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TABLE OF CONTENTS ABSTRACT.......................................................................................................................iii TITLE ............................................................................................................................... vii TABLE OF CONTENTS.................................................................................................... 1 LIST OF TABLES.............................................................................................................. 3 LIST OF FIGURES ............................................................................................................ 4 LIST OF FILES .................................................................................................................. 6 CHAPTER 1: Introduction. ................................................................................................ 7 CHAPTER 2: From Biomedicine to Natural History Research: EST Resources for Ambystomatid Salamanders. ............................................................................................ 10 Introduction................................................................................................................... 10 Materials and Methods.................................................................................................. 12 Results and Discussion ................................................................................................. 15 CHAPTER 3: A comprehensive EST Linkage Map for Tiger Salamander and Mexican Axolotl: Enabling Gene Mapping and Comparative Genomics in Ambystoma ............... 48 Introduction................................................................................................................... 48 Materials and Methods.................................................................................................. 50 Results........................................................................................................................... 53 Discussion..................................................................................................................... 55 CHAPTER 4: Sal-Site: Integrating New and Existing Ambystomatid Salamander Research and Informational Resources............................................................................. 68 Introduction................................................................................................................... 68 Salamander Genome Project (SGP).............................................................................. 69 Ambystoma EST Database (AESTdb) .......................................................................... 69 Ambystoma Gene Collection (AGC)............................................................................. 71 Ambystoma Genetic Map & Marker Collection (AMAP) ............................................ 71 CHAPTER 5: Evolution of Salamander Life Cycles: A Major-Effect Quantitative Trait Locus Contributes to Discrete and Continuous Variation for Metamorphic Timing...... 76 Introduction................................................................................................................... 76 Materials and Methods.................................................................................................. 78 Results........................................................................................................................... 80 Discussion..................................................................................................................... 83 CHAPTER 6: Gene Order Data from a Model Amphibian (Ambystoma): New Perspectives on Vertebrate Genome Structure and Evolution.......................................... 90 Introduction................................................................................................................... 90 1
Materials and Methods.................................................................................................. 91 Results........................................................................................................................... 94 Discussion..................................................................................................................... 97 Conclusions................................................................................................................. 102 CHAPTER 7: MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes. ........................................................................................ 113 Introduction................................................................................................................. 113 Methods....................................................................................................................... 115 Results and Discussion ............................................................................................... 118 Summary..................................................................................................................... 123 An Additional Note..................................................................................................... 123 CHAPTER 8: Bird and Mammal Sex Chromosome Orthologs Map to the Same Autosomal Region in a Salamander (Ambystoma) ......................................................... 132 Introduction................................................................................................................. 132 Materials and Methods................................................................................................ 134 Results and Discussion ............................................................................................... 137 CHAPTER 9: Amphibian Sex Determination: Segregation and Linkage Analysis Using Members of the Tiger Salamander Species Complex (Ambystoma mexicanum and A. t. tigrinum). ........................................................................................................................ 145 Introduction................................................................................................................. 145 Materials and Methods................................................................................................ 147 Results......................................................................................................................... 150 Discussion................................................................................................................... 153 CHAPTER 10: Future Directions. .................................................................................. 161 Comparative Genomics............................................................................................... 161 met............................................................................................................................... 162 Sex............................................................................................................................... 163 REFERENCES ............................................................................................................... 164 Vita.................................................................................................................................. 181 2
