1. Construct and use dichotomous keys to identify organisms.

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1 OBJECTIVE SHEET SYSTEMATICS AND CLASSIFICATION 1. Construct and use dichotomous keys to identify organisms. 2. Clarify the purpose behind systematics and phylogeny. 3. Identify the structures of a phylogenetic tree including an ancestral node, sister taxa, outgroup, and polytomy. 4. Identify the difference between Monophyletic, Paraphyletic, and Polyphyletic groups when comparing species. 5. Recognize the problem of classification due to convergent evolution (analogy) rather than to shared ancestry (homology) 6. Discus how gene similarities in DNA as well as the use of Molecular Clocks aids in the development of more accurate Phylogenies. 7. Construct a cladogram based on derived characteristics. 8. Define scientific name and the binomial system of nomenclature. 9. Identify the general characteristics of each of the five most common Kingdoms. 10. Explain the Modern classification of Organisms by identifying the characteristics of the Three-Domain System. 11. Classify a human being using Taxons 1

2 This Phylogenetic Tree depicts the evolutionary relationships of about 3,000 species throughout the Tree of Life. Less than 1 percent of known species are depicted. Sorry to tell you, but it s not all about you. Share the Earth. 2

3 Systematics One of the great challenges of modern science is to understand the history of ancestordescendant relationships that unites all forms of life on Earth, from the earliest singlecelled organisms to the complex organisms we see around us today. All organisms share many biological characteristics. They are composed of one or more cells, carry out metabolism and transfer energy with ATP, and encode hereditary information in a single type of molecule called DNA. Yet, there is also a tremendous diversity of life ranging from bacteria and amebas to blue whales and giant sequoia trees. For generations, biologists have tried to group organisms based on shared characteristics. The most meaningful groupings are based on the study of evolutionary relationships among organisms. New methods for constructing evolutionary trees and a sea of molecular sequence data are leading to improved evolutionary hypotheses to explain life s diversification. The reconstruction and study of evolutionary relationships is called systematics. By looking at the similarities and differences between species, systematists can construct an evolutionary tree or phylogeny, which represents a hypothesis about probable patterns of evolutionary relationships among species. Branching Diagrams Depict Evolutionary Relationships Darwin envisioned that all species were descended from a single common ancestor, and that the history of life could be depicted as a branching tree. He referred to his tree as descent with modification. This is a drawing depicted from one of Darwin s notebooks, written in 1837 as he developed his ideas and shook the world with his momentous book that he called On the Origin of Species. Darwin viewed life as a branching process akin to a tree, with species on the twigs, and evolutionary change represented by the branching pattern displayed by a tree as it grows. As one works down the tree, the joining twigs and branches reflects the pattern of common ancestry back in time to the single common ancestor of all life. 3

4 Dissecting the Parts of a Phylogenetic Tree In the diagram below, each branch point represents the divergence of two evolutionary lineages from a common ancestor. Each taxon (organism name) is depicted solely by it evolutionary relationship to other taxa being compared in the tree. Taxa B and C are known as sister taxa, that is, groups of organisms that share an immediate common ancestor (branch point 4) and are each other s closest evolutionary relatives. The lineage leading to taxa D-F includes a polytomy, a branch point from which more than two descendent groups emerge. A polytomy indicates that the evolutionary relationships among the descendant taxa are not yet clear. As new evidence arises from sources such as fossils or molecular DNA sequencing, a new sister taxa may be proposed and branch point 5 may be revised and changed to look like branch points 3 and 4. Taxon G known as the outgroup or basal taxon exhibit the least amount of derived features from the other taxons. 4

5 How Do Biologists Use Phylogenetic Trees? When biologists select a group of organisms to study or compare, they use a phylogenetic tree to determine their evolutionary relatedness to each other. The tree is usually constructed by comparing DNA sequences, studying fossil remains, morphology, and even physiological characteristics. Organisms with similar structures (morphologies) or DNA sequences are likely to be more closely related than organisms with different structures or sequences. Monophyletic Paraphyletic Polyphyletic Group Group Group (a clade) Any group of organisms that are selected to be studied belong to one of three groups in a phylogenetic tree. A Monophyletic group includes the common ancestor and all descendants of that ancestor. Monophyletic groups are usually referred to as a clade. A Paraphyletic group includes the common ancestor and some, but not all, of the ancestor s descendants. A Polyphyletic group does not include the common ancestor of the group 5

