Chordate Origins and Evolution: The Molecular Evolutionary Road to Vertebrates

Front-Matter_2016_Chordate-Origins-and-Evolution
	Chordate Origins and Evolution: The Molecular Evolutionary Road to Vertebrates
Copyright_2016_Chordate-Origins-and-Evolution
	Copyright
Preface_2016_Chordate-Origins-and-Evolution
	Preface
Chapter-1---Deuterostomes-and-Chordates_2016_Chordate-Origins-and-Evolution
	1 - Deuterostomes and Chordates
		1.1 A Brief Background
		1.2 Deuterostomes and Chordates
			1.2.1 Deuterostomes
			1.2.2 Ambulacraria
			1.2.3 Chordates
			1.2.4 Olfactores
		1.3 Deuterostome Phyla
			1.3.1 Echinoderms
			1.3.2 Hemichordates
			1.3.3 Cephalochordates
			1.3.4 Urochordates (Tunicates)
			1.3.5 Vertebrates
		1.4 Conclusions
Chapter-2---Hypotheses-on-Chordate-Origin_2016_Chordate-Origins-and-Evolutio
	2 - Hypotheses on Chordate Origins
		2.1 The Annelid Theory
		2.2 The Auricularia Hypothesis
		2.3 The Calcichordate Hypothesis
		2.4 The Pedomorphosis Scenario: Was the Ancestor Sessile or Free-Living
		2.5 The New Inversion Hypothesis
		2.6 The Enteropneust Hypothesis
			2.6.1 A New Enteropneust Hypothesis
		2.7 The Aboral-Dorsalization Hypothesis
		2.8 Conclusions
Chapter-3---Fossil-Records_2016_Chordate-Origins-and-Evolution
	3 - Fossil Records
		3.1 The Cambrian and Ediacaran Periods
		3.2 Crown, Stem, and Total Groups
		3.3 Fossil Records of Invertebrate Deuterostomes
			3.3.1 Echinoderms
			3.3.2 Hemichordates
			3.3.3 Cephalochordates
			3.3.4 Urochordates (Tunicates)
		3.4 Fossil Records of Vertebrates
			3.4.1 Cyclostome-Like Fossils
			3.4.2 Early Vertebrate Fossils
			3.4.3 Conodont Elements
		3.5 Conclusions
Chapter-4---Molecular-Phylogeny_2016_Chordate-Origins-and-Evolution
	4 - Molecular Phylogeny
		4.1 Molecular Phylogeny of Metazoans
		4.2 Molecular Phylogeny of Deuterostome Taxa
			4.2.1 Ambulacraria and Chordata: Two Major Groups of Deuterostomes
			4.2.2 Cephalochordates Came First Among Chordates and Then Urochordates + Vertebrates as Olfactores
			4.2.3 Timing of the Emergence of Deuterostome Groups
		4.3 Relationships Within Each Deuterostome Phylum
			4.3.1 Echinoderms
			4.3.2 Hemichordates
			4.3.3 Cephalochordates
			4.3.4 Urochordates (Tunicates)
			4.3.5 Vertebrates
		4.4 Xenacoelomorpha
		4.5 MicroRNAs
		4.6 Conclusions
Chapter-5---Comparative-Genomics-of-Deuteros_2016_Chordate-Origins-and-Evolu
	5 - Comparative Genomics of Deuterostomes
		5.1 Genome Decoding
		5.2 Genomic Features of Five Representative Deuterostome Taxa
			5.2.1 Echinoderm Genomes
			5.2.2 Hemichordate Genomes
			5.2.3 Cephalochordate Genome
			5.2.4 Urochordate Genomes
				5.2.4.1 Ciona intestinalis
				5.2.4.2 Oikopleura dioica
			5.2.5 Vertebrate Genomes
				5.2.5.1 Lampreys
				5.2.5.2 Elephant Shark
				5.2.5.3 Fish
		5.3 Gene Families in Deuterostomes and the Ancestral Gene Set
			5.3.1 Gene Families in Deuterostomes
			5.3.2 Expansion of Gene Families in Deuterostomes
		5.4 Exon-Intron Structures
		5.5 Synteny
			5.5.1 Macrosynteny
			5.5.2 Microsynteny
		5.6 Conserved Noncoding Sequences
		5.7 Repetitive Elements
		5.8 Taxonomically Restricted Genes
		5.9 Conclusions
Chapter-6---The-Origins-of-Chordates_2016_Chordate-Origins-and-Evolution
	6 - The Origins of Chordates
		6.1 Evaluation of Hypotheses for Chordate Origins
			6.1.1 How Do We Interpret Deuterostome Evolution
			6.1.2 The Chordate Ancestor Was Free-Living
			6.1.3 The Auricularia Hypothesis Is Not Supported
			6.1.4 The Calcichordate Hypothesis Cannot Be Accepted
			6.1.5 The Annelid Hypothesis Is Not Related to the Origins of Chordates
			6.1.6 The Enteropneust Hypothesis and Inversion Hypothesis Need Reconsideration
		6.2 The Pharyngeal Gene Cluster and the Origin of Deuterostomes
		6.3 Hox and Chordate Evolution
			6.3.1 Ambulacrarian Hox Genes
			6.3.2 Cephalochordate Hox Genes
			6.3.3 Urochordate Hox Genes
			6.3.4 Vertebrate Hox Genes
				6.3.4.1 Cyclostome Hox Genes
				6.3.4.2 Gnathostome Hox Genes
			6.3.5 Deuterostome Posterior Hox Genes: An Unsolved Origin
		6.4 ParaHox Genes
