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31 Table 2.3: Presumptive human chromosome 17 loci that were mapped in <strong>Ambystoma</strong> Marker ID Primers a Diagnosis b LG c Symbol d RefSeq ID e E6E6 F-GAAAACCTGCTCAGCATTAGTGT R-TCTATTACCATAGCATTAATTGGCAG ASA ul PFN1 NP_005013 E-34 E5G5 F-CTATTTCATCTGAGTACCGTTGAATG R-TAATGTAGAACTAAATGGCATCCTTC E-CCATGGTGCAGGAAGAGAGCCTATAT PE (A) 23 CGI-125 NP_057144 E-56 Rpl19 F-GTCTCATTATCCGCAAACCTGT R-ATTCTCATCCTCCTCATCCACGAC SP 1 RPL19 NP_000972 E-67 Krt24 F-CCTAGAACATTACCAAAACAGACTCA R-AATGAAGAAGTATTGCATGTGAGAAC RD (Dpn II) 1 KRT10 NP_061889 E-17 Krt17 F-GAACTTGTTGGCAGGTTTCTCTT R-CTAGTGATAGGTTGGACATACCAGAG RD (AciI) 1 KRT17 NP_000413 E-146 E10C4 F-CTCCACTATTTAAAGGACATGCTACA R-TTAATATAGCACAACATTGCCTCATT E-TGCTACATTAATGTAATAAACGGCATCATC PE (A) 1 SUI1 NP_005792 E-48 E6E11 F-AAGAGAAGTTCCTAGATGAGTTGGAG R-TGAAGAGAGAACTCAAAGTGTCTGAT E-TCATGTTTTGCTCTGCTGTGCAGT PE (A) 1 HSPC009 NP_054738 E-26 E9A10 F-TGATAGTTTCTGGATTAAGACGAGTG R-CTTAGAGCCATTGTTACAAGATGTTC E-GTGATCTAGTGGGATCAAACCCTAAAGACC PE (T) 1 FLJ13855 NP_075567 E-15 E10C9 F-AAAGTGCCAAGAAGGAGATTAACTT R-GAGCTCAGAAAACAAGGCAGTAAC E-AAATGGATCTACGAGTAGACCTTGACCC PE (T) 9 NME1 NP_000260 E-71 31 E-value f
32 Marker ID Primers a Table 2.3 (continued) 32 Diagnosis b LG c Symbol d RefSeq ID e E-value f E9C9 F-GAGTCTCCTTTAGGATTGACGTATCT PE (T) 23 FLJ20345 NP_060247 E-17 R-GCTATGTGAGCAGAGATAAAAGTCAG E-GTTACAGCATCAGTGGGATGTGGTATGT E8C9 F-AGGATACCAACCTCTGTGCTATACAT PE (C) 15 H3F3B NP_005315 E-66 R-TAAATGTATTTACAAACCGAAAGCAA E-CGTGGCGAGCGTGCCTAGT E9C4 F-GTGGTTATTTGTAACATTTCGTTGAC PE (A) 8 SFRS2 NP_003007 E-40 R-AATTACATTTGGGCTTCTCAATTTAC E-TTTTTAAACGCGTAAAAATGTTAACAGA E6C5 F-CCGTAAATGTTTCTAAATGACAGTTG PE (G) 2 ACTG1 NP_001605 0 R-GGAAAGAAAGTACAATCAAGTCCTTC E-GATTGAAAACTGGAACCGAAAGAAGATAAA a – Sequences are 5' amplification primers, 3' amplification primers, or primer extension probes, and are preceded by F-, R-, and E- respectively. b – Genotyping methods are abbreviated: allele specific amplification (ASA), size polymorphism (SP), restriction digestion (RD), primer extension (PE). Diagnostic restriction enzymes and diagnostic extension bases are provided in parentheses. c – <strong>Ambystoma</strong> linkage group ID. "ul" designates markers that are unlinked. d – Official gene symbols as defined by the Human Genome Organization Gene Nomenclature Committee http://www.gene.ucl.ac.uk/nomenclature/. e – Best BLASTX hit (highest e-value) from the human RefSeq database using the contig from which each marker was designed as a query sequence. f – Highest E-value statistic obtained by searching contigs, from which EST markers were designed, against the human RefSeq database.
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 35 and 36: 28 Table 2.2 (continued) Locus ID F
Page 37: 30 Table 2.2 (continued) Locus ID F
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
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
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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
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Fissions derived within the mammali
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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
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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
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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
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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.
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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
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Sakata, N, Y. Tamori, M. Wakahara,
Page 185 and 186:
Straus, N. A., 1971 Comparative DNA
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(superorder Afrotheria) reveals the
Page 189:
Page, R. B., J. R. Monaghan, A. K.
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