph Bielawski, Alastair Simpson, Ed Susko] and Faculty of Computer Science [Robert Beiko, Christian Blouin]. The main focus of the Centre’s research is understanding how microbial genomes evolve and diversify, however the research programs collectively span computational biology, computer science, statistical modeling and comparative genomics, with a strong focus on method and theory.

The Centre was officially approved by the Dalhousie Senate in June, 2008 with the mission to foster collaborations amongst a ‘group’ of nine comparative genomics/bioinformatics and microbial evolution researchers at Dalhousie. Specifically, the CGEB Centre’s goals are to: 1) recruit new world-class comparative genomics/bioinformatics researchers to Dalhousie, 2) recruit top-notch postdoctoral fellows and Ph.D. students to CGEB labs through the provision of Tula Foundation stipends and research allowances, 3) create a CGEB seminar series to attract world- class speakers to interact with CGEB principal investigators and trainees, 4) fund CGEB trainees to attend and present their work at national and international scientific meetings, and, 5) provide a framework that promotes collaborations between CGEB members and attract external research funding. Over the last year and a half we have

1 met or exceeded all of these goals. This Annual Report records the achievements of the Centre to date, the highlights of which are summarized below.

CGEB research productivity, funding and collaborations. During the period of 2008-2009 inclusive, CGEB researcher have published a total of 99 manuscripts in peer-reviewed journals (pp. 9-15), including contributions in high impact journals such as Science, Proceedings of the National Academy of Sciences USA, Trends in Ecology and Evolution and Current Biology. The fact that 55 of these publications are from 2009 (as of Oct. 1st) underscores the tremendous positive impact CGEB has made on our collective research output in the last year. The international profile of CGEB researchers is further demonstrated by the 57 invited presentations given at international conferences or invited seminars from 2008 to 2009 (32 in 2009 and 25 in 2008). Furthermore, in the last two years CGEB members have been awarded a number of prestigious Honours and Distinctions (see p. 27). The CGEB trainees (postdocs, graduate students and undergraduates) have also been productive beyond their contribution to publications. They have presented their results at international meetings (a total of 44 seminars or posters presented in 2008-2009), and, in the process, gained invaluable presentation and networking skills. The CGEB Trainee Travel/Meetings funds provided by the Tula Foundation have been of great benefit in supporting the latter activities.

A large portion of CGEB research efforts is directed at development of computer software tools for evolutionary modeling analyses and bioinformatics. In the last year and a half, 15 ‘open-source’ software tools (or suites of tools) for analysis of genomic data have been created, published and made available to the international scientific community through free web access (see pp. 16-18).

CGEB researchers have also been extremely successful in attracting external funding, garnering a total of ~$2,930,600 of external grant support in total over 2008 and 2009 from Natural Sciences and Engineering Research Council of Canada, Canadian Institutes for Health Research, Canada Foundation for Innovation, the Canadian Institute for Advanced Research, as well as the Tula Foundation.

Finally, CGEB has greatly facilitated collaborative interactions between the member researchers leading to joint publications, software development and grant applications (see p. 23). The CGEB journal club, joint lab meetings, seminar series and, in future, the annual mixer/poster session will continue to foster CGEB collaborations and synergy.

CGEB faculty recruitment. With the financial help from the Tula Foundation and the Canadian Institute for Advanced Research (CIFAR) Program in Microbial Biodiversity, we created a new CGEB position within the Department of Biochemistry and Molecular Biology. After an international job search we hired Dr. Claudio Slamovits to join the Department and CGEB as an Assistant Professor as of July 2009. The comparative genomics themes of Dr. Slamovits’ research program fits well with activities of the CGEB community.

2 CGEB postdoc and student recruitment and training. Since we first received the trainee funds from the Tula Foundation we have recruited seven top-notch postdoctoral fellows and two Ph.D. students to fill these positions. The importance of these Tula-sponsored trainees to the success of our research programs cannot be over-stated. As these individuals are often already accomplished young scientists, they bring new techniques/knowledge to CGEB labs, as well as help train the younger, less experienced students in the labs (thereby gain invaluable supervisory experience). This is especially important to the success of the CGEB labs because the number of trainees collectively has increased to a total of 67 (see pp. 28-30).

Although we have been successful in recruiting the ‘first wave’ of trainees to CGEB labs, some aspects of the current policies and procedures relating to postdoctoral training at Dalhousie poses a significant risk to the future abilities of CGEB researchers to recruit top-notch postdocs. Specifically, the lack of a postdoctoral trainees benefits package and current three-year restriction of the ‘academic postdoc’ designation (that enables these individuals to claim their stipend as non-taxable fellowship income) will make it difficult for us to compete with other institutions to attract top-notch candidates. We have twice pointed out the flaws of the current system to the Faculty of Graduate Studies in charge of postdoctoral training (see attached letters in Appendix B), and we hope that changes in the policies will be made to address these issues.

CGEB seminar series. The CGEB Seminar Series is in full swing and has hosted seven well-attended seminars from internationally recognized researchers (see p. 36) with two more scheduled to occur in the next few months. The Seminar Series has expanded to include sponsorship of symposia in meetings held at Dalhousie University by paying for the travel and accommodation of the guest speakers. In return, CGEB members are free to choose the topic of the symposium and the speakers that will present. So far we have sponsored three such symposia (see pp. 36-37), two of which occurred in the context of national or international society meetings (International Society for Evolutionary Protistology/Society of Protozoologists and the Canadian Society for Ecology and Evolution).

New CGEB activities and future directions. So far, group CGEB activities have consisted of a journal club, monthly group lab meetings where CGEB PIs or trainees describe their ongoing research and the CGEB seminar series. Owing to the increasing size of the CGEB group, we are planning to host an annual CGEB poster night mixer to promote intra-CGEB networking and collaboration. If we can procure sufficient additional funding, this event could grow into an annual retreat meeting with invited external speakers. Another future activity may be to co- or fully sponsor workshops in comparative genomics and phylogenomics methodologies; the purpose of this would be to promote the acquisition of new skills and again allow CGEB researchers to interact with other internationally renowned scientists. These and other future directions are being actively discussed amongst the CGEB membership (see pp. 38-39).

3 II. CGEB Membership (2009)

DIRECTOR • Andrew Roger, Prof. Biochemistry and Molecular Biology

STEERING COMMITTEE • Andrew Roger, Prof. Biochemistry and Molecular Biology • Michael W. Gray, Prof. Biochemistry and Molecular Biology • W. Ford Doolittle, Prof. Biochemistry and Molecular Biology

CGEB MEMBERSHIP • Andrew Roger, Prof. Biochemistry and Molecular Biology • Michael Gray, Prof. Biochemistry and Molecular Biology • Ford Doolittle, Prof. Biochemistry and Molecular Biology • Ed Susko, Prof. Mathematics and Statistics • John Archibald, Assoc. Prof. Biochemistry and Molecular Biology • Alastair Simpson, Assoc. Prof. Biology • Joseph Bielawski, Assoc. Prof. Biology, and Mathematics and Statistics • Christian Blouin, Assoc. Prof. Computer Science, and Biochemistry and Molecular Biology • Robert Beiko, Asst. Prof. Computer Science • Claudio Slamovits (new 2009), Asst. Prof. Biochemistry and Molecular Biology

CENTRE ADMINISTRATOR • Wanda Danilchuk, Biochemistry and Molecular Biology

4 III. FINANCIAL STATUS OF THE CENTRE

The Centre’s administration (i.e. 50% administrator’s salary, seminar series fund, and student travel funds) is supported by funding from the Tula Foundation at $50,000/year for 8 years, 2007-2015 (see Table A. below). The other 50% of the administrator’s salary is covered by contributions from the Faculties of Medicine, Science and Computer Science, and the office of VP, Academic & Provost. Five-year financial commitments from Dalhousie were established and annual installments for years 1 and 2 have been received (see Table B. below).

A. Tula Foundation Contributions

Fiscal Year 50% salary of Seminar Series Trainee Travel/ (August 1-July 30) administrator Fund Meetings Fund TOTAL Year 1: 2007-2008 $25,000 $15,000 $10,000 $50,000 Year 2: 2008-2009 $25,000 $15,000 $10,000 $50,000 Year 3: 2009-2010 $25,000 $15,000 $10,000 $50,000 Year 4: 2010-2011 $25,000 $15,000 $10,000 $50,000 Year 5: 2011-2012 $25,000 $15,000 $10,000 $50,000 Year 6: 2012-2013 $25,000 $15,000 $10,000 $50,000 Year 7: 2013-2014 $25,000 $15,000 $10,000 $50,000 Year 8: 2014-2015 $25,000 $15,000 $10,000 $50,000 Total: $400,000

The Seminar Series Fund enables us to invite world-renowned scientists to present seminars at Dalhousie University. The Travel to Meetings Fund enables our CGEB trainees to attend scientific meetings and workshops.

The Centre is also supported by individual research grants from the Tula Foundation to each CGEB faculty member for postdoc trainees ($44,000/year) or graduate student trainees ($25,000/year). In addition, these grants provide a research allowance for each trainees’ lab ($20,000/year for molecular biology PDFs, $5,000/year for computational PDFs, $2,500/year for computational PhDs). These grants are awarded for five years.

In summary, the Tula Foundation has invested over $3,000,000 in the CGEB centre.

B. Dalhousie Faculty Contributions

Fiscal Year Faculty of VP, Academic Faculty Faculty of (April 1-March 31) Medicine & Provost of Science Comp. Sci. TOTAL Year 1: 2008-2009 $15,000 $10,000 N/A N/A $25,000 (received) Year 2: 2009-2010 $15,000 $10,000 $1,000 $1,000 $27,000 (received) Year 3: 2010-2011 $10,000 $10,000 $6,000 $3,000 $29,000 Year 4: 2011-2012 $10,000 $10,000 $7,000 $4,000 $31,000 Year 5: 2012-2013 $10,000 $10,000 $8,000 $5,000 $33,000 Total: $145,000

5 C. CGEB New Opportunities Fund

Another source of funds available to finance CGEB activities is our New Opportunities Fund. This is a “special purpose account” (# 6-8292) that was opened to receive transfers of revenue that was generated from CGEB faculty activities. The purpose of this fund is to provide additional partial funding or ‘seed’ monies for CGEB activities, the costs of which either exceed existing allocated funds (e.g. the Trainee Travel/Meeting fund, the Seminar Series fund) or one-time events/activities/opportunities that fall under the CGEB mandate. For example, in 2008, the New Opportunities Fund sponsored student travel awards at the international ISEP meeting held at Dalhousie campus that had major CGEB faculty and trainee involvement. Furthermore, through this fund CGEB co-sponsored the Mitochondria, Ribosomes & Cells meeting at Dalhousie in 2008 with the Canadian Institute for Advanced Research (CIFAR) (see pp. 36-37 for details under “CGEB Meeting Sponsorships”). To date these funds have also been used for costs associated with recruitment of potential trainees to CGEB labs (e.g. interview travel and accommodation costs), as well as CGEB website design and maintenance (see http://www.cgeb.dal.ca).

The first source of revenue for this fund came from the Society for Molecular Biology and Evolution Conference which resulted in a net income of $39,181.46. Second, Drs. Doolittle & Gray had been maintaining an account from a conference in 1981 that had generated a net revenue of $10,073.15. In 2008 they generously donated these funds to the CGEB New Opportunities Fund. Finally, another symposium (“Mitochondria, Ribosomes & Cells” in 2008) generated net revenue of $106.01.

The current balance is $40,123.29.

6 IV. CGEB GOVERNANCE

CGEB Governance structure and policies (see Appendix A) have been working smoothly since the creation of the Centre. As the Centre has only ten current members and maintains no core Centre-specific research facilities or equipment, governance is not onerous and no problems with our procedures have surfaced.

According to our governance guidelines, the CGEB Director is to meet annually with the ‘Deans Committee’ for discussion regarding Centre operations and directions. Although official approval for CGEB was given in June 2008, we did not convene a ‘Deans Committee’ meeting in June 2009 because both the Faculty of Medicine and Faculty of Science were in a transition period moving to the leadership of new Deans. We thought that the best course of action was to wait until Dr. Tom Marrie (Dean of Medicine) and Dr. Chris Moore (Dean of Science) had assumed their positions this summer and to arrange for a meeting in the Fall. The Deans committee meeting will be arranged for late October or November, 2009.

Since the official designation of CGEB as a University centre, we have had two ‘biannual’ CGEB members meetings attended by all PIs. In these meetings we have constructed additional policies and procedures relating to Centre activities, trainee recruitment, disbursement of Tula-sponsored postdoc and PhD fellowships. These are briefly summarized below:

A. Recruitment and vetting of potential Tula-sponsored Trainees. Once a CGEB member has found a suitable candidate to fill the Tula-sponsored postdoc or Ph.D. student position, he/she will send the CV of the candidate to the Director and Steering committee who will adjudicate the application. If they find that the candidate is acceptable as a Tula-sponsored trainee, the member is informed and the CGEB Administrator (Wanda Danilchuk) liaises with Research Services, Financial Services and the Tula Foundation to set up the appropriate accounts in anticipation of the trainee’s start date.

B. Disbursement of Trainee Travel/Meeting Funds. The $10,000 annual budget for CGEB trainee travel/attendance at meetings is divided equally amongst CGEB labs. If any monies are left over from the previous year, then these monies get rolled into the next year and added to new $10,000 allotment. The total is then divided by ten (total number of CGEB labs) which becomes that years ‘allocation’ for each lab.