		6.5 Conclusions
Chapter-7---The-New-Organizers-Hypothesis-for-Ch_2016_Chordate-Origins-and-E
	7 - The New Organizers Hypothesis for Chordate Origins
		7.1 Chordate Features
		7.2 The New Organizers Hypothesis of Chordate Origins
		7.3 Cephalochordate Embryogenesis: Primitive Chordate Body-Plan Formation
		7.4 Chordate Features and Molecular Developmental Mechanisms
		7.5 The Notochord: A Mesodermal Novelty
			7.5.1 Brachyury: A Key Transcription Factor for Notochord Formation
			7.5.2 Regulatory Networks of Brachyury
		7.6 Somites (Myotomes): A Mesodermal Novelty
		7.7 The Postanal Tail: A Mesodermal Novelty
		7.8 The Dorsal Central Nervous System: An Ectodermal Novelty
			7.8.1 The Gene Regulatory Network for Neural Development
			7.8.2 Regionalization of the Central Nervous System
		7.9 Hatschek’s Pit: An Ectodermal Novelty
		7.10 The Endostyle: An Endodermal Novelty
		7.11 Conclusions
Chapter-8---The-Dorsoventral-Axis-Inversion-Hypothesis--_2016_Chordate-Origi
	8 - The Dorsoventral-Axis Inversion Hypothesis: The Embryogenetic Basis for the Appearance of Chordates
		8.1 Spemann’s Organizer, the Nieuwkoop Center, and the Three-Signal Model
			8.1.1 Spemann’s Organizer
			8.1.2 The Nieuwkoop Center
			8.1.3 The Three-Signal Model
		8.2 Axial Patterning of Deuterostome Body Plans
			8.2.1 The Animal-Vegetal Axis and Formation of Endomesoderm
			8.2.2 The Anteroposterior Axis
			8.2.3 The Dorsoventral Dimension and the Inversion Hypothesis
			8.2.4 Left-Right Asymmetry and the Nodal Signal
		8.3 Interpretation of the Dorsoventral-Axis Inversion Hypothesis
			8.3.1 Nodal Function in Mesoderm Formation
			8.3.2 Interpretation of the Dorsoventral-Axis Inversion
		8.4 Conclusions
Chapter-9---The-Enteropneust-Hypothesis-and-Its-_2016_Chordate-Origins-and-E
	9 - The Enteropneust Hypothesis and Its Interpretation
		9.1 The Stomochord and Other Organs Proposed as Antecedents to the Notochord
			9.1.1 The Stomochord
			9.1.2 The Pygochord
			9.1.3 The Annelid Axochord
		9.2 The Nervous System of Enteropneusts
			9.2.1 The Dorsal Collar Cord
			9.2.2 Gene Expression Profiles in Epidermis along the Anteroposterior Axis
			9.2.3 Gene Expression Profiles along the DV Axis
		9.3 The Spemann’s Organizer-Like System in Hemichordates
		9.4 Interpretations of the Enteropneust Hypothesis
		9.5 Conclusions
Chapter-10---Chordate-Evolution--An-Extension-of-th_2016_Chordate-Origins-an
	10 - Chordate Evolution: An Extension of the New Organizers Hypothesis
		10.1 Evolution of Vertebrates
			10.1.1 Neural Crest
				10.1.1.1 Evolution of the Neural Crest and Its Gene Regulatory Network
			10.1.2 The Placodes
				10.1.2.1 The Evolution of the Placode and Its Gene Regulatory Network
			10.1.3 The Cardiopharyngeal Field
			10.1.4 Cartilage and Bone
			10.1.5 Adaptive Immune System
		10.2 Evolution of Urochordates
			10.2.1 Precocious Mode of Embryonic Development
			10.2.2 Asexual Reproduction of Colonial Ascidians
			10.2.3 Pluripotent Stem-Like Cells for Bud Formation
			10.2.4 The Development of Colony Specificity
		10.3 Conclusion
Chapter-11---How-Did-Chordates-Originate-and-_2016_Chordate-Origins-and-Evol
	11 - How Did Chordates Originate and Evolve
		11.1 The Three-Phylum System of Chordates
		11.2 Mechanisms Involved in Origination of Deuterostome Novelties
		11.3 Horizontal Gene Transfer
			11.3.1 Acquisition of Cellulose Biosynthetic Ability and Urochordate Evolution
			11.3.2 Genes Encoding Enzymes Involved in Sialic Acid Metabolism
		11.4 The Significance of Gene Duplication in Deuterostome Evolution
		11.5 Significance of Domain Shuffling in Chordate Evolution
		11.6 The Significance of Structural Genes in Metazoan Evolution
		11.7 The Phylotypic Stage
		11.8 Conclusions
Chapter-12---Summary-and-Perspective_2016_Chordate-Origins-and-Evolution
	12 - Summary and Perspective
		12.1 Summary
		12.2 Perspective
References_2016_Chordate-Origins-and-Evolution
	References
Index_2016_Chordate-Origins-and-Evolution
	Index
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