GB2-Q3-Chapter-3-Evolutionary Relationship PDF

Systematics Based on CHAPTER Evolutionary Relationships of Organisms Q3 GENERAL BIOLOGY 2 3 D I S C U S S I O N : EVOLUTIONA RY RELATION...

Systematics Based on CHAPTER Evolutionary Relationships of Organisms Q3 GENERAL BIOLOGY 2 3 D I S C U S S I O N : EVOLUTIONA RY RELATIONSHIP Homo luzonensis: new species of ancient human discovered in the Philippines A species of small, ancient human, Homo luzonensis, has been described from the Philippines. It means a new branch has been added to the human evolutionary tree. The discovery of the fossils has been made in Callao Cave on the island of Luzon, Philippines, and echoes those made in 2004 when the diminutive human species Homo floresiensis was revealed. At the time, H. floresiensis sent shockwaves through the archaeological world as many questioned the likelihood of a small human species living on the island of Flores in Southeast Asia, but this latest find appears to feed into that narrative. The researchers have found 13 bones dating to about 67,000 years ago from at least three separate individuals in the sediment of a cave. These have been attributed to a new species of human called Homo luzonensis. The size of these remains suggests that the humans to whom they once belonged were also short of stature, not unlike those identified from H. floresiensis. Prof Chris Stringer, a merit researcher at the Museum and expert on human evolution, says, 'Given the small sample of fossils, some scientists will question the wisdom of creating a new species based on such limited material. 'Others such as me wonder whether the Luzon finds might eventually turn out to be a variant of the already known Homo floresiensis. We know that island isolation can be a catalyst for some odd evolutionary changes, including reversions to apparently primitive states. 'Nevertheless, for the moment it is probably reasonable to accept the new species while awaiting more finds.' Human evolution: a branching tree In recent years, the timeline of human evolution has shifted from being that of a simple tree as new species evolved and branched off, to something of a thicket. More and more ancient human species have been found to survive to within the last 100,000 years, suggesting that in some places, at least, there may have been significant overlap between our own ancestors and these ancient species. Southeast Asia, in particular, was once home to numerous species of human. In an early migration out of Africa, the incredibly successful Homo erectus made it to China and Indonesia, while it is thought that the more enigmatic Denisovans (a relative of the Neanderthals) may even have reached the vicinity of Papua New Guinea. The seafaring ability of these early humans was often called into question, until H. floresiensis was found on of the island of Flores. When the small humans were alive, there would have been a deep channel isolating the island, raising the question of whether the species' ancestors rafted across or were actively exploring the region. The presence of H. in the Philippines only adds to this, as the island of Luzon has never been attached to the Asian mainland, meaning that their ancestors must have crossed the ocean somehow. Meet Homo The cave in which H. was found was first explored in 2003. When the researchers uncovered nothing of note after excavating a few of the sediment they abandoned the site. With no reason to assume that ancient humans had once made it over to Luzon, there was no reason to explore further. That was until the human remains found on Flores hit the headlines. Suddenly, it was shown that ancient humans could reach these seemingly inaccessible islands, so the researchers went back to Callao Cave in 2007 to dig a little deeper. In a layer of animal bones that dated to 67,000 years ago, they made the discovery of a nearly complete human foot bone. Further excavations revealed more human material. Prof Philip Piper from the Australian National University, and co-author of the paper published in Nature, says, 'The fossil remains included adult finger and toe bones, as well as teeth. We also recovered a child's femur. There are some really interesting features - for example, the teeth are really small. 'The size of the teeth generally - though not always - reflect the overall body-size of a mammal, so we think Homo was probably relatively small too. 'Exactly how small we don't know yet. We would need to find some skeletal elements from which we could measure body-size more precisely.' The features of the remains show an intriguing mix of both modern and ancient aspects. For example, while the teeth look more like those of modern humans, the hands and feet seem to match more closely with the australopithecines, who last walked the earth some two million years ago in Africa. The finding of the remains of another short human on a different Southeast Asian Island, coupled with the primitive features, raises intriguing questions. Are the ancient humans on Flores and those on Luzon closely related? Or are they separate species that have both succumbed to island dwarfism? 'Some will argue that the primitive features of H. are evidence of a pre-Homo dispersal out of Africa, perhaps more than two million years ago,' says Chris. 'H. and H.luzonensis would represent some of the last survivors of that primitive early wave, lingering on at the fringes of the inhabited world. 