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About this book
About this book
Of relevance to both systematic and evolutionary biologists, Reconstructing the Tree of Life: Taxonomy and Systematics of Species-Rich Taxa draws from taxonomy and phylogenetics to provide both a systematics and evolutionary biology perspective. Detailing a broad range of organisms, the text addresses the task of reconstructing and making best use of the tree of life. Featuring the contributions of leading experts, who examine recent progress and consider future developments, it also discusses global diversity issues and the taxonomic problems of dealing with large and species-rich taxa.
INTRODUCTION TO THE SYSTEMATICS OF SPECIES RICH GROUPS, T.R. Hodkinson and J.A.N. ParnellIntroductionWhat is a Species Rich Group?Reconstructing and Using the Tree of LifeTaxonomy of Species Rich GroupsConclusions: Blame Evolution and PoliticiansReferencesTAXONOMY/SYSTEMATICS IN THE TWENTY-FIRST CENTURY, F.R. SchramHistorical WailingsUsing TechnologyInstitutional IssuesHuman CapitalThe Biodiversity CrisisWhat to Do?Concluding RemarksAcknowledgementsReferencesASSEMBLING THE TREE OF LIFE: MAGNITUDE, SHORTCUTS AND PITFALLS, O. Seberg and G. PetersenIntroductionThe Scale of the ProblemShortcuts in Systematics: DNA TaxonomyThe Identification ProblemInstability of Linnaean NamesTaxonomic BiasThe 'Taxonomic Impediment'Inadequacy of Taxonomic Data and Standards in Existing DatabasesConclusionAcknowledgementsReferencesEVOLUTIONARY HISTORY OF PROKARYOTES: TREE OR NO TREE? J.O. McInerney, D.E. Pisani, M.J. O'Connell, D.A. Fitzpatrick, and C.J. CreeveyA Brief History of Prokaryotic SystematicsThe Ribosomal RNA RevolutionConflicting TreesMethodological DevelopmentsAn Emerging Consensus?The Prokaryotic Influence on the EukaryoteConclusions, Future Directions and Open QuestionsAcknowledgementsReferencesSUPERTREE METHODS FOR BUILDING THE TREE OF LIFE: DIVIDE-AND-CONQUER APPROACHES TO LARGE PHYLOGENETIC PROBLEMS, M. Wilkinson and J.A. CottonIntroductionDivide-and-conquer MethodsEffective OverlapFast Quartet-based Supertree ConstructionConclusionReferencesTAXON SAMPLING VERSUS COMPUTATIONAL COMPLEXITY AND THEIR IMPACT ON OBTAINING THE TREE OF LIFE, O.R.P. Bininda-Emonds and A. StamatakisIntroductionMaterials and MethodsResultsDiscussionConclusionsAcknowledgementsReferencesTOOLS TO CONSTRUCT AND STUDY BIG TREES: A MATHEMATICAL PERSPECTIVE, M. SteelTrees (and networks) of LifeConstructing Supertrees and SupernetworksAn Application for Large Trees: Phylogenetic DiversityConcluding CommentsAcknowledgmentsReferencesTHE ANALYSIS OF MOLECULAR SEQUENCES IN LARGE DATA SETS: WHERE SHOULD WE PUT OUR EFFORT? W.C. WheelerThe Problem Presented by Unaligned Sequence DataCladogram Search HeuristicsHomology Determination HeuristicsExample DataComparisonsWhat is Happening in Large Data Sets?AcknowledgmentsReferencesSPECIES-LEVEL PHYLOGENETICS OF LARGE GENERA: PROSPECTS OF STUDYING COEVOLUTION AND POLYPLOIDY, N. R?nsted, E. Yektaei-Karin, K. Turk, J. J. Clarkson and M. W. ChaseIntroduction: Prospects of Studying Large GeneraCoevolution of Figs and their Pollinating WaspsLow Levels of Variation in Standard MarkersLow Copy Nuclear Markers: The Ideal ToolsUsing AFLP and other Fingerprinting TechniquesDouble Dating of Fig and Wasp Lineages: Evidence for CodivergenceIncongruence in Phylogenetic Trees: Effects of Polyploids and HybridsConclusionsAcknowledgmentsReferences