C. Seminar Series. All CGEB members are invited to suggest (to the Director) potential seminar series speakers covering their areas of interest. If the Director approves the choice, the speakers are invited by the CGEB member who will serve as host for the speaker’s visit. While the speaker is at Dalhousie, CGEB members (and their trainees) are invited to meet with the speaker and/or have lunch/dinner with them in order to promote interaction and discussion. An honorarium of $500 is given to each seminar speaker. Where possible, CGEB will partner with a member’s home department to co-sponsor high-profile speakers.

7 The membership has decided to extend the Seminar series fund to cover sponsorship (or co-sponsorship) of dedicated symposia at meetings held at Dalhousie in the area of interest of several of the CGEB membership. These symposia can be part of larger international meetings held in Halifax. However, if CGEB sponsors or co-sponsors a symposium, all CGEB members and trainees may attend without paying meeting fees (although usually many of them are already registered to attend the meeting). CGEB members are free to make proposals of CGEB sponsorship of these symposia at any time and the Director decides on the eligibility in consultation with the membership and steering committee. The CGEB seminar speakers invited, and symposia sponsored, to date are listed on pp. 36-37.

D. The ‘CGEB Associate’ position. At the last CGEB members meeting the possibility of adding a new category of CGEB affiliation was discussed. A proposal for a ‘CGEB Associate’ category was voted on and unanimously supported. CGEB Associates were defined as faculty members at Dalhousie University whose research is aligned closely with CGEB goals and who may be active collaborators of CGEB members, in some cases co-supervising trainees. The CGEB Associate status does not entitle the faculty member to any financial contributions from the Centre, nor entitle them to Tula-sponsored trainee positions. However, Associates and their trainees will be invited to all Centre activities (i.e. sponsored talks, symposia, workshops etc), can suggest seminar speakers and will be able to participate in co-supervision of Tula-sponsored trainees with a CGEB member to whom the trainee monies are awarded. We hope this category makes it possible to expand the impact and interactions of the Centre without diluting its financial resources. To become a CGEB Associate, a CGEB member will ‘sponsor’ the candidate and circulate their CV to the membership and provide a brief justification as to why the individual deserves Associate status. The Director will decide on the appointment in consultation with the membership and the Steering Committee.

8 V. PUBLICATIONS BY CGEB FACULTY AND TRAINEES (includes published, in press & accepted papers: total of 99 for 2008-present)

Note: for each publication listed below, CGEB faculty members are highlighted in bold face type and CGEB trainees’ names are underlined.

Year 2009:

Archibald, J.M. 2009. Genomics. Green evolution, green revolution. Science 324: 191-92. Archibald, J.M. 2009. Secondary endosymbiosis. In Encyclopedia of Microbiology, M. Schaechter (Ed.), pp. 438-446, Oxford: Elsevier. Archibald, J.M. 2009. The origin and spread of eukaryotic photosynthesis—evolving views in light of genomics. Botanica Marina 52: 95-103. Archibald, J.M. 2009. The puzzle of plastid evolution. Curr. Biol. 18: 663-665. Archibald, J.M. and Lane, C.E. 2009. Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. J. Hered. 100: 582-590. Archibald, J.M. & Hoef-Emden, K. 2009. Phylum Cryptophyta (Cryptomonads). In Handbook of Protoctista, 2nd Ed., L. Margulis (Ed.), Jones & Bartlett Publishers (in press). Beiko, R.G. and Ragan, M.A. 2009. Untangling hybrid phylogenetic signals - HGT and artifacts of phylogenetic reconstruction. In Horizontal Gene Transfer: Genomes in Flux, M. Gogarten, J.P. Gogarten, and L. Olendzenski (Eds.), Methods in Molecular Biology Series, Humana Press, NJ. Blouin, C., Perry, S., Lavell, A., Susko, E. and Roger, A.J. 2009. Reproducing the manual annotation of multiple sequence alignments using an SVM classified. Bioinformatics, Sept. 21 [Epub ahead of print]. Burki, F., Inagaki, Y., Brate, J., Archibald, J.M., Keeling, P.J., Cavalier-Smith, T., Sakaguchi, M., Hashimoto, T., Horak, A., Kumar, S., Klaveness, D., Jakobsen, K. S., Pawlowski, J. and Shalchian-Tabrizi, K. 2009. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Gen. Biol. Evol. 2009: 231-238. Chan, C.X, Darling, A.C., Beiko, R.G. and Ragan, M.A. 2009. Are protein domains modules of lateral genetic transfer? PLoS ONE 4: e4524. Curtis, B.A. & Archibald, J.M. 2009. Problems and progress in understanding the origins of mitochondria and plastids. In Symbiosis and Stress, J. Seckbach & M. Grube (Eds.), Springer-Verlag. Dipippo, J.L., Nesbo, C.L., Dahle, H., Doolittle, W.F., Birkland, N.-K. and Noll, K.M. 2009. Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerotic heterotroph isolated from oil production fluid. Int. J. Syst. Evol. Microbiol. [Epub ahead of print]. Doolittle, W.F. 2009. Eradicating typological thinking in prokaryotic systematics and evolution. In Cold Spring Harbor Symposia on Quantitative Biology, Vol. 74 (Evolution: The Molecular Landscape), Aug. 10 [Epub ahead of print]. Doolittle, W.F. 2009. The practice of classification and the theory of evolution, and what the demise of Darwin’s Tree of Life Hypothesis means for both of them. Phil. Trans. Roy. Soc. Lond. Series B, 364: 2221-2228. Doolittle, W.F. and Zhaxybayeva, O. 2009. Metagenomics and the units of biological organization. Bioscience, in press.

9 Doolittle, W.F. and Zhaxybayeva, O. 2009. On the origin of prokaryotic species. Genome Res. 19: 744-756. Dunn, K.A., Bielawski, J.P., Ward, T.J., Urquhart, C. and Gu, H. 2009. Reconciling ecological and genomic divergence among lineages of Listeria under an “extended mosaic genome concept.” Mol. Biol. Evol., Aug 10 [Epub ahead of print]. Elias, M. and Archibald, J.M. 2009. The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus. Gene 442: 63-72. Gawryluk, R.M. and Gray M.W. 2009. A split and rearranged nuclear gene encoding the iron-sulfur subunit of mitochondrial succinate dehydrogenase in Euglenozoa. BMC Res. Notes 2: 16. Gawryluk, R.M. and Gray, M.W. 2009. An ancient fission of mitochondrial cox1. Mol. Biol. Evol., Sept. 18 [Epub ahead of print]. Gaston, D., Tsaousis, A.D. and Roger, A.J. 2009. Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data. Methods Enzymol. 457: 21-47. Hampl, V., Hug, L., Leigh, J.W., Dacks, J.B., Lang, B.F., Simpson, A.G.B. and Roger, A.J. 2009. Phylogenetic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci USA 106: 3859- 3864. Hopkins, J. and Archibald, J. M. 2009. Plastid evolution and the nuclear genomic 'footprint' of red and green algal endosymbionts. In Red algae in the age of genomics, J. Seckbach & M. Grube (Eds.), Springer-Verlag, in press. Hug, L. A. Stechmann, A. and Roger A.J. 2009. Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes. Mol. Biol. Evol. (in press) Jezbera, J., Sharma, A.K., Brandt, U., Doolittle, W.F. and Hahn, M.W. 2009. ‘Candidatus Planktophila limnetica’, an Actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton. Int. J. Syst. Evol. Microbiol., July 23 [Epub ahead of print]. Joss, M.J., Koenig, J.E., Labbate, M., Polz, M.F., Gillings, M.R., Stokes, H.W., Doolittle W.F. and Boucher, Y. 2009. ACID: annotation of cassette and integron data. BMC Bioinformatics 21: 118. Kamikawa, R., Sanchez-Perez, G.F., Sako, Y., Roger, A.J. and Inagaki, Y. 2009. Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes. Mol Phylogenet Evol. 53: 565-570. Kim, E. and Archibald, J. M. 2009. Diversity and evolution of plastids and their genomes. In The Chloroplast-interactions with the environment, A.S. Sandelius & H. Aronsson (Eds.), pp. 1-39, Springer. Koenig, J.E., Sharp, C., Dlutek, M., Curtis, B., Joss, M., Boucher, Y. and Doolittle, W.F. 2009. Integron Gene Cassettes and Degradation of Compounds Associated with Industrial Waste: The Case of the Sydney Tar Ponds. PLoS One, 4: e5276. Lane, C.E. and Archibald, J.M. 2009. Reply to Bodyl, Stiller and Mackiewicz: Chromalveolate plastids: direct descent or multiple endosymbioses? Trends Ecol. Evol. 24: 121-122. MacDonald, N., Parks, D. and Beiko, R. SeqMonitor: Influenza analysis pipeline and visualization. PLoS Currents: Influenza, RRN: 1040.

10 Moore, C.E. and Archibald, J.M. 2009. Nucleomorph genomes. Ann. Rev. Genet., Aug. 17 [Epub ahead of print]. Morine, M., Gu, H., Myers, R. and Bielawski, J.P. 2009. Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth. J. Mol. Evol. 68: 506-515. Nesbo, C.L., Bapteste, E., Curtis, B., Dahle, H., Lopez, P., Macleod, D., Dlutek, M., Bowman, S., Zhaxybayeva, O., Birkeland, N.K. and Doolittle, W.F. 2009. The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J. Bacteriol. 191: 1974-1978. Ota, S., Silver, T.D., Archibald, J.M., & Ishida, K.-I. 2009. Lotharella oceanica sp. nov.— a new planktonic chlorarachniophyte studied by light and electron microscopy. Phycologia 48: 317-325. Park, J.S., Kolisko, M., Heiss, A.A., Simpson, A.G.B. 2009. Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n.g., n.sp., a deep-branching relative of diplomonads. J Euk. Microbiol. 56: 373-84. Park, J.S., Simpson, A.G.B., Brown, S. and Cho, B.C. 2009. Ultrastructure and molecular phylogeny of two heterolobosean amoebae. Protist 160: 265-283. Parks, D.H. and Beiko, R.G. 2009. Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context. Geoinformatics 2009, Fairfax, VA. Parks, D.H., MacDonald, N. and Beiko, R. 2009. Tracking the evolution and geographic spread of Influenza A. PLoS Currents: Influenza, RRN: 1014. Parks, D.H., Porter, M., Churcher, S., Wang, S., Blouin, C., Whalley, J., Brooks, S. and Beiko, R.G. 2009. GenGIS: A geospatial information system for genomic data. Genome Res., July 17 [Epub ahead of print]. Ragan, M.A. and Beiko, R.G. 2009. Lateral genetic transfer: open issues. Philosophical Trans. Royal Soc. London B, Biol. Sci. 364: 2241-2251. Roger, A.J. and Simpson, A.G.B. 2009. Evolution: revisiting the root of the eukaryote tree. Curr Biol. 19: R165-167. Rowe, D.L., Dunn, K.A., Adkins, R.M. and Honeycutt, R.L. 2009. Molecular clocks keep dispersal hypotheses afloat: evidence for transatlantic rafting by rodents. J. Biogeog. [Epub ahead of print] Sharma, A.K., Sommerfeld, K., Bullerjahn, G.S., Matteson, A.R., Wilhelm, S.W., Jezbera, J., Brandt, U., Doolittle, W.F. and Hahn, M.W. 2009. Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria. ISME 3: 726-37. Simpson A.G. & Cepicka, I. 2009. Amitochondriate protists (Diplomonads, Parabasalids and Oxymonads). In Encyclopedia of Microbiology, 3rd Ed., pp. 545-557, Elsevier. Susko, E. 2009. Bootstrap support is not first order correct. Syst. Biol. 58: 211-233. Susko, E. and Roger, A.J. 2009. Statistical analysis of expressed sequence tags. Methods Mol Biol. 533: 277-87. Walsh, D.A and Sharma, A.K. 2009. Molecular Phylogenetics: Testing evolutionary hypotheses. In Bacteriophages: Methods and Protocols Volume 2: Molecular and Applied Aspects, M. Clokie & A. Kropinski (eds.), Humana Press, pp. 131-168. Wang, H., Susko, E. and Roger, A.J. 2009. PROCOV-SPR: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis. BMC Evol. Biol. 9: 225.

11 Whalley, J., Brooks, S. and Beiko, R.G. 2009. Radie: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree. Bioinformatics 25: 672- 673. Wu, J. and Susko, E. 2009. General Heterotachy and Distance Method Adjustments. Mol. Biol. Evol. Aug 17 [Epub ahead of print]. Zhaxybayeva, O. 2009. Detection and quantitative assessment of horizontal gene transfer. Methods Mol. Biol. 532: 195-213. Zhaxybayeva, O., Swithers, K., Lapierre, P., Fournier, G., Bickhard, D., DeBoy, R.T., Nelson, K.E., Nesbø, C.L., Doolittle, W.F., Gogarten, J.P. and Noll, K.M. 2009. On the chimeric nature, thermophilic origin and phylogenetic placement of the Thermotogales. Proc. Natl. Acad. Sci. 106: 5865-5870. Zhaxybayeva, O., Doolittle, W.F., Papke, R.T. and Gogarten, J.P. 2009. Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol. Evol. [Epub ahead of print].