'Others would prefer to regard these island forms as descendants of Homo erectus, subject to isolation and island dwarfing over a considerable period of time.' Only with the discovery of more ancient human remains on both Luzon and other Southeast Asian islands will the answers to some of these questions begin to be. (Source: https://www.nhm.ac.uk/discover/news/2019/april/new-species-of-ancient-human-discovered-in-the-philippines.html)  INTRODUCTION All life on Earth arose from a single common molecule. The sequence of bases in a gene ancestor and our genes reflects this shared determines the order of amino acids in a protein, ancestry. As species differentiated over and the order of amino acids acts as the blueprint evolutionary time, the DNA sequences in their for protein assembly. Because the DNA sequence genes acquired slight changes. According to determines a protein's amino acid sequence, a evolutionary theory, these changes accumulate gene shared by two closely related organisms over time: species that diverged from each other should have similar, or even identical, amino acid long ago have more differences in their DNA than species that diverged recently. Scientists use this sequences. The sequences of amino acids in a degree of difference as a molecular clock to help protein determine its function. The more similar the them predict how long species split apart from one sequence between two organisms, the more similar another. In general, scientists say the longer two the function of their protein, the more similar their species split, the more distantly related they are. function in each organism. That is because closely Scientists collect accurate information that related species most likely diverged from one allows them to make evolutionary connections another recently in the evolutionary span. Thus, among organisms. Darwin proposed that the they have not had as much time to accumulate evolutionary history of life forms a branching tree random mutations in their genetic codes. For years, with many levels, in which all species can be traced scientists have used DNA and amino acid back to an ancient common ancestor. Phylogeny sequences to decipher relationships between describes the evolutionary relationships between closely related species, such as different types of groups of organisms being compared. reptiles, birds, and even bacteria. The approach, Morphologic evidence (form and function) and called "molecular phylogeny," compares genetic evidence among others are used by sequence data and ranks organisms' degree of scientist to trace evolutionary relationships among relatedness based on the differences in their DNA organisms. 3.1.1 CLADISTICS You have learned from the previous lesson Scientist organize traits using a system that similar structures can be either homologous or called cladistics. This system sorts of organisms analogous. Homologous structures are structures into clades: groups of organisms that descended that are similar in related organisms because they from a single ancestor. A diagram showing were inherited from a common ancestor while evolutionary relationships within one or more clades analogous structures are structures that are is called a cladogram. Consider the cladogram of similar in unrelated organisms. The structures are insect phylogeny shown in figure 1. According to similar because they evolved to do the same job, this cladogram, beetles were the first insect to not because they were inherited from a common branch off from a common ancestor. Then, the ancestor. For example, the bones in the front flipper group that includes wasps, bees, and ants of a whale are homologous to the bones in the branched off. Finally, flies branched off from their human arm. These structures are not analogous. common ancestor with butterflies and moths. All insects can be considered a clade because they The wings of a butterfly and the wings of a bird are have a common ancestor. Butterflies, moths, and analogous but not homologous. Some structures flies can also be considered a clade for the same are both analogous and homologous: the wings of reason. a bird and the wings of a bat are both homologous Figure 1. Cladogram of and analogous. Scientists must determine which Insect Phylogeny. Based type of similarity a feature exhibits to decipher the on this cladogram, flies shared a more recent phylogeny of the organisms being studied. common ancestor with butterflies and moths than either group shared 3.1 CLADISCTICS Cladogram Definition with other insects. What other evolutionary A cladogram is the relationships does the With the advancement of DNA technology, graphical representation cladogram reveal? Retrieved from: the area of molecular systematics, which describes of the hypothetical https://tinyurl.com/xzf the use of information on the molecular level relationship (phylogenetic h392u including DNA analysis, has blossomed. Recall that relationship) between DNA is a molecule made up of four types of units different groups of organisms. It is used in the called bases. The four bases—adenine (A), phylogenetic analysis of organisms to determine the evolutionary relationship between them. The cytosine (C), guanine (G) and thymine (T)— cladogram is derived from Greek words clados and collectively make up the DNA "alphabet." Genes gramma where ‘clados’ means branch and are distinct locations along the length of a DNA ‘gramma’ means characters. It is an unscaled representation of a phylogenetic analysis where Nodes indicate the bifurcating branch point of only the topography of the diagram matters. divergence in all cladograms. However, it doesn’t have any time axis and is Thus, a node exists in each point where a group instead a simple diagram that summarizes a pattern of organisms divides or separate into further of characters among different organisms. Although different groups. a cladogram includes hypothetical ancestors to derive a relationship, it is the starting point for Clade/Ingroup further analysis. Clades