Chapter 10 Genome Evolution This chapter covers whole--genome sequencing, the evolution of genome size, the genome structure

of viruses, Bacteria, Archaea, and Eukaryotes. How to test for genome level selection and the C--value paradox about different genome sizes not relating to the complexity of the organism also will be introduced. Evolutionary genomics is defined here as the field of studying population genetics at the genome level and exploring the entire evolution of genomes over time. Whole-Genome Sequencing Whole--genome sequencing technology is one of the most important advancements in science in the past half century. This section details a short history of genome sequencing with a summary of current data available. We now have over 100 eukaryotic and over 1,000 prokaryotic genomes sequenced. What can we learn from all the data that is being collected? Resolving the Paradoxes of Genome Size C value paradox This section addresses the C value paradox and discrepancy between genome size and complexity. At first look, non--coding DNA accounts for much of the discrepancy, and among complex organisms there are somewhat similar amounts of coding DNA. However, the problem is more complex, and one hypothesis is that a balance must be found between replication speed and transposable elements proliferation. Organisms control it differently, and that becomes the variation in genome size. Michael Lynch hypothesized that population size and the ability to excise deleterious mutations also plays a role. Another paradox is that of gene number. As multicellular organisms increase in complexity, they do not increase the number of genes but do seemingly increase in transcription factors, suggesting that regulation of genes is more important than the number of genes. Why would regulation be more important than gene number in multicellular eukaryotic organisms? Why would population size be critical in genome size and buildup of non-- coding DNA? Content and Structure of Viral Genomes The genome structure of viruses is extremely diverse; some are made of DNA, others of RNA. Additionally, both types can be either single or double stranded. Because many viruses are RNA based, they are limited in size, with the upper end of RNA--based genomes about 30 kb. For DNA--based viruses, the upper end is 1000 kbstill very small for a genome. Viral genomes conserve space by overlapping genes as shown in Figures 10.9 and 10.10. Discussion Point: Because viruses have so much variation in their genomes, do you think they are all from the same lineage anciently, or could they have evolved multiple times? Content and Structure of Bacterial and Archaeal Genomes

Though Archaea is more closely related to Eukaryota, their genomes are very similar to Bacteria and so the text considers these two prokaryotic genomes together in this section. Prokaryotic genomes have 85%90% protein coding regions, lack introns, have few pseudogenes, and very few transposable elements. Along with their main circular chromosome, prokaryotes carry plasmids, which are small nonessential circular pieces of DNA. In prokaryotes, the size of their genome is very tightly correlated with the number of genes. Prokaryotes exchange genetic material with other organisms through horizontal (or lateral) gene transfer (HGT) by way of transduction, transformation, or conjugation (defined in text and illustrated in Figure 10.16). Though it can have negative impacts, HGT is a very important process in prokaryote evolution because it is not limited by species but allows an organism access to the entire bacterial genetic domain. Prokaryotic genomes show codon bias, especially toward genes that are the most highly expressed, and a large range of GC content. Hypotheses are offered to explain both phenomena. Content and Structure of Eukaryotic Nuclear Genomes Transposable Elements (transponsons) Transposons facilitate their own replication and movement within the genome

This section begins with an overview of the multiple genomes in Eukaryotes and a summary of what is found in all the different types of DNA that is stored within the eukaryotic genome. Transposable elements are defined, along with their types: Conservative: cut and paste Nonconservative: copy and paste LINE-1 elements: Retrotransposons SINE elements. Transposons are selfish genetic elements and their three methods of replicating themselves are explained and outlined in Figure 10.30. A critical point here is that these elements do not exist because they benefit the host organism; rather, they act as their own entity and survive at a cost to the host. The eukaryotic genome also differs from prokaryotes in their chromosome structure, which is reviewed alongside a hypothesis of the origin of centromeres and a discussion about the evolutionary consequences of having chromosomes. Introns also pose a significant difference from prokaryotes, and the text reviews hypotheses about their utility, why they exist, and why they might have arisen in the genome. Local recombination rates and recombination hotspots in the genome also are discussed.

Consequences of Transposition Loss of gene function Changes in gene order or chromosome structure Inversions, tanslocations, deletions, rearrangements

The centromere drive model Noncentomeric histones, highly conserved DNA histones at centromeres evolving rapidly

 Tests for Selection The different methods of testing for selection in DNA sequences of whole genomes is tackled here, as is distinguishing between purifying and positive selection and understanding ratios of nonsynonymous to synonymous changes in coding sequence. When the ratio is: (1) less than one, then purifying selection is taking place, (2) very close to one, then nearly neutral selection is taking place, (3) greater than one, then positive selection is happening. The text illustrates this principle with an example of positive selection in the Hawaiian silversword alliance group of plants. Another example of selection is provided in which selection is detected in specific amino acids of the protein sialidase from avian pathogens. To increase sensitivity for detecting positive selection, the McDonaldKreitman test is introduced to compare allele substitutions between species to the pattern of allelic polymorphism within species. This test, used on the genome level to characterize the types of selection operating on populations, has helped us understand the evolutionary differences between humans and chimps. Looking at broader patterns such as the distribution of allele frequencies enables scientists to see past selection events because allele frequencies are easily calculated by effective population size and mutation rate. When frequencies deviate from the distribution predicted, it is a sign of past selection events. Recent events of positive selection can be detected by finding blocks of extended haplotypes because a gene under intense positive selection will drag the nearby portions of the genome along with it.