Avian Molecular Evolution and Systematics

by Mindell

• ISBN13: 9780124983151
• ISBN10: 0124983154
• Format: Hardcover
• Copyright: 1997-05-05
• Publisher: Elsevier Science

Summary

The use of DNA and other biological macromolecules has revolutionized systematic studies of evolutionary history. Methods that use sequences of nucleotides and amino acids are now routinely used as data for addressing evolutionary questions that, although not new questions, have defied description and analysis. The world-renowned contributors use these new methods to unravel particular aspects of the evolutionary history of birds. Avian Molecular Evolution and Systematics presents an overview of the theory and application of molecular systematics, focusing on the phylogeny and evolutionary biology of birds. New, developing areas in the phylogeny of birds at multiple taxonomic areas are covered, as well as methods of analysis for molecular data, evolutionary genetics within and between bird populations, and the application of molecular-based phylogenies to broader questions of evolution. Key Features * Contains authoritative contributions from leading researchers * Discusses the utility of different molecular markers for questions of avian evolution, involving populations and higher-level taxa * Applies molecular-based phylogenies of birds and molecular population genetics data to broad questions of organismal and molecular evolution. * Compares and contrasts molecular and morphological data sets

Table of Contents

Contributors	xiii	(4)
Preface	xvii
PART I Molecular Sequences and Evolutionary History in Birds	4	(247)
1 Molecular Evolution of the Mitochondrial Genome	4	(26)
Thomas W. Quinn
I. Introduction	4	(1)
II. Mitochondria: An Ancient Legacy	4	(1)
III. The Vertebrate Mitochondrial Genome	5	(1)
IV. Avian Mitochondrial Genomes	6	(5)
A. An Altered Gene Order throughout Aves	6	(4)
B. Other Features of the Avian Mitochondrial Genome	10	(1)
V. Major Genomic Features as Characters for Phylogenetic Analysis	11	(6)
A. Two Approaches to Phylogenetic Analysis Using DNA Sequence Information	11	(2)
B. The Sister Taxon to Birds: Evidence from Comparisons of DNA Sequence and "Genomic Landmarks"	13	(3)
C. Other Potentially Informative Characters	16	(1)
VI. Intergenomic Transfer of Mitochondrial Sequences	17	(6)
A. Nuclear Homologs of Mitochondrial DNA: Not Unusual	17	(1)
B. An Avian Numt	18	(1)
C. Numts as a Challenge for Studies of Avian Phylogenetics	19	(3)
D. Opportunities Provided by Numts	22
VII. Conclusion	23	(1)
References	23	(7)
2 DNA Microsatellites as Genetic Markers at Several Scales	30	(21)
David B. McDonald
Wayne K. Potts
I. Introduction	30	(1)
II. Technical Overview	30	(4)
A. Generating a Size-Selected Plasmid Genomic Library	32	(1)
B. Library Enrichment Techniques	33	(1)
C. Screening the Library for Microsatellite-Bearing Clones	33	(1)
D. Genotyping	33	(1)
E. Microsatellite Mutations	34	(1)
III. The Range of Scales	34	(5)
A. Among Genes	34	(2)
B. Among Individuals	36	(1)
C. Among Populations	36	(2)
D. Among Species	38	(1)
E. Among Genera and Higher Taxa	38	(1)
F. Temporal Scales (Ancient DNA)	39	(1)
IV. Cautions for Data Analysis	39	(2)
V. Case Histories	41	(2)
A. Relatedness among Partners in Male Long-Tailed Manakins	41	(1)
B. Gray Seals	42	(1)
C. Domestic and Bighorn Sheep	42	(1)
VI. Summary and Conclusions	43	(1)
References	43	(6)
Appendix I	49	(2)
3 Mitochondrial Control Region Sequences as Tools for Understanding Evolution	51	(33)
Allan J. Baker
H. Dawn Marshall
I. Introduction	51	(2)