are groups of organisms or genes that include the most recent common ancestor of all Features of a Cladogram its members and all of the descendants of that The trees that result from the cladistic analysis most recent common ancestor. are relative statements of relationship and do A clade is made up of an ancestor and all its not indicate ancestors or descendants. E.g., it descendants. hypothesizes that birds and mammals are It includes a particular node and all its connected related but not that mammals evolved from branches. birds or that birds evolved from mammals. In a cladogram, branch lengths are not Taxon/Outgroup proportional to the number of evolutionary A taxon or an outgroup is the most distantly changes and thus have no phylogenetic meaning. The external taxa of a cladogram related group of animals that isn’t necessarily a line up neatly in a row or a column. clade. Cladograms are generated by the analysis of This functions as a point of reference or morphological characters of the organisms and comparison for the rest of the cladogram. DNA or RNA sequencing data. Recently, however, computational phylogenetics is also Branches used in the combination of the existing A branch in a cladogram is a line that connects characters for the generation of cladograms. all the other parts of the cladogram. Cladograms are the assumptions for the The branch length in some cases represents preparation of phylogenetic trees. the extent of divergence or the extent of the Even though cladograms are of different relationship among different taxa. shapes, they all consist of lines that branch off from other lines representing the hypothetical Trait, Feature or Character ancestors of different organisms. Attributes of an organism that are expressed by genes and/or influenced by the environment. Parts of a Cladogram Traits include physical attributes of an organism A cladogram is a diagram consisting of the following such as hair color, leaf shape, size etc., and parts: behavioral characteristics such as bird nesting. Clade/ Branch/es How to Make a Cladogram? Ingroup (Constructing Cladograms) As discussed, cladograms can be generated Taxon/ either based on the morphological characteristics Outgroup or molecular evidence like DNA, RNA or protein sequencing. Therefore, on the basis of the characters used in Node the cladograms, these can be made in two different ways, by using morphological/structural characters and by using molecular characters. Traits/Features/Characters Root Root A root is the initial common ancestors of all the organisms in a cladogram. A root is the starting point for any given cladogram. However, the root might also indicate that it comes from some other larger clades. Node Each node is a hypothetical ancestor that gives rise to two or more daughter taxa. Figure 2. Parts of a Cladogram Retrieved from: https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules /Phylogenetics/phylo7.html Using Morphological/Structural Characters There are three steps that will help you build a cladogram. Thumb: Human Step One “The Table”: Hair: Tiger First, you need to make a “characteristics chart” Legs: Frog that helps you analyze which characteristics each Backbone: Catfish species has. Fill in a “x” for yes it has the trait and “o” for “no” for each of the organisms below. Outgroup: Slug Then you count how many times you wrote yes for each characteristic. Those characteristics with a Step Three “The Cladogram”: This step converts large number of “yeses” are more ancestral the Venn Diagram into cladogram. The traits are characteristics because they are shared by many. written on the main line, and species go on the Those traits with fewer yeses, are shared derived branches. On the cladogram below, try to put all the characters, or derived characters and have characters and the species in the correct evolved later. evolutionary history. Tiger Human Frog Catfish Opposable Thumb Slug Hair Step Two “The Venn Diagram”: This step will help you to learn to build cladograms, Legs but once you figure it out, you may not always need to do this step. Backbone Draw a multi-circular Venn diagram. You will need as many circles as there are characters. 3.2 TREE OF LIFE: THREE DOMIAN SYSTEM Organisms that ever existed on this planet are related to other organisms in a branching evolutionary pattern called the tree of life. To Start with the character that is shared by all the decipher this relatedness between the diversity of taxa on the outside. (You will want to make this a organisms, both living and extinct, “tree thinking” is large circle.) invaluable. Tree thinking, or phylogenetic thinking, helps us unknot the branching evolutionary relationships between surviving or extant species, while thinking about the passage of time and the ancestors of each of those living species. Thumb Hair Legs Backbone Inside each box, write the species that have only that set of characters. Thumb: Human Hair: Tiger Figure 3. Phylogenetic tree of life built using ribosomal Legs: Frog RNA sequences, after Carl Woese. Backbone: Catfish Retrieved from: https://images.app.goo.gl/mLiLy4xtr28ZKyQx5 On the outside of the Venn Diagram, write the The Three Domain System, developed by outgroup. This is a group of organisms that do not Carl Woese in 1990, is a system for classifying share any traits and serve as a comparison to the biological organisms. As scientists learn more about phylogeny you are looking at. Venn Diagram organisms, classification systems change. Genetic Example: sequencing has given researchers a whole new way of analyzing relationships between organisms. immune system. They are also important for the The current Three Domain System groups recycling of nutrients in the