Genomes and Their Evolution

1. Chapter 21 Genomes and Their Evolution Questions prepared by Jung ChoiGeorgia Institute of Technology Louise PaquinMcDaniel College

2. Which of the following seems to be the known upper and lower size limits of genomes? • 1-2900 Mb • 1500-40,000 Mb • 1-580,000 Mb • 100 – 120,000 Mb • 100- 200,000 Mb

3. Genome SequencingWhich of these criteria have been used in selecting species whose genomes have been sequenced? • The species should be relevant for human health or well-being. • The species should have a relatively small genome. • The species should have an important ecological role. • The species may yield key evolutionary insights. • All of the above.

4. Genome Annotation and Gene PredictionIn sequencing the human genome (the first vertebrate genome to be sequenced), how were most protein-coding exons and genes identified and annotated? • by identifying long open reading frames • by identifying DNA sequences that were conserved in human, yeast, nematode, and fruit fly genomes • by mapping human mutations to the genomic DNA sequence • by comparison to human cDNA and EST sequences • all of the above

5. Comparative GenomicsOn average, the human and chimpanzee DNA sequences differ by 12 nucleotide substitutions per 1,000 base pairs (bp). Fossil evidence suggests that the hominid lineage diverged from the great apes 6 million years ago. Therefore, • the human lineage accumulated 2 mutations per 1,000 bp per million years. • a human protein-coding gene of 300 amino acids evolved through an average of 12 mutation events. • the mutation rate for humans is 2 mutations per 1,000 bp per million years. • All of the above are true. • None of the above are true.

6. Human EvolutionGiven the high degree of sequence similarity between the human and chimpanzee genomes, what might be the most important factor that drove hominid evolution in the past 6 million years? • small changes in proteins that affect their function or activity in important ways • changes in regulatory sequences that affect the timing and level of expression of genes • evolution of a few novel protein-coding genes that play key roles in neural development • gene duplication events that selectively expanded a set of genes favoring development of human traits • all of the above

7. Human Evolution Hypothesis TestingWhat experimental technique could be used to test the hypothesis that humans and chimpanzees have significantly different patterns of gene expression? • comparison of promoter DNA sequences • hybridization of RNA from various human and chimpanzee tissues to a DNA microarray containing all 21,000 human genes • analysis of single nucleotide polymorphisms (SNPs) in human and chimpanzee populations • comparison of human disease alleles to chimpanzee homologues

8. TransposonsThe human genome has about 7,000 Alu elements not found in chimpanzees, whereas the chimpanzee genome has about 2,300 Alu elements not found in humans. How might the Alu elements influence human evolution? • They may affect levels of expression of adjacent genes. • They may create new alternative splicing variants of a protein. • They may promote recombination events that induce chromosomal rearrangements, deletions, and duplications. • all of the above • none of the above: Alu elements are “junk” DNA

9. PseudogenesMany pseudogenes in vertebrate genomes lack introns. What process may account for such pseudogenes? • gene duplication followed by DNA splicing to remove introns • recombination between duplicated copies of genes • reverse transcription of a processed mRNA and insertion of the cDNA copy to a new chromosomal location • duplication events that involve just the exons • unequal crossing over between duplicated copies of genes