Biodiversity Informatics S. Sreekumar, Safeer PM, Biju CK, Raveendran M,

1. TBGRI Biodiversity Informatics S. Sreekumar, Safeer PM, Biju CK, Raveendran M, Parvathy Sankar & Krishnan PN Bioinformatics Centre, Tropical Botanic Garden & Research Institute Palode, Thiruvananthapuram E-mail:tbgri@sancharnet.in Web site : www.tbgri.orgwww.bioinfotbgri.org Bioinformatics Centre TBGRI

2. TBGRI What is Biodiversity Biological diversity means the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part. This include diversity within species, between species and ecosystems. Bioinformatics Centre TBGRI

3. Elements of Biodiversity TBGRI Bioinformatics Centre TBGRI

4. TBGRI Types of Biodiversity Alpha diversity : The total number of species coexisting in a region Beta diversity : As habitats change along climatic and topographic gradients, new species turn over takes place Gamma diversity : High species turn-over rate with distances between sites of similar habitats Bioinformatics Centre TBGRI

5. TBGRI Bioinformatics Centre TBGRI

6. Plant diversity in India and the world TBGRI Bioinformatics Centre TBGRI

7. Animal diversity in India and the World TBGRI Bioinformatics Centre TBGRI

8. TBGRI • What are microorganisms • Organisms microscopic in dimensions, includes Viruses, Bacteria, Algae, Fungi and Protozoa • United States patent office includes plant and animal cells besides Viruses, Bacteria, Fungi and Protozoa • Microbes are patentable as per WTO and Indian patent laws Bioinformatics Centre TBGRI

9. TBGRI Microorganisms in the world Bioinformatics Centre TBGRI

10. TBGRI Microorganisms described in India Bioinformatics Centre TBGRI

11. TBGRI • Biodiversity issues and profiles • Identifications • Quantifications • Distributions • Endemism • Hotspots and Warm spots Bioinformatics Centre TBGRI

12. TBGRI • What are ‘Hotspots’ • Areas having rich endemism and are facing extreme threat perception • Hotspot areas occupy about 8% of world geographical area but hold 46% of total world species • Includes major tropical forests, relict temperate mediterranean ecosystems Bioinformatics Centre TBGRI

13. TBGRI • Hotspots versus agrobiodiversity • Hotspot centres do not include major and Vavilovian centres of origin and do not encompass major agrobiodiversity ecosystems of the world. • As a paradigm ‘Hotspot’ concept helps conservation of endemic and threatened tropical ecosystems and does not protect agrobiodiversity • The driving force for the evolution and domestication of wild species took place in the deforested woodlands and grasslands through human intervention and environmental determinism Bioinformatics Centre TBGRI

14. Biodiversity Hotspots TBGRI Bioinformatics Centre TBGRI

15. Biodiversity Hotspots TBGRI Total endemic species 124,035 i.e., 46% of world species (270,000) Bioinformatics Centre TBGRI

16. TBGRI • What are ‘Warm spots’ • Areas holding vast genetic resources, predomesticates, agro-pastural woodlands and grasslands which are modified or co-evolved with man’s determinism and environmental stresses. • These warm spot areas are in or adjacent to the cradles of human civilisations. Bioinformatics Centre TBGRI

17. TBGRI India is one of the twelve mega diversity countries in the world In India species richness is often accompanied by enormous genetic diversity found within individual species. This makes India one of the Vavilovian Centres of diversity and origin of about 167 crop plants and the primary or secondary centres of domestication of a few animals. Bioinformatics Centre TBGRI

18. TBGRI Ecosystem wise, India has 42 vegetation types, 16 major forest types, 10 biogeographical zones and 25 hot spots of endemic centres Bioinformatics Centre TBGRI