Year 2008:

Archibald, J.M. 2008. Genome evolution: remnant algal genes in ciliates. Curr. Biol. 18: R663-R665. Archibald, J.M. 2008. The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. USA 51: 20049-20050. Bao, L., Gu, H., Dunn, K.A. and Bielawski, J.P. 2008. Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of molecular evolution. Mol. Biol. Evol. 25: 1995-2007. Bapteste, E., Susko, E., Leigh, J., Ruiz-Trillo, I., Bucknam, J. and Doolittle, W.F. 2008 Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol. Biol. Evol. 25: 83-91. Beiko, R.G. 2008. Small but mighty: microbial communities and a second wave of genomics. Canadian Chemical News, Nov-Dec 2008. Beiko, R.G. and Ragan, M.A. 2008. Detecting lateral genetic transfer: a phylogenetic approach. In Bioinformatics (J. Keith, Ed.), Methods in Molecular Biology Series, Humana Press, NJ. Beiko, R.G., Doolittle, W.F., and Charlebois, R.L. 2008. The impact of reticulate evolution on genome phylogeny. Systematic Biol. 57: 844-56. Beiko, R.G., Whalley, J., Wang, S., Clair, H., Smolyn, G., Churcher, S., Porter, M., Blouin, C. and Brooks, S. 2008. Spatial Analysis and Visualization of Genetic Biodiversity. Free and Open Source Software for Geoinformatics (FOSS4G) 2008, Cape Town. Cavalier-Smith, T., Chao, E.E, Stechmann, A., Oates, B., Nikolaev, S. 2008. Planomonadida ord. nov. (Apusozoa): ultrastructural affinity with Micronuclearia podoventralis and deep divergences within Planomonas gen. nov. Protist 159: 535- 562. Chan, C.X., Beiko, R.G. and Ragan, M.A. 2008. Large-scale detection of recombination in nucleotide sequences. In Proceedings of the International Conference on Mathematical Biology 2007 (eds., K.A. Mohd Atan & I.S. Krishnarajah), Kuala Lumpur. AIP Conf. Proc. 971: 101-104.

12 Cuvelier, M. L., Ortiz, A., Kim, E., Moehlig, H., Richardson, D., Heidelberg, J.F., Archibald, J.M. and Worden, A. 2008. Widespread distribution of a unique marine protistan lineage. Env. Microbiol. 10: 1621-1634. Doolittle, W.F. 2008. Microbial evolution: stalking the wild bacterial species. Current Biol. 18: R565-567. Doolittle, W.F., Nesbo, C.L., Bapteste, E. and Zhaxybayeva, O. 2008. Lateral gene transfer. In Evolutionary Genomics and Proteomics, M. Pagel & A. Pomiankowski (eds.), pp. 45-79, Sinauer. Fong, M. & Archibald, J.M. 2008. Evolutionary dynamics of light-independent protochlorophyllide oxidoreductase (LIPOR) genes in the secondary plastids of cryptophyte algae. Euk. Cell 7: 550-553. Gogarten, P.J., Fournier, G. and Zhaxybayeva, O. 2008. Gene transfer and the reconstruction of life’s early history from the molecular record. Space Science Reviews, 135: 115-131. Hamblin, K., Standley, D.M., Rogers, M.B., Stechmann, A., Roger, A.J., Maytum, R. and van der Giezen, M. 2008. Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol. Microbiol. 68: 1395-1405. Hamel, L., Nahar, N., Poptsova, M.S., Olga Zhaxybayeva and Gogarten, J.P. 2008. Unsupervised learning in detection of gene transfer. J. Biomed. Biotech. 2008: 472719. Hampl, V. & Simpson, A.G.B. 2008. Possible mitochondria-related organelles in poorly- studied ‘amitochondriate’ eukaryotes. In J. Tachezy (Ed.), Hydrogenosomes and mitosomes: mitochondria of anaerobic eukaryotes, pp. 265-282, Springer Verlag. Hampl, V., Silberman, J.D., Stechmann, A., Diaz-Triviño, S., Johnson, P.J. and Roger, A.J. 2008. Genetic evidence for a mitochondriate ancestry in the amitochondriate flagellate Trimastix pyriformis. PLoS ONE 3: e1383. Hickey, G., Dehne, F., Rau-Chaplin, A. and Blouin, C. 2008. SPR distance computation for unrooted trees. Evol. Bioinform. 4: 17-27. Hoef-Emden, K. and Archibald, J.M. 2008. Cryptophytes. Tree of Life web project. http://tolweb.org/Cryptophtytes/ Keeling, P.J. and Archibald, J.M. 2008. Organelle evolution: What’s in a name? Curr. Biol. 18: R345-R347. Keeling, P.J., Leander, B.S. & Simpson A.G. 2008. Eukaryotes. Tree of Life web project. http://www.tolweb.org/Eukaryotes/3 Khan, H. & Archibald, J.M. 2008. Lateral transfer of introns in the cryptophyte plastid genome. Nucleic Acids Res. 36, 3043-3053. Kim, E., Lane, C. E., Curtis, B. A., Kozera, C., Bowman, S. and Archibald, J.M. 2008. Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics 9: 215. Koenig, J.E., Boucher, Y., Charlebois, R.L., Nesbo, C., Zhaxybayeva, O., Bapteste, E., Spencer, M., Stokes, H.W., and Doolittle, W.F. 2008. Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Env. Microbiol. 10: 1024-38. Kolisko, M., Cepicka, I., Hampl, V., Leigh, J., Roger, A.J., Kulda, J., Simpson, A.G.B. and Flegr, J. 2008. Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, α-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads. BMC Evol. Biol. 8: 205.

13 Lane, C.E. and Archibald, J.M. 2008. New members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae). J. Phycol. 44: 339-450. Lane, C.E. and Archibald, J.M. 2008. The eukaryotic Tree of Life: endosymbiosis takes its TOL. Trends Ecol. Evol. 23: 268-275. Leander, B.S. and Simpson A.G.B. 2008. Euglenozoa. Tree of Life web project. http://www.tolweb.org/Euglenozoa/2405 Leigh, J., Susko, E., Baumgartner, M. and Roger, A.J. 2008. Testing congruence in phylogenomic analysis. Syst. Biol. 57: 104-115. Lin, S., Zhang, H. and Gray, M.W. 2008. RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery. In RNA and DNA Editing: Molecular Mechanisms and Their Integration into Biological Systems (Smith, H.C., ed.), pp. 280-309, Wiley Press. Phipps, K., Lane, C.E., Donaher, N. and Archibald, J.M. 2008. Nucleomorph genome karyotype diversity in the cryptophyte genus Cryptomonas. J. Phycol. 44: 11-14. Ruiz-Trillo, I., Roger, A.J., Burger, G., Gray, M.W. and Lang, B.F. 2008. A phylogenomic investigation into the origin of metazoa. Mol. Biol. Evol. 25: 664-672. Sanchez-Perez, G., Hampl, V., Simpson, A.G.B. and Roger, A.J. 2008. A new divergent type of eukaryotic methionine adenosyltransferase is present in multiple distantly related secondary algal lineages. J. Euk. Microbiol. 55: 374-381. Sharma, A.K., Zhaxybayeva, O., Papke, R.T. and Doolittle, W.F. 2008. Actinorhodopsins: Proteorhodopsin-like gene sequences found predominantly in non-marine environments. Environ Microbiol. 10: 1039-56. Simpson A.G. 2008. Jakobida (including sub-pages). Tree of Life web project. http://www.tolweb.org/Jakobida/97407 Simpson, A.G.B., Perley, T.A. and Lara, E. 2008. Lateral transfer of the gene for a widely used marker, α-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata). Mol. Phylogenet. Evol. 47: 366-377. Stechmann, A., Hamblin, K., Perez-Brocal, V., Gaston, D., Richmond, G.S., van der Giezen, M., Clark, C.G. and Roger, A.J. 2008. Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes. Curr. Biol. 18: 580-585. Sullivan, M.B., Coleman, M.L., Quinlivan, V., Rosenkrantz, J.E., Defrancesco, A.S., Tan, G., Fu, R., Lee, J.A., Waterbury, J.B., Bielawski, J.P. and Chisholm, S.W. 2008. Portal protein diversity and phage ecology. Env. Microbiol. 10: 2810-2823. Susko, E. 2008. On the distributions of bootstrap support and posterior distributions for a star tree. Syst. Biol. 57: 602-612. Wang, H.C., Li, K.M., Susko, E. and Roger A.J. 2008. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol. Biol. 8: 331. Wang, H.C., Susko, E., Spencer, M. and Roger, A.J. 2008. Topological estimation biases with covarion evolution. J. Mol. Evol. 66: 50-60. Ward, T.J., Ducey, T.F., Usgaard, T., Dunn, K.A. and Bielawski, J.P. 2008. Multilocus genotyping assays for single nucleotide polymorphism-based subtyping of Listeria monocytogenes isolates. Applied Environ. Microbiol. 74: 7629-7642. Watkins, R.F. and Gray M.W. 2008. Sampling gene diversity across the supergrouip Amoebozoa: large EST data sets from A. castellanii, H. vermiformis, P. polycephalum, H. dachnaya and Hyperamoeba sp. Protist 159: 269-281.

14 Wu, J., Susko, E. and Roger, A.J. 2008. An independent heterotachy model and its implications for phylogeny and divergence time estimation. Mol. Phylogenet. Evol. 46: 801-806.

15 VI. CGEB SOFTWARE DEVELOPMENT

Program name: PROCOV-SPR (Protein COVarion analysis) Authors: Huai-chun Wang, Ed Susko and Andrew Roger Description: A maximum likelihood phylogenetic inference program that implements a variety of rates-across-sites and covarion models and allows tree- searching using the SPR function. http://www.mathstat.dal.ca/~hcwang/Procov/

Program name: QmmRAxML (Q-matrix mixture RAxML) Authors: Huai-chun Wang, Ed Susko and Andrew Roger Description: A maximum likelihood phylogenetic inference program that implements a mixture model with any number of rate (Q) matrices and frequency vectors. Captures the 'site specific' nature of protein evolution. http://www.mathstat.dal.ca/~hcwang/QmmRAxML/

Program name: CONCATERPILLAR Authors: Jessica W. Leigh, Ed Susko and Andrew Roger Description: A program that implements hierarchical likelihood ratio test and a clustering algorithm for testing phylogenetic congruence between partitions of a phylogenomic dataset. http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm

Program name: Barrel-o-Monkeys Authors: Jessica W. Leigh and Andrew Roger Description: A series of Python scripts that automate repetitive tasks in bioinformatics that are so simple, but annoying, that a monkey could do them. http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm

Program name: RAADdet Authors: Jessica W. Leigh, Ed Susko and Andrew Roger Description: A program that implements novel methods for adjusting for rates-across-sites in an amino acid Log-Det distance calculation. http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm

Program name: CBOrg Authors: Daniel Gaston and Andrew Roger Description: A tool that does comparative BLAST analyses on a set of input sequences to determine if their gene products are targeted to mitochondria or hydrogenosomes versus elsewhere in the cell. http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm

Program: GenGIS - A Geospatial Information System for Genetic Data Authors: Parks, D.H., Porter, M., Churcher, S., Wang, S., Blouin, C., Whalley, J., Brooks, S., Beiko, R.G. Description: GenGIS is a bioinformatics application that allows users to combine

16 digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. http://kiwi.cs.dal.ca/GenGIS/Main_Page

Program: Radié Authors: Whalley, J., Brooks, S. and Beiko, R.G. Description: Radié is a Java tool that allows characters to be visualized against the background of a phylogenetic tree. http://kiwi.cs.dal.ca/~beiko/software-and-data/radie

Program: Codeml FE Authors: Bielawski research group Description: A modification of the program codeml (Yang, 1997) that implements 11 new fixed effect models of codon evolution. www.bielawski.info

Program: LiBaC (Likelihood Based Clustering) Authors: Bielawski research group Description: Implements a novel statistical technique to group sites according to similarities in the underlying process of molecular evolution. LiBaC is a generalization of the statistical technique called “model based clustering” to Markov models of codon evolution. www.bielawski.info

Programs for cross validation on codon models of evolution Authors: Joey Mingrone & Joe Bielawski Description: Implemented a suite of programs for using cross validation as a method to assess model based classification of individual codon sites to different groups based on the strength of natural selection pressure. http://awarnach.mathstat.dal.ca/repos

Programs for bootstrapping codon models of evolution Authors: Joey Mingrone & Joe Bielawski Description: Employs bootstrapping as a method to assess model based classification of individual codon sites to different groups based on the strength of natural selection pressure. This work is in progress, but software is made available at http://awarnach.mathstat.dal.ca/repos as it is being developed.

Programs and scripts for automated analysis of genomic data Authors: Bielawski research group Description: A suite of over 50 Perl programs for bioinformatic analysis. The newest programs allow automation of many methods for genome scale computational analysis. We have established a web site for public access to some of these programs (24 of the most commonly used programs) and supporting documentation.

