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Phylogenetics: Theory and Practice of Phylogenetic Systematics 2nd edition [Hardback]

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(University of Kansas), (University of Kansas, Lawrence)
  • Formāts: Hardback, 432 pages, height x width x depth: 257x183x28 mm, weight: 930 g
  • Izdošanas datums: 19-Jul-2011
  • Izdevniecība: Wiley-Blackwell
  • ISBN-10: 0470905964
  • ISBN-13: 9780470905968
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  • Bibliotēkām
  • Formāts: Hardback, 432 pages, height x width x depth: 257x183x28 mm, weight: 930 g
  • Izdošanas datums: 19-Jul-2011
  • Izdevniecība: Wiley-Blackwell
  • ISBN-10: 0470905964
  • ISBN-13: 9780470905968
Citas grāmatas par šo tēmu:
The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come.

This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeographythe purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics.

The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes:





Parsimony and parsimony analysis



Parametric phylogenetics including maximum likelihood and Bayesian approaches



Phylogenetic classification



Critiques of evolutionary taxonomy, phenetics, and transformed cladistics



Specimen selection, field collecting, and curating



Systematic publication and the rules of nomenclature





Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

Recenzijas

The volume is impressively broad in its coverage of modern systematics, including topics such as nomenclature, curatorial practices, and publication, in addition to the basic principles and methods of phylogenetic inference.  (The Quarterly Review of Biology, 1 March 2014)

 