19. TBGRI In India - about 5725 endemic taxa of angiosperm (33.5% of Indian flora) Hot spots of endemic species in India 1. Andaman group of islands 2. Nicobar group of islands 3. Agasthyamala hills 4. Anamala - high ranges 5. Palni hills 6. Nilgiris-Silent Valley-Wyanad-Kodagu 7. Shimoga-Kanara 8. Mahabaleshwar-Khandala Ranges 9. Konkan -Raigad 10. Marathwada-Satpura 11. Torupati-Cuddappa-Nallamalai hills 12. Vizagapatanam-Ganjam-Jeypore hills 13. Southern Deccan (leeward side) 14. Chotanagpur Plateau 15. Kathiawar-Kutch 16. Rajasthan-Aravalli hills 17. Khasia-Jaintia hills 18. Patkoi-Manipur-Lushai hills 19. Assam 20. Arunachal Pradesh Himalaya 21. Sikkim Himalayas 22. Garhwal-Kumaon Himalaya 23. Lahul-Himachal Pradesh Himalaya 24. Kashmir-Ladak Himalaya 25. Nepal Himalaya Bioinformatics Centre TBGRI

20. TBGRI • Hottest of hot spots in India • Eastern Himalayas • Western Ghats Bioinformatics Centre TBGRI

21. TBGRI Western Ghats Lying along the west coast of Peninsular India in the north-south direction from the mouth of Tapti river in Gujarat to Kanyakumari in Tamil Nadu. It forms a continuous series of hills except 30 km wide Pallakkad gap, which separate the Nilgiri hills from Anamali Geographic position - 8o 20’ – 20o 40’ N Latitude 73o – 77o E Longitude Length - 1600 km Area - 1,00,000 km2 Altitude - 150 – 2695 m Rain fall - 1000 – 7000 mm Temperature - 5 – 10 oC to 25 – 30oC Bioinformatics Centre TBGRI

22. TBGRI Western Ghats – Peaks Kalsubai - 1646 m Banasuram - 2060 m Vavulmala - 2339 m Doddabetta - 2637 m Devarmala - 1922 m Anamudi - 2695 m Agasthyamala - 1868 m Bioinformatics Centre TBGRI

23. Southern tropical thorn forest - 200 – 300 m Southern tropical dry deciduous forest - 200 – 500 m Grasslands of lower altitudes - 200 – 500 m Southern tropical moist deciduous forest - 300 – 700 m Tropical semi-evergreen forest - 500 – 800 m Southern tropical wet-evergreen forest - 800 – 1500 m Subtropical montane forest - above 1500 m Grasslands of high altitudes - above 1500 m Western Ghats – Vegetation types TBGRI Bioinformatics Centre TBGRI

24. Western Ghats – Floristic diversity TBGRI • Angiosperms – 4000 sp. • Gymnosperms – 4 sp. • Pteridophytes – 350 sp. • Bryophytes – 400 sp. • Lichens – 550 sp. • Algae – 400 sp. • Fungi – 5500 sp. Bioinformatics Centre TBGRI

25. TBGRI • BIODIVERSITY AND ITS BENEFITS • Agriculture • Functioning ecosystem • Economic value- extractable products, fuels, medicines, materials for shelter, food and energy • Compounds, genes & species for industry • Ecosystems- climate regulation, hydrological and chemical cycles in soils • Recreation- social, ethical, spiritual, cultural and economic goods and services Bioinformatics Centre TBGRI

26. Why rich biodiversity in India? TBGRI • Strategic position having connection with adjacent floristic regions • Vast stretch of geographic area of 329 m ha; 7500 km long coast line. • Diverse habitats – dry deserts, cold deserts, al pine, temperate, tropical habitats, wetland areas (4.1 million ha.), mangroves. • Diverse ecological conditions (High rainfall area, coldest place on earth etc.). Altitude varying from sea level to the highest mountain ranges of the world. • Gondawana connection. • Himalaya as an active speciation zone. • 12 biogeographic regions representing 3 basic biomes and 2 natural realms as identified by Udvardy (1975). Bioinformatics Centre TBGRI

27. TBGRI Biodiversity use value Bioinformatics Centre TBGRI

28. TBGRI • Increase in the biodiversity from the appearance of the first organism • The increase has not been continuous • Present day biodiversity stands at an estimated 13.5 million species with only 1.75 million of these currently described • The present extent of biodiversity is contributed by only a relatively few groups of organisms • Human kind has been, and continues, to be, instrumental in the erosion of biodiversity • The biodiversity crisis may be current rather than imminent • Erosion of biodiversity varies from region to region Bioinformatics Centre TBGRI

