You have isolated a gene that is important for the production of milk and wish to study its regulation. You examine the genomes of human, mouse, dog, chicken, pufferfish, and yeast and note that all genomes except yeast have an orthologous gene.
How would you identify the regulatory elements important for the expression of your isolated gene in mammary glands?

Consider the phylogenetic trees below pertaining to three related species (A, B, and C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene Z, gene duplications have occurred in all species. Define orthology and paralogy relationships for the different Z genes.

Consider the phylogenetic trees below pertaining to three related species (A, B, and C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene Y, a gene duplication occurred in the lineage leading to A after it diverged from that, leading to B and C. Are genes AY1 and AY2 orthologous or paralogous? Are genes AY1 and BY orthologous or paralogous? Are genes BY and CY orthologous or paralogous?

Consider the phylogenetic trees below pertaining to three related species (A, B, and C) that share a common ancestor (last common ancestor, or LCA). The lineage leading to species A diverges before the divergence of species B and C.

For gene X, no gene duplications have occurred in any lineage, and each gene X is derived from the ancestral gene X via speciation events. Are genes AX, BX, and CX orthologous, paralogous, or homologous?

You have isolated a gene that is important for the production of milk and wish to study its regulation. You examine the genomes of human, mouse, dog, chicken, pufferfish, and yeast and note that all genomes except yeast have an orthologous gene.

What does the existence of orthologous genes in chicken and pufferfish tell you about the function of this gene?

When the human genome is examined, the chromosomes appear to have undergone only minimal rearrangement in the 100 million years since the last common ancestor of eutherian mammals. However, when individual humans are examined or when the human genome is compared with that of chimpanzees, a large number of small indels and SNPs can be detected. How are these observations reconciled?

Symbiodinium minutum is a dinoflagellate with a genome size that encodes more than 40,000 protein-coding genes. In contrast, the genome of Plasmodium falciparum has only a little more than 5000 protein-coding genes. Both Symbiodinium and Plasmodium are members of the Alveolate lineage of eukaryotes. What might be the cause of such a wide variation in their genome sizes?

Researchers have compared candidate loci in humans and rats in search of loci in the human genome that are likely to contribute to the constellation of factors leading to hypertension [Stoll, M., et al. (2000). Genome Res. 10:473–482]. Through this research, they identified 26 chromosomal regions that they consider likely to contain hypertension genes. How can comparative genomics aid in the identification of genes responsible for such a complex human disease? The researchers state that comparisons of rat and human candidate loci to those in the mouse may help validate their studies. Why might this be so?

Homology can be defined as the presence of common structures because of shared ancestry. Homology can involve genes, proteins, or anatomical structures. As a result of 'descent with modification,' many homologous structures have adapted different purposes.

Under what circumstances might one expect proteins of similar function to not share homology? Would you expect such proteins to be homologous at the level of DNA sequences?