LG 4.1.pdf

1 Subject Code: Biology 3 Exploring Diversity Module Code: Module 4 (Evolutionary History and an Organism’s Genome) Lesson Code: Lesson 4.1 (Deducing Information Present from an Organism’s Geno...

1 Subject Code: Biology 3 Exploring Diversity Module Code: Module 4 (Evolutionary History and an Organism’s Genome) Lesson Code: Lesson 4.1 (Deducing Information Present from an Organism’s Genome) Time Limit: 60 minutes (2 sessions) TARGET ( (2 mins) After completing this module, you are expected to: 1. Evaluate how an organism’s genome reflect its evolutionary history 2. Use the information of a gene in interpreting evolutionary events 3. Appreciate the role of molecular evidence in tracing evolutionary history. HOOK (3 mins) Have you heard the news about the Golden State killer, who was convicted through the use of DNA technology? This was a man who was charged with various criminal cases as early as the 1970’s but was just only recognized and found guilty in the year 2018. Decades of searching was put to an end when California police officers decided to submit a sample DNA from the crime scene to a DNA database for comparison. Molecular technology has now revolutionized the way crimes are solved. With the help of DNA testing as well, cases such as paternity testing has also been done in a more accurate, non- invasive and faster approach. Comparison of DNA has allowed a more efficient way of solving crimes and paternity cases. Do you have any idea how this is being done? What DNA sequence is used for comparison? Know more about this in the following section. IGNITE (25 mins) Embedded in the genome are DNA sequences that codes instructions for specific living functions that are pass through from parent to offspring. In the process of evolution, these DNA sequences may undergo alterations through the processes of mutation and recombination. Mutation occurs when a DNA sequence has undergone a deletion or insertion of nucleotide bases. Recombination on the other hand occurs as a result of restructuring of a part of a genome. These changes in the gene contribute to genome evolution when they are passed from parents to offspring during reproduction. Because of this, molecular sequences have been valued as a useful approach in tracing the evolutionary history of a genome or of organisms in general. WHAT MAKES MOLECULAR COMPARISON VALUABLE? molecular data helps in comparing relationship between two distant group of organisms that do not share common morphological attributes; genomic approach allows reconstruction of anomalous or unresolved phylogenetic trees COMPARING RELATIONSHIP BETWEEN DISTANT GROUPS OF ORGANISMS Although organisms are not closely related to one another, they can still share genes in common. These common genes are referred to as conserved genes. Typically, these are DNA sequences that codes for critical functions in the development of an organism (ex: genes that codes for ATP production). The percentage of genes conserved in an organism are being used to show evolutionary relationship (see Figure 1). PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology ___: SY 2020-21  2 Figure 1. Genes Conserved (%) between humans and different animals. From “Evolutionary Relationships,” by Cornell, B, 2016. RECONSTRUCTION OF ANOMALOUS/UNRESOLVED TREES With genomic data of most organisms now made available in gene banks, scientists are now able to provide hypotheses to resolve anomalous trees. Anomalous trees are unrooted, which means that they can show us relationship among organisms but not their ancestry. To create an inferred tree from an anomalous tree, one should be able to identify an outgroup. An outgroup is an organism that shares homologous structures with all organisms in the tree but found to exist earlier than the organisms in the tree. Let us take for example the phylogenetic trees below. The tree on the left shows as an unresolved unrooted tree. Let us say the genes represented by the letters comes from human, chimpanzee, gorilla and orangutan. If we reconstruct this tree to make it rooted, we have to find a gene sequence that is homologous to these four. Based on gene evidences, we can put baboon as the outgroup. By this time, we have resolved the tree by DNA analysis. This tree is now known as an inferred tree, analyzed using genomic data. Figure 2. Reconstruction of unresolved tree (left panel) to an inferred tree (right) using an outgroup. Adapted from “Molecular Phylogenetics,” by Brown, TA. 2002. WHAT MOLECULAR SEQUENCES ARE USED IN MAKING COMPARISONS AMONG SPECIES FOR PHYLOGENETIC CONSTRUCTION/RECONSTRUCTION? Non-coding regions of the DNA are best used since this is where mutations typically occur Amino acid sequences of proteins are also being used (ex: cytochrome C) Some examples used by scientists are mitochondrial and genomic data, including messenger RNA, transfer RNA and ribosomal RNA PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology ___: SY 2020-21  3 WHAT DETERMINES THE TYPE OF DNA SEQUENCE TO BE USED FOR COMPARISON? Choosing the sequences to compare depends on the kind of relationship the scientist is trying to determine. For instance, when trying to deduce the relationship among groups of organisms that have diverge million years ago, a DNA sequence that mutates relatively slow will be used, such as the DNA that codes for ribosomal RNA. In contrast, when trying to compare the relationship of closely related organisms, mitochondrial DNA that mutates relatively fast are used to show evolutionary events. Earlier, we have found that both nucleic acid and amino acid sequences can be used to trace evolutionary history of organisms. Let us now look at some commonly used nucleic acid sequences and amino acid sequence utilized by scientists for genetic comparisons. Cytochrome c a protein that is loosely attached to the inner membrane of the mitochondria important in the processes of cell death (apoptosis) and metabolic pathway of oxidative phosphorylation is made up of 112 amino acids, 19 of