Page 1 and 2: ABSTRACT OF DISSERTATION Jeramiah J
Page 3 and 4: ABSTRACT OF DISSERTATION AMBYSTOMA:
Page 5 and 6: RULES FOR THE USE OF DISSERTATIONS
Page 7: AMBYSTOMA: PERSPECTIVES ON ADAPTATI
Page 11 and 12: LIST OF FIGURES Figure 2.1, Results
Page 13 and 14: LIST OF FILES File Name Size Supple
Page 15 and 16: under which the female phenotype is
Page 17 and 18: CHAPTER 2: From Biomedicine to Natu
Page 19 and 20: Materials and Methods cDNA library
Page 21 and 22: minimum 100 bp match length, and 85
Page 23 and 24: indeed, there were approximately tw
Page 25 and 26: Informatic searches for regeneratio
Page 27 and 28: To identify SNPs between species, i
Page 29 and 30: ESTs and to assess likelihood that
Page 31 and 32: Table 2.1: Tissues selected to make
Page 33 and 34: 26 Table 2.2 (continued) Locus ID F
Page 39 and 40: 32 Marker ID Primers a Table 2.3 (c
Page 41 and 42: 34 Table 2.6: Top 20 contigs with t
Page 43 and 44: Table 2.8: Functional annotation of
Page 45 and 46: 38 Table 2.9: Ambystoma contigs tha
Page 47 and 48: 40 TABLE 2.9 (continued) Ambystoma
Page 49 and 50: 42 Table 2.9 (continued) Ambystoma
Page 51 and 52: Table 2.10 (continued) A. mexicanum
Page 53 and 54: Figure 2.3: Results of BLASTN and T
Page 55 and 56: CHAPTER 3: A comprehensive EST Link
Page 57 and 58: Materials and Methods Study species
Page 59 and 60:
additionally constrained to flank a
Page 61 and 62:
linkage groups that consisted of on
Page 63 and 64:
combined map length of LG1 and LG2
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needed to elucidate fully the effec
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and BLAST alignments can also be ob
Page 69 and 70:
Table 3.2: Distribution of markers
Page 71 and 72:
Figure 3.1: Statistical tests for M
Page 73 and 74:
Figure 3.2 (continued) 66
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CHAPTER 4: Sal-Site: Integrating Ne
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elated databases. To create the AES
Page 79 and 80:
as hyperlinks to separate marker fi
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Figure 4.1 - Schematic showing the
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CHAPTER 5: Evolution of Salamander
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metamorphic timing. These results s
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coding sequence for this EST was ob
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modes in WILD2, all individuals wer
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Genetic basis of discrete variation
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met alleles that increase or decrea
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Figure 5.1: Larval and adult phases
Page 97 and 98:
CHAPTER 6: Gene Order Data from a M
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sequence alignments between transla
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Results Identification of putative
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N=309 for Ambystoma-human), and 2)
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identifiable between Ambystoma and
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and more variable rates of genome r
Page 109 and 110:
Fissions derived within the mammali
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Table 6.2: Distribution of human/Am
Page 113 and 114:
Figure 6.2: Frequency distributions
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Figure 6.5: Oxford plot of the posi
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Page 119 and 120:
Figure 6.10: Oxford plot of the pos
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evolution) that has evolved since t
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Sequence Alignment Similarity searc
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Software Requirements: MapToGenome
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substantial proportion of zebrafish
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segments within which linear order
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shows much stronger correspondence
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Figure 7.2: Oxford plots of alignme
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Figure 7.4: Plot of the λ values f
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Figure 7.6: Oxford plots of vertebr
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CHAPTER 8: Bird and Mammal Sex Chro
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(XCR) (Graves, 1995; Ross et al, 20
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uild 2.1 (http://www.ncbi.nih.gov/m
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identified between amniote sex chro
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evidence for ancestral linkage of X
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Figure 8.1: An abridged phylogeny o
Page 151 and 152:
Page 153 and 154:
etween sex chromosomes, or by gene
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Rearing conditions At approximately
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AGGGCCTTCACATATTTTTCTGCAAAATAT). Th
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were females (respectively, Z A. me
Page 161 and 162:
Localization of the major sex-deter
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and possibly other members of the t
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Table 9.1: Segregation of sex among
Page 167 and 168:
Figure 9.3: Diagram of the crossing
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Other amphibians As genetic maps be
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REFERENCES Adrian, E. K. Jr. and B.
Page 173 and 174:
Collins, J. P., J. L. Brunner, J. K
Page 175 and 176:
Gardiner, D. M., M. A. Torok, L. M.
Page 177 and 178:
Humphrey, R.R., 1957 Male homogamet
Page 179 and 180:
Licht, L. E., L. A. Lowcock, 1991 G
Page 181 and 182:
Ohno, S., 1967 Sex chromosomes and
Page 183 and 184:
Sakata, N, Y. Tamori, M. Wakahara,
Page 185 and 186:
Straus, N. A., 1971 Comparative DNA
Page 187 and 188:
(superorder Afrotheria) reveals the
Page 189:
Page, R. B., J. R. Monaghan, A. K.
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