1. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini MOLECULAR EVOLUTION Questo documento è pubblicato sotto licenza Creative Commons Attribuzione – Non commerciale – Condividi allo stesso modo http://creativecommons.org/licenses/by-nc-sa/2.5/deed.it

2. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 1. Homologous genes Genes with similar functions can be found in a diverse range of living things. Genes with similar functions can be found in a diverse range of living things. The great revelation of the past 20 years has been the discovery that the actual nucleotide sequences of many genes are sufficiently well conserved that homologous genes—that is, genes that are similar in their nucleotide sequence because of a common ancestry—can often be recognized across vast phylogenetic distances. The great revelation of the past 20 years has been the discovery that the actual nucleotide sequences of many genes are sufficiently well conserved that homologous genes—that is, genes that are similar in their nucleotide sequence because of a common ancestry—can often be recognized across vast phylogenetic distances. For example, unmistakable homologs of many human genes are easy to detect in such organisms as nematode worms, fruit flies, yeasts, and even bacteria. For example, unmistakable homologs of many human genes are easy to detect in such organisms as nematode worms, fruit flies, yeasts, and even bacteria.

3. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 2. Similarity of nucleotide sequences Homologous genes are ones that share a common evolutionary ancestor, revealed by sequence similarities between the genes. These similarities form the data on which molecular phylogenies are based. Homologous genes fall into two categories: Homologous genes are ones that share a common evolutionary ancestor, revealed by sequence similarities between the genes. These similarities form the data on which molecular phylogenies are based. Homologous genes fall into two categories:  Orthologous genes are those homologs that are present in different organisms and whose common ancestor predates the split between the species.  Paralogous genes are present in the same organism, often members of a recognized multigene family, their common ancestor possibly or possibly not predating the species in which the genes are now found. A pair of homologous genes do not usually have identical nucleotide sequences, because the two genes undergo different random changes by mutation, but they have similar sequences because these random changes have operated on the same starting sequence, the common ancestral gene. A pair of homologous genes do not usually have identical nucleotide sequences, because the two genes undergo different random changes by mutation, but they have similar sequences because these random changes have operated on the same starting sequence, the common ancestral gene. Two DNA sequences with 80% sequence identity

4. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 3. Reconstructing extinct gene sequences For closely related organisms such as humans and chimpanzees, it is possible to reconstruct the gene sequences of the extinct, last common ancestor of the two species. For closely related organisms such as humans and chimpanzees, it is possible to reconstruct the gene sequences of the extinct, last common ancestor of the two species. The close similarity between human and chimpanzee genes is mainly due to the short time that has been available for the accumulation of mutations in the two diverging lineages, rather than to functional constraints that have kept the sequences the same. The close similarity between human and chimpanzee genes is mainly due to the short time that has been available for the accumulation of mutations in the two diverging lineages, rather than to functional constraints that have kept the sequences the same. Evidence for this view comes from the observation that even DNA sequences whose nucleotide order is functionally unconstrained — such as the third position of “synonymous” codons — are nearly identical. Evidence for this view comes from the observation that even DNA sequences whose nucleotide order is functionally unconstrained — such as the third position of “synonymous” codons — are nearly identical.

5. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 4. Human and chimpanzee leptin genes For convenience, only the first 300 nucleotides of the leptin coding sequences are given. Only 5 codons (of 441 nucleotides total) differ between these two sequences, and in only one does the encoded amino acid differ. The corresponding sequence in the gorilla is also indicated. In two cases, the gorilla sequence agrees with the human sequence, while in three cases it agrees with the chimpanzee sequence. Leptin is a hormone that regulates food intake and energy utilization in response to the adequacy of fat reserves.

6. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 5. The ancestor sequence What was the sequence of the leptin gene in the last common ancestor of human and chimpanzee? What was the sequence of the leptin gene in the last common ancestor of human and chimpanzee? We know from other evidences that human and chimpanzee are more closely related one to each other than any of them to gorilla We know from other evidences that human and chimpanzee are more closely related one to each other than any of them to gorilla An evolutionary model that seeks to minimize the number of mutations postulated to have occurred during the evolution of the human and chimpanzee genes would assume that the leptin sequence of the last common ancestor was the same as the human and chimpanzee sequences when they agree An evolutionary model that seeks to minimize the number of mutations postulated to have occurred during the evolution of the human and chimpanzee genes would assume that the leptin sequence of the last common ancestor was the same as the human and chimpanzee sequences when they agree When they disagree, it would use the gorilla sequence as a tie-breaker. Therefore, the sequence of the common ancestor underwent three substitutions (at position 2, 4 and 5 of the five differences) in the human lineage, and two substitutions (at positions 1 and 3) in the chimpanzee lineage When they disagree, it would use the gorilla sequence as a tie-breaker. Therefore, the sequence of the common ancestor underwent three substitutions (at position 2, 4 and 5 of the five differences) in the human lineage, and two substitutions (at positions 1 and 3) in the chimpanzee lineage

7. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 6. Which individual’s DNA have to be compared? In comparisons between two species that have diverged from one another by millions of years, it makes little difference which individuals from each species are compared. In comparisons between two species that have diverged from one another by millions of years, it makes little difference which individuals from each species are compared.  For example, typical human and chimpanzee DNA sequences differ from one another by 1%. In contrast, when the same region of the genome is sampled from two different humans, the differences are typically less than 0.1%. For more distantly related organisms, the inter-species differences overshadow intra-species variation even more dramatically. However, each “fixed difference” between the human and the chimpanzee (i.e., each difference that is now characteristic of all or nearly all individuals of each species) started out as a new mutation in a single individual. How does such a rare mutation become fixed in the population, and hence become a characteristic of the species rather than of a particular individual genome? However, each “fixed difference” between the human and the chimpanzee (i.e., each difference that is now characteristic of all or nearly all individuals of each species) started out as a new mutation in a single individual. How does such a rare mutation become fixed in the population, and hence become a characteristic of the species rather than of a particular individual genome?

8. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 7. A mosaic of small DNA pieces The answer to the previous question depends on the functional consequences of the mutation. If the mutation has a significantly deleterious effect, it will simply be eliminated by purifying selection and will not become fixed. (In the most extreme case, the individual carrying the mutation will die without producing progeny.) The answer to the previous question depends on the functional consequences of the mutation. If the mutation has a significantly deleterious effect, it will simply be eliminated by purifying selection and will not become fixed. (In the most extreme case, the individual carrying the mutation will die without producing progeny.) Conversely, the rare mutations that confer a major reproductive advantage on individuals who inherit them will spread rapidly in the population. Because humans reproduce sexually and genetic recombination occurs each time a gamete is formed, the genome of each individual who has inherited the mutation will be a unique recombinational mosaic of segments inherited from a large number of ancestors. Conversely, the rare mutations that confer a major reproductive advantage on individuals who inherit them will spread rapidly in the population. Because humans reproduce sexually and genetic recombination occurs each time a gamete is formed, the genome of each individual who has inherited the mutation will be a unique recombinational mosaic of segments inherited from a large number of ancestors. The selected mutation along with a modest amount of neighboring sequence — ultimately inherited from the individual in which the mutation occurred — will simply be one piece of this huge mosaic. The selected mutation along with a modest amount of neighboring sequence — ultimately inherited from the individual in which the mutation occurred — will simply be one piece of this huge mosaic.

9. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 8. Functional Constraint Changes to genes that diminish an organism's ability to survive and reproduce are typically removed from the gene pool by the process of natural selection. Changes to genes that diminish an organism's ability to survive and reproduce are typically removed from the gene pool by the process of natural selection. Portions of genes that are especially important are said to be under functional constraint and tend to accumulate changes very slowly over the course of evolution. Portions of genes that are especially important are said to be under functional constraint and tend to accumulate changes very slowly over the course of evolution. Different portions of genes do accumulate changes at widely differing rates that reflect the extent to which they are functionally constrained. Different portions of genes do accumulate changes at widely differing rates that reflect the extent to which they are functionally constrained.  Changes at the nucleotide level of coding sequence that do not change the amino acid sequence of a protein are called synonymous substitutions.  In contrast, changes at the nucleotide level of coding sequence that do change the amino acid sequence of a protein are called nonsynonymous substitutions.

10. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 9. The molecular clock The integrated phylogenetic trees support the basic idea that changes in the sequences of particular genes or proteins occur at a constant rate, at least in the lineages of organisms whose generation times and overall biological characteristics are quite similar to one another. This apparent constancy in the rates at which sequences change is referred to as the molecular-clock hypothesis. Molecular clocks have a finer time resolution than the fossil record and are a more reliable guide to the detailed structure of phylogenetic trees than are classical methods of tree construction, which are based on comparisons of the morphology and development of different species. For example, the precise relationship among the great-ape and human lineages was not settled until sufficient molecular-sequence data accumulated in the 1980s to produce the tree that was shown

11. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 10. Rate of molecular evolution The constant rate of neutral substitution predicts that, if the number of nucleotide differences between two species is plotted against the time since their divergence from a common ancestor, the result should be a straight line with a slope equal to μ. The constant rate of neutral substitution predicts that, if the number of nucleotide differences between two species is plotted against the time since their divergence from a common ancestor, the result should be a straight line with a slope equal to μ. That is, evolution should proceed according to a molecular clock that is ticking at the rate μ. That is, evolution should proceed according to a molecular clock that is ticking at the rate μ. Because molecular clocks run at rates that are determined both by mutation rates and by the amount of purifying selection on particular sequences, a different calibration is required for genes replicated and repaired by different systems within cells. Because molecular clocks run at rates that are determined both by mutation rates and by the amount of purifying selection on particular sequences, a different calibration is required for genes replicated and repaired by different systems within cells. Most notably, clocks based on functionally unconstrained mitochondrial DNA sequences run much faster than clocks based on functionally unconstrained nuclear sequences because of the high mutation rate in mitochondria. Most notably, clocks based on functionally unconstrained mitochondrial DNA sequences run much faster than clocks based on functionally unconstrained nuclear sequences because of the high mutation rate in mitochondria.

12. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 11. Nucleotide substitutions in the β-globin gene A plot of synonymous and nonsynonymous substitutions for the β- globin gene. The slope for nonsynonymous substitutions is much lower than that for synonymous changes, which means that the mutation rate to nonsynonymous substitutions is much lower than that to synonymous ones. A plot of synonymous and nonsynonymous substitutions for the β- globin gene. The slope for nonsynonymous substitutions is much lower than that for synonymous changes, which means that the mutation rate to nonsynonymous substitutions is much lower than that to synonymous ones.

13. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 12. Differences among nucleotide substitution rates Nucleotide substitution rates differ among different portions of the genes Nucleotide substitution rates differ among different portions of the genes Highest rates are typical of pseudogenes, lowest rates are characteristic of non-synonymous substitutions Highest rates are typical of pseudogenes, lowest rates are characteristic of non-synonymous substitutions

14. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 13. Effect of functional constraints Average pairwise divergence among different regions of the human, mouse, rabbit, and cow beta-like globin genes

15. Genetica per Scienze Naturali a.a. 08-09 prof S. Presciuttini 14. Different clok rates in different proteins Another prediction of neutral evolution is that different proteins will have different clock rates, because the metabolic function of some proteins will be much more sensitive to changes in their amino acid sequence. Proteins in which every amino acid makes a difference will have smaller values of the neutral mutation rate than will proteins that are more tolerant of substitution. A comparison of the clocks for fibrinopeptides, hemoglobin, and cytochrome c. That fibrinopeptides have a much higher proportion of neutral mutations is reasonable because these peptides are merely a nonmetabolic safety catch, cut out of fibrinogen to activate the blood- clotting reaction. From a priori considerations, why hemoglobins are less sensitive to amino acid changes than is cytochrome c is less obvious