17 Program: MANUEL Authors: C. Blouin, S. Perry, A. Lavell, E. Susko & A.J. Roger Description: An SVM-based multiple sequence annotation offered through a web interface. http://fester.cs.dal.ca/manuel/

Program: spr distance Authors: D. Hickey, Dehne, Rau-Chaplin & C. Blouin Description: An FTP-like algorithm to evaluate the length of the shortest SPR path between two phylogenetic trees. http://peta.cs.dal.ca/blouinlab/node/7

18 VII. INVITED PRESENTATIONS FROM CGEB FACULTY

Year 2009:

Roger, A.J. 109th General Meeting of the American Society For Microbiology, Philadelphia, PA, May 2009. Shaking the Tree of Life Symposium. Roger, A.J. Perspectives on the Tree of Life Workshop, Dalhousie University, Halifax, NS, July 2009. Deconstructing deconstructions on the Tree of Life: why a tree of microbes might be realizable, meaningful and useful. Roger, A.J. Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program Annual Meeting, Asilomar, CA, June 2009. Diversity of mitochondrion-like organelles. Roger, A.J. Canadian Society for Ecology and Evolution & Genetics Society of Canada Annual Meeting, Dalhousie University, Halifax, NS, May 2009. Problems and progress in understanding deep eukaryotic phylogeny with phylogenomic approaches. Roger, A.J. Departmental “Darwin Day” Seminar, Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, February 2009. Early eukaryote phylogeny and evolution: New paradigms and challenges. Archibald, J.M. Annual Meeting of the Society for General Microbiology, Heriot- Watt University, Edinburgh, Scotland, September 2009. The eukaryotic Tree of Life: Endosymbiosis takes its TOL. Archibald, J.M. 9th International Phycological Congress, Tokyo, Japan, August 2009. Endosymbiotic gene transfer and genome evolution in secondary plastid- containing algae: insights from cryptophytes and chlorarachniophytes. Archibald, J.M. 17th Annual Meeting of the Society for Molecular Biology and Evolution, Iowa City, Iowa, June 2009. Vanishing nucleomorph genomes: Where do they go and how do they do it? Archibald, J.M. Perspectives on the Tree of Life Workshop, Dalhousie University, Halifax, NS, May 2009. Genomic threads in the tapestry of photosynthetic life: implications for ‘tree thinking.’ Archibald, J.M. IGERT Program in Comparative Genomics Annual Symposium, University of Arizona, Tuscon, Arizona, May 2009. The eukaryotic Tree of Life: Endosymbiosis takes its TOL. Archibald, J.M. Canadian Institute for Advanced Research, Junior Fellow Academy Meeting, Toronto, ON, April 2009. Integrated Microbial Biodiversity Program. Archibald, J.M. University of Geneva, Departmental of Zoology and Animal Biology Seminar Series, Geneva, Switzerland, March 2009. Bonsai genomics: the remnant nuclear genomes of cryptophyte and chlorarachniophyte algae. Archibald, J.M. Annual Meeting of the American Association for the Advancement of Science (AAAS), Darwin ‘Mania’ Symposium (organelles), Chicago, February 2009. Symbiosis as an evolutionary driver: mergers of cells and genomes. Beiko, R. Perspectives on the Tree of Life Workshop, Dalhousie University, Halifax, NS, July 2009. If a tree exists in the forest, does it something something?

19 Beiko, R. Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program Annual Meeting, Asilomar, CA, June 2009. GenGIS: Geospatial analysis and visualization of microbial diversity. Beiko, R. Universite Laval, Quebec, March 2009. The geography of microbial genetic diversity. Bielawski, J.P. Workshop on Molecular Evolution, Woods Hole, MA, July 2009. Estimating the strength and direction of natural selection pressure acting on protein coding genes, and, Tutorial on analyzing gene sequences for presence of sites evolving under adaptive evolution. Bielawski, J.P. The European Workshop on Molecular Evolution, Cesky Krumlov, South Bohemia, Czech Republic, January 2009. Phylogenetic methods to detect the signature of selection, and Software demonstration: PAML: phylogenetic analysis by maximum likelihood. Doolittle, W.F. Norman H. Giles Distinguished Lecturer, University of Georgia, Genetics Dept., Athens, GA, March 2009. How stands the Tree of Life. Doolittle, W.F. Microbiology Department, University of Georgia, Athens, GA, March 2009. On the origin of (prokaryotic) species. Doolittle, W.F. Darwin Series Lecture, Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati, April, 2009. The Tree of Life and its current travails, and Departmental Seminar: Species, for Prokaryotes. Doolittle, W.F. 74th Cold Spring Harbor Symposium on Quantitative Biology, NY, May 2009. Species, domains and the Tree of Life: are they real? Doolittle, W.F. Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program Annual Meeting, Asilomar, CA, June 2009. Two metagenomics-driven discoveries: mesotogas and actinorhodopsins. Doolittle, W.F. Marine Biological Laboratory, Microbial Diversity Course Lectures, Woods Hole, MA, July 2009. The Tree of Life, and Species. Doolittle, W.F. Perspectives on the Tree of Life Workshop, Dalhousie University, Halifax, July 2009. Tree of Life, Tree of Cells, LUCA and other questionable entities. Doolittle, W.F. Department of Philosophy, Dalhousie University, Halifax, August 21, 2009. Tree of Life, Tree of Cells, LUCA and other questionable entities. Doolittle, W.F. 10th Anniversary RiboClub Meeting, Sherbrooke, Quebec, September 22-23, 2009. Why are molecular machines such as the editosome, the spliceosome and the ribosome so ridiculously complex? Gray, M.W. Joint Symposium of Germany Academy of Sciences Leopoldina,SFB 429 and SFB-TR1, Free University of Berlin, September 20-23, 2009. Genomics vs. proteomics: two views of mitochondrial evolution. Gray, M.W. International Conference for Plant Mitochondrial Biology (ICPMB), Grandlibakken Conference Center & Lodge, Lake Tahoe, CA, May 2009. First among equals: evolution of the plant mitochondrial genome. Simpson A.G.B. 12th International Congress of Protistology, Buzios, Brazil, August 2009. What do Carpediemonas and like organisms tell us about the evolution of parasitic diplomonads? Slamovits, C. 12th International Congress of Protistology, Buzios, Brazil, August 2009. Lateral gene transfer, endosymbiosis and genome evolution.

20 Susko, E. Canadian Society for Ecology and Evolution & Genetics Society of Canada Annual Meeting, Dalhousie University, Halifax, May 2009. Properties of bootstrapping and posterior probabilities for a Star Tree.

Year 2008:

Roger, A.J. ICREA Conference on the Origin and Early Evolution of Metazoans. Barcelona, Spain. The power and pitfalls of a phylogenomic analyses in understanding early eukaryote evolution. Roger, A.J. International Symposium on Evolutionary Protistology, University of Tsukuba, Japan. Diversity of genomes and organelles of anaerobic protists. Roger, A.J. Mitochondria, Ribosomes and Cells: A Symposium in Honour of Mike Gray, Dalhousie University, Halifax, July 2008. The diversity of mitochondrion- derived organelles in eukaryotes. Roger, A.J. From RNA to Humans: A Symposium on Evolution, The Rockefeller University, New York, May 2008. The deep evolutionary history of eukaryotes. Roger, A.J. Darwin Day Symposium, National Evolutionary Synthesis Centre (NESCent). Deep phylogeny and the origins of eukaryotes. Archibald, J.M. Tree of Life Workshop, Dalhousie University, Halifax, 2008. Cryptophytes. Archibald, J.M. Mitochondria, Ribosomes and Cells: A Symposium in Honour of Mike Gray, Dalhousie University, Halifax, July 2008. Endosymbiosis and eukaryotic genome evolution. Archibald, J.M. Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program Annual Meeting, Lac Carling, Quebec, May 2008. Nucleomorph genomes: where are we now? Archibald, J.M. International Symposium on Protist Biology, University of Tsukuba, Japan. Protist diversity and the eukaryotic Tree of Life: endosymbiosis takes its TOL. Archibald, J.M. Department of Biology, Seminar Series, Dalhousie University, Going, going, not quite gone: the weird and wonderful world of endosymbiotic nuclear genomes. Beiko, R. Nova Scotia Agricultural College, NS, September 2008. Genes from my father (and my neighbours): evolutionary networks of microorganisms. Beiko, R. Mitochondria, Ribosomes and Cells: A Symposium in Honour of Mike Gray, Dalhousie University, Halifax, NS, July 2008. Failogenomics. Beiko, R. Society for Molecular Biology and Evolution 2008 Annual Meeting, Barcelona, Spain, June 2008. Lateral gene transfer and genome phylogeny. Bielawski, J.P. Workshop on Molecular Evolution, Marine Biological Laboratory, Woods Hole, MA, July 2008. Estimating the strength and direction of natural selection pressure acting on protein coding genes, and, Tutorial on analyzing gene sequences for presence of sites evolving under adaptive evolution. Blouin, C. Acadia University, Wolfville, NS. Exploring the optimization landscape of maximum likelihood phylogenies. Doolittle, W.F. From RNA to Humans: A Symposium on Evolution, The Rockefeller University, New York, May 2008. Barking up the wrong tree: the dangers of reification in molecular phylogenetics and systematics.

21 Doolittle, W.F. Medical Humanities Day Forum, Dalhousie University – co-participant in Ethics Panel Discussion, May 2008. Doolittle, W.F. Microbiome Workshop, Toronto, Ontario, June 2008. Microbial genomics. Doolittle, W.F. Microbial Diversity Course Symposium, Marine Biological Laboratory, Woods Hole, MA, June 2008. Doolittle, W.F. Atlantic OMICS Symposium, Moncton, NB, August 2008. Lateral genomics, bacterial species and the Tree of Life. Doolittle, W.F. Marker Lectureship, Evolutionary Biology, Pennsylvania State University, October 2008. The Tree of Life: what does it really mean?, and Entry-level metagenomics. Gray, M.W. Protist 2008 (ISOP59/ISEPXVII), Dalhousie University, Halifax, NS, July 2008. Spectacular and bizarre: RNA editing and its evolution in protists. Gray, M.W. Gordon Research Conference on Mitochondria & Chloroplasts, University of New England, Biddeford, ME, August 2008. Two views of mitochondrial evolution: genomics vs. proteomics. Simpson, A.G.B. Tree of Life Web Project Protist Diversity Workshop, Halifax, 2008. Introduction to Excavata; Jakobids. Simpson, A.G.B. Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program Annual Meeting, Lac Carling, Quebec, May 2008. The evolution and diversity of anaerobic excavates.

22 VIII. COLLABORATIVE INTERACTIONS BETWEEN CGEB MEMBERS

In the last two years, collaborative interactions amongst CGEB labs have flourished. Evidence of this can be seen in the 16 publications in 2008-2009 (pp. 9-15) that were co-authored by two or more CGEB members and their trainees. Below a short summary is provided of the collaborations that are ongoing within CGEB:

Archibald and Gray are working on the analysis and annotation of cryptophyte nuclear and organellar genome data coming from the Joint Genome Institute. They are co-PIs on an NSERC Strategic Opportunities Grant to sponsor this work and co-supervise Tula-sponsored postdoc Dr. Goro Tanifuji (allocated to Gray).

Blouin and Beiko have been involved in the development of methods (e.g. the software tool GenGIS) that integrate geospatial data with genomic (and metagenomic) data.

Beiko and Archibald are developing phylogenomic methods for analysing eukaryote and prokaryote genomic data to be integrated into the MOA database. They co-supervise M.Sc. student Rob Eveleigh.

Roger and Gray are working together to elucidate the origin and function of enzymes of anaerobic energy metabolism in the aerobic amoeba Acanthamoeba castellanii.

Susko, Roger, and Blouin have worked on the development of methods for curating protein alignments (e.g. the development of the software tool MANUEL) and site- independent models of protein evolution that take into account structural information.

Susko and Roger have been developing tools for phylogenomic analysis (e.g. CONCATERPILLAR), sophisticated models of protein evolution (e.g. QmmRAxML and PROCOV-SPR), methods for assessing the quality of EST data and theoretical contributions to the understanding of molecular evolution. They co-supervise Tula- sponsored postdoc Dr. Huaichun Wang (allocated to Susko).

Roger and Beiko began a collaboration this summer to determine whether an ancient vertical phylogenetic signal exists for core proteins in the domain Bacteria or if it has been completely erased as some have claimed.

Roger and Simpson are collaborating on understanding the phylogeny and evolution of the most enigmatic eukaryote supergroup – the Excavata by EST surveys and phylogenomic analysis. They co-supervise Ph.D. student Martin Kolisko.

Doolittle, Bielawski and Beiko teamed up to write a CIHR grant application entitled “Beyond species: modeling and mapping microbial diversity and function with marker genes, genomes and metagenomes” that was submitted in the Sept. 2009 operating grants competition.

Susko and Doolittle have collaborated over the last few years in developing methods with Eric Bapteste (former PDF) to probe the extent of lateral gene transfer in prokaryotic genome evolution.

23 IX. CURRENT EXTERNAL RESEARCH GRANTS AND FUNDING

Collectively, CGEB faculty members have received ~$2,930,600 from external research grants and funding for the period 2008-2009. Grants involving one or more CGEB faculty (as co-applicants) were only included for the P.I. in the above total.

A.J. Roger: 2008-2013 Canadian Institutes for Health Research, Operating Grant – “Major transitions in eukaryotic cell evolution”: $719,381 over 5 years 2007–2015 Tula Foundation, Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB) Administrator salary, Seminar Series and Student Travel Grant: $50,000/year for 8 years 2007–2012 Tula Foundation, CGEB Molecular Biology Research Fellowship (funding for one postdoctoral fellowship plus research expenses): $64,000/year for 5 years 2007–2009 E.W.R. Steacie Fellowship Supplement, NSERC - “Determining the super-kingdoms of eukaryotes”: $238,624 over 2 years 2005 – 2010 Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant – “Phylogenomic approaches to ancient relationships amongst eukaryotes”: $41,300/year for 5 years 2004 – 2008 Alfred P. Sloan Foundation Research Fellowship – “Understanding genome and proteome evolution”: $40,000 USD total 2003 – 2008 Canadian Institutes for Health Research, Operating grant – "The origins and evolution of genes and organelles in eukaryotes": $107,815/year for 5 years

J.M. Archibald: 2009-2013 NSERC Discovery Grant —“Genome and proteome evolution in nucleomorph-containing algae”: $34,000/year 2008-2010 NSERC Special Research Opportunities Program Grant—“Impact of secondary endosymbiosis on eukaryotic genome evolution”: Year 1 $113,050; Year 2 $106,050 2008-2010 CIHR & NS/CIHR Regional Partnership Program Operating Grant— “The causes and consequences of genome reduction in eukaryotes”: $100,000 Year 1; $76,615 Year 2 2007-2012 Tula Foundation – funding for one CGEB postdoctoral fellowship ($44,000/year) plus research allowance ($20,000/year), for 5 years 2007-2012 Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity—annual funds in support of research: $35,000/year 2007-2010 US Department of Energy’s Joint Genome Institute (JGI) Community Sequencing Program (CSP_LOI_19044)—“Impact of Secondary Endosymbiosis on Genome Evolution and Cell Biology: A Cryptomonad and a Chlorarachniophyte Nuclear Genome”: ~1,000,000 USD (in kind contribution – not included in above total).