global ecosystem as organisms primarily based on differences in they are primary decomposers. They have unique ribosomal RNA (rRNA) structure. Ribosomal RNA cell wall composition and rRNA type. They are is a molecular building block for ribosomes. Under grouped into five main categories: this system, organisms are classified into three Proteobacteria: This phylum contains the domains and six kingdoms. It is generally thought largest group of bacteria and includes E. coli, that all cells came from a common ancestor cell Salmonella, Heliobacter pylori, and Vibrio. termed the last universal common ancestor bacteria. (LUCA). It eventually evolved into the domains Cyanobacteria: These bacteria are capable of Archaea, Bacteria, and Eukarya while the kingdoms photosynthesis. They are also known as blue- are Archaebacteria (ancient bacteria), Eubacteria green algae because of their color. (true bacteria), Protista, Fungi, Plantae, and Firmicutes: These gram-positive bacteria Animalia. include Clostridium, Bacillus, and mycoplasmas (bacteria without cell walls.) ARCHAEA DOMAIN Chlamydiae: These parasitic bacteria reproduce This Archaea domain contains single-celled inside their host's cells. Organisms include organisms. Archaea have genes that are like both Chlamydia trachomatis (causes chlamydia STD) bacteria and eukaryotes. Because they are very and Chlamydophila pneumoniae (causes similar to bacteria in appearance, they were pneumonia.) originally mistaken as bacteria. Like bacteria, Spirochetes: These corkscrew-shaped bacteria archaea are prokaryotic organisms and do not have exhibit a unique twisting motion. Examples a membrane-bound nucleus. They also lack internal include Borrelia burgdorferi (cause Lyme cell organelles, and many are about the same size disease) and Treponema pallidum (cause as and similar in shape to bacteria. Archaea syphilis.) reproduce by binary fission, have one circular chromosome, and use flagella to move around in EUKARYA DOMAIN their environment as do bacteria. Archaea differ The eukarya domain includes eukaryotes or from bacteria in cell wall composition and differ from organisms that have a membrane-bound nucleus. both bacteria and eukaryotes in membrane Eukaryotes have rRNA that is distinct from bacteria composition and rRNA type. These differences are and archaeans. Plant and fungi organisms contain substantial enough to warrant that archaea have a cell walls that are different in composition than separate domain. Archaea are extreme organisms bacteria. Eukaryotic cells are typically resistant to that live under some of the most extreme antibacterial antibiotics. Organisms in this domain environmental conditions. This includes within include protists, fungi, plants, and animals. hydrothermal vents, acidic springs, and under Arctic Examples include algae, amoeba, molds, yeast, ice. Archaea are divided into three main phyla: ferns, mosses, flowering plants, sponges, Crenarchaeota, Euryarchaeota, and Korarchaeota. insects, and mammals. Crenarchaeota include many organisms that are hyperthermophiles and thermoacidophiles. These archaea thrive in environments with great 3.3 PHYLOGENETIC TREE temperature extremes (hyperthermophiles) and in A phylogenetic tree is a hypothetical visual extremely hot and acidic environments representation of the relationship between different (thermoacidophiles.) organisms, showing the path through evolutionary Archaea known as methanogens are of the time from a common ancestor to different Euryarchaeota phylum. They produce methane descendants. Trees can represent relationships as a byproduct of metabolism and require an ranging from the entire history of life on earth, down oxygen-free environment. to individuals in a population. Trees that show Little is known about Korarchaeota archaea as species help us understand how new species form few species have been found living in places such from common ancestral species. The process of as hot springs, hydrothermal vents, and obsidian new species formation, called speciation, is the pools. starting point for a discussion of biological diversity. The natural endpoint will be extinction. Speciation BACTERIA DOMAIN leads to an evolutionary pattern that is something Bacteria are classified under the Bacteria like a forking road. A lineage may continue for many Domain. These organisms are generally feared generations and then splits, with each resulting because some are pathogenic. However, bacteria lineage taking its own path. Some paths end up are essential to life as some are part of the human leading to dead ends (extinction) while others microbiota. These bacteria perform vital functions, diverge many more times, leading to new lineages. such as enabling us to properly digest and absorb The result of this process is a tree-like structure that nutrients from the foods we eat. Bacteria that live on links together all species that have ever lived on the skin prevent pathogenic microbes from planet Earth. colonizing the area and aid in the activation of the  Step 2: Compare the sequences, to see how similar they are to each other. Start with sequence A and B, then C, and so on. Make a table showing the differences between sequences. The completed table is shown below. Figure 4. Hypothetical Phylogenetic Tree The horizontal branches in Figure 4 represent a lineage, which is a taxon, shown at the tip, and all its ancestors. The nodes or branch points are where lineages diverge, representing a speciation event from a common ancestor. The root node represents the most recent common ancestor of all the taxa represented on the tree. For example, branch point 3 represents the common ancestor of taxa A, B, and C. The position Step 3: Identify the sequences