6 On Making More Accurate Phylogenetic Trees Constructing Phylogenetic trees that represent a true picture of the evolutionary history of life is understandably a challenge. Revision is a constant reality for Biologists. This is a good thing, as self-correction occurs as data from a variety of sources accumulates. A potential source of confusion in constructing a phylogeny is similarity between organisms that is due to convergent evolution called analogy rather than to shared ancestry called homology. Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages. Distinguishing between homology and analogy is critical in reconstructing phylogenies. Consider bats and birds, both of which have adaptations that enable flight. Because they both have wings, one might think that bats are more closely related to birds than they are to cats, which cannot fly. But a closer examination reveals that a bat s wing is more similar to the forelimbs of cats and other mammals than to a bird s wing. Bats and birds shared a common tetrapod ancestor over 320 mya. Thus, although the underlying skeletal systems of birds and bats are homologous, their wings are not. Flight is enabled in different ways stretched membranes in the bat wing versus feathers in the bird wing. Fossil evidence also documents that bat wings and bird wings arose independently from the forelimbs of different tetrapod ancestors. Thus, with respect to flight, a bat s wing is analogous, not homologous, to a bird s wing. Analogous structures that arose independently are also called homoplasies. A typical clue to distinguishing between homology and analogy is the complexity of the characters being compared. The more elements that are similar in two complex structures, the more likely it is that the structures evolved from a common ancestor. For instance, the skulls of an adult human and an adult chimpanzee both consist of many bones fused together. The composition of the skulls match almost perfectly, bone for bone. It is highly improbable that such complex structures, matching in so many details, have separate evolutionary origins. More likely, the genes involved in the development of both skulls were inherited from a common ancestor. This leads to a powerful realization; that if two structures being compared (such as human and chimp skulls) are homologous, then so must the genes that produce them. 6

7 These two mole-like burrowing creatures evolved independently from each other and are a classic example of analogous structures evolving through the means of convergent evolution. Because they live in similar environments, they have evolved structures that serve them well in their environment. Despite having vastly different internal anatomy, physiology, and reproductive structures, they both managed to independently evolve a long body, large front paws, small eyes, and a pad of thick skin that protects their nose. Biologists can search for homology between genes amongst two different organisms. Genes are DNA sequences of nucleotide bases of A,T,C, and G. If the gene from two organisms being compared contains a lot of similar sequences, then it is highly probable that the gene is homologous and the gene in both organisms was inherited from a common ancestor. 7

8 Applying Phylogeny Understanding phylogeny can have practical applications. Investigating whether whale meat samples purchased in a market had been illegally harvested from the whale species protected under international law rather than from species that can be harvested legally, such as Minke whales from the Southern hemisphere. This phylogeny indicated that meat from humpback, fin, and North Atlantic Minke whales caught in the North was being sold illegally in some Japanese fish markets. This analysis indicated that DNA sequences of six of the unknown samples were most closely related to DNA sequences of whales that are not legal to harvest. 8

9 Cladistics In reconstructing phylogenies, the first step is to distinguish homologous features from analogous features (since only the former reflect evolutionary history). Organisms are classified by putting them in monophyletic groups called clades, each of which includes an ancestral species and all of its descendants. Clades are identified using shared derived characters. A derived trait is one that differs from its form in the common ancestor of a lineage. A node on a tree indicates a derived feature. As a result of descent with modification, organisms both share characteristics with their ancestors and differ from them. As an example, all mammals have backbones, but the presence of a backbone does not distinguish mammals from other vertebrates because all vertebrates have backbones. The backbone predates the branching of the mammalian clade from other vertebrates. Thus, we say that for mammals, the backbone is a shared ancestral character, a character that originated in an ancestor of the taxon. In contrast hair is a character shared by all mammals but not found in their ancestors. Thus, in mammals, hair is considered a shared derived character, an evolutionary novelty unique to the mammal clade. Molecular Clocks How is it that biologists can estimate that two organisms, such as humans and chimps shared a common ancestor about 6 mya? They rely on a concept called the molecular clock. Molecular clocks take advantage of the notion that particular genes mutate at fairly constant rates. This known rate of gene mutation allows biologists to compare fossil evidence from around the world with predicted changes in body form and function. The molecular clock here allows us to predict that species B and C shared a more recent common ancestor than they did with species A due to analysis of the positions of their mutations. If a gene is essential for life (such as those involved in cellular respiration) biologists expect there would be less mutations in this gene as they would be harmful mutations and the organism would not likely survive. Less essential genes may have mutations that have little or no effect on the fitness of the organism and may therefore have a faster rate of mutation. 9

