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35 Table 2.7: Top 20 contigs with the most assembled ESTs. (A. t. tigrinum) Contig ID # ESTs Best Human Match E-value TigCluster_6298_Contig1 654 (NM_000519) delta globin E-38 TigCluster_10099_Contig2 193 (NM_001614) actin, gamma 1 propeptide 0 TigCluster_6470_Contig1 167 (NM_000558) alpha 1 globin E-39 TigCluster_9728_Contig2 142 (NM_000477) albumin precursor E-140 TigCluster_6594_Contig1 117 (NM_001402) eukaryotic translation elongation f1 0 TigCluster_5960_Contig1 91 (NM_001101) beta actin; beta cytoskeletal actin 0 TigCluster_7383_Contig1 77 (NM_001614) actin, gamma 1 propeptide 0 TigCluster_6645_Contig1 76 (NM_001063) transferrin 0 TigCluster_7226_Contig4 74 (NM_006009) tubulin, alpha 3 E-160 TigCluster_7191_Contig1 67 (NM_019016) keratin 24 E-89 TigCluster_10121_Contig1 64 (NM_005141) fibrinogen, beta chain preproprotein 0 TigCluster_6705_Contig1 63 (NM_000558) alpha 1 globin E-39 TigCluster_7854_Contig1 62 (NM_021870) fibrinogen, gamma chain is<strong>of</strong>orm E-121 TigCluster_6139_Contig1 52 (NM_001404) eukaryotic translation elongation f1 0 TigCluster_7226_Contig2 51 (NM_006009) tubulin, alpha 3 0 TigCluster_10231_Contig1 44 (NM_003018) surfactant, pulmonary-associated prot. E-08 TigCluster_6619_Contig1 36 (NM_000041) apolipoprotein E E-38 TigCluster_7232_Contig2 35 (NM_003651) cold shock domain protein A E-46 TigCluster_5768_Contig1 34 (NM_003380) vimentin E-177 TigCluster_9784_Contig3 32 |XP_218445.1| similar to RIKEN cDNA 1810065E05 E-15 35
Table 2.8: Functional annotation <strong>of</strong> contigs A. mexicanum A. t. tigrinum Molecular Function (0016209) antioxidant (0016209) 25 29 binding (0005488) 3117 2578 chaparone (0003754) 100 85 enzyme regulation (003023) 193 223 motor (0003774) 73 75 signal transduction (0004871) 344 375 structural protein (0005198) 501 411 transcriptional reg. (0030528) 296 221 translational reg. (0045182) 94 59 bone remodeling (0046849) 8 8 circulation (0008015) 23 78 immune response (000695) 182 263 respiratory ex. (0009605) 254 288 respiratory in. (0009719) 72 58 stress (0006950) Biological Process (0008150) Cellular (0009987) 263 320 activation (0001775) 4 6 aging and death (0008219) 158 148 communication (0007154) 701 696 differentiation (0030154) 31 20 extracellular mat. (0043062) 4 4 growth and main. (0008151) 1731 1445 migration (0016477) 8 14 motility (0006928) Developmental (0007275) 163 154 aging (0007568) 32 21 embryonic (0009790) 6 1 growth (0040007) 2 2 morphogenesis (0009653) 350 272 pigment (0048066) 13 26 post embryonic (0009791) 8 13 reproduction (0000003) 42 27 36
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 and 8: AMBYSTOMA: PERSPECTIVES ON ADAPTATI
Page 9 and 10: Materials and Methods..............
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: 34 Table 2.6: Top 20 contigs with t
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
Page 65 and 66: needed to elucidate fully the effec
Page 67 and 68: 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
Page 75 and 76: CHAPTER 4: Sal-Site: Integrating Ne
Page 77 and 78: elated databases. To create the AES
Page 79 and 80: as hyperlinks to separate marker fi
Page 81 and 82: Figure 4.1 - Schematic showing the
Page 83 and 84: CHAPTER 5: Evolution of Salamander
Page 85 and 86: metamorphic timing. These results s
Page 87 and 88: coding sequence for this EST was ob
Page 89 and 90: modes in WILD2, all individuals wer
Page 91 and 92: Genetic basis of discrete variation
Page 93 and 94:
met alleles that increase or decrea
Page 95 and 96:
Figure 5.1: Larval and adult phases
Page 97 and 98:
CHAPTER 6: Gene Order Data from a M
Page 99 and 100:
sequence alignments between transla
Page 101 and 102:
Results Identification of putative
Page 103 and 104:
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
Page 111 and 112:
Table 6.2: Distribution of human/Am
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Figure 6.2: Frequency distributions
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Figure 6.5: Oxford plot of the posi
Page 117 and 118:
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
Page 127 and 128:
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
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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
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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
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Figure 9.3: Diagram of the crossing
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Other amphibians As genetic maps be
Page 171 and 172:
REFERENCES Adrian, E. K. Jr. and B.
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Collins, J. P., J. L. Brunner, J. K
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Gardiner, D. M., M. A. Torok, L. M.
Page 177 and 178:
Humphrey, R.R., 1957 Male homogamet
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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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