Broughton, RichardZhang, Feifei2015-08-032015-08-032015-08http://hdl.handle.net/11244/15475Physiological processes may serve as mechanistic links between organismal genotypes and phenotypes. Accordingly, adaptations in genes involved in energy metabolism pathways may facilitate the evolution of organismal physiology and behavior with diverse energy requirements. Oxidative phosphorylation (OXPHOS) is one of the most ancient and conserved physiological functions and the major source of ATP in eukaryotic cells. My dissertation research explores how the genes involved in the OXPHOS system evolve from four perspectives: 1) investigating the co-evolution between mitochondrial and nuclear OXPHOS genes in fishes and mammals; 2) how natural selection affects OXPHOS genes in fishes with different swimming performance; 3) how environmental factors (temperature and salinity) and a life history trait (migration) affect the rates of evolution of mitochondrial OXPHOS genes in fishes; and 4) what are the patterns of positive natural selection on mitochondrial OXPHOS genes across bony fishes? The OXPHOS pathway is composed of protein subunits encoded by both mitochondrial and nuclear genomes. The successful interaction of OXPHOS proteins encoded by both genomes plays a central role in the maintenance of OXPHOS function. Under the compensatory model, deleterious substitutions at one nucleotide site could be compensated by a subsequent (or simultaneous) substitution at an interacting site. Generally, the mitochondrial genome evolves faster than the nuclear genome. If nonsynonymous substitutions of mitochondrial genes drive corresponding nonsynonymous substitutions of nuclear OXPHOS genes, one expects to see the acceleration of dN (nonsynonymous substitution rate) in nuclear OXPHOS genes relative to most nuclear genes not involved in OXPHOS. In Chapter 1, I examined the substitution rates of 13 mitochondrial OXPHOS genes, 60 nuclear OXPHOS genes, and 77 nuclear non-OXPHOS genes in 7 fishes and 40 mammals. I found that dN (mitochondrial OXPHOS genes) > dN (60 nuclear OXPHOS genes) > dN (77 nuclear non-OXPHOS genes), which supports the compensatory evolution hypothesis. However, results from two (out of five) OXPHOS complexes did not fit this pattern when analyzed separately. I found that the dN of nuclear OXPHOS genes for “core” subunits (those involved in the major catalytic activity) was lower than that of “noncore” subunits, whereas there was no significant difference in dN between genes for nuclear non-OXPHOS and core subunits. This latter finding suggests that compensatory changes play a minor role in the evolution of OXPHOS genes and that the observed accelerated nuclear substitution rates are due largely to reduced functional constraint on noncore subunits. Fishes exhibit extreme variation in swimming performance, ranging from “high-performance” tunas and billfishes to largely sedentary species like seahorses and flounders. Positive natural selection at the gene level (DNA sequence) favors adaptive substitutions that could benefit the fitness of the whole organism. Evidence of positive selection on OXPHOS genes has been associated with evolution of a variety of energetically demanding characteristics such as the origin of large brains in anthropoid primates, powered flight in bats, and adaptation to cold environment in polar bears. In Chapter 2, I examined all major branches on a phylogeny of fishes with diverse swimming performance, testing whether positive natural selection on mitochondrial and nuclear OXPHOS genes was associated with high-performance fishes. The results were not as predicted: positive selection was associated with branches leading to fishes with low and moderate performance, while negative (purifying) selection dominated on branches leading to fishes with high-performance. This result indicates a complicated evolutionary scenario of fish swimming and it could be possible that positive selection favors changes leading to low OXPHOS efficiency in low performance fishes. Understanding the factors that affect the rates of nucleotide substitution is central to evolutionary biology, population genetics, and mutation research. How the evolution of mitochondrial genes is affected by environmental factors or life history traits has not been examined in vertebrates at a broad phylogenetic scale. Fishes exhibit great variation in thermal environments (tropical, subtropical, temperate, and deep cold water), salinity (fresh water, brackish, and salt water), and migration (anadromous, catadromous, amphidromous, oceanodromous, potamodromous, and non-migratory) and the newly published fish tree of life provides a broad evolutionary background for such analyses. In Chapter 3, I investigated how the substitution rates of mitochondrial protein-coding genes are correlated with thermal environment, salinity, and migratory ability in 972 fish species. I found that tropical fishes have the highest dS and dN, while deep cold water fishes have higher dS and dN than subtropical and temperate fishes. This results suggest that substitution rates may not be only affected by temperature value (high or low), but may also be affected by the stability of the temperature (constant or variable). Similar patterns were also found among fishes from different salinity levels: fishes that can live in both freshwater and salt water (variable salinity environment) have lower dN and dS than fishes that live only in either freshwater or salt water (stable salinity environment). Migratory fishes have lower substitution rates than non-migratory fishes. This is probably because migratory fishes with high energy demands usually have high OXPHOS efficiency, thus OXPHOS genes are under strong constraint with low tolerance for substitutions. Among different types of migratory fishes, amphidromous fishes have the highest dN and dS, but the reason for this observation is not clear. The recently developed codon based branch-site model using maximum likelihood is a powerful tool for detecting positive selection on protein-coding sequences, providing an effective means of identifying the plausible candidate genes or residues for further testing. The OXPHOS pathway is the primary source of ATP in eukaryotic cells and ample evidence has shown positive selection on mitochondrial OXPHOS genes on branches leading to organisms with high energy demands or organisms that are well adapted to cold environments. To test if this is a general pattern, in Chapter 4, I identified 11 groups of bony fishes with some interesting characteristics that incur high energy costs (and two groups are adapted to cold environments), and examined the evidence for positive selection on mitochondrial OXPHOS genes on branches leading to the target group, its sister group, and the most recent common ancestor. In most cases, positive selection was found to be associated with the target group, but various patterns were identified. It appears that the pattern of positive selection is case specific and was determined by the particular evolutionary history of each group. Though there are many challenges to studying the molecular evolution of genes involved in OXPHOS due to its complexity, much can be learned about the functional importance and unique bi-genome composition of this fundamental system. More research is needed on nuclear OXHOS gene sequences, protein crystal structures, and direct measurement of OXPHOS efficiency. Studying OXPHOS opens a window to increase our understanding of basic life processes.Biology, Evolution, Natural Selection