WORKSHOP: Phylogenetic Biology
Professor R Geeta, Botany Department, Delhi University, Delhi 110007
Across the world, there is a growing interest in biology that is often focused on the areas of genomics and
biodiversity. These areas have important applied aspects: for instance, in 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) is missing from this work. The need for such ‘tree-thinking’ in biology is
widely recognized, and its lack is comparable with an absence 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, http://www.ncbi.nlm.nih.gov/) and biodiversity (e.g.,
GBIF, http://www.gbif.org/). It is also critical for understanding the exceptionally rich and diversified
flora and fauna of India. 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. Conceptual foundations need to be built up and strengthened, as
these areas are hardly taught in the universities, colleges, or schools.
The workshop being proposed would consist of lecture and practical sessions (computer lab.) to familiarize
participants with the theory and practice of phylogenetics. The aim would be to introduce the basic ideas
and introduce some sophisticated methods of analysis to allow students and researchers to be able to
effectively use the enormous resources available on the internet today and to access recent literature.
Tentative Programme
(L) Lecture; (P) Practical
Day
10:00-11:00
11:30-13:00
14:00-15:30
16:00-17:00
1
Introduction:
Trees and
Tree-thinking
(L)
Reading, interpreting and
manipulating tree
topology [Manual,
Mesquite] (P)
Building Trees:
Maximum Parsimony
(L)
Maximum Parsimony,
MP (P):
--Manual
--PAUP
2
Using Trees (L)
Comparative Methods
(L)
Molecular Evolution,
Models (L)
3
Molecular data
(L)
Mesquite: Character
optimization,
interpretation (P)
MEGA: GenBank, BLAST,
Alignment (P)
Maximum Likelihood
(ML) and Bayesian
methods (L)
Neighbour Joining,
ML Analysis (P)
--MEGA, PAUP