with the least of branch points 4 to the right of 3 indicates that taxa differences between them. We will infer that these B and C diverged after their shared lineage split are the sequences which are closely related to each from the lineage leading to taxon A. Taxa B and C other. The table above shows that sequence A and are sister taxa, groups of organisms that share an C and sequence B and E has the least differences. immediate common ancestor (branch point 4) and hence are closest relatives. Step 4: Draw the first groupings on the tree. Group Basal taxon refers to a lineage that A and C together to show the fact that these two diverges early in the history of a group and hence, sequences reflect the closest relationship with one like taxon G, lies on a branch that originates near another. Do the same with sequence B and E the common ancestor of the group. The lineage A leading to taxa D–F includes a polytomy, a branch C point from which more than two descendant groups B emerge. A polytomy signifies that evolutionary relationships among the taxa are not yet clear. Two E species are more related if they have a more recent common ancestor, and less related if they have a Step 5: Rework the table by combining the two less recent common ancestor. group sequences closest to each other as one individual. Then, determine the average difference BUILDING PHYLOGENETIC TREES that A and C show to each of the other sequences. To construct a tree, we’ll compare the DNA For example, both A and B showed 9 differences sequences of different species. Evolutionarily just like B and C, so, the average difference of the related species have a common ancestor. Before two sequences is 9. A and D showed 4 differences they split into separate species, they had the same while C and D had 5 differences, so, the average DNA. But as species evolve and diverge, they will difference of the two sequences is 4.5. Add the B/ E accumulate changes in the DNA sequences. We grouping and use the same process to complete the can use these changes in the DNA to tell how table. For example, B and E has an average closely related two species are. If there aren’t very difference of 9 in comparison to A/C. B to D and D many differences, they’re probably closely related. to E has an average difference of 6. If there are a lot of changes, they might be more distant relatives. Step 1: Align the DNA sequences that you’re going to compare together. Make sure you are comparing the same gene. This sequence alignment is often done with the help of computer programs. The strategy is to find the alignment that has the most matches and the least mismatches. Step 6: Identify the sequences with the least Figure 4 does not indicate that taxon C evolved differences between them based on the new table. from taxon B or vice versa. We can only infer that We can see that the A/ C group has only 4.5 the lineage leading to taxon C and the lineage differences to D, so this is the next close leading to taxon B both evolved from the common relationship in our tree. ancestor. That ancestor, which is now extinct, was A neither taxon B nor taxon C. C Organisms are classified based on their D different characteristics such as morphological and molecular level. They are grouped for the purpose B of identification and phylogenetic analysis. E Monophyletic, paraphyletic and polyphyletic are three groups that can be identified in phylogenetic Step 7: Rework the table again with the A/ C/ D trees. The monophyletic group consists of a most group together. Complete the table with the same recent common ancestor and its entire process. The average difference of A/ C to B is 9 descendants. It is a natural group that is found in while the average difference B/ E to D is 6. So, the phylogeny. The paraphyletic group consists of a average difference of A/ C/ d to B/ E is 7.5. most recent common ancestor and some of its descendants. The polyphyletic group is an unnatural assemblage of unrelated organisms who lack a most recent common ancestor. Step 8: Identify the group with the least differences based on the newly reworked table. A/ C/ D group with the B/ E group has the least differences with the average of 7.5, so, we can add this in our tree. Taxon 1 Taxon 2 Taxon 3 A (Monophyletic) (Paraphyletic) (Polyphyletic) Figure 5. Three groups in identifying Phylogenetic Tree C D B 3.4 TAXONOMY E Early Classification Schemes Sequence F has an average difference of 10 and is Humans have probably always classified equally distantly related with all the other life. Thousands of years ago, people designated sequences. plants, animals, and fungi by whether they were A tasty and safe to eat, of medicinal value, or were foul-tasting or even poisonous. An early taxonomist C was Greek philosopher Aristotle (384–322 B.C.), D who organized five hundred types of animals B according to habitat and body form. His designations were rather subjective: he considered E animals that gave birth to live young and had lungs F as the pinnacle of living perfection. By the sixteenth century, explorers had Points to remember about Phylogenetic Trees discovered so many new species that Aristotle's It is intended to show patterns of descent, not plan could no longer suffice. Newer schemes phenotypic similarity. Although closely related continued to be based on what people could see, organisms often resemble one another due to but the characteristics considered were often more their common ancestry, they may not if their mystical than scientific. For example, an early- lineages have evolved at different rates or faced sixteenth-century botanical classification assigns a very different environmental conditions. high-ranking order to plantain (banana) because The