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pufferfish). In particular, the analyses that are presented within Chapter 6 on the
distribution of genes that presumably derive from a common ancestral gene that was
located within the genome of the species common ancestor; such genes are known as
orthologs. Comparing the orders of orthologs among these species reveals features of
ancestral genomes that have been conserved through time and permits an estimation of
the relative rates of genome rearrangement that have been experienced by different
vertebrate lineages. In Chapter 7, the methods that were used to identify orthologs in
Chapter 6 are improved somewhat and developed into a formal computer program called
MapToGenome. Chapter 8 presents what is arguably the most controversial finding that
has arisen from comparison of gene orders between Ambystoma and other vertebrates.
This is that the sex chromosomes of birds and mammals (which were presumed to have
evolved from independent ancestors, e.g. Fridolffson et al, 1998; Nanda et al, 1999;
Ellegren, 2000; Nanda et al, 2000; Graves et al, 2002; Nanda et al, 2002; Kohn et al,
2004; Handley et al, 2004; Khil and Camerini-Otero, 2005; Kohn et al, 2006) share many
orthologs with a single salamander linkage group. The distribution of orthologs on this
linkage group and within the genomes of other vertebrate species is highly consistent
with shared ancestry of the avian and mammalian sex chromosomes.
In Chapter 9, I describe experiments that have identified the location of the major
sex-determining factor of A. mexicanum. The fairly uniform patterns of recombination
that are observed within sex-linked regions of the genome imply that this sex-determining
factor evolved relatively recently, in contrast to the deep ancestry of avian and
mammalian sex chromosomes. I conclude this dissertation with a final chapter that
outlines some future avenues of research that can be extended from the works that are
described in Chapters 2-9.
Copyright © Jeramiah J. Smith 2007
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