About Book

Global biodiversity is being lost at an unprecedented rate as a result of human activities, and decisions must be taken now to combat this trend. Taxonomy is a long-range research needs more care and attention, with high degree of technical and scientific skills for producing effective results. In fact, taxonomy deals with the principals involved in the study of classification of organisms. Taxonomy consists of three main parts: classification (arrangement of organisms based on similarity), nomenclature (naming of the organisms) and identification (determining whether an organism belongs to the group under which it is classified and named). Using morphological, behavioural, genetics and biochemical observations, taxonomists identify, describe and arrange species into classifications, including those that are new to science. Modern taxonomy uses database technologies to search and catalogue classifications and their documentation. This book provides an overview of the theory and practice of modern taxonomy, with associated biodiversity studies. It attempts to redress the balance by providing an introduction to the taxonomic theory upon which the identification procedure is based. The book studies, analyses and upholds the pillars of taxonomy and its utmost significance in modern times. It deals with genetic features, microbial diversity, chemotaxonomy, molecular taxonomy, endemic species, taxonomy of lepidoptera, genus alstroemeria and methanogenic diversity. It also provides insight into effective ways of organizing taxonomic information. In the book, constant effort has been made to make the understanding of the difficult concepts of this field as easy and informative as possible for the readers. It aims to serve as a resource guide for researchers and facilitate the study of this discipline.

Preface............................................................................................................v

Chapter 1 Methanogenic Diversity and Taxonomy in the Gastro

Intestinal Tract of Ruminants ................................................................1

Abstract...................................................................................................1

1. Introduction............................................................................................2

2. Major rumen microbes.........................................................................2

3. Methane production in ruminants and its contribution to

greenhouse gases...................................................................................3

4. Methanogenic archaeal population in gastro-intestinal tract of

ruminants................................................................................................3

5. Effect of diet on diversity of rumen methanogens........................5

6. Methanogen diversity inside rumen and/feces under similar

conditions of diet..................................................................................7

7. Methanogenic archaeal population in pseudo ruminants like

camelids................................................................................................11

8. Biotechnological applications of extremophiles............................12

Chapter 2 Molecular Phylogeny and Taxonomy of Lepidoptera with Special Reference to Influence of Wolbachia Infection in the

Genus Polytremis......................................................................................21

Abstract.................................................................................................21

1. Introduction to molecular phylogeny and taxonomy of

Lepidoptera..........................................................................................22

2. The phylogeny of the butterfly genus Polytremis.......................22

3. Taxonomic status of two sibling species of Polytremis

(Lepidoptera: Hesperiidae)................................................................26

4. The application of mitochondrial genome and microsatellite

DNA in Polytremis.............................................................................33

5. Wolbachia infection and influence in Polytremis species...........36

Acknowledgements.............................................................................42

Chapter 3 Molecular Taxonomy: Use of Transcriptional Profiles to Identify

Different ALS Subtypes..........................................................................47

Abstract.................................................................................................47

1. Introduction..........................................................................................48

2. Amyotrophic lateral sclerosis: an overview..................................49

3. Transcriptional analysis in ALS.......................................................51

4. Toward a molecular classification of SALS patients: our

experience.............................................................................................51

5. Conclusion............................................................................................74

Chapter 4 Chemotaxonomy of Actinobacteria.......................................................81

Abstract ................................................................................................81

1. Introduction..........................................................................................81

2. Amino acid of cell wall.....................................................................82

3. Sugar of whole cell hydrolytes........................................................86

4. Polar lipids...........................................................................................90

5. Menaquinones......................................................................................93

6. Mycolic acid.........................................................................................95

7. Fatty acids.............................................................................................96

8. Gas chromatography of fatty acids...............................................100

Acknowledgements...........................................................................104

Chapter 5 Modern Taxonomy for Microbial Diversity.....................................111

1. Introduction........................................................................................111

2. Biogeography of microbial diversity.............................................112

3. Microbial evolution...........................................................................113

4. Microbial phylogeny.........................................................................113

5. The prokaryotic microbes — Bacteria and archaea...................114

6. The species concept..........................................................................115

7. Polyphasic taxonomy.......................................................................115

8. The eukaryotic microbes — Fungi................................................123

9. Uncultured microorganisms............................................................124

10. Taxonomy of viruses........................................................................125

11. Conclusions & perspectives............................................................125

Chapter 6 Bovine Papillomaviruses — Taxonomy and Genetic Features....132

1. Introduction........................................................................................132

2. Taxonomic classification of PVs.....................................................133

3. Genomic organization......................................................................134

4. Viral proteins.....................................................................................138

5. Clinical conditions in cattle.............................................................140

6. Diversity of BPVs..............................................................................142

7. New BPV types.................................................................................144

8. Co-infections and heterologous infections.....................................147

9. Vaccines against BPV.......................................................................147

10. Conclusion..........................................................................................149

Acknowledgements...........................................................................149

Chapter 7 Towards an Integrative Taxonomy of the Genus Alstroemeria (Alstroemeriaceae) in Chile: A Comprehensive Review...............159

Abstract...............................................................................................159

1. Introduction........................................................................................160

2. Methods..............................................................................................161

3. Taxonomy and distribution of the genus Alstroemeria in

Chile.....................................................................................................161

4. Cytogenetic studies in Chilean Alstroemeria..............................170

5. Molecular studies in Alstroemeria................................................176

6. Concluding remarks.........................................................................185

Acknowledgements...........................................................................186

A. Appendix.......................................................................................186

Chapter 8 Endemic Species of the Family Poaceae in Chile: Taxonomy, Distribution, and Conservation...........................................................201

Abstract...............................................................................................201

1. Introduction........................................................................................202

2. Materials and methods....................................................................202

3. Results.................................................................................................202

Acknowledgements...........................................................................224

Citation......................................................................................................233

Index...........................................................................................................235

About Author

Stefano Boyd obtained his M.Sc. Degree in Biology & Ph.D. in Cell Biology from Public University of Camerino. He has written dozens of journals and articles on biotechnology, evolutionary biology, genetics and cell biology. He is serving as a Research Scientist at University College, Giessen. His main interests are cellular microbiology, bioremediation, and applied microbiology, drug discovery for infectious diseases and surveillance and molecular epidemiology of rising drug resistant pathogens. Boyd has traveled and lectured extensively throughout Europe and the America; primarily for higher education.