sequence of branching in a tree does not "more than any other plant, it bears witness to God's necessarily indicate the actual (absolute) ages of omnipotence." John Ray (1627–1705) was an the species. We should interpret the diagram English naturalist who classified more than twenty solely in terms of patterns of descent. No thousand types of plants and animals. His highly assumptions should be made about when species descriptive method distinguished animals by their evolved or how much change occurred in each hoofs, nails, claws, teeth, and toes. Yet the inability lineage. to see microscopic distinctions and reliance on Do not assume that a taxon on a phylogenetic tree superficial similarities led him to group together evolved from the taxon next to it. Refer to figure 3. algae, lichens, fungi, and corals. A lichen is a compound organism that consists of an alga and a fungus, but a coral is an animal. Carolus Linnaeus (1707–1778) is the best-known taxonomist. Heavily influenced by John Ray, Linnaeus compared, contrasted, and meticulously listed types of organisms from his earliest childhood. He started his first botanical listing at age eight, which evolved into a series of publications called Systema Naturare, reaching twenty-five hundred pages by its tenth edition. Linnaeus distinguished plants by their sexual parts. He is most noted The table above illustrates how four species are classified using the present classification system. (Note that it is standard practice to italicize the genus for introducing the binomial name for a and species names) species, which includes an organism's genus and "specific epithet," an adjective that describes the species in some way. The human animal, according to Linnaeus's scheme, is Homo sapiens, sapiens meaning "wise." LINNAEAN SYSTEM OF CLASSIFICATION The evolution of life on Earth over the past 4 billion years has resulted in a huge variety of species. For more than 2,000 years, humans have been trying to classify the great diversity of Note: Most of us are accustomed to the Linnaean system of classification that assigns every organism a kingdom, phylum, class, order, family, genus and life. The science of classifying species. The Linnaean method is artificial since organisms are classified based organisms is called taxonomy. on morphological similarities and evolutionary relationships. Classification is an important step in understanding the present diversity and past evolutionary history of life on Earth. All modern classification systems have their roots in the Linnaean classification system. It was developed by Swedish botanist Carolus Linnaeus in the 1700s. He tried to classify all living things that were known at his time. He grouped together organisms that shared obvious physical traits, such as number of legs or shape of leaves. For his contribution, Linnaeus is known as the “father of taxonomy.” The Linnaean system of classification consists of a hierarchy of groupings, called taxa (singular, taxon). Taxa range from the kingdom to the species (see tables). The kingdom is the largest and most inclusive grouping. It consists of organisms that share just a few basic similarities. Figure 6. The Linnaean Classification Diagram Examples are the plant and animal kingdoms. The species is the smallest and most exclusive first letter is always capitalized (e.g. Canis) while the grouping. It consists of organisms that are similar specific epithet is not capitalized (e.g. familiaris). enough to produce fertile offspring together. Closely One can distinguish a species name from the way it related species are grouped together in a genus. is written. Species name can be in bold letters or underlined or italicized. Binomial Nomenclature Nomenclature refers to the practice of Examples: assigning scientific names. Binomial comes from the words “bi” meaning “two” and “nomen” meaning “name”. A species name consists of two parts: the genus or generic name and the specific epithet. The  3.5 RECOMBINAT DNA The REs cut the DNA molecules at a limited number of specific locations. It can TECHNOLOGY recognize the restriction site and cuts both DNA strands at precise points with a sticky Humans have successfully domesticated end (single-stranded end). These short selected plants and animals particularly in choosing extensions can form hydrogen-bonded base the desired traits. Traits that were considered pairs with complementary sticky ends on valuable (i.e. high fruit yield; high milk production, any other DNA molecules cut with the same etc.) were sought out and propagated. The enzyme (refer to figure 7). Here are the processes involved may include classical breeding common examples of REs: practices such as controlled pollination of plants a. EcoR1 (from Escherichia coli) cuts at and the mating of animals with desired traits. In 5’ GAATTC 3’ today’s modern science, molecular biology 3’ CTTAAG 5’ techniques are being employed in the insertion and b. BamH1 (from Bacillus expression of proteins in different organisms for amyloliquefaciens) cuts 5’ at various purposes. Genetic engineering involves the GGATTC 3’ use of molecular techniques to modify the traits of 3’ CCTAAG 5’ the target organism. The modification of traits may II. Selection of an appropriate vector or vehicle involve: which would propagate the recombinant A. Introduction of new traits into an organism DNA A new trait may develop after the gene The most common vector used in responsible for the trait is inserted. Ex. glowing propagating the desired gene (e.g. circular mice- inserted with the bioluminescent gene plasmid in bacteria with a foreign gene of from jellyfish interest) is the bacteria and yeast. These B. Enhancement of a present trait by increasing