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AMBYSTOMA: PERSPECTIVES ON ADAPTATION AND THE EVOLUTION OF VERTEBRATE GENOMES ________________________________________________ ABSTRACT OF DISSERTATION ________________________________________________ A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Arts and Sciences at the University of Kentucky By Jeramiah James Smith Lexington, Kentucky Director: Dr. S. Randal Voss, Associate Professor of Biology Lexington, Kentucky 2007 Copyright © Jeramiah James Smith 2007 ii
ABSTRACT OF DISSERTATION AMBYSTOMA: PERSPECTIVES ON ADAPTATION AND THE EVOLUTION OF VERTEBRATE GENOMES Tiger salamanders, and especially the Mexican axolotl (Ambystoma mexicanum), are important model organisms in biological research. This dissertation describes new genomic resources and scientific results that greatly extend the utility of tiger salamanders. With respect to new resources, this dissertation describes the development of expressed sequence tags and assembled contigs, a comparative genome map, a webportal that makes genomic information freely available to the scientific community, and a computer program that compares structure features of organism genomes. With respect to new scientific results, this dissertation describes a quantitative trait locus that is associated with ecologically and evolutionarily relevant variation in developmental timing, the evolutionary history of the tiger salamander genome in relation to other vertebrate genomes, the likely origin of amniote sex chromosomes, and the identification of the Mexican axolotl sex-determining locus. This dissertation is concluded with a brief outline of future research directions that can extend from the works that are presented here. Keywords: Ambystoma, Genome, Metamorphosis, Evolution, Sex Copyright © Jeramiah J. Smith 2007 iii
Page 1: ABSTRACT OF DISSERTATION Jeramiah J
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 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
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Figure 2.3: Results of BLASTN and T
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CHAPTER 3: A comprehensive EST Link
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Materials and Methods Study species
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additionally constrained to flank a
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linkage groups that consisted of on
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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
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Table 3.2: Distribution of markers
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Figure 3.1: Statistical tests for M
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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
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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
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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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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,
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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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