II. Sequence Organization and Evolution	53	(11)
A. Control Region Sequence Data and Structural Features	53	(8)
B. Sequence Evolution	61	(3)
III. Population Structure and Intraspecific Taxonomy	64	(13)
A. Global Phylogeography of the Dunlin	66	(3)
B. Bottlenecking and Recent Population Expansion in Knots	69	(1)
C. Colonization Routes of Chaffinches in the Atlantic Islands	70	(3)
D. Intraspecific Variation in Canada Geese	73	(1)
E. Phylogeography of Gray-Crowned Babblers	74	(1)
F. Recent Mixing of Lineages in Adelie Penguins and in Snow Geese	75	(2)
IV. Higher Level Systematics	77	(2)
References	79	(5)
4 The Window of Taxonomic Resolution for Phylogenies Based on Mitochondrial Cytochrome b	84	(37)
William S. Moore
Victor R. DeFilippis
I. Introduction	84	(3)
A. Avian Phylogenies Inferred from Mitochondrial DNA	84	(1)
B. Objectives of This Study	85	(1)
C. Properties of DNA Sequences That Are Ideal for Recovering Phylogenies	86	(1)
II. Materials and Methods	87	(1)
A. Producing Sequence Data	87
III. Results	88	(17)
A. Sequences	88	(1)
B. Phylogenetic Analysis	88	(4)
C. Base Composition	92	(2)
D. Pairwise Comparisons among Divergent Sequences	94	(4)
E. The Relationship between Transitions and Transversions	98	(2)
F. The Relationship between Taxonomic Divergence and Saturation of Transversions	100	(2)
G. The Relationship between Taxonomic Divergence and Amino Acid Substitutions	102	(1)
H. Short Internodes, Long Terminal Branches, and Phylogenetic Resolution	102	(2)
I. Rate Variation within Lineages	104	(1)
J. How Much Sequence in a Pilot Study	105	(1)
IV. Discussion	105	(4)
A. The Window of Taxonomic Resolution for Avian Phylogenies	105	(2)
B. Molecular Clock	107	(1)
C. Conclusions and Advice	107	(2)
References	109	(5)
Appendix I	114	(1)
Appendix II	115	(6)
5 Phylogeny and Evolution of 12S rDNA in Gruiformes (Aves)	121	(38)
Peter Houde
Alan Cooper
Elizabeth Leslie
Allan E. Strand
Gabriel A. Montano
I. Introduction	121	(6)
A. The Birds	122	(3)
B. The Gene	125	(2)
II. Methods	127	(7)
A. DNA Sequence Data	127	(6)
B. Phylogeny Reconstruction	133	(1)
III. Phylogenetic Inferences	134	(8)
A. Results	134	(5)
B. Discussion	139	(3)
IV. Molecular Evolution	142	(10)
A. Sequence Divergence	142	(2)
B. Evolutionary Dynamics of 12S rDNA	144	(4)
C. Character Evolution of 12S rDNA	148	(4)
V. Implications of 12S Evolution for Phylogenetic Inference	152	(1)
VI. Summary	153	(1)
References	154	(5)
6 Phylogeny of the Pelacaniformes: Molecular Systematics of a Privative Group	159	(14)
Douglas Siegel-Causey
I. Introduction	159	(5)
A. The Problem of the Putatively Privative Pelecaniformes	160	(3)
B. The Enigma of Balaeniceps	163	(1)
II. Methods	164	(2)
A. Data Sets and Analysis	164	(2)
III. Results	166	(1)
A. Molecular Evidence	166	(1)
B. Morphological and Behavioral Evidence	167	(1)
IV. Discussion	167	(3)
References	170	(3)
7 The Phylogeny of Ratite Birds: Resolving Conflicts between Molecular and Morphological Data Sets	173	(41)
Krista Lee
Julie Feinstein
Joel Cracraft
I. Introduction	173	(3)
II. Materials and Methods	176	(5)
A. Taxa	176	(1)
B. DNA Extraction and Sequencing	177	(3)
C. Phylogenetic Analysis	180	(1)
III. Results	181	(5)
A. Morphological Analysis	181	(3)
B. Sequence Analysis	184	(1)
C. Total Evidence Solution	185	(1)
IV. Discussion	186	(4)
A. Ratite Interrelationships: Morphological Data	186	(1)
B. Why Do Molecular and Morphological Data Conflict?	187	(3)
V. Conclusions	190	(2)
References	192	(4)
Appendix I	196	(13)
Appendix II	209	(5)
8 Phylogenetic Relationships among and within Select Avian Orders Based on Mitochondrial DNA	214	(37)
