Training

R Geeta, iBiologist, Chennai

Phylogenetic Biology

A growing interest in biology worldwide is often focused on the areas of genomics and biodiversity. These areas have important applied aspects: for instance, the discovery and development of new pharmaceuticals, and biological conservation. The areas receive much attention in India, where increasing numbers of bright, young biologists are making their mark in rapidly developing fields such as biotechnology. However, an important component phylogenetics (establishing and understanding the relationships between species) often is missing from this work. The need for such ‘tree-thinking’ in biology is widely recognized and its lack is comparable with a lack of statistics in modern biology.

Phylogenetics is essential for interpreting large amounts of information from different species, such as found in databases of DNA sequences (e.g., GenBank) and biodiversity (e.g., GBIF). It is also critical for understanding the exceptionally rich and diversified flora and fauna of India, as well as in the rest of the world. Millions of years ago, India broke away from Africa, and later became connected to Asia. Because of this, India’s biodiversity can only be understood in relation to organisms from Africa, Eurasia, China and Malayasia. Phylogenetic methods are critically important for a good understanding of the past and, therefore, planning for the future and conservation of biodiversity.

However, the paucity of expertise makes this a difficult task at present. The problem is not due to a lack of awareness of the importance of phylogenetics, but rather limited exposure to the concepts and methods used in this area of biology. While some research groups have developed skills in the area, conceptual foundations may need to be strengthened. These ideas are hardly taught at all in the universities, colleges, or schools. Teachers are a key element for spreading the ideas and skills related to phylogenetics; however most teachers have never had a course on the topic, and their immediate experience does not put them in contact with practitioners in the field. Direct exposure is essential for teachers to be effective communicators of phylogenetic ideas and skills. Teaching teachers is the best strategy to rapidly propagate ‘tree-thinking’ among biologists.

I have participated in introductory workshops across India (see list below), either by myself or in collaboration with others. The objective of these workshops is to familiarize participants with the theory and practice of phylogenetics. Lecture and practical hands-on sessions at the computer are used to introduce basic phylogenetic concepts and methods that should allow teacher-researchers to read the recent literature and to be able to effectively use the enormous resources available on the internet today.

 Workshop on Phylogenetic Biology

Exemplary schedule

Day	10:00-11:00 Lecture	11:30-13:00 Practicals	14:00-15:30 Lecture	16:00-17:00 Practicals
1	Introduction: Trees and Tree-thinking	Reading, interpreting, manipulating trees: Manual, Mesquite	Building Trees: Maximum Parsimony (MP)	MP analysis: Manual, PAUP
2	Sequence Analysis, BLAST, Alignment: NCBI, MEGA	Pairwise Distances, Molecular Evolution, Models	Distance, Neighbour Joining (NJ), MEGA, PAUP	Maximum Likelihood (ML): MEGA, PAUP
3	Using Trees: Applications	Character  optimization, interpretation	Mesquite

Resource Person at Workshops

• “Introduction to Evolutionary Biology and Phylogenetic Methods.” Workshop for teachers and researchers, Dr. M.G.R. Educational And Research Institute, Chennai, 23-25 April, 2019
• “Phylogenetics.” SERB Workshop in Evolutionary Biology, JNCASR, Bengaluru, 15-16 March, 2019.
• “Integrative Taxonomy: Recent Developments.” Departments of Botany and Environmental Sciences, organised with Prof. Radhey Sharma, funded by AICOPTAX-MOEFF&CC, 14-23 November, 2017.
• “Trees and Tree-Thinking,” National Workshop on “Bioinformatics and Data Mining,” National Institute of Plant Genetic Resources (NIPGR), New Delhi, 22nd March, 2017. 
• “Phylogenetic Biology: Trees in Ecology and Conservation.” Young Ecologists Talk and Interact (YETI), Amity University, Noida, UP, 17 January, 2016.
• “Phylogenetic Biology.” Workshop for students and researchers in Biology, Department of Botany, Sikkim University, Gangtok, 23-25 September, 2015.
• “Modern Trends in Molecular Phylogeny.” (With Ullasa Kodandaramaiah, IISER, Thiruvananthapuram). National workshop, sponsored by Science and Engineering Research Board and Kerala State Council for Science, Technology and Environment, at the Department of Botany, University of Calicut, Calicut. 15-20 March, 2015.
• “Phylogenetic Biology.” Workshop for Researchers in Palaeobotany, Birbal Sahni Institute of Palaeobotany, Lucknow. 2-3 March, 2015.
• “Phylogenetic Biology: Trees and Tree-thinking.” Workshop for Life Science Educators, Homi Bhabha Centre for Science Education, TIFR, Mumbai. 5 January, 2015.
• “Molecular Phylogeny Workshop.” Department of Genetic Engineering, SRM University, Chennai. 18-19 July, 2014.
• “Phylogenetic Systematics: Principles and Practice.” Workshop for Biology Researchers, Goa University, Taleigao, Goa. 24-25 Aug, 2013.
• “Phylogenetic Systematics: Principles and Practice.” Workshop for Biology Researchers, Department of Botany, Shivaji University, Kolhapur. 8-10 November, 2012.
• “Phylogenetics: Principles and Practice.” Workshop for Life Sciences Faculty, University of Delhi: ILLL, Department of Botany, DBT Star College Scheme (SGTB Khalsa College)” 27-28 August, 2011.
• “Phylogenetic Biology.” A course for College Teachers and Research Scholars, sponsored by the Indian Academy of Sciences and Evolution Unit, Mysore University, Mysore. July 10-22, 2006. (With John Wiens, SUNYSB, Stony Brook, NY).