24 2006-2009 Canada Foundation for Innovation (CFI) Institutional Infrastructure Operating Fund (IOF)—“Laboratory for microbial genome analysis”: $37,442 total over 3 years 2004-2009 NSERC - Discovery Grant —“Genome reduction in eukaryotes”: $36,390/year

R. Beiko: 2009-2012 Genome Canada, Competition in Applied Genomics Research – “BEEM: Bioproducts and enzymes from environmental metagenomes”: total $5,000,000 over 3 years (co-applicant with Elizabeth Edwards, P.I. – not included in above total) 2008-2013 Tula Foundation – funding for one PhD student trainee ($25,000/year) plus research allowance ($2,500/year) for 5 years 2007-2011 NSERC - Discovery Grant, “New computational methods for metagenomics”: $115,000 total over 4 years 2007-2011 Canada Research Chairs (CRC) – “Canada Research Chair (Tier II) in Bioinformatics”: $500,000 total over 4 years 2007-2010 Australian Research Council – Discovery Grant – “Metagenomics and the genetic basis of ecology and evolution of communities”: $210,000 over 4 years (co-applicant with L.L. Blackall, P.I. – not included in above total) 2006-2010 Genome Atlantic – “Computational analysis of genomic and metagenomic data”: $226,000 total over 4 years

J. Bielawski: 2009-2013 NSERC – Discovery Grant – “Evolutionary analysis of protein diversification: model improvement, assessment and application to real data”: $145,000 total over 4 years 2007-2012 Tula Foundation – funding for one postdoctoral fellowship ($44,000/year) plus research allowance ($5,000/year) for 5 years

C. Blouin: 2009-2014 CFI (Infrastructure Operating Funds) – “A high performance computational platform for bioinformatics”: $12,000/year 2008-2013 Tula Foundation – funding for PhD student trainee ($25,000/year) plus research allowance ($2,500/year) for 5 years 2004-2009 NSERC – Discovery Grant - “Phylogenetics and the emergence of structural patterns in proteins”: $24,000/year

W.F. Doolittle: 2006-2009 Canadian Institutes for Health Research – “Integron metagenomics”: $141,917/year 2008-2011 Tula Foundation – funding for one postdoctoral fellowship ($44,000/year) plus research allowance ($20,000/year) for 2.5 years

M.W. Gray: 2009-2011 Tula Foundation – funding for one postdoctoral fellow trainee ($44,000/year) plus research allowance ($20,000/year) for 2.5 years

25 2004-2009 Canadian Institutes for Health Research – “A combined biochemical and genomics approach to investigate the function of a mitochondrial tRNA editing system & the mitochondrial proteome”: $161,979/year

A.G.B. Simpson: 2009-2014 NSERC - Individual Discovery Grant – “Microbial eukaryote diversity and evolution in extraordinary environments”: $34,000/year 2007-2011 Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity—annual funds in support of research: $23,000/year 2008-2013 Tula Foundation – funding for one postdoctoral fellowship ($44,000/year) plus research allowance ($20,000/year) for 5 years 2008-2013 CIHR Operating Grant – (co-applicant with Andrew Roger, P.I.: $143,876/yr – counted for A.J. Roger only in above total) 2008 NSERC - Research Tools Grant (co-applicant with Ian Meinertzhagen, P.I.: $150,000 – not included in above total) 2004-2009 NSERC - Individual Discovery Grant – “The evolution and diversity of eukaryotic cells”: $32,700/year

E. Susko: 2008-2013 NSERC – Discovery Grant - “Statistical evolutionary bioinformatics”: $21,000/year 2008-2013 Tula Foundation – funding for one postdoctoral fellowship ($44,000/year) plus research allowance ($5,000/year) for 5 years 2006-2009 Canadian Institutes for Health Research – “Integron metagenomics”: $141,917/year (co-applicant with W.F. Doolittle, P.I. – counted for W.F. Doolittle only in above total) 2003-2008 NSERC – Discovery Grant - “Mixture models and molecular evolution”: $19,000/year

26 X. HONOURS/AWARDS/DISTINCTIONS [includes those received during 2008-2009, ongoing salaried fellowships and scholarships, and lifetime fellowships and honorary memberships]

Andrew Roger: • Director, Centre for Comparative Genomics & Evolutionary Bioinformatics (CGEB), Dalhousie University (2008-2011) • Fellow, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program (2007-2012) • NSERC E.W.R. Steacie Memorial Fellowship (2007-2009) • Peter Lougheed/CIHR New Investigator Salary award (2004-2009)

John Archibald: • Fellow, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program (2009-2012) • New Investigator Award, Canadian Institutes of Health Research (5-year salary award, 2008-2013) • Award of Excellence in Basic Research, Dalhousie Medical Research Foundation, Dalhousie University (2008): $7,000 • Scholar, Canadian Institute for Advanced Research - Integrated Microbial Biodiversity Program (2007-2009)

Robert Beiko: • Canada Research Chair in Bioinformatics (2007-2012): $100,000/year

Joseph Bielawski: • Faculty of Science, Killam Prize, Dalhousie University (2008-2009): $2,000 • Genome Atlantic Research Chair, Department of Biology (2003-2008)

W. Ford Doolittle: • Elected Member, The Norwegian Academy (2009-present) • Institute Fellow, Canadian Institute for Advanced Research (2008-present) • Elected Member, U.S. National Academy of Sciences (2002-present) • Canada Research Chair in Comparative Microbial Genomics (2001-2008): $200,000/year • Fellow, American Academy of Microbiology (1999-present) • Fellow, The Royal Society of Canada (1991-present) • Fellow, American Association for the Advancement of Science (1985-present)

Michael Gray: • Canada Research Chair in Genomics and Genome Evolution (2001-2008) • Fellow, The Royal Society of Canada, Academy of Sciences (1996-present)

Alastair Simpson: • Scholar/Fellow, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program (2007-2012): $23,000/year (research allowance)

27 XI. SUPERVISION OF RESEARCH TRAINEES

A total of 67 students and postdoctoral fellows are either currently being supervised (or were supervised) in the labs of CGEB faculty members for the period 2008-present. Note: Tula-funded trainees’ names are highlighted in boldface type.

CGEB Faculty Member Name and Type of Trainee Andrew Roger Anastasios Tsaousis, Postdoctoral Fellow Biochemistry and Molecular Biology Alexandra Stechmann, Postdoctoral Fellow Huaichun Wang, Postdoctoral Fellow (co- supervised with E. Susko – see below) Ivica Tamas, Postdoctoral Fellow Jessica Leigh, PhD student (now a PDF at Universite Pierre et Marie Curie) Michelle Leger, PhD student Dan Gaston, PhD student Martin Kolisko, PhD student (co-supervised with A. Simpson – see below) Liwen Zhou, PhD student (co-supervised with E. Susko – see below) Javier Alfaro, MSc student Courtney Stairs, Honours student – now an MSc student Peter Walker, Honours student Grant Stevens, Honours student Andrew Evans, Undergraduate co-op student

John Archibald Eunsoo Kim, Postdoctoral Fellow Biochemistry and Molecular Biology Julia Hopkins, Postdoctoral Fellow Goro Tanifuji, Postdoctoral Fellow (co- supervised with M. Gray – see below) Bruce Curtis, PhD student Robert Eveleigh, MSc student Natalie Donaher, MSc student Christa Moore, MSc student Tyler Mills, Honours student Matthew MacDowell, Honours student Matt Hood, Co-op student

Christian Blouin, Computer Science Julia Frenette, PhD student Haibin Liu, PhD student Michael Lo, MSc student Gregory Smolyn, M.C.S. student Karina Haupt, visiting MSc student Allan Lavell, NSERC USRA student Joshua Litven, NSERC USRA student

28

CGEB Faculty Member Name and Type of Trainee

Robert Beiko, Computer Science Dennis Wong, PhD student Kathryn Duffy, PhD student Norman MacDonald, PhD student Donovan Parks, PhD student Christopher Whidden, PhD student Scott Perry, MSc student Sylvia Churcher, Honours student (co-supervised with Hong Gu) – now an MSc student Isabel Gao, Honours student (co-supervised with Hong Gu) Catherine Holloway, NSERC USRA student Mike Porter, Undergraduate RA student Jeremy Gallant, Undergraduate RA student Harman Clair, Undergraduate RA student Suwen Wang, Undergraduate RA student

Joseph Bielawski, Biology Katherine Dunn, Postdoctoral Fellow Rachael Bay, PhD student Caroline Urqhardt, MSc student Joseph Mingrone, Honours student – now an MSc student Alyssa Byers-Heinlein, Honours student Hannah Zimmering, Undergraduate student

W. Ford Doolittle Olga Zhaxybayeva, Postdoctoral Fellow Biochemistry and Molecular Biology Adrian Sharma, PhD student (now PDF at MIT) Jeremy Koenig, PhD student (now PDF at Cornell) Christine Sharp, Honours student

Michael Gray Goro Tanifuji, Postdoctoral Fellow (co- Biochemistry and Molecular Biology supervised with J. Archibald – see above) Ryan Gawryluk, PhD student

Alastair Simpson, Biology Jong Soo Park, Postdoctoral Fellow Aaron Heiss, PhD student Martin Kolisko, PhD student (co-supervised with A. Roger – see above) Laura MacDonald, Honours student Gillian Forbes, Honours student Karla Grimm, Honours student Greg Macmullin, NSERC summer student Abrar Nebgaban, summer student

29

CGEB Faculty Member Name and Type of Trainee

Claudio Slamovits Gillian Gile, Postdoctoral Fellow Biochemistry and Molecular Biology Renny Lee, PhD student

Edward Susko Huaichun Wang, Postdoctoral Fellow (co- Mathematics and Statistics supervised with A. Roger – see above) Liwen Zhou, PhD student (co-supervised with A. Roger – see above) Jihua Wu, PhD student Yifei Hu, MSc student Goldis Radajapalipour, MSc student

30 XII. CONTRIBUTIONS FROM CGEB TRAINEES

This section includes abstracts, posters, and seminar presentations (total of 44) by CGEB students and postdocs at national and international meetings, conferences and workshops. Travel and attendance was sponsored in part by CGEB (Tula) funds.

Note: CGEB trainees’ names are underlined and the presenter’s name is in bold.

A. Conference and Seminar Presentations

Duffy, K., Beiko, R. & Zeh, N. “Improvements to the BLOSUM amino acid substitution model,” CIFAR - Integrated Microbial Biodiversity Program Annual Meeting, Asilomar, California, June, 2009 (poster presentation).

Duffy, K., Beiko, R. & Zeh, N. “The BLOSUM matrix model: Does greedy clustering underestimate substitution probabilities?”, ISMB 2008, Toronto, July 2008 (poster presentation).

Dunn, K. “Testing "genome concepts" in ecologically divergent species of Listeria: implications for the bacterial speciation problem”, Department of Biology, Seminar Series, Dalhousie University, November 20, 2008 (oral presentation).

Gaston, D. & Roger, A.J. “A Likelihood Based Mixture Model Method of Identifying Functionally Divergent Protein Residues”, CIFAR Integrated Microbial Biodiversity Program Meeting, Carling Lake Resort, May 2008 (poster presentation).

Gaston, D. & Roger, A.J. “A Likelihood Based Mixture Model Method of Identifying Functionally Divergent Protein Residues”, Protist 2008 (ISEP/ISOP) Meeting, Halifax, NS, July 2008 (poster presentation).

Gaston, D., Wang, H., Susko, E. & Roger, A.J. “FunDi: A Phylogenetic Mixture- Model Approach to Predicting Functionally Divergent Protein Residues”, Society for Molecular Biology and Evolution Meeting, Iowa City, June 2009 (oral presentation). Received Graduate Student Travel Award.

Gaston, D., Wang, H., Susko, E. & Roger, A.J. “FunDi: A Phylogenetic Mixture- Model Approach to Predicting Functionally Divergent Protein Residues”, Dalhousie University, Department of Biochemistry and Molecular Biology, Departmental Seminar, 2009 (oral presentation).

Gawryluk, R.M.R., Spencer, D.F. & Gray, M.W. “A proteomic investigation of the Acanthamoeba castellanii mitochondrial electron transport chain”, Leopoldina Symposium – Molecular Genetics of Mitochondria and Chloroplasts, Berlin, September 20-23, 2009 (poster presentation).

31 Heiss, A.A., Walker, G. & Simpson, A.G.B. “The ultrastructure of Ancyromonas, a eukaryote without supergroup affiliation.” Protist 2008/ISEPXVII/ISOP 59 Meeting, Dalhousie University, Halifax, July 21-26, 2008 (oral presentation).

Kim, E., Yubuki, N., Leander, B. & Graham L.E. “Episymbioses involving three new genera of heterotrophic stramenopiles flagellages: Apoikia lindahli nov. comb. (Chrysophyceae), Filos agilis gen. et sp. nov. (Bicosoecida), and Nanos amicus gen. et sp. nov. (Bicosoecida)”, Protist 2008 Conference, Halifax, Canada, July 2008 (oral presentation).

