Major topics in molecular evolution fundamentals of molecular biology pdf the rates and impacts of single nucleotide changes, neutral evolution vs. 20th century with comparative biochemistry, and the use of “fingerprinting” methods such as immune assays, gel electrophoresis and paper chromatography in the 1950s to explore homologous proteins.
The content and structure of a genome is the product of the molecular and population genetic forces which act upon that genome. This hedgehog has no pigmentation due to a mutation. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, and translocations. Because mutations are extremely rare, they accumulate very slowly across generations. While the number of mutations which appears in any single generation may vary, over very long time periods they will appear to accumulate at a regular pace.
The resulting independent inheritance of genes results in more efficient selection, meaning that regions with higher recombination will harbor fewer detrimental mutations, more selectively favored variants, and fewer errors in replication and repair. Recombination can also generate particular types of mutations if chromosomes are misaligned. Damaged bases are first excised, the damaged strand is then aligned with an undamaged homolog, and DNA synthesis repairs the excised region using the undamaged strand as a guide. Gene conversion is often responsible for homogenizing sequences of duplicate genes over long time periods, reducing nucleotide divergence. Some existing variants have no effect on fitness and may increase or decrease in frequency simply due to chance. Many genomic features have been ascribed to accumulation of nearly neutral detrimental mutations as a result of small effective population sizes.
With a smaller effective population size, a larger variety of mutations will behave as if they are neutral due to inefficiency of selection. Selection can be the product of natural selection, artificial selection, or sexual selection. The principles of population genetics apply similarly to all types of selection, though in fact each may produce distinct effects due to clustering of genes with different functions in different parts of the genome, or due to different properties of genes in particular functional classes. For instance, sexual selection could be more likely to affect molecular evolution of the sex chromosomes due to clustering of sex specific genes on the X, Y, Z or W. Examples of such selfish elements include transposable elements, meiotic drivers, killer X chromosomes, selfish mitochondria, and self-propagating introns.
Genome size is influenced by the amount of repetitive DNA as well as number of genes in an organism. Explanations for the so-called paradox are two-fold. First, repetitive genetic elements can comprise large portions of the genome for many organisms, thereby inflating DNA content of the haploid genome. Secondly, the number of genes is not necessarily indicative of the number of developmental stages or tissue types in an organism.
An organism with few developmental stages or tissue types may have large numbers of genes that influence non-developmental phenotypes, inflating gene content relative to developmental gene families. Neutral explanations for genome size suggest that when population sizes are small, many mutations become nearly neutral. There is little evidence to suggest that genome size is under strong widespread selection in multicellular eukaryotes. Genome size, independent of gene content, correlates poorly with most physiological traits and many eukaryotes, including mammals, harbor very large amounts of repetitive DNA.
Birds, unlike humans, produce nucleated red blood cells, and larger nuclei lead to lower levels of oxygen transport. Bird metabolism is far higher than that of mammals, due largely to flight, and oxygen needs are high. Hence, most birds have small, compact genomes with few repetitive elements. Many bacteria have also experienced selection for small genome size, as time of replication and energy consumption are so tightly correlated with fitness. Many transposable elements are related to viruses, and share several proteins in common. Reduced linkage through creation of additional chromosomes should effectively increase the efficiency of selection.