these are arranged exactly in the same sequential position in organisms that have been tested the difference in the sequential identity and position of the remaining 93 amino acids in cytochrome c is attributed to mutations that took place during the process of evolution Figure 3. Cytochrome C difference between a human and a mouse rRNA (ribosomal RNA) commonly used because it changes relatively slow based on rRNA, fungi were found to be closer to animals than to green plants mDNA (mitochondrial DNA) mutates rapidly useful for exploring recent evolutionary events is present in both males and females but only the females can pass it to their offspring (maternal inheritance) useful in tracing the ancestry of races and identifying origins and relationships of organisms ex: Pima of Arizona, Yanomami of Venezuela and Maya of Mexico are closely related based on mitochondrial DNA comparative studies made by scientists PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology ___: SY 2020-21  4 Figure 4. Mitochondrial DNA passed from mother to child (single lineage) with males as carriers. From “Mitochondrial DNA tutorial,” by Genebase, 2020. HOW IS THE INFORMATION OF A GENE BEING USED TO INTERPRET EVOLUTION? In a phylogenetic tree represented by branches, each branch will show a period of genetic mutation. Given that a gene can mutate in a constant rate, we can then deduce the number of evolutionary changes that took place in a present organism just by counting the difference in their nucleic acid sequences. We just need to know the constant rate of mutation of a gene used for phylogenetic construction to interpret the time it took for the gene to diverge from a certain point in its evolution. To illustrate this better, let us look at this simple phylogenetic tree: Figure 5. DNA between two species changing at a constant rate of once per 25 million years. From “Understanding Evolution,” by University of California Museum of Paleontology, 2008. Figure 5 shows a gene that mutates at a rate of once per 25 million years. Given a sample set of gene sequences for 2 different species (see center panel), we can see that there was only one gene mutation that took place during the 25 million year- time frame (encircled nucleotide). If evolution continues at a constant rate, two gene mutations will now be observed for each species after 50 million years (see last panel). Thus, if we use molecular sequences to interpret evolutionary process, we can say that the higher the number of mutations or changes in the nucleotides or amino acid sequences, the farther is their relationship. This concept of genes evolving at different rates are represented by molecular clocks, which will be discussed further in the next module. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology ___: SY 2020-21  5 NAVIGATE (25 mins) Note: This assessment is graded It’s your time to test what you’ve learned. Provide what is asked on the following items. 1. If you are asked to compare the genetic sequences between monkeys and fungi, what molecular sequence are you going to use? Why? How about comparing genetic sequences of monkeys to humans, what genetic sequence will you use? Provide an explanation. 2. How is mitochondrial DNA inherited? Compare the inheritance pattern of a mitochondrial DNA to that of a nuclear DNA. 3. Stefan has launched a paternity suit to determine whether he is the father of an orphan residing in a monastery. Can mitochondrial DNA be used to trace the paternity? Explain. 4. Using the amino acid sequences in Cytochrome C provided in the following table, list the amino acid differences between a human and a selected animal; a. human and chicken =______ b. human and rabbit = ______ c. human and pony = ______ 5. Based from the genetic comparison you did in item no. 4, describe the relationship of humans to the compared animals. PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology ___: SY 2020-21  6 KNOT (5 mins) In summary, we have learned that; A genome contains the evolutionary history of an organism Genomic comparison is a more reliable approach that allows reconstruction of anomalous or unresolved phylogenetic trees Genetic evolution occurs at different rates among species belonging to the same lineage. For example, ribosomal RNA is being used to compare distant groups of species because it changes relatively slow, while mitochondrial DNA is being used likewise when comparing two closely related organisms. Comparing nucleotide or amino acid sequences of two or more species can provide data on the species’ evolutionary relationship. The branches of phylogenetic trees reflect genetic changes which can then be use to deduce the history of evolution among organisms. Mitochondrial DNA can only be inherited by the child from his/her mother. Males can be carriers but any mutations inherited by the father would never pass to his child. REFERENCES Brown, TA. (2002). Genomes. 2nd edition. Oxford: Wiley-Liss. Chapter 16, Molecular Phylogenetics. Retrieved from: https://www.ncbi.nlm.nih.gov/books/NBK21122/. Cornell, B. (2006). Evolutionary relationships. Retrieved from http://www.vce.bioninja.com.au/aos-4-change- over-time/evolution/evolutionary-relationships.html). Genebase, (2020). Mitochondrial DNA tutorial. Retrieved from https://www.genebase.com/learning- center/ancestry-mtdna/mitochondrial-dna-tutorial/. Reece, J., Urry, L., Cain, M., Wasserman, S., Minorsky, P., and Jackson, R. (2011). An organism’s evolutionary history is documented in its genome. In Campbell Biology, 9th Edition, pp. 594. University of California Museum of Paleontology, (2008). Understanding Evolution. Retrieved from (https://www.genebase.com/learning-center/ancestry-mtdna/mitochondrial-dna-tutorial/) Prepared by: JULNAFE B. LIBO-ON Position: SST 1 Campus: Western Visayas Campus Reviewed by: LANI M. SUYOM Position: SST IV Campus: Central Luzon Campus Approved by: MICHELLE DUCUSIN Position: SST V Campus: Ilocos Region Campus PHILIPPINE SCIENCE HIGH SCHOOL SYSTEM Biology ___: SY 2020-21