On the Origin of Phyla

Preface
Part One- Evidence of the Origins of Metazoan Phyla
1. The Nature of Phyla
Phyla Are Morphologically Based Branches of the Tree of Life
Concepts of Animal Phyla Have Developed over Hundreds of Years
The Concept of Homology Is Basic to Determining Animal Relationships
Linnean and Hennigian Taxa Have Different Properties
Genealogical Histories Can Be Traced in Trees, Which Are Positional Structures
Morphological Entities within Metazoan Bodies, Such as Cells, Can Be Positioned in Trees
Trees Composed of Individual Organisms Can Be Incredibly Complicated
Trees Composed of Species Are Much Simpler
Trees Can Be Formed of Linnean Taxa above the Species Level
Molecular Information Can Position Morphologically Based Taxa in a Tree
Natural Biological Hierarchies Are Nested Structures of Functional Entities That
Emerge When Complex Systems Are Organized
There Are Four Major Types of Hierarchical Structure
Hierarchies Help Sort Out Relations among Biological Features
Novel Phenomena Emerge at Successive Hierarchical Levels * The Effects of Levels upon One Another Are Quite Asymmetrical
Natural Hierarchies Are Formed by Trees
An Ecological Hierarchy of Biotic Entities Is Formed by the Tree of Life
Hierarchies of Genes Can Be Mapped onto the Somatic and Ecological Hierarchies
The Linnean Hierarchy Is Quasi-Natural
Trees and Hierarchies Have Very Distinct Properties
Cladistics Is a Systematics Based on Trees
Some Cladistic Terms Are Hypotheses as to the Evolutionary Status of Characters
In Cladistic Classifications, Branch Points May Define Sister Taxa That Are Holophyletic
Phyla Have Split Personalities
Molecular Branchings Can Define Clades, while Morphological Features Define Linnean Taxa
Bodyplans Consist of Evolutionarily Disparate Features
Bodyplans Are Polythetic
Important Bodyplan Features May Be Plesiomorphies or Synapomorphies, and May Be Homoplasies
Systematic Hierarchies and Trees: A Summary
2. Design Elements in the Bodyplans of Phyla
Cells Are the Basic Building Blocks of Metazoan Bodies
Cytoskeletons Provide the Framework for Cytoarchitectures
Metazoan Cells Have Descended from Protistans, Probably Choanoflagellate-Like
Cells Are Integrated into Tissues by Protein Bindings or Matrices
Extracellular Matrix Supports Metazoan Tissues
In Most Metazoan Tissues, Cells Are Connected or Anchored by Protein Molecules
Metazoans Have Several Major Types of Tissues
Most Tissues Are Epithelial or Connective
Muscle Tissue May Be either Epithelial or Connective
Nervous Tissues Are Not Organized either as Epithelia or as Connective Tissues
Multinucleate (Syncytial) Tissues Are Found in Many Disparate Phyla
Organs and Organ Systems Are Formed of Tissues
Organisms Are Best Understood as Developmental Systems
Cleavage and Cell Differentiation Are Linked in Most Metazoan Ontogenies
Gastrulation Gives Rise to Ectodermal and Endodermal Germ Layers
Middle Body Layers Range from Simple Sheets of Extracellular Matrix to
Mesodermal Germ Layers
Pseudocoels and Hemocoels Are Body Cavities That Lie on the Site of the Blastocoel
Coeloms Are Body Cavities That Lie within Mesoderm
Some Coeloms Function as Hydrostatic Skeletons * Some Coeloms Are Adjuncts to Organs
Larval Stages Commonly Possess Bodyplans of Their Own
Many Bodyplan Features Reflect Locomotory Techniques
In Soft-Bodied Forms, Locomotory Devices Range from Cilia to Limbs
"Hard" Skeletons May Complement or Replace the Biomechanical Functions of Fluid Skeletons
Symmetry and Seriation Are the Principal Descriptors of Body Style
Symmetry Is Imparted by Repetition of Parts across Planes or along Radii
Anteroposterior Regionation Involves Seriation, Segmentation, and Tagmosis
Evolutionary Changes in Body Size Occur throughout Metazoan History
Area/Volume Ratios Are Sensitive to Most Size Changes
Life Is Different at High versus Low Reynolds Numbers
Morphological Complexity Is Not a Simple Topic
3. Development and Bodyplans
The Evolution of Developmental Systems Underpins the Evolution of Bodyplans The English Language and Genomes Both Have Combinatorial, Hierarchical Structures
In Narrative English the Immensity of Combinations Inherent in the Alphabet Is Constrained within a Hierarchy
Hierarchical Constraints Also Operate within Metazoan Genomes
The Metazoan Gene Is a Complex of Regulatory, Transcribed, and Translated Parts
Transcribed Gene Regions Are Processed to Produce mRNA
Cis-Regulatory Elements Mediate Transcription
Regulatory Signals Are Produced by Trans-Regulatory Systems
Transcription Factors Bind to Enhancers
Trans-Regulators Are Controlled by Signals That Ultimately Arise from Other Regulatory Genes
Genomic Complexity Is a Function of Gene Numbers and Interactions
Metazoan Genomes Display Surprising Patterns of Similarities and Differences among Taxa
Some Functional Classes of Genes Are Broadly Similar across Metazoan Phyla
Bodyplans Are Patterned by Sequential Expressions of High-Level Regulatory Genes
Anteroposterior Axis Specification and Patterning Genes Are Found throughout Eumetazoa
Dorsoventral Axis Specification and Patterning Genes Are Similar across Bilateria
Organogenesis Involves Positioning by Patterning Genes and Development via Gene Cascades Controlled by Selector Genes
Signaling Pathways, Like Individual Genes, Are Recruited for a Variety of Tasks
Developmental Genomes May Evolve on Many, Semidecomposable Levels
Evolution of Cis-Regulatory Elements Entails Effects That Differ from the Evolution of Transcribed Genes
Regulatory Variation May Be Maintained by Several Unique Mechanisms
Units of Selection in Developmental Evolution Include Semi-independent Modules