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ADVANCED PHYLOGENETIC WORKSHOPS IN 2017

Workshops focussing on training researchers and students in phylogenetic theory and the application of phylogenetic methods in taxonomy, systematics and evolutionary studies have been presented biannually at FABI since 2004. Two advanced phylogenetic workshops are planned for this year. A major objective for the workshops is to provide hands on experience in the use of databases available on the world-wide-web and the different software, both commercial and freeware, currently available for evolutionary biologists. The workshops cater for researchers that have a basic to advanced background in the field.

Dates:

  • Advanced Phylogenetics Workshop 1: 29 May to 2 June 2017
  • Advanced Phylogenetics Workshop 2: 6 to 10 November 2017

Click here for the Registration form

Outline:

The following is a broad outline of the topics that will be treated during the workshop:

  • File formats
  • Sequence alignments
  • Dealing with gaps
  • Everything about trees (phylogenetic)
  • Testing for partition homogeneity
  • Evolutionary models
  • Parsimony
  • Maximum likelihood
  • Bayesian phylogenetic inferences
  • Other interesting topics (e.g. molecular dating and hypothesis testing)

Software:

Experience will be gained in using the following software*:

  • BioEdit
  • MAFFT
  • PAUP*
  • jModelTest
  • RAXML and PHYML
  • MrBayes
  • Tracer
  • TreeView
  • BEAST

*Other software that are of value to the workshop will be demonstrated if time permits.

Prerequisite for attending the workshop:

  • Ability to operate in the DOS command line environment
  • Basic knowledge in phylogenetic analyses. Beginners workshops are available for researchers with no or limited background in phylogenetics. Please follow this link to get more information about introductory workshops.

Payment and registration:

The cost for this workshop is R 4400-00 per person and should be paid before the workshop commences.

Workshop 1
Closing date for registration of attendees outside of FABI: 15 April 2017
Closing date for payment: 30 April 2017**

Workshop 2
Closing date for registration of attendees outside of FABI: 1 October 2017
Closing date for payment: 15 October 2017**

**If no payment is received by the specified date, the applicant will lose their reservation.

Cost of the workshop includes workshop material, light lunches each day and coffee/tea in the morning. Unfortunately, we can accommodate only 15 people per workshop.

For more information please contact Dr. Martin Coetzee (This email address is being protected from spambots. You need JavaScript enabled to view it.).

Centre of Excellence in Tree Health Biotechnology (CTHB)
Forestry and Agricultural Biotechnology Institute (FABI)