organisms are widely used because they the expression of the desired gene can reproduce exponentially in a short A present trait that is slightly expressed may be period. enhanced after the insertion of an enhancer III. Ligation of the gene of interest with the gene. Ex. golden rice-naturally rice can vector synthesize beta-carotene in low concentration The ligation of the two DNA strands (e.g., but may be enhanced after inserted with a gene from animal and cut bacterial plasmid) is from the plants with high beta-carotene (e.g., permanently sealed by an enzyme DNA carrots) which is a precursor of Vitamin A ligase. This catalyzes the formation of synthesis. Golden rice helps in solving Vitamin covalent bonds of the sugar phosphate A deficiency in children. Insufficient Vit. A lead backbones that results in a stable to blindness. recombinant DNA molecule (e.g., bacterial C. Enhancement of a present trait by disrupting plasmid). the inhibition of the desired genes’ IV. Transfer of the recombinant plasmid into a expression host cell The expression of the trait may be disrupted by The cell carries out replication to make huge introducing an inhibitor (stops/ slows down the copies of the recombined plasmid. The expression of the trait) like the ripening recombinant plasmid can be transferred processes in tomatoes. Ex. In Flavr-Savr through biolistic, heat shock treatment, or tomatoes- an inhibitor (i.e., antisense RNA) electroporation depending on the recipient disrupts the expression of the enzyme that organism. causes degradation of pectin in cell walls, V. Selection process to screen the cells thereby delaying the softening of the fruit thus, containing the gene of interest increasing the shelf life. Cells containing the gene will be screened through selection markers like antibiotic gene, fluorescent gene, or through a polymerase chain reaction of the plasmids. VI. Sequencing of the gene to find out the primary structure of the protein Once the cells with the gene have been identified, DNA sequencing is employed to separate pieces of DNA that differ in length Figure 7. Genetically modified organisms: Golden rice by only one base. The most common (www.irri.org) and Flavr Savr tomato (http://ucce.ucdavis.edu/) technique is through gel electrophoresis GENERAL OUTLINE OF RECOMBINANT DNA wherein the DNA to be sequenced is placed TECHNOLOGY at one end of a gel - a slab of a gelatin-like I. Cutting or cleavage of target DNA sequence substance. by restriction enzymes (REs) or restriction endonucleases  Figure 8. Biolistic method in plants. (https://www.intechopen.com/chapters/30876) Figure 7. Steps in recombinant DNA technology (https://creativecommons.org/licenses) Figure 9. Heat shock vs. Electroporation of Plasmid Insertion Methods of plasmid insertion to the target (https://www.thermofisher.com) organism 1. Biolistic. In this technique, a “gene gun” is used METHODS TO SCREEN RECOMBINANT CELLS to fire DNA-coated pellets on plant tissues 1. Selection of plasmid DNA containing cells (Figure 8). Cells that survive the bombardment A selection marker (e.g., AMP ampicillin and can take up the expression plasmid-coated resistance gene) is included in the plasmid DNA pellets and acquire the ability to express the (refer to Figure 3). This allows only “transformed” designed protein. cells to survive in the presence of the antibiotic 2. Plasmid insertion by Heat Shock Treatment. (e.g., ampicillin). Plating the plasmid-cell solution This technique is used to transfer plasmid DNA on antibiotic-containing media will select for into the bacteria. The cell is exposed to a “heat these “transformants” and only allow plasmid- shock” (rapid rise and drop of temperature) which containing cells to grow and propagate into increases and decreases the pore sizes in the colonies. membrane. The plasmid DNA near the 2. Selection of transformed cells with the membrane surface is taken into the cells by this desired gene process. The cells that took up the plasmids Certain inserted genes within the plasmids acquire new traits and are said to be provide visible proof of their presence. Some “transformed”. inserted genes also produce colored (e.g., 3. Electroporation. This technique follows a chromogenic proteins) or fluorescent products similar methodology as Heat Shock Treatment, that label the colonies/cells with the inserted but the expansion of the membrane pores is gene. done through an electric “shock”. This method is 3. Polymerase Chain Reaction (PCR) detection commonly used for the insertion of genes into of plasmid DNA mammalian cells. Figure 5 in the next page The presence of the desired gene in the inserted shows the differences in heat shock and plasmids may be confirmed using PCR electroporation technique of plasmid insertion to amplification. The DNA from the cells will be used the host cell. in producing large copies of the gene which will  confirm the presence of the gene in the samples. loss of enzyme function. Each cycle of PCR doubles (A detailed discussion on the steps of PCR is the amount of the target sequence. found in the succeeding pages). Detection of the A typical PCR experiment uses about 35 presence of the SARSCOV 2 or the COVID-19 cycles of amplification. This increases the original virus in the swab or saliva of the patient use RT- amount of the target sequence by 235 (i.e. ~34 PCR or Reverse Transcriptase-Polymerase billion) times. Unlike DNA replication in vivo, PCR Chain Reaction. However, before the DNA reactions do not use too many helper enzymes such amplification of the said virus, its genetic material as helicases and gyrases to help denature and must undergo reverse transcription (meaning stabilize the template DNA strands. The cyclic from RNA to