Department Of Botany

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    DNA Barcoding and phylogography of brown seaweeds of coasts of indian subcontinent
    (Central University of Punjab, 2013) Bhushan, Satej; Bast, Felix
    Algae are one of the diverse groups of ubiquitous autotrophs. Their use as food was more or less initially confined to few East Asian and South American countries like China, Japan, Korea, Chile, Argentina and Brazil, but with the increased demand and limited supply for food combined with the medicinal properties of the marine macroalgae, they started getting the attention of policy makers and researchers alike all around the world. Brown seaweeds (Phaeophyceae) are mostly marine and characterized by presence of pigment fucoxanthin which gives them its coloured appearance. The present work aims to provide detailed molecular analysis of the brown seaweeds found in Indian coastal regions to study and characterize it taxonomically which has not been done till now in Indian context. Out of all the samples processed, one invasive species was detected, Sargassum zhangii, which is the first report of this algal species outside Chinese waters. The conspecificity was confirmed by a multi-faceted approach, including comparative morphology, microscopy, genetic distance analysis and computational phylogenetics using Maximum Likelihood and Bayesian Inference methods.
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    Tutorial on Phylogenetic Inference – 1
    (Indian Academy of Science, 2015) Bast, Felix
    Phylogenetic Inference is a statistical technique to trace the evolutionary legacy of a wide range of subjects including biological taxa (species), biomolecules, languages, ancient texts and so on. In Part 1 of the tutorial, we begin with an introduction to this field and discuss phenetics and cladistics — two major techniques used for phylogenetic inference. A number of fundamental concepts for understanding phylogenetic inference are introduced. In Part 2, we will learn models of molecular evolution and methods of phylogenetic inference, concluding with a worked-out example.
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    Tutorial on Phylogenetic Inference Part-2
    (Indian Academy of Science, 2015) Bast, Felix
    Phylogenetic Inference (PI) is a statistical technique to trace the evolutionary legacy of a wide range of subjects; including biological taxa (species), biomolecules, languages, ancient texts and so on. The first part 1 of this tutorial introduced a number of fundamental concepts including phenetics, cladistics, homology, homoplasy, synapomorphy, symplesiomorphy, orthology and paralogy. In this part, we will learn about models of molecular evolution, choosing the best model, overview of various genetic loci used in PI, methods of PI (including distance matrix method, NJ, and discrete data methods ML, MP and BI), issue of lineage sorting and conclude with a worked-out example.
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    Chloroplast DNA phylogeography of holy basil (Ocimum tenuiflorum) in Indian subcontinent
    (2014) Bast, Felix; Rani, Pooja; Meena, Devendra
    Ocimum tenuiflorum L., holy basil "Tulsi", is an important medicinal plant that is being grown and traditionally revered throughout Indian Subcontinent for thousands of years; however, DNA sequence-based genetic diversity of this aromatic herb is not yet known. In this report, we present our studies on the phylogeography of this species using trnL-trnF intergenic spacer of plastid genome as the DNA barcode for isolates from Indian subcontinent. Our pairwise distance analyses indicated that genetic heterogeneity of isolates remained quite low, with overall mean nucleotide p-distance of 5?10-4. However, our sensitive phylogenetic analysis using maximum likelihood framework was able to reveal subtle intraspecific molecular evolution of this species within the subcontinent. All isolates except that from North-Central India formed a distinct phylogenetic clade, notwithstanding low bootstrap support and collapse of the clade in Bayesian Inference. North-Central isolates occupied more basal position compared to other isolates, which is suggestive of its evolutionarily primitive status. Indian isolates formed a monophyletic and well-supported clade within O. tenuiflorum clade, which indicates a distinct haplotype. Given the vast geographical area of more than 3 million km 2 encompassing many exclusive biogeographical and ecological zones, relatively low rate of evolution of this herb at this locus in India is particularly interesting. ? 2014 Felix Bast et al.
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    Phylogenetics: Tracing the Evolutionary Legacy of Organisms, Metastatic Clones, Bioactive Compounds and Languages
    (OMICS, 2015) Bast, Felix
    Since its inception seventy-five years ago, the field of phylogenetics has steadily been expanding to contribute in a number of scientific fields including biogeography, medicinal chemistry, forensics, transcriptomics, cancer biology and even linguistics, in addition to systematic biology -for which it was originally erupted by Willi Hennig. In this invited editorial contributed to the Journal of Phylogenetics and Evolutionary Biology a big picture of this ever evolving field is expounded. Application of phylogenetic inference in biosystematics, phylogeography, phylogenetic selection of target taxa in medicinal chemistry, cancer phylogenetics, and linguistic phylogeny are reviewed with a personal perspective summarizing contribution to this interdisciplinary field from my group. Parametric methods such as Maximum Likelihood and Bayesian Inference have dramatically improved for last one decade, yet empirical solutions to some of the most fundamental issues, including homoplasmy and lineage sorting, remains to be materialized.