David P. Mindell
Michael D. Sorenson
Christopher J. Huddleston
Hector C. Miranda, Jr.
Alec Knight
Steven J. Sawchuk
Tamaki Yuri
I. Introduction	214	(1)
II. Issues in Phylogenetic Analyses	215	(4)
A. Constraints on Molecular Evolution	215	(3)
B. Sampling of Characters and Taxa	218	(1)
III. Methods	219	(6)
A. Study Characters and Taxa	219	(3)
B. Phylogenetic Analyses	222	(3)
IV. Results and Discussion	225	(16)
A. Phylogenetic Placement of Anseriformes and Galliformes	225	(3)
B. Relationships among Neognath Orders	228	(2)
C. Placement of Buttonquail, Hoatzin, and Flamingoes	230	(3)
D. Relationships among Passeriformes	233	(1)
E. Relationships among Anseriformes and Galliformes	233	(2)
F. Relationships among Falconiformes and Strigiformes	235	(6)
V. Conclusions	241	(2)
References	243	(8)
PART II Applying Phylogeny and Population Genetics to Broader Issues	251	(124)
9 Relevance of Microevolutionary Processes to Higher Level Molecular Systematics	251	(28)
Scott V. Edwards
I. Introduction	251	(2)
II. Molecular Variability	253	(9)
A. The Specter of Polymorphism	253	(5)
B. Pattern of Nucleotide Substitution	258	(4)
III. Population Processes	262	(11)
A. Gene and Species Trees	266	(1)
B. Permanent Effects of Incomplete Lineage Sorting and Hybridization	266	(1)
C. Dating Biogeographic Events: Coalescence in Subdivided Populations	267	(4)
D. Selection	271	(2)
IV. Conclusion	273	(1)
References	274	(5)
10 Phylogeny in Studies of Bird Ecology, Behavior, and Morphology	279	(22)
Frederick H. Sheldon
Linda A. Whittingham
I. Introduction	279	(2)
II. Accurate Phylogenetic Estimates and Historical Ecology	281	(4)
A. An Example of the Phylogenetic Framework Approach	283	(2)
III. Application of the Comparative Approach to Classic Problems of Evolution	285	(9)
A. Adaptation	285	(6)
B. Phylogenetic Constraints	291	(3)
IV. Summary	294	(2)
References	296	(5)
11 Phylogeographic Studies of North American Birds	301	(24)
Robert M. Zink
I. Introduction	301	(1)
II. Allozymic Studies of Avian Geographic Variation	302	(1)
III. The DNA Revolution in Intraspecific Studies	303	(2)
IV. Phylogeographic Studies in Birds	305	(9)
A. Nature of Variation	305	(5)
B. Haplotype Phylogenies and Directionality	310	(1)
C. Estimates of Gene Flow	310	(1)
D. Description and Significance of Genetic Variation among Populations	311	(3)
V. Comparative Phylogeography	314	(6)
A. Method	314	(1)
B. Some Avian Results	315	(3)
C. Mismatch Distributions and Population Histories	318	(2)
D. Comparative Phylogeography and the History of Communities	320	(1)
VI. Prospectus	320	(1)
References	321	(4)
12 The Speciation of South American and African Birds in Montane Regions	325	(20)
Michael S. Roy
Jose Maria Cardoso da Silva
Peter Arctander
Jaime Garcia-Moreno
Jon Fjeldsa
I. Introduction	325	(1)
II. The Model Hypothesis	326	(2)
A. Basic Assumptions	326	(1)
B. Method	327	(1)
III. Old and New Species in South America	328	(2)
IV. Old and New Species in Africa	330	(2)
V. Implications for the Model	332	(1)
VI. Case Studies of Biogeographic Patterns in Tropical Mountains	333	(6)
A. The Andes	333	(1)
B. East African Mountains	334	(5)
VII. Discussion and Summary	339	(2)
References	341	(4)
13 Studies of Avian Ancient DNA: From Jurassic Park to Modern Island Extinctions	345	(30)
Alan Cooper
I. Introduction	345	(1)
II. Review of Ancient DNA Research	346	(3)
A. Techniques	347	(2)
III. Systematics and Paleoecological Applications	349	(19)
A. Ratite Systematics	349	(13)
B. Paleoecological Studies	362	(6)
IV. Summary	368	(1)
V. Future Research	368	(1)
References	369	(6)
Index	375