DNA using the enzyme reverse heating of the samples is meant to provide the transcriptase) because it is an RNA virus. This is physical separation of the template DNA strands done to obtain the complementary DNA which through heat denaturation of the inter-strand H- can undergo base pairing of the PCR primer. bonds. Running the DNA through PCR cycles produces multiple copies of the gene which confirms the Steps in Polymerase Chain Reaction presence of the virus in the sample hence the Step 0: Undenatured Template at Temp ~ 54 °C patient is considered positive. The complementary sequences of template double- stranded (ds) DNA strands are held together by H- POLYMERASE CHAIN REACTION (PCR) bonds. PCR amplification is an in-vitro (occur outside a living organism) method that simulates Step 1: Template denaturation at Temp ~ 95 °C DNA replication in vivo (occur inside a living The H-bonds between DNA complementary organism). It utilizes a thermostable (heat-resistant) sequences are broken producing single-stranded DNA polymerase that builds single-stranded DNA (ss) DNA strands that serve as the template. strands to unwind DNA templates. PCR uses repeated cycles of incubation at different temperatures to promote the unwinding of the DNA Step 2: Primer Annealing at Temp ~ 54 °C template (~95°C); the annealing of a primer (a (dependent on primer melting temperature) ~20bp oligonucleotide sequence (recall RNA H-bonds are formed between complementary primers in DNA replication) into the single-stranded sequences on the primers and the target DNA (ssDNA) template strand (~54 - 60°C); and the sequences. extension of the generated ssDNA strand through the binding of complementary bases to the template Step 3: New DNA strand elongation at Temp ~ 72 strand (~72°C). The thermostability of the °C polymerase allows it to survive the repeated cycles The two new dsDNA strands are formed by the of denaturation, annealing, and extension with little elongation of the generated ssDNA and the H- bonds between the complementary sequences on these new strands and their templates. Each of the new dsDNA strands is made up of one old strand from the original template, and one new strand that was generated as a reverse complement of the template. This is called semiconservative replication of the sequence. Step 4: Repeat step 1 to 3 for N number of cycles (N is usually 35) Each new DNA undergoes another cycle of PCR usually until 35 cycles producing multiple copies of DNA in each cycle. PCR may be used to detect the presence of the desired gene in an organism. Depending on the primer design, the expected product may represent only a specific region of the gene or the entire gene itself. The first case is useful for the detection of the gene, or the detection of organisms with that specific gene within a sample. The second case is useful for the amplification of the entire gene for Figure 10. Steps in Polymerase Chain Reaction eventual expression in other organisms. The direct (https://creativecommons.org/licenses) amplification/copying of a full gene is part of the The figure summarizes the steps of Polymerase Chain process for “cloning” that gene. Some genes Reaction. Observe what happens to the DNA and how many provide economically, and industrially important strands are produced after one cycle. products (e.g. insulin-coding genes; genes for collagen degradation). In some cases, scientists blood clots, can be inserted into the genome of a would want to put these genes into organisms for goat in such a way that the transgene’s product is the expression of their products. One example secreted in the animal’s milk. However, some would be the insertion of an insulin coding gene genetically engineered microbes are important in from the human genome into bacteria. This allows mining (cleaning up highly toxic wastes), oil spills, the “transformed” bacteria to now produce human and wastewater treatment. insulin as a product. This technology promises a lot Genetic engineering promises a lot of of applications in different fields which improves the benefits to humans especially for the improvement lives of humanity. of agricultural productivity and food quality. However, as responsible consumers, we must Applications of Recombinant DNA technology remember that these products might bring potential Recombinant DNA technology is the joining harm to humans, animals, and the environment as together of DNA molecules from two different well. That is why consumption of GM plants and species. The recombined DNA molecule is inserted animals and even the use of genetically engineered into a host organism to produce new genetic pharmaceutical products poses a lot of ethical combinations (new or improved traits) that are of issues until now. value to science, medicine, agriculture, and industry. This is the basis for the development of genetically modified organisms (GMOs). GMOs are organisms whose genome has been engineered in the laboratory to favor the expression of desired physiological traits or the generation of desired biological products. The table below shows examples of modified traits using cloned genes and their applications: Figure 11. Recombinant Products. Human Insulin injection (https://www.sedico.net) and HGH (https://dfwantiagingwellness.com) Most of the genetically modified organisms are plants. Some of these are drought, salinity, frost, and herbicide-resistant plants that promote high crop production which is of great help to the growing human population of the world. There are also transgenic animals that serve as “pharmaceutical factories” which helps in the mass production of proteins. For example, a transgene for a human blood protein such as antithrombin, which prevents