Preface to the Second Edition xiii
Preface to the First Edition xv
Chapter 1 Introduction
1(22)
Phylogenetic Propositions
3(3)
Topics Covered
6(1)
Terms and Concepts
7(9)
Disciplines
8(1)
Organisms and Grouping of Organisms
9(2)
Phylogenetic History and Evolution
11(2)
Attributes of Organisms
13(2)
Classification
15(1)
Philosophy and Systematics
16(5)
The Form of Phylogenetic Hypotheses
19(2)
Chapter Summary
21(2)
Chapter 2 Species and Speciation
23(43)
What Is It to Be a Species?
24(3)
Species as Kinds
24(2)
Species as Sets
26(1)
Species as Individuals
27(1)
Species Concepts
27(12)
Process-Based Concepts
29(1)
The Evolutionary Species Concept
30(2)
Justifications for the ESC
32(1)
Variations on the ESC
33(1)
Process-Based Concepts Emphasizing Reproductive Isolation
34(2)
Phylogenetic Species Concepts
36(1)
Some Additional Species Concepts
37(1)
Sorting through Species Concepts
38(1)
Speciation: Modes and Patterns
39(11)
Allopartic Speciation
41(1)
Allopartic Mode I: Vicariance
42(2)
Allopatric Speciation, Mode II Peripatric Speciation
44(1)
Distinguishing between Allopatric Modes of Speciation
44(5)
Parapatric Speciation
49(1)
Sympatric Speciation
49(1)
Identifying Modes of Speciation in the Fossil Record
50(4)
The Evolutionary Species Concept, Speciation, and Ecology
54(1)
Empirical Methods for Determining Species Limits
54(11)
Nontree-Based Methods
55(6)
Tree-Based Methods
61(4)
Chapter Summary
65(1)
Chapter 3 Supraspecific Taxa
66(19)
Concepts of Naturalness and Supraspecific Taxa
67(1)
The Natural Taxon
68(2)
Monophyly, Paraphyly and Polyphyly
70(2)
Hennig's Concepts Placed in History
72(1)
Natural Higher Taxa as Monophyletic Groups sensu Hennig (1966)
73(1)
Logical Consistency: The Hallmark of Proposed Natural Classifications
74(6)
Paraphyletic Groups Misrepresent Character Evolution
80(1)
Paraphyly and Polyphyly: Two Forms of Nonmonophyly
81(2)
Node-Based and Stem-Based Monophyly: Same Concept Different Graphs
83(1)
Chapter Summary
83(2)
Chapter 4 Tree Graphs
85(22)
Phylogenetic Trees
87(4)
Stem-Based Phylogenetic Trees
87(2)
Node-Based Phylogenetic Trees
89(2)
Cyclic Graphs
91(1)
Cladograms
92(7)
Nelson Trees in Phylogenetics
92(1)
From Nelson Trees to Phylogenetic Trees
93(6)
Gene Trees
99(1)
Individuals versus Sets of Individuals Used in an Analysis
99(1)
Representing Character Evolution on Trees
100(1)
Unrooted Trees and Their Relationship to Phylogenetic Trees
101(1)
Node Rotation
102(1)
Other Kinds of Tree Terminology
103(1)
Concepts of Monophyly and Trees
104(2)
Chapter Summary
106(1)
Chapter 5 Characters and Homology
107(45)
A Concept of Character
107(2)
Character States as Properties
109(1)
Shared Character States
110(1)
Historical Character States as Properties
111(1)
Ahistorical Kind Properties
112(1)
Historical Groups and Natural Kinds
113(1)
Homology
114(8)
Haszprunar's Homology Synthesis
115(2)
Concepts of Homology in Systematics
117(1)
Phylogenetic Characters and Phylogenetic Homology: An Overview
118(1)
Taxic Homologies as Properties of Monophyletic Groups
119(2)
Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series
121(1)
Discovering and Testing Homology
122(10)
Patterson's Tests
124(1)
Similarity and Remane's Criteria
124(1)
Similarity in Position: Morphology
124(1)
Similarity in Position: Molecular Characters
125(4)
Special or Intrinsic Similarity
129(2)
Stacking Transformations: Intermediate Forms
131(1)
Conjunction
132(4)
Phylogenetic Homology (Forging Congruence between Hennig's and Patterson's Views)
136(1)
Avoiding Circularity: How Congruence Works
136(1)
Working with Characters
137(13)
Qualitative versus Quantitative Characters: Avoiding Vague Characters
139(1)
Morphometrics and Phylogenetics
140(4)
Characters, Transformation Series, and Coding
144(3)
Complex Characters or Separate Characters?
147(1)
Missing Data
147(2)
Homology and "Presence-Absence" Coding
149(1)
Chapter Summary
150(2)
Chapter 6 Parsimony and Parsimony Analysis
152(51)
Parsimony
152(2)
Parsimony: Basic Principles
153(1)
Kinds of Parsimony
154(1)
Classic Hennigian Argumentation
154(12)
Polarization
156(6)
Example 1 The Phylogenetic Relationships of Leysera
162(4)
A Posteriori Character Argumentation
166(1)
Algorithmic versus Optimality Approaches
166(2)
Optimality-Driven Parsimony
168(1)
Determining Tree Length
169(2)
Finding Trees
171(5)
Random Addition Searches
172(1)
Rearranging Tree Topologies
173(2)
The Parsimony Ratchet
175(1)
Simulated Annealing
176(1)
Optimizing Characters on Trees
176(3)
ACCTRAN Optimization
177(1)
DELTRAN Optimization
178(1)
Summary Tree Measures
179(9)
Example 2 Olenelloid Trilobites
184(4)
Evaluating Support
188(5)
Using Consensus Techniques to Compare Trees
193(2)
Statistical Comparisons of Trees
195(1)
Weighting Characters in Parsimony
196(3)
A Priori Weighting
196(2)
Weighting by Performance
198(1)
Weighting by Character Elimination
199(1)
Weighting: Concluding Remarks
199(1)
Phylogenetics Without Transformation?
199(3)
Chapter Summary
202(1)
Chapter 7 Parametric Phylogenetics
203(26)
Maximum Likelihood Techniques
205(14)
Simplicity
209(1)
Likelihood in Phylogenetics: An Intuitive Introduction
210(2)
Likelihood in Phylogenetics: A More Formal Introduction
212(6)
Selecting Models
218(1)