10 The cladogram above shows proposed phylogenetic relationships for some animal species. Selected derived characters are indicated by the labels on the left of the diagram. Using the number 1 to indicate the presence of a character and the number 0 to indicate its absence, what character values are entered into the table below for each species? Give your answer as a five-digit number. Vertebral Column Hinged Jaws Four walking legs Amnion Hair Turtle Bass Leopard The table below right shows the ancestral and derived states of 5 traits (a through e) for 6 species. For each box in the cladogram, write in a number (1-6) to indicate where that species should be positioned in the cladogram. Note: circles in the cladogram show where specific derived traits appeared. (-) = ancestral state, (+) = derived state 10

11 Classical Taxonomy Linnaeus s Hierarchical Classification Ref Carolus Linnaeus ( ) devised a system to put into the diversity of life. He started the science of taxonomy. First he assigned each species a scientific name composed of two names = binomial nomenclature. Each name is made up of the genus and species name in Latin. Sometimes a third name is included to give credit to the discoverer. Secondly, he adopted a filing system for grouping species into a hierarchy of increasingly general categories. Although, he used only three categories (one in bold), we commonly use all the ones below: KINGDOM PHYLUM CLASS ORDER FAMILY GENUS SPECIES The purpose of taxonomy (the identification and classification of species) is to: Sort out closely related organisms and assign them to separate species, describing the characteristics that distinguish one species from another. Each taxonomic category from Kingdom all the way to Species is called a TAXON. 11

12 DOMAIN EUKARYA Grizzly bear Black bear Giant panda Red fox Abert squirrel Coral snake Sea star KINGDOM Animalia PHYLUM Chordata CLASS Mammalia ORDER Carnivora FAMILY Ursidae GENUS Ursus SPECIES Ursus arctos The Kingdom taxon contains the greatest number of organisms as it is the least specific while the species taxon is the most specific. The Species designation is the only taxon that occurs naturally as organisms decide for themselves whom they want to reproduce with to make fertile offspring with under natural conditions. 12

13 The Five Kingdom System (with Archetista) Traditionally, a five-kingdom classification system was introduced in which all living things can fit into, based on their complexity and the methods by which their nutritional needs are met. KINGDOM CHARACTERISTICS Monera Protista Fungi Plantae Bacteria and Cyanobacteria- All monerans are single-celled. Unlike other cells, the monerans lack a nucleus, and other organelles. They are all prokaryotic. Ameba, Euglena, Paramecia Protists are mainly unicellular organisms that have a membrane-bound nucleus and many other organelles. Some are colonial and multicellular. All protists are eukaryotic. Mushrooms, water mole, bread mold fungi are non-motile and cannot photosynthesize. They are heterotrophic as they absorb nutrients from a living or non-living source. Fungi differ from plants in the way the cell wall is made, in their method of reproduction, and even in their body structure. Includes the mosses, ferns, grasses, shrubs, flowering plants and trees most photosynthesize and contain chloroplasts. All plant cells have a membrane-enclosed nucleus and cell walls that contain a substance called cellulose. Animalia All members of the animal kingdom are multicellular. The cells have a discrete nucleus that contains chromosomes. Most animals can move and depend on organic materials for food. Excluding the very simple species, most animals reproduce by means of gametes called egg and sperm cells. Archetista Viruses although not living and acellular, the structure of viruses can evolve to produce drastic changes. Viruses have a protein coat surrounding either DNA or RNA. This sixth kingdom is sometimes used for convenience. Linnaeus s system is still used somewhat today but it has its limitations. Using Linnaeus s system of taxons, taxonomists have always tried to group organisms according to biologically important characteristics. But which similarities and differences are most important? 13

14 The Three-Domain System Using the molecular clock model, scientists have grouped modern organisms according to how long they have been evolving independently. The modern day method of classification includes a new taxon called a domain. The three domains are the domain Bacteria, domain Archaea, and domain Eukarya. List the characteristics that distinguish members of the domain Bacteria from members of the domain Archaea in your notebook. 14

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