Koenig, J.E., Sharp, C., Boucher, Y. & Doolittle, W.F. “Environmental assessment of integron gene cassettes present in a tar pond”, American Society for Microbiology general meeting, Boston, MA, June 2008 (oral presentation).

Kolisko, M., Silberman, J.D., Cepicka, I., Yubuki, N., Takishita, K., Inagaki, Y., Roger, A.J. & Simpson, A.G.B. “New isolates of Carpediemonas-like organisms and phylogeny of Excavata.” XIIIth Meeting of the International Congress of Protistology, Buzios, Brazil, August 2009 (poster presentation).

Kolisko, M., Park, J.S., Silberman, J.D., Roger, A.J. & Simpson, A.G.B. “Molecular phylogeny of new Carpediemonas-like organisms”, Protist 2008, Halifax, July 21-26, 2008 (oral presentation).

Leger, M.M., Hug, L.A. & Roger, A.J. “A novel mitochondrion-derived organelle in the jakobid Andalucia incarcerata, Protist 2008 Meeting, Dalhousie University, July 2008 (poster presentation).

Leger, M.M., Hug, L.A. & Roger, A.J. “A hydrogenosome in the free-living excavate Andalucia incarcerata, XIIIth Meeting of the International Congress of Protistology, Buzios, Brazil, August 2009 (poster presentation).

Leger, M.M. “Exploring the functions of mitochondrion-derived organelles”, Departmental Seminar, Dalhousie University, May 2009 (oral presentation).

Mingrone, J. “Assessing the reliability of codon evolution models”, Cameron Conference, Dalhousie University, February 2009 (oral presentation).

Moore, C. “454 pyrosequencing the nucleomorph genome of Chroomonas mesostigmatica CCMP 1168: introns, synteny, and gene density", CIFAR – Integrated Microbial Biodiversity Program Annual Meeting, Asilomar, CA, June 16-19, 2009 (poster presentation).

Park, J.S., Simpson, A.G.B., Brown, S. & Cho, B.C. “Ultrastructure and Molecular Phylogeny of Three Extremely Halophilic Heterolobsea”, CIFAR - Integrated Microbial Biodiversity Program Annual Meeting, Carling Lake Resort, Quebec, Canada, May 7-9, 2008 (poster presentation).

32 Park, J.S., Simpson, A.G.B. & Cho, B.C. “The isolation and identification of three extremely halophilic Heterolobosea from high salinity waters”, Protist 2008, Halifax, July 21-26, 2008 (oral presentation).

Parks, D.H. & Beiko, R.G. “Quantitative Visualizations of Hierarchically Organized Data in a Geographic Context”, 27th International Conference on Geoinformatics, Fairfax, Virginia, 2009 (oral presentation). Received CPGIS 2009 Best Student Paper Award.

Parks, D.H. & Beiko, R.G. “Exploring Marine Microbial Community Diversity”, Canadian Society for Ecology and Evolution (CSEE) and Genetics Society of Canada (GSC) Conference, Halifax, 2009 (poster presentation).

Sharma, A.K. “Metagenomics, pure cultures and rhodopsin-based phototrophy”, Departmental Seminar, Dalhousie University, February 2009 (oral presentation).

Sharma, A.K., Bullerjahn, G. S., Sommerfeld, K. & Doolittle, W.F. “Rhodopsin Sequence Diversity Recovered from the Surface Waters of the Great Lakes Superior and Erie”, 108th General Meeting for the American Society of Microbiology (ASM), June 2, 2008 (poster presentation).

Sharp, C., Doolittle, W.F. & Koenig, J.E. “Discovery of a novel integron in the Arthrobacter genus: a potential agent of xenobiotic degradation? Society for Molecular Biology and Evolution, Barcelona, Spain, June 2008 (poster presentation).

Stairs, C.A.W., Tsaousis, A.D. & Roger, A.J. “Unique subcellular localization of mitochondrial proteins in the mitochondrion related organelle of Mastigamoeba balamuthi”, CIFAR - Integrated Microbial Biodiversity Program Annual Meeting, Asilomar, California, June 17-20, 2009 (poster presentation).

Tsaousis, A.D., Stechmann, A. & Roger, A.J. “The Fe/S biosynthetic pathways of Blastocystis sp.”, Protist 2008, Dalhousie University, July 21-26, 2008 (oral presentation).

Tsaousis, A.D., Stechmann, A., Gaston, D., Walker, P.B., Lithgow, T. & Roger, A.J. “A functional TOM70 in Blastocystis and related stramenopiles suggests it was part of the ancestral core mitochondrial protein import apparatus”, Leopolidina Symposium: Molecular Genetics of Chloroplasts and Mitochondria, Berlin, Germany, September 20-23, 2009 (poster presentation).

Tsaousis, A.D., Stechmann, A., Gaston, D., Walker, P.B., Perley, T., Stairs, C.A.W. & Roger, A.J. “The unique mitochondrion related organelle of Blastocystis”, XIII International Congress of Protistology, Armação dos Búzios, Rio de Janeiro, Brazil, August 23-28, 2009 (oral presentation). Awarded Walter Colli Prize 2009.

33 Walker, P.B., Tsaousis, A.D. & A.J. Roger. “A unique feature of the mitochondrial protein import machinery in Blastocystis”, Protist 2008, Halifax, Canada, July 21-26, 2008 (poster presentation).

Wang H-C, Susko, E, & Roger A.J. “QmmRAxML: a New Phylogenetic Program Implementing Site-specific Amino Acid Frequencies Model for Phylogenetic Inference”, Protist 2008 Conference, Dalhousie University, July 21-26, 2008 (oral presentation).

Wang, H-C, Susko, E. & Roger, A.J. “A Model-based Approach for Detecting Covarion Positions in a Protein Family”, SMBE Annual Meeting, Iowa City, June 3-7 2009 (oral presentation).

Wong, D.H.J. & Beiko, R. “Phylogenomic and metabolic analysis of microbial EBPR communities”, Canadian Society for Ecology and Evolution, Dalhousie University, May 2009 (poster presentation).

Wong, D.H.J., Parks, D.H., Churcher, S. & Beiko, R.G. “Exploring the World of Microbes using new Genomic Methods and Software Tools”, 5th Annual Sustainability and Environmental Research Symposium, Dalhousie University, March, 2009 (poster presentation).

B. Invited Oral Presentations from CGEB Trainees

Kim, E. “Ultrastructure and molecular phylogeny of the heterotrophic euglenid Petalomonas sphagnophila and its photosynthetic endosymbionts”, International Symposium on Protistology, Tsukuba, Japan, November 2008.

Kim, E. & Archibald, J.M. “Diversity and evolution of plastids and their genomes” Chloroplast Workshop, Gothenburg, Sweden, June 2008.

Kolisko, M., Park, J.S., Silberman, J.D., Roger, A.J. & Simpson, A.G.B. New isolates of Carpediomonas-like organisms and the phylogeny of Excavata”, International Symposium on Protistology, Tsukuba, Japan, 2008.

Sharma, A.K. “Mining metagenomic datasets and culture collections to understand the ecology of rhodopsin-based phototrophy”, Department of Civil and Environmental Engineering, MIT, Boston, MA, April 9, 2009.

Tsaousis, A.D. “Characterization of Blastocystis organellar proteins in the mitochondrion of T. brucei”, Mitochondrion of Trypanosoma brucei enters the post – proteomic era, Trest, Czech Republic, September 27-30, 2009.

Tsaousis, A.D. “Evolution and function of microsporidian mitosome”, Department of Protistology, Charles University, Prague, Czech Republic, October 14, 2008.

34 Tsaousis, A.D. “Evolution and function of mitochondrial-like organelles”, Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic, October 7, 2008.

Tsaousis, A.D. “The microsporidian mitosome is an energy parasite”, CIFAR - Integrated Microbial Biodiversity Program Annual Meeting, Carling Lake Resort, Quebec, May 7-9, 2008.

Zhaxybayeva, O. “Evolutionary Bioinformatics in Postgenomic and Metagenomic Eras”, Computer Science and Biology Departments, Memorial University, St. John’s, NL, March 30, 2009.

Zhaxybayeva, O. “Tree, Coral or Potato of Life”, Biology Department, Mount Allison University, Sackville, NB, October 28, 2008.

35 XIII. OTHER ACTIVITIES OF THE CENTRE

A. CGEB Seminar Series

The following invited speakers presented seminars in the Department of Biochemistry & Molecular Biology and Department of Biology at Dalhousie. These were sponsored (or co-sponsored) by funding from the Tula Foundation.

• (upcoming) Dr. Graham Bell, McGill University, November 2009 “The genomics of fitness in yeast”

• Dr. John McCutcheon, University of Arizona, May 2009 "Big surprises from small genomes: the unusual genomic properties of bacterial symbionts in sap-feeding insects"

• Dr. Thomas Schwartz, MIT, April 2009 "Taming a monster: toward the atomic structure of the nuclear pore complex"

• Dr. William Hanage, Imperial College London, February 2009 "Hyper-recombination, species, and the acquisition of antibiotic resistance"

• Dr. Peter Gogarten, University of Connecticut, November 2008 "Phylogenetics in light of horizontal gene transfer"

• Dr. Elizabeth Edwards, University of Toronto, September 2008 "Bioremediation metagenomics"

• Dr. Jeffrey Parsons, Memorial University, March 2008 "Classification in Science: Toward Some Unifying Principles"

• Dr. Philip Bourne, University of California-San Diego, December 2007 "Evolutionary insights from protein structure"

B. CGEB Meeting Sponsorships

CGEB made contributions to the following symposia and meetings through our Seminar Series Fund from the Tula Foundation and our CGEB New Opportunities Fund.

• sponsored a symposium “Principles and Practice of Phylogenomic Inference” at the Canadian Society for Ecology and Evolution/Genetics Society of Canada Meeting, Dalhousie University, Halifax, May 2009. Speakers: Henner Brinkmann (U. Montreal), Nicolas Lartillot (U. Montreal), Stephane Aris-Bourne (U. Ottawa), Brian Golding (McMaster). CGEB Seminar Series Fund contribution: $4,794.23

36 • sponsored a symposium “Protist Phylogenomics” at the Protist 2008 Meeting (ISOP59/ISEPXVII), Dalhousie University, Halifax, July 2008. Speakers: Jessica Kissinger (U. Georgia), Martin Embley (Newcastle), Jan Andersson (Uppsala), Yuji Inagaki (U. Tsukuba) CGEB Seminar Series Fund contribution: $8,377.57

• co-sponsored a symposium “Structure and processing of RNAs” at the Mitchondria, Ribosomes & Cells: A Symposium in Honour of Mike Gray, Dalhousie University, Halifax, July 3-4, 2008. Speakers: Maurille Fournier (U. Mass.), Tony Russell (U. Lethbridge), Franz Lang (U. Montreal), James Collings (M.D., Hampton) CGEB New Opportunities Fund contribution: $3,992.74

• CGEB New Opportunities Fund provided $4,000 to ISEP for student travel awards at the Protist 2008 Meeting (ISOP59/ISEPXVII), Dalhousie University, Halifax, July 2008.

C. CGEB Joint Lab Meetings

In 2009 we instituted a new schedule of CGEB joint lab meetings that include all ten CGEB labs’ faculty members, undergraduate and graduate students, postdocs, and lab personnel. These meetings are held on the first Thursday of every month, to be continued on a year-round basis.

The purpose of these meetings is to introduce CGEB faculty and trainees to the ever-expanding group of trainees in the various labs. Faculty members and/or their students and postdocs provide an overview of their research program in a seminar-style format, with adequate time allotted for questions, constructive criticism and open discussion throughout.

D. CGEB Journal Club

The CGEB Journal Club was initially formed in 2007 by several postdocs/PIs in the Department of Biochemistry and has now expanded to include all CGEB labs’ trainees and faculty members who are interested in participating. These meetings are held on a bi-weekly basis throughout the year. Participants select and present a current research paper for discussion. A number of trainees have stated that this experience has been invaluable and an integral part of their overall training.

37 XIV. FUTURE DIRECTIONS

The main goals of the establishment of CGEB Centre were to: 1) advance the research programs of its members, 2) enhance recruitment/training of world- class postdocs and PhD students in CGEB labs, 3) promote collaborations between CGEB members, 4) leverage additional support for comparative genomics and bioinformatics research at Dalhousie, and 5) provide opportunities for seeking additional research funds from granting agencies through CGEB collaborations. From the progress described in this report, it should be clear that CGEB has already been spectacularly successful in advancing each of these goals. So a major future direction is, in fact, to do even more of the same!

Nevertheless, at our recent biannual CGEB members meeting, a number of future CGEB activities were proposed, including:

A. An annual CGEB poster session and social ‘mixer’, perhaps associated with the talk of one of the more eminent invited speakers in the CGEB Seminar Series. Now that CGEB has grown to 10 members and 67 trainees, it has become difficult for ‘everyone to know everyone’. This mixer would allow members, trainees (and the new ‘Associates’, see p. 8) to meet each other and discuss areas of mutual interest provoked by the poster session that could lead to future collaborations. A wine and cheese service would function as an added incentive for trainee attendance. Financing for this mixer could be drawn from the ‘New Opportunities Fund’.