Bayesian Analysis
219(7)
Interpreting Models in a Phylogenetic Context
226(1)
Chapter Summary
227(2)
Chapter 8 Phylogenetic Classification
229(31)
Classificaitons: Some General Types
230(3)
Classification of Natural Kinds
230(1)
Historical Classifications (Systematizations)
231(2)
Convenience Classifications
233(1)
Biological Classifications
233(1)
Constituents and Grouping in Phylogenetic Classifications
233(1)
The Linnean Hierarchy
234(11)
Definition of Linnean Higher Categories
235(1)
Conventions for Annotated Linnean Classifications
236(5)
Ancestors in Phylogenetic Classification
241(3)
Species and Higher Taxa of Hybrid Origin
244(1)
Alternative Methods of Classifying in the Phylogenetics Community
245(3)
The PhyloCode
248(7)
PhyloCode Controversies
250(3)
Stability of Names Relative to Clade Content
253(2)
Proper Names of Taxa
255(2)
The Future of Linnean Nomenclature
257(1)
Alternative "Schools" and Logical Consistency
258(1)
Chapter Summary
258(2)
Chapter 9 Historical Biogeography
260(56)
The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence
261(3)
Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes
264(1)
The Importance of Vicariance in the Context of Evolutionary Theory
265(1)
The Importance of "Dispersal" in Phylogenetic Biogeography
265(6)
Geodispersal: Not Dispersal
266(4)
Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal
270(1)
Areas and Biotas
271(7)
"Area" as It Relates to Phylogenetic Biogeographic Analysis
274(3)
The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa
277(1)
Conclusions
278(1)
Analytical Methods in Phylogenetic Biogeography
278(2)
Historical Biogeography Using Modified Brooks Parsimony Analysis
280(13)
Overview of MBPA
282(3)
Steps 1 and 2 Fitch Optimization of Area States on a Phylogeny
285(3)
Area Distributions
288(1)
Step 3.1 The Vicariance Matrix
288(1)
Step 3.2 The Dispersal Matrix
289(1)
Steps 4 and 5 MBPA Analyses and Comparison
290(3)
Alternative Biogeographic Methods
293(4)
How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota
297(4)
Statistical Approaches to Biogeographic Analysis
301(4)
Tracking Biogeographic Change within a Single Clade
305(2)
Phylogeography: Within Species Biogeography
307(1)
The Biogeography of Biodiversity Crises
308(2)
A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography
310(1)
Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal?
310(2)
The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal
312(2)
Chapter Summary
314(2)
Chapter 10 Specimens and Curation
316(15)
Specimens, Vouchers, and Samples
316(3)
The Need for Voucher Specimens
317(1)
Access to Specimens
318(1)
Previous Literature
318(1)
Systematic Collections
318(1)
Access to Specimens in the Age of the Internet
318(1)
Collecting and Collection Information
319(3)
Field Data
321(1)
The Systematics Collection
322(4)
Loans and Exchanges
322(1)
Curation
323(1)
Receipt of Specimens, Accessing the Collections, and Initial Sorting
323(1)
Sorting and Identifying
324(1)
Cataloging
324(1)
Storage
324(1)
Arrangements of Collections
324(1)
Type Specimens
324(1)
Catalogs
325(1)
What Is in a Catalog?
325(1)
The Responsibility of Curators
326(1)
The Importance of Museum Collections
326(1)
Integrating Biodiversity and Ecological Data
327(2)
A Simple Example: Range Predictions
328(1)
Predicting Species Invasions
329(1)
Global Climate Change
329(1)
Chapter Summary
329(2)
Chapter 11 Publication and Rules of Nomenclature
331(18)
Kinds of Systematic Literature
331(3)
Descriptions of New Species
331(1)
Revisionary Studies
332(1)
Keys
332(1)
Faunistic and Floristic Works
332(1)
Atlases
333(1)
Catalogs
333(1)
Checklists
333(1)
Handbooks and Field Guides
334(1)
Taxonomic Scholarship
334(1)
Phylogenetic Analyses
334(1)
Access to the Literature
334(3)
Literature in Zoology
334(1)
Literature in Botany
335(2)
Publication of Systematic Studies
337(8)
Major Features of the Formal Taxonomic Work
338(1)
Name Presentation
338(1)
Synonomies
339(1)
Material Examined
340(1)
The Diagnosis
340(1)
The Description
341(1)
Illustrations and Graphics
341(1)
Comparisons and Discussion
342(1)
Distributional Data
342(1)
Etymology
343(1)
Keys
343(1)
Indented Key
344(1)
Bracket Key
344(1)
The Rules of Nomenclature
345(3)
Basic Nomenclatural Concepts
346(1)
Priority
346(1)
Correct Name and Valid Name
346(1)
Synonyms
347(1)
Homonyms
347(1)
Conserved Names (Nomen conservadum)
347(1)
Limits of Priority
347(1)
Names and Name Endings
347(1)
Types
347(1)
Chapter Summary
348(1)
Literature Cited 349(41)
Index 390
Professor Wiley is Emeritus Professor of Ecology and evolutionary Biology at the University of Kansas.  Currently he works in the University of Kansas Natural History Museum.  Professor Wiley's distinguished career is marked by hundreds of peer-reviewed papers, a continuous string of research grants, including his current NSF grant, "Assembling the Euteleost Tree of Life," and the publication of 5 books.  

Professor Lieberman is an Invertebrate Paleontologist at University of Kansas.  Professor Lieberman has also authored five books as well as numerous peer reviewed publications.  His long string of research grants culminates most recently with an NSF grant to study "Revisionary systematic of Cheirurid Trilobites."