29. TBGRI • Factors affecting Biodiversity – Direct / immediate causes • Exploitation of wild living organisms • Expansion of agriculture, forest and aquaculture • Habitat loss and fragmentation • Species introductions • Pollution of soil, water and atmosphere • Global climatic change Bioinformatics Centre TBGRI

30. TBGRI • Factors affecting Biodiversity – Indirect cause • Growth of human population • Human social organisation • Unscrupulous natural resource consumption • Global trade culture • Lack of strategy to value the environment • Inequity in ownership, management & flow of benefits Bioinformatics Centre TBGRI

31. TBGRI • Current global environmental trends • Unsustainable use of renewable resources • Increasing greenhouse gas emissions • Reduction in natural areas and biodiversity • Increasing use of chemicals • Escalating use of energy • Unplanned urbanization • Disruption of global biogeochemical cycles • (UNEP 1997) Bioinformatics Centre TBGRI

32. TBGRI • International efforts • Biodiversity Conventions, Trade related intellectual property rights (TRIPS) and General agreement on tariffs and trade(GATT)-give guidelines and regulations for biological resource use. Bioinformatics Centre TBGRI

33. TBGRI • Biodiversity Information management - Issues • Biodiversity information is very complex, voluminous and rapidly proliferating. • The biodiversity data can be categorised in to different types such as molecular sequences, gene diversity, individuals, species, higher taxa, population, habitats, ecosystems, biomes, etc. • Management of complex and voluminous data of biodiversity is very difficult. • Biodiversity data are scattered and not organised for further studies. • At present it is very difficult to get a comprehensive picture of the genetic wealth of our nation. • Application of Bioinformatics tools is the best solution to the above problems. Bioinformatics Centre TBGRI

34. TBGRI Bioinformatics ? Medicine Biology Bioinformatics Maths + Physics + Statistics Computer + Information technology Bioinformatics is an emerging field of science Bioinformatics evolved from the convergence of Biology, Computer science, Information technology, Mathematics, Physics, Statistics and Medicine. Bioinformatics Centre TBGRI

35. TBGRI Bioinformatics uses computational algorithms for database creation, data management, data warehousing, data mining and global communication networks. To understand the links between pieces of information from research areas such as molecular biology, structural biochemistry, enzymology, cell biology and physiology, bioinformatics uses computational power to catalog, organise and structure these pieces into biologically meaningful entities. These “entities” are reflection of the cellular organisation of life and its common denominator – that all life evolved from a common ancestral form. Bioinformatics Centre TBGRI

36. TBGRI Bioinformatics Definition ? Bioinformatics is an interdisciplinary field, therefore this newly emerging discipline has variously defined by different authors. “Bioinformatics is the design and development of computer based technology that support life sciences” Bioinformatics definition – Oxford English Dictionary (Molecular) bio –informatics: bioinformatics is conceptualising biology in terms of molecules (in the sense of physical chemistry) and applying “informatics techniques” (derived from disciplines such as applied maths, computer science and statistics) to understand and organise the information associated with these molecules, on a large scale. In short, bioinformatics is a management information system for molecular biology and has many practical applications. Bioinformatics Centre TBGRI

37. TBGRI • Principles of Bioinformatics • The data produced by the thousands of research teams all over the world are collected and organised in databases specialised for particular subjects. Well known e.g., GDB, SWISS-PORT, Genebank and PDB. • Analyse the collected data by using computational tools/techniques • Development of appropriate computational software/tools for programming and analysing the biological data. Bioinformatics Centre TBGRI

38. TBGRI Sub-disciplines within Bioinformatics The development of new algorithms and statistics with which to assess relationships among members of large data sets. The analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures The development and implementation of tools that enable efficient access and management of different types of information Bioinformatics Centre TBGRI