B. An annual 2-3 day CGEB retreat with seminars/posters presented by CGEB members, Associates and trainees, as well as a handful of guest speakers (~70- 80 individuals). Ideally this retreat would occur offsite, perhaps in a remote resort hotel (e.g. Whitepoint Beach Resort). This way all of those involved are more likely to attend all talks and participate in all events and the intensity of the interactions is thereby increased. By inviting several high profile speakers with similar research interests, connections could be forged with these outside groups and give CGEB a higher international profile. This idea was stimulated by the apparent success of similar-style retreats coordinated annually by the Tula- funded Centre for Microbial Diversity and Evolution (CMDE) at UBC that were attended by new CGEB member Claudio Slamovits. Obviously, we would have to seek additional monies to support this annual activity as its projected cost (~$20,000/year) extends well beyond the current CGEB Budget.

C. Co-sponsorship of targeted workshops with the Canadian Institute for Advanced Research Integrated Microbial Biodiversity Program and the Canadian Institute for Health Research Institute of Genetics. Several potential hands-on workshops could be held to train those at CGEB in particular areas of interest. One potential workshop that is in the works (funded by CIFAR) focuses on the growing field of eukaryotic microbial genomics and genome annotation. All CGEB members could attend and learn ‘hands-on’ skills for assembling, annotating and analyzing whole eukaryotic genomes – a task that has been made affordable by the advent of cheap ‘Next Generation’ sequencing technology.

38

D. Co-sponsorship of a Phylogenomics Meeting. An international meeting involving experts in comparative genomics, phylogenetics and bioinformatics could be held at Dalhousie and some costs (e.g. invited speakers) could be offset by CGEB. A similar conference was held in Quebec a few years ago and was a resounding success.

39

APPENDIX A:

CGEB GOVERNANCE POLICY APPENDIX A: GOVERNANCE

Proposed Governance of CGEB

The purpose of CGEB is to stimulate research and collaboration among its members. The streamlined management structure we propose is designed to ensure fair and efficient operation. The organizational structure of CGEB will consist of a Deans Committee, a Director, a Steering Committee, and the Membership. The terms of reference for these bodies are outlined below.

I. DEANS COMMITTEE

The Deans Committee will meet annually with the Director, providing advice on operation and direction of the Centre, and identifying emerging opportunities for CGEB to advance its research and training goals at Dalhousie University. The Deans committee will be headed by the ‘Presiding Dean’ (initially the Dean of the Faculty of Medicine) and, with the other Deans, will be ultimately responsible for the Centre management and budget. The Presiding Dean will also advise the Director on matters relating to the operation of the Centre as issues arise. The Deans Committee will appoint new Directors in consultation with the Steering Committee and the CGEB Membership. The Deans Committee will consist of: Vice President, Research (or designate), ex-officio; Dean of Medicine (or designate), Presiding; Dean of Science (or designate); Dean of Computer Science (or designate).

II. DIRECTOR

The Director is ultimately responsible for decisions relating to Centre business and will chair the Steering Committee and supervise a Centre Administrator who will coordinate CGEB group meetings and meetings of the Deans Committee and Steering Committee, as well as prepare and receive Centre-related correspondence and assist in accounts-keeping. The Director will report to the Presiding Dean on all matters relating to Centre operation and budget and will meet with the Deans Committee annually. The Director position will normally be held for a three-year term but this term may be renewed on the recommendation of the Deans Committee. When required, a new Director will be selected by the Deans Committee, based on advice received from the CGEB membership.

III. STEERING COMMITTEE

The Steering Committee will be made up of the Director and two other faculty members in the CGEB group. The Steering Committee will be responsible for advising the Director on matters such as the disbursement of Tula Foundation-supported postdoctoral and graduate student positions to CGEB faculty, as outlined in the main text of the proposal. Furthermore, the Director will consult with the Steering Committee on any decisions substantially affecting CGEB before a final decision is made by the Director. The term for membership on the Steering Committee is three years, but reappointment of an individual whose term has been completed is possible providing the Membership approves.

IV. CGEB MEMBERSHIP

The CGEB Membership will have scheduled meetings bi-annually to discuss Centre business, and make/vote on recommendations to the Steering Committee and the Deans Committee regarding new CGEB members, nominations for Director, Steering Committee membership, and new opportunities for CGEB.

Proposed Composition of the Initial CGEB Management Structure

I. DEANS COMMITTEE • Vice President, Research (or designate), ex-officio • Dean of Medicine (or designate), Presiding • Dean of Science (or designate) • Dean of Computer Science (or designate)

II. DIRECTOR • Andrew Roger, Biochemistry and Molecular Biology

III. STEERING COMMITTEE • Andrew Roger, Biochemistry and Molecular Biology • Michael W. Gray, Biochemistry and Molecular Biology • W. Ford Doolittle, Biochemistry and Molecular Biology

IV. CGEB MEMBERSHIP • Andrew Roger, Biochemistry and Molecular Biology • Michael Gray, Biochemistry and Molecular Biology • Ford Doolittle, Biochemistry and Molecular Biology • John Archibald, Biochemistry and Molecular Biology • Alastair Simpson, Biology • Joseph Bielawski, Biology, and Mathematics and Statistics • Robert Beiko, Computer Science • Christian Blouin, Computer Science, and Biochemistry and Molecular Biology • Ed Susko, Mathematics and Statistics • (new) Assistant Professor, Biochemistry and Molecular Biology (job search underway)

V. CENTRE ADMINISTRATOR • Wanda Danilchuk, Biochemistry and Molecular Biology

APPENDIX B:

LETTERS TO FGS REGARDING “POLICIES AND PROCEDURES” GOVERNING POSTDOCTORAL TRAINEES AT DALHOUSIE UNIVERSITY DEPARTMENT OF BIOCHEMISTRY & MOLECULAR BIOLOGY FACULTY OF MEDICINE, SIR CHARLES TUPPER MEDICAL BLDG HALIFAX, NOVA SCOTIA, CANADA B3H 1X5 PHONE: (902) 494-2480 FAX: (902) 494-1355 WWW.BIOCHEM.DAL.CA

March 27, 2009

Dr. Sunny Marche Associate Dean Faculty of Graduate Studies Dalhousie University

Dear Dr. Marche,

Re: Postdoctoral Fellows - Concerns and Issues for Inclusion at PDF Meeting in Ottawa

I was unavailable to attend the meetings where you asked for input in regulations regarding postdoctoral researchers that you will take forward to a meeting in Ottawa. In a letter dated October 27, 2008, my colleagues and I in the Centre for Comparative Genomics and Evolutionary Bioinformatics, outlined our points of view on many issues relevant to postdoc regulations at Dalhousie University. Although we did not receive a reply to our letter, we hope that the information and arguments we provided in that letter help to clarify the key importance of postdoctoral researchers and their training to the competitiveness of Dalhousie University as a research institution.

In lieu of attending the meeting you had on March 20th, I am writing this letter to re- emphasize some issues regarding postdoctoral researchers that I feel are extremely important to take forward to the discussion in Ottawa:

1) A large fraction (maybe more than 50%) of postdoctoral researchers in the biomedical and biological sciences at Dalhousie University (and most Canadian Universities) are not Canadians or landed immigrants. It is part of scientific culture to encourage Ph.D. students to explore postdoctoral research opportunities outside of their institution and often outside of the country as a way to broaden their horizons/experience and forge international collaborative connections. As a result, many Canadians travel to the US and Europe for postdocs, and many postdocs in Canada come from other countries. These postdocs significantly contribute to the research activities of our laboratories. They not only bring new ideas and techniques to Canadian labs, but, in exchange, they gain invaluable experience from the Canadian labs they are completing their postdocs in. It is therefore extremely important that whatever rules/legislations are adopted for postdocs in Canada, that they continue to allow easy access for non-Canadians to pursue their postdoctoral training in Canada. If, for instance, postdocs become classified as employees, then this could cause major problems with hiring foreign postdocs as each prospective supervisor would have to go through onerous and time-consuming HRDC screening to prove that a “Canadian” applicant was not equally qualified etc. This is inappropriate as the postdoctoral position is not a regular job; it is a training position. Furthermore, preventing foreign postdocs from coming to Canada will have terrible downstream negative consequences for competitiveness of Canadian researchers relative to their colleagues in the US and the EC. We would be deprived of opportunities to benefit from scientific knowledge from other countries, as well as future collaborative opportunities when the postdocs return to their home countries.

In case you are not convinced, I can tell you from personal experience that since 1999, I have supervised 16 postdoctoral fellows in my laboratory. Only three of the 16 are Canadian citizens -- the 13 others were foreign. Of the 16, three are currently in my lab as postdocs, nine have obtained full-time faculty positions at reputable universities and three of them are doing a second postdoc in Europe. I maintain mutually beneficial and productive research collaborations with seven of my former postdocs at universities in Canada, the US, Japan, Sweden and Spain. My own research successes, such as the award of an Alfred P. Sloan Foundation fellowship in 2004, a Peter Lougheed/CIHR New Investigator Fellowship in the same year and, most recently, an NSERC Steacie Fellowship in 2007, are in a large part due to my previous and current collaborative work with these excellent postdoctoral researchers from all over the world. I can honestly say that the synergy between my own expertise and that of the postdocs and graduate students that I have supervised was key to the success of my research group at Dalhousie and key to the ultimate success of these trainees in getting jobs.

2) The length of the postdoctoral training period should not be too short. The current rules for ‘academic’ PDFs at Dalhousie are too restrictive given that postdocs (especially ones in interdisciplinary environments) need a lot of time to gain the appropriate training to become effective researchers, fund-raisers, teachers and administrators. In our Oct. 28th letter, I outlined in detail the reasons for this. I would simply add here that, if a length limit were to be imposed, I would suggest a minimum of six years for a postdoc position. In previous group discussions you have hosted on this issue, you raised the question of why we even need postdocs – “shouldn’t a PhD be qualification enough?”, you asked. The answer is a definite “no”, and it is not because we are not training Ph.D. students properly. In biomedical/biological sciences, laboratory research takes a very long time and learning the theory and methods of a field takes both hands-on experience and critical review of the literature. Many postdocs are trying to branch-out from their PhD work to new sub- fields and learn new techniques (to diversify their research abilities). Add to those tasks, the need for a postdoc to: i) learn how to manage/supervise trainees in a lab setting (PI’s in biomedical science often have 8-10 trainees in total), ii) learn how to set up a lab, iii) learn how to write grants, iv) learn how to budget for research activities, and v) learn how to teach. It’s analogous to the situation with medical doctors. Why isn’t medical school enough? Why do they have to do 3-4 years of residency? I, for one, would not want to be operated on, by a student fresh out of medical school with no residency experience. I think an analogy like this might help the non-scientists at the Ottawa meeting understand the situation a bit better.

3) The issue of taxation of postdoc stipends. Aside from the serious problems associated with foreign postdocs being designated as employees, I believe that making postdoctoral fellowships taxable will seriously decrease our competitiveness at attracting world-class postdoctoral trainees to Canadian universities. For Canadians and landed immigrants, the benefits package (and CPP plus EI) may be seen as reasonable compensation for paying taxes. However, for the large fraction of postdocs who are non-Canadians, then the contributions are ultimately useless. For these individuals, having a tax-free income of $40,000/year (a typical postdoc salary) is extremely competitive with the remuneration available in the US and the EC. We have to realize that researchers in Canada are competing with these other countries to attract excellent postdoctoral trainees – so a competitive advantage in the size of stipends that we pay goes a long way towards attracting good people to Canada. This is especially important now that the US is injecting huge amounts of money into NSF and NIH. In Canada, operating grant funding for NSERC and CIHR has been undercut (and redirected) in the last federal budget.

4) Benefits. Assuming postdocs are not ultimately designated as employees, I strongly feel that the university should help negotiate a benefits package for postdocs. Graduate students have a benefits package and it is important that the same benefits are extended to postdoctoral researchers. Again, this is essential if we are to be competitive in attracting excellent postdoctoral researchers to Dalhousie.

5) Regulation of the postdoctoral training position. From our lab manager Katrin Sommerfeld who attended your March 20th meeting in the Kellogg Library, I learned that you made a suggestion that the postdoctoral training process become more regulated or structured. I must admit that I am wary of any further complexities being introduced into postdoctoral research training. The postdoc period is one of the only times in a researcher’s life when he/she can fully devote him/herself to doing research and learning the ‘ropes’ of day to day scientific management without endless interruptions in the form of teaching, meetings, courses, committees, etc. Furthermore, faculty members who supervise postdocs already spend a lot of time in activities supporting the “structured” training of undergrads and graduate students (i.e. teaching graduate courses, attending graduate student presentation courses, thesis supervisory committees, etc.). The training of a postdoc is thankfully free of this structure. The ‘advanced’ level of the training required for postdocs benefits from flexibility and it should be tailored to the individual needs of the trainee. Certainly, offering seminars/courses on professional development for postdocs (such as the one you teach) is a welcome enrichment to the postdoc training experience. However, formalizing the training beyond this is both undesirable and unnecessary. Please keep in mind that although some postdoc supervisors may not be doing a ‘good job’, many of us put a lot of effort into this kind of training; these efforts and abilities should not be ignored. Researchers raise the funds that support the stipends of postdocs and their research activities. It is important that we have not only this responsibility, but also the authority to carry out the training in a way that maximizes mutual benefit to the postdoc and the research program we are managing.