Lectures at Symposia, Courses and Workshops

• “Phylogenetic Trees and Tree-thinking.” DST-SERB sponsord workshop on “Molecular Phylogenetics,” Department of Plant Biology and Biotechnology, Loyola College, Chennai, 18-19 February, 2020.
• “Phylogenetic Biology – What, Why and How?” Workshop on “Molecular Taxonomy”, ILS Bhuvaneshwar, 12 March, 2019.
• “Phylogenetic Biology or, So Now you have a Phylogenetic Tree – What Next?” Symposium, Indian Science Congress, University of Mumbai, Mumbai. 6 January 2015.
• “An introduction to Phylogenetic Reconstruction.” Training Workshop on Evolutionary Approaches to Biodiversity Science, ATBC 2013 Meeting, Aceh, Indonesia. 16-17 March 2013.
• “Phylogenetic Methods.” Workshop on Evolutionary Applications to Biodiversity Science, ATBC 2012 Meeting, Bonito, Brasil, 16-18 June 2012.
• “Species Complexes and Phylogenetic Trees.” National Workshop on Systematcs and Species Complexes, CEMDE, University of Delhi, 6 February, 2012.
• “Trees and Tree-thinking.” Bioinformatics Workshop, Zakir Hussain College, University of Delhi, Delhi, 19 January, 2012.
• “Trees and Tree-thinking.” Bioinformatics Workshop, Ramjas College, University of Delhi, Delhi, 27 September, 2011.
• “Phylogenetic Systematics and Evolutionary Biology.” National Workshop on Taxonomy and Evolution, CEMDE, University of Delhi, 15 March, 2011.
• “Phylogenetic Biology.” National Workshop on Genomics and Biodiversity, ADNAT and CCMB, Hyderabad, Hyderabad, 7-8 March, 2011.
• “Phylogenetic Biology: Making Sense of Biology in the Light of Evolution.” National Workshop on “Use of Bioinformatics in Agriculture/Plant Sciences, NIPGR, New Delhi, India. March, 2010.
• “Phylogenetic Systematics.” National Workshop on Taxonomy, CEMDE, University of Delhi, Delhi, India. March, 2010.
• “Molecular Systematics.” National Consultation on “Advancing the Science of Taxonomy in India for Biodiversity Conservation” ATREE, Bangalore, India. 23 February, 2010.
• “Phylogenetics, Phylogenetic Diversity and Conservation Decisions.” National Workshop on Taxonomy, CEMDE, University of Delhi, Delhi, India. 6 January 2010.
• “Phylogenetic Diversity and Conservation Decisions.” Consultation workshop on Conservation Planning for Rhododendrons of Eastern Himalaya, Winrock International India and Whitley Fund for Nature, UK, at TERI, Delhi. 28 October 2009.
• “Phylogenetic Biology.” National Workshop on Molecular Systematics, Department of Botany, University of Delhi, Delhi, India, 8 October 2009.
• “Evolutionary Biology: The study of Biodiversity.” Course for undergraduate students, Vivekananda College, Chennai. 2007.