RIG: Genome Size and Karyotype Evolution in Esociform Fishes

University Of Florida, Gainesville FL

Investigators

Abstract

The goal of this research is to determine factors that played a role in shaping the observed variation in genome size and karyotype among the fishes of the order Esociformes, a lineage that includes the widely recognized Northern Pike. Classical cytogenetic studies have demonstrated extensive diversity in the genomic characteristics of the species in this group of fishes. This variability, coupled with emerging consensus on the evolutionary relationships of the group makes it an ideal testing ground for emerging ideas on the underlying mechanisms and consequences of evolution at the chromosome and genome levels. The knowledge, data and materials that this project will generate will provide the foundation for broader investigations of the mode and tempo of chromosome and genome evolution in fishes, the most species-rich vertebrate lineage. The research has two specific goals: a) to determine the characteristics of the expansion of the genome in the esociform genus Umbra; and b) to produce protocols and reagents necessary for molecular cytogenetic studies of esociforms and their closest relatives. In the long term, these protocols may be applied to other lineages that exhibit unique features of genomic organization. The genome of two of the three species of Umbra comprise approximately two times as much DNA as those observed in other esociform genera. Determining the factors that contribute to this genome expansion is significant in light of the recently renewed interest in hypothesized relationships between organismal evolution and genome size. Preliminary data point to the amplification of some transposable element (TE) populations as a primary force leading to genome expansion in Umbra. The current project is designed to test that hypothesis using several complementary lines of evidence. Southern and dot blot experiments will reveal the relative contributions of different genomic components to genome expansion. Deep sequencing of PCR-targeted cloning experiments and phylogenetic analyses will be used to characterize the diversity and relative age of TE populations in representative esociform genomes. Finally, fluorescence in situ hybridization observations will help define features of any putative relationships between changes in genome size and karyotypic arrangement. Another interesting aspect of genomic variation among esociforms is the apparent change in chromosomal stability that underlies the diversity of karyotypes in the group. Specifically, classical cytogenetic studies and fossil evidence indicate that the karyotypes of members of the genus Esox have remained virtually unchanged for more than 60 million years; while at the other extreme, different populations of the esociform Dallia pectoralis show divergent karyotypes. Overall, diploid chromosome numbers among esociforms range from 22 to 78. This variability in karyotype and karyotypic stability highlights the value of the study of chromosome evolution in esociforms to uncover characteristics of the mechanisms that shape genome variation. This project initiates the task of determining the mode and rate of chromosomal evolution in esociforms through the development and application of chromosome specific DNA probes. This effort will also help determine the utility of cytogenetic data in fish phylogenetics. This project will examine processes that shape genetic variability at the scale of chromosomes and genomes. The research focuses on one group of fishes that is known to possess extensive and interesting diversity in their chromosomal and genomic characteristics. The insights gained from this work will lead to increased understanding of the mechanisms that are responsible for generating some of the genetic diversity that characterizes life and that constitutes the fuel for biological evolution. This research will help foster the professional development of a beginning investigator who is a member of a group underrepresented in science and a graduate student, who will gain hands-on experience with a set of scientific tools that currently are not in widespread use among evolutionary biologists in the U.S. Thanks to the investigator's affiliation with a natural history museum and his participation in its educational activities, the project's results will be made promptly and conveniently available to the general public.