Sincerely yours,

Andrew J. Roger Associate Professor Director, Centre for Comparative Genomics and Evolutionary Bioinformatics Department of Biochemistry and Molecular Biology Dalhousie University Halifax, N.S. B3H 1X5 Tel: 902-494-2620 Fax: 902-494-1355 cc: Dr. Carolyn Watters, Dean of Graduate Studies Dr. Martha Crago, Vice President (Research) Dr. David Byers, Head, Biochemistry & Molecular Biology Dr. Chris McMaster, Assistant Dean, Graduate & Postdoctoral Studies DEPARTMENT OF BIOCHEMISTRY & MOLECULAR BIOLOGY FACULTY OF MEDICINE, SIR CHARLES TUPPER MEDICAL BUILDING HALIFAX, NOVA SCOTIA, CANADA B3H 1X5 PHONE: (902) 494-2480; FAX: (902) 494-1355 WWW.BIOCHEM.DAL.CA

October 27, 2008

Dr. Carolyn Watters, Dean Dr. Sunny Marche, Associate Dean Faculty of Graduate Studies Dalhousie University

Dear Dr. Watters and Dr. Marche,

We are writing to you regarding the new “PDF Policy and Procedures” that the Faculty of Graduate Studies has implemented, partially in response to the changes in the income tax status of postdoctoral fellows. While we are pleased that FGS is taking a proactive role in enhancing the postdoctoral training environment of the university, we are concerned that the new PDF policy was developed with limited initial input from faculty members, who are the primary educators of postdoctoral trainees and who, for the most part, pay their stipends from their research grants.

The change in the Income Tax Act that allows PDFs to claim their stipends as non-taxable fellowship award income is a great opportunity to make postdoctoral training in Canada more attractive to excellent candidates worldwide. Dalhousie’s research community could potentially benefit from this new policy. However, because the FGS PDF policy in its current form does not reflect the diversity of the requirements of postdoctoral fellowships in the different fields of research at Dalhousie (in particular in the life and biomedical sciences), it will have a serious negative impact on our competitiveness in attracting the best PDFs to our university and retaining them.

Our chief concerns with the policy are that: i) it specifies an overly restrictive ‘three year from PhD completion’ eligibility requirement for PDF candidates, ii) the overall length of the academic PDF tenure is far too short, and, iii) the distinction between academic PDFs and research PDFs is artificial and creates an unfavourable ‘two tier’ system. Below we explain in detail the difficulties with these aspects of the PDF policy and the changes necessary to improve it.

1) Eligibility of candidates for postdoctoral fellowships at Dalhousie. The new PDF policy states that: “Individuals who have completed a Ph.D. within three years from the date of application…., are eligible for consideration as an academic PDF or a research PDF…..”

There are several problems with these requirements. First, many excellent candidates for PDFs in our research groups will exceed the 3-year eligibility limit. This is because it is becoming standard in the life/biomedical sciences for PDFs to complete several multi-year postdoctoral stints in different laboratories or industry. This is not simply because PDFs cannot find jobs within the first three years, rather it is because a productive career in competitive biomedical research nowadays often requires that PDFs master a number of different subfields and gain experience in a number of different research environments. Moreover, completing multiple postdoctoral stints is likely to become more and more common as the funding opportunities and competitiveness in inter-disciplinary research increase.

The research environment in the biomedical sciences also reflects this changing reality for postdocs. In the biomedical sciences, professors not only teach, conduct research and become involved in administration, they also typically spend a substantial amount of time and effort in managing their research group. Biomedical research is often accomplished by large teams (often >10 trainees/group) managed by the faculty member. To sustain these activities and equip his/her research facilities the faculty member must also spend a substantial amount of time applying for grant funding from multiple sources. Since the grant award success rates at agencies such as the Canadian Institutes of Health Research (CIHR) have dipped as low as 13%, this means that repeated attempts are usually made before a grant is secured. The training of a PDF in the biomedical research setting includes preparation for leading group projects, learning how to prepare competitive grant applications, and developing mentoring skills through helping in supervision of undergraduates and graduate students involved in the group projects. As a result, it often takes more than one three-year postdoctoral fellowship for an individual to not only carry out their independent research and publish it in reputable journals, but also develop the grantsmanship, supervisory skills and independence sufficient to be able to function as a successful faculty member.

Indeed, current job searches in biomedical departments often ‘pass over’ those with only a few years of postdoctoral experience in favour of individuals with longer and more diverse PDF experiences. To give an example, a minimum requirement of at least two years postdoctoral experience was specified in the advertisement for an entry-level probationary tenure-track position in a recent job search by the Dept. of Biochemistry and Molecular Biology. Several of the excellent candidates who had completed even three years of postdoctoral study were seen by the search committee as too inexperienced to handle the full responsibilities of a biomedical research-intensive faculty position. The top candidate (who was offered and subsequently accepted the position) had a total of six years of postdoctoral experience obtained at a Canadian university. Under the current PDF policy at Dalhousie it would not have been possible for an excellent researcher such as this individual to have completed comparable postdoctoral training at Dalhousie after the first three years of his PDF. Yet this is exactly the type of top-notch young scientist we wish to attract and train as a postdoctoral fellow.

Note that the Dalhousie ‘three years out of PhD policy’ for eligibility is actually more restrictive than the eligibility requirements for postdocs being paid from CIHR operating research grants (the CIHR limit for starting a postdoc is within five years of obtaining a doctoral degree and there is no limit on subsequent duration). Furthermore, other granting agencies and foundations (e.g. the Tula Foundation discussed below) do not have any eligibility limit. Since many other Canadian universities will not institute PDF eligibility requirements (or they will make requirements more in line with the granting council guidelines), they will have an advantage in recruiting the excellent PDFs that are ineligible to complete postdoc fellowships at Dalhousie University under this new policy.

2 Finally, we would like to question the rationale of PDF eligibility limits beyond the straightforward requirement of a doctoral degree. If an individual has a Ph.D. from a reputable institution and seeks postdoctoral training under a faculty researcher at Dalhousie University, and that faculty member is willing, and permitted (under granting agency guidelines) to pay their fellowship stipend, why should FGS impose arbitrary eligibility rules that disqualify the candidate? What purpose do these eligibility rules serve? It seems more appropriate that the faculty member responsible for supervising the postdoc, and funding his/her stipend, should also have the authority to decide if that candidate has the appropriate background for the position of a PDF in his/her research group. Eliminating eligibility rules like these would have the added benefit of saving the time and efforts of the FGS staff currently responsible for reviewing various aspects of the PDF applications to ensure they meet the requirements.

2) The time restriction on academic PDFs and the artificial distinction between academic and research PDFs.

A second, and equally serious problem with the current PDF policy concerns the length of the academic postdoc tenure and the designation of two classes of postdocs. According to the policy, postdoctoral researchers are eligible to be academic postdocs for only three years at Dalhousie. After that time, they must either leave, or their position can be ‘renewed’ but at that point they may only stay on as a research postdoc for a maximum of three more years. Clearly the motivation for erecting these two classes is related to the Canada Revenue Agency’s discussion of postdoc fellowships in the interpretation bulletin, IT75R4, of the Income Tax Act. In parts 11 and 12 of this bulletin a distinction is made regarding the primary purpose of a fellowship for doctoral and postdoctoral candidates. If the “primary purpose of the award is to further the education and training of the recipient in his or her individual capacity…” then the fellowship stipend is an award and is not taxable income. If, on the other hand, the “primary purpose of the award is to carry out research for its own sake….the award is considered to be a research grant….” and the doctoral candidate or postdoc must report his/her stipend as taxable income. Clearly, the former type of trainee coincides with the concept of an ‘academic PDF’ and the latter with a ‘research PDF’ as outlined in the PDF Policy (pg 2). Note, however, that the CRA documentation does not explicitly suggest such a classification be made at the educational institution. Furthermore, CRA’s policy applies equally to the activities of both doctoral and postdoctoral candidates.

Unfortunately, interpreting the CRA regulations is difficult since, in reality, doctoral students and PDFs carry out research both for the purposes of furthering their own education/training and for the sake of advancing research: there is no natural dividing line between these two goals and neither is obviously primary. FGS has clearly decided to deal with this problem with regard to doctoral candidates by classifying them all as ‘academic’. However, for postdocs, the PDF policy instead makes an artificial distinction between ‘academic’ and ‘research’ streams that coincides with a three-year limit for the former before re- classification as the latter. As we have argued above, a three-year limit on postdocs is unreasonable when considering the reality of what many PDFs must learn to become trained for the next stage of their careers in the life and biomedical sciences. Furthermore, the classifications of ‘academic’ and ‘research’ PDFs will be extremely detrimental to a healthy training environment. For example, consider an excellent PDF who, in order to get the most out of her training at Dalhousie (i.e. her research project is by necessity longer term or she needs to learn more skills), has decided to continue her postdoc for a total of 4-5 years. The

3 supervisor also feels this extension is important and wishes to renew the postdoc for years 4-5. Here is the problem. Assuming the stipend is ~$40,000/year, in year 3, the fellowship income the postdoc receives incurs no tax. In years 4 and 5, however, at a time when the postdoc has more training/expertise than when she started, her income becomes taxable and now her take-home pay (after tax) falls to roughly ~$35,000. In effect, the postdoc is doing the same work as before but now, with even more experience under her belt, is effectively making ~$5000 less. This policy is a very poor way to reward this PDF for her excellent work and, in practice, it will be extremely demoralizing. Those PDFs who are supporting families are likely to be even harder hit under these circumstances. Furthermore, if they are working in a lab with academic postdocs, research postdocs become ‘second-class citizens’ whose take-home pay is substantially less than the other PDFs, despite their greater knowledge and experience.

Another undesirable result of the above policy is that supervisors will feel pressured to increase the stipend of the research PDF in years 4+ to compensate for the lost income relative to years 1-3. However, many researchers do not have sufficient grant funds to accommodate this. Those who do stand to lose precious research dollars (~$6000- $7000/year to compensate for the loss) from their grants, research dollars that were not originally designated to be used for this purpose. One might be tempted to suggest that researchers might pay academic postdocs $5000 (or so) less to begin with and then increase the pay to research postdocs to avoid this situation. However, under these circumstances we would lose the competitive edge relative to other Canadian universities that the new tax legislation provides, because our starting postdoc stipend offers would be very low. Furthermore, some granting agencies stipulate minimum PDF stipends limiting how low initial offers can be (e.g. CIHR lower limits on PDF stipends are $36,750 p.a.).

The problems described above can be avoided if, as was decided in the case of doctoral students, FGS were to designate all PDFs as ‘academic postdocs’ whose primary purpose is to advance their education/training and do away with the 3-year length restrictions on academic postdocs. We see no real justification for a limit on postdoc lengths: CRA certainly does not specify anything like this in the agency’s fellowship bulletin and it is far from clear what purposes these limits serve. If one purpose is to prevent unscrupulous exploitation of junior personnel by discouraging their timely application for independent positions, there must be better, case-by-case ways of dealing with this concern (if it is indeed a justified one), possibly through the creation of a postdoc ombudsman or the formation of postdoc unions. It is our position that faculty members responsible for paying and training PDFs are themselves in the best position to decide how long a PDF should last. This is the system that Dalhousie has operated with for years and that has presumably contributed to its ranking by The Scientist as one of the best places in the world for postdoctoral training. We should not try to fix something that is not broken.

If FGS deems that a limit is really needed, then we suggest that it should be minimally restrictive so as to maximize flexibility and enhance Dalhousie’s competitiveness for PDF recruitment relative to other Canadian and American universities. A maximal length of eight years would be reasonable and would avoid over-burdening FGS staff with repeated renewal exception requests. Furthermore, special attention should be paid to non-Canadian postdocs (who make up a large fraction of the life science/biomedical PDFs at Dalhousie) who must obtain a special work permit and cannot be designated as research associate employees.

4 Finally, we would like to explain why we feel this issue is so important. As members of the newly minted interdisciplinary Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB, see http://www.cgeb.dal.ca), we have had the good fortune to receive a sizable grant (>$3,000,000 over eight years) from the Tula Foundation (see attached letter from Dr. Eric Peterson, President of the Tula Foundation). More than half of these monies are dedicated to postdoctoral fellowships, each of which may last as long as five years, with the eligibility of candidates to be entirely decided at the discretion of CGEB researchers. This grant was offered to the CGEB group in recognition of the internationally renowned accomplishments of our research teams over the past decades. The grant is meant to strengthen our ability to attract and train world-class postdoctoral fellows and Ph.D. students. The FGS PDF policy was implemented after these monies were awarded and we feel that the issues identified and discussed above could have a serious negative impact on our ability to achieve our research and training goals. It is especially problematic for us because the fields of genomics and bioinformatics are explicitly interdisciplinary and often require PDFs from diverse career paths and backgrounds, and who need extra time as postdocs to master several fields. Importantly, we are concerned that the overly restrictive PDF policy may hamper our chances of receiving additional monies from the Tula Foundation in the future.

To summarize, all postdoctoral trainees and faculty members at Dalhousie University would be best served by a PDF policy that is flexible with respect to eligibility requirements, does not unduly restrict the length of postdoctoral training periods, enriches the PDF training experience, and maximizes a PDF’s chances to succeed in his/her chosen career. We ask that you carefully consider our arguments above and act to modify the FGS PDF policy along these lines.

Sincerely,

Andrew J. Roger Associate Professor Director, Centre for Comparative Genomics and Evolutionary Bioinformatics Department of Biochemistry and Molecular Biology

W. Ford Doolittle Professor Emeritus Department of Biochemistry and Molecular Biology

Michael W. Gray Professor Department of Biochemistry and Molecular Biology

5

John M. Archibald Associate Professor Department of Biochemistry and Molecular Biology

Alastair G. B. Simpson Associate Professor Department of Biology

Joseph Bielawski Associate Professor Department of Biology/Department of Mathematics and Statistics

Edward Susko Professor Department of Mathematics and Statistics

Christian Blouin Associate Professor Faculty of Computer Science

Robert Beiko Assistant Professor Faculty of Computer Science cc: Dr. Martha Crago, Vice President (Research) Dr. Alan Shaver, Vice President (Academic & Provost) Dr. Christopher McMaster

Encl:

6