New Publications

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Human ZR, Crous CJ, Roets F, Venter SN, Wingfield MJ, de Beer ZW. (2017) Biodiversity and ecology of flower-associated actinomycetes in different flowering stages of Protea repens. Antonie van Leeuwenhoek 10.1007/s10482-017-0942-3
Wingfield BD. (2017) The peer review system has flaws. But it’s still a barrier to bad science. The Conversation http://bit.ly/2holsgS
McTaggart AR, Beasley DR, Wingfield MJ, Wood AR, Pretorius ZA, Drenth A, Shivas RG, Roux J. (2017) A dynamic, web-based resource to identify rust fungi (Pucciniales) in southern Africa. MycoKeys 26:77-83. 10.3897/mycokeys.26.14602
De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA. (2017) Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii. Frontiers in Microbiology 8(1755) 10.3389/fmicb.2017.01755
Jami F, Wingfield MJ, Gryzenhout M, Slippers B. (2017) Diversity of tree-infecting Botryosphaeriales on native and non-native trees in South Africa and Namibia. Australasian Plant Pathology 10.1007/s13313-017-0516-x
Stewart JE, Ross-Davis AL, Graҫa RN, Alfenas AC, Peever TL, Hanna JW, Uchida JY, Hauff RD, Kadooka CY, Kim MS, Cannon PG, Namba S, Simeto S, Pérez CA, Rayamajhi MB, Lodge DJ, Arguedas M, Medel-Ortiz R, López-Ramirez MA, Tennant P, Glen M, Machado PS, McTaggart AR, Carnegie AJ, Klopfenstein NB, Cleary M. (2017) Genetic diversity of the myrtle rust pathogen (Austropuccinia psidii) in the Americas and Hawaii: Global implications for invasive threat assessments. Forest Pathology 10.1111/efp.12378
Roodt D, Lohaus R, Sterck L, Swanepoel RL, Van de Peer Y, Mizrachi E. (2017) Evidence for an ancient whole genome duplication in the cycad lineage. PLOS ONE 12(9):e0184454. 10.1371/journal.pone.0184454
Liebhold AM, Brockerhoff EG, Kalisz S, Nuñez MA, Wardle DA, Wingfield MJ. (2017) Biological invasions in forest ecosystems. Biological Invasions 10.1007/s10530-017-1458-5
Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. (2017) A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Scientific Reports 7:9747. 10.1038/s41598-017-09617-z
McTaggart AR, Shuey LS, Granados GM, du Plessis E, Fraser S, Barnes I, Naidoo S, Wingfield MJ, Roux J. (2017) Evidence that Austropuccinia psidii may complete its sexual life cycle on Myrtaceae. Plant Pathology 10.1111/ppa.12763
Wondafrash M, Slippers B, Garnas J, Hurley BP. (2017) Parasitoid assemblage associated with a North American pine weevil in South Africa. Agricultural and Forest Entomology 10.1111/afe.12246
Nzuki I, Katari MS, Bredeson JV, Masumba E, Kapinga F, Salum K, Mkamilo GS, Shah T, Lyons JB, Rokhsar DS, Rounsley S, Myburg AA, Ferguson ME. (2017) QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii. Frontiers in Plant Science 8(1168) 10.3389/fpls.2017.01168
Mostert D, Molina AB, Daniells J, Fourie G, Hermanto C, Chao C-P, Fabregar E, Sinohin VG, Hossain MDS, Masdek N, Visarto P, Rajapakse C, Thanh DT, Thangavelu R, Li C, Yi G, Wei Y, Mostert L, Viljoen A. (2017) The distribution and host range of the banana Fusarium wilt fungus, Fusarium oxysporum f. sp. cubense, in Asia. PLoS ONE 12(7):24. 10.1371/journal.pone.0181630
Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME. (2017) QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert. Theoretical and Applied Genetics 10.1007/s00122-017-2943-z
Fraser S, McTaggart AR, Wingfield MJ, Roux J. (2017) Effect of temperature, leaf wetness and the developmental stage of host tissue on infection of Acacia mearnsii by Uromycladium acaciae (Pucciniales). Australasian Plant Pathology 10.1007/s13313-017-0503-2
Jankowiak R, Strzałka B, Bilański P, Linnakoski R, Aas T, Solheim H, Groszek M, De Beer ZW. (2017) Two new Leptographium spp. reveal an emerging complex of hardwood-infecting species in the Ophiostomatales. Antonie van Leeuwenhoek 10.1007/s10482-017-0905-8
Ozturk KI, Chettri P, Dupont P-Y, Barnes I, McDougal RL, Moore GG, Sim A, Bradshaw RE. (2017) Evolution of polyketide synthesis in a Dothideomycete forest pathogen. Fungal Genetics and Biology 10.1016/j.fgb.2017.07.001
Wilken PM, Steenkamp ET, Wingfield MJ, De Beer ZW, Wingfield BD. (2017) Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered. Fungal Biology Reviews 31:199-211. 10.1016/j.fbr.2017.05.003
Bush SJ, Dittrich-Schröder D, Neser S, Gevers C, Baffoe KO, Slippers B, Hurley BP. (2017) First record of Quadristichus mendeli, a parasitoid of Leptocybe invasa, in South Africa. Southern Forests 10.2989/20702620.2017.1318347
Beukes CW, Palmer M, Manyaka P, Chan W-Y, Avontuur JR, Van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. (2017) Genome data provides high support for generic boundaries in Burkholderia sensu lato. Frontiers in Microbiology 8 10.3389/fmicb.2017.01154
Hurley BP, Slippers B, Sathyapala S, Wingfield MJ. (2017) Challenges to planted forest health in developing economies. Biological Invasions 10.1007/s10530-017-1488-z
Bouwer MC, Slippers B, Wingfield MJ, Allison JD, Rohwer ER. (2017) Optimization of Pheromone Traps for Coryphodema tristis (Lepidoptera: Cossidae) . Journal of Economic Entomology 10.1093/jee/tox171
du Plessis E, McTaggart AR, Granados GM, Wingfield MJ, Roux J, Pegg GS, Makinson J, Purcell M, Ali M. (2017) First report of myrtle rust caused by Austropuccinia psidi on Rhodomyrtus tomentosa (Myrtaceae) from Singapore. Plant Disease 10.1094/PDIS-04-17-0530-PDN
Hussey SG, Loots MT, van der Merwe K, Mizrachi E, Myburg AA. (2017) Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. Scientific Reports 7:3370. 10.1038/s41598-017-03665-1
Wingfield MJ, Barnes I, De Beer ZW, Roux J, Wingfield BD, Taerum SJ. (2017) Novel associations between ophiostomatoid fungi, insects and tree hosts: current status—future prospects. Biological Invasions 10.1007/s10530-017-1468-3
Vivas M, Kemler M, Mphahlele MM, Wingfield MJ, Slippers B. (2017) Maternal effects on phenotype, resistance and the structuring of fungal communities in Eucalyptus grandis. Environmental and Experimental Botany 140:120-127. 10.1016/j.envexpbot.2017.06.002
Miller A, Cai L, Crous PW, De Beer ZW, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, Lumbsch HT, May TW, Rossman AY, Schoch CL, Seifert KA. (2017) Mycologists' committees strongly support changes to the governance of fungal nomenclature. IMA Fungus 8(1):(9)-(11). PDF
Linnakoski R, Forbes KM, Wingfield MJ, Pulkkinen P, Asiegbu FO. (2017) Testing projected climate change conditions on the Endoconidiophora polonica / Norway spruce pathosystem shows fungal strain specific effects. Frontiers in Plant Science 8:883. 10.3389/fpls.2017.00883 PDF
Crous CJ, Burgess TI, Le Roux JJ, Richardson DM, Slippers B, Wingfield MJ. (2017) Ecological disequilibrium drives insect pest and pathogen accumulation in non-native trees. AoB Plants 9:plw081. 10.1093/aobpla/plw081
Mbenoun M, Garnas JR, Wingfield MJ, Begoude Boyogueno AD, Roux J. (2017) Metacommunity analyses of Ceratocystidaceae fungi across heterogeneous African savanna landscapes. Fungal Ecology 28:76-85. 10.1016/j.funeco.2016.09.007