39. TBGRI Dr. Margaret Oakley Dayhoff (1925-1983) was a pioneer in the use of computers in chemistry and biology, beginning with her Ph. D thesis project in 1948.  Her work was multi-disciplinary, and used her knowledge of chemistry, mathematics, biology and computer science to develop an entirely new field, the Bioinformatics.  She is credited today as a founder of the field of Bioinformatics.  Dr. Dayhoff was the first woman in the field of Bioinformatics.  Bioinformatics Centre TBGRI

40. Applications of Bioinformatics TBGRI Bioinformatics Centre TBGRI

41. Schematic outlining how scientists can use bioinformatics to aid rational drug discovery TBGRI • MLH1 (human gene encoding a mismatch repair protein (mmr)) on short arm of chromosome 3. • Through linkage analysis and its similarity to mmr genes in mice, the gene has been implicated in nonpolyposis colorectal cancer. • from nucleotide sequence, the amino acid sequence of the encoded protein can be determined using translation software. • Sequence search techniques used to find homologues in model organisms, and based on sequence similarity, it is possible to model the structure of the human protein on experimentally characterised structures. • Docking algorithms design molecules that could bind the model structure, leading for biochemical assays to test their biological activity on the actual protein. Bioinformatics Centre TBGRI

42. TBGRI Bioinformatics Centre TBGRI

43. TBGRI Bioinformatics Centre TBGRI

44. TBGRI • The important applications of bioinformatics in biodiversity are: • The complex and voluminous data of biodiversity can be digitised for easy accession, analysis and interpretation. • It makes easy survey, documentation and measurement of biodiversity data. • Based on the available data, future biodiversity of a particular area can be predicted and model can be formulated by computational methods, thereby appropriate measures can be taken for its conservation and sustainable utilisation. • It helps to predict species invasions using ecological niche modeling. • The electronic information may serve as the raw material for augmenting future developments in all areas of biology. • The digital databases can easily provide the current status of the biodiversity of a particular area. Bioinformatics Centre TBGRI

45. TBGRI • The biodiversity extinction rate can be easily documented and theoretical studies and modeling can be formulated for its conservation on priority basis. • The computational analysis makes easy understanding of the phylogenetic relationship among the species/individuals. • Through internet biodiversity databases can be linked together and the information can be shared. • The researchers can easily identify the priority materials for their studies. • The potential indigenous material can be easily identified for biotechnological intervention. Bioinformatics Centre TBGRI

46. TBGRI Bioinformatics resources on the Web Bioinformatics Centre TBGRI

47. TBGRI • Recently several web sites providing biodiversity information • Biodiversity databases in the web can be broadly classified into the following groups • Global databases • Geographical, regional and national databases • Databases for specific taxonomic group • Government, scientific and advocacy organisations promoting biodiversity study • Other resources. Bioinformatics Centre TBGRI

48. Global Databases SPECIES 2000 TBGRI Established in 1994 by the International Union of Biological Sciences (IUBS), in co-operation with the Committee on Data for Science and Technology (CODATA) and the International Union of Microbiological Societies (IUMS). It was subsequently endorsed by the UNEP Biodiversity Work Programme 1996-1997, and associated with the Clearing House Mechanism of the UN Convention on Biological Diversity. • Enumerating taxonomic indexes of all known species of organisms (animals, plants, fungi and microbes) on Earth. http://www.sp2000.org Bioinformatics Centre TBGRI

49. Global Database TBGRI Global Biodiversity Information Facility (GBIF) A long term project of the International Organisation for Economic Cooperation and development, is building “ an interoperable network of biodiversity databases and information technology tools” the structure of which is summarized in the project’s business plan http://www.gbif.org/ Bioinformatics Centre TBGRI

50. Global Database The Tree of Life (ToL) TBGRI • Launched on 5 January 1996 • The Tree of Life (ToL) is a collaborative effort of biologists from all over the world (21 countries). • More than 4000 World Wide Web pages contained 948 pages, housed in seven computers on two continents. • Information about the diversity of organisms on Earth, their evolutionary history (phylogeny), and characteristics • Each page contains information about a particular group of organisms ToL pages are linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, thus illustrates the genetic connections between all living things http://tolweb.org/tree/phylogeny.html Bioinformatics Centre TBGRI