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Zachary McAllister

on 24 March 2015

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Transcript of Classification

For billions of years, life on Earth has been constantly changing. Natural selection and other processes have led to a staggering diversity of organisms. A tropical rainforest, for example, may support thousands of species per acre. Recall that a species is a population of organisms that share similar characteristics and can breed with one another and produce fertile offspring. Biologists have identified well over 1 million species so far. They estimate that anywhere between 2 and 100 million additional species have yet to be discovered.
To study this great diversity of organisms, biologists must give each organism a name. Biologists must also attempt to organize living things into groups that have biological meaning. To study the diversity of life, biologists use a classification system to name organisms and group them in a logical manner. Scientists have developed a discipline known as taxonomy to accomplish this task.
In the discipline known as taxonomy, scientists classify organisms and assign each organism a universally accepted name. By using a specific name, biologists can be certain that everyone is discussing the same organism. When taxonomists classify organisms, they organize them into groups that have biological significance. In a good system of classification, organisms placed into a particular group are more similar to one another than they are to organisms in other groups.
Assigning Names
By the 18th century, European scientists recognized that referring to organisms by common names was confusing. Common names vary among languages and even among regions within a single country. The animal below is often called a cougar, but could also be called a mountain lion, puma, or panther. The picture on the right is a female human, but some modern humans would also label her as a cougar!
Early Efforts
To eliminate confusion, scientists agreed to use a single name for each species. Because 18th-century scientists understood Latin and Greek, they used those languages for scientific names. The first attempts at standard scientific names often described the physical characteristics of a species in great detail. As a result, these names could be twenty words long! Another drawback was the fact that different scientists described different characteristics.
Binomial Nomenclature
A Swedish botanist, Carolus Linnaeus developed a two-word naming system called binomial nomenclature. This system is still in use today. In binomial nomenclature, each species is assigned a two-part scientific name. The scientific name is always written in italics. The first word is capitalized, and the second word is lowercased. For example, a grizzly bear is called . The first part of the name, , is the genus to which the organisms belongs. A genus is a group of closely related species. The genus contains 5 other types of bears. The second part of the name distinguishes the specific species of the genus.
Ursus arctos
Linnaeus's System
Linnaeus's hierarchical system of classification includes seven levels. They are - from smallest to largest - species, genus, family, order, class, phylum, and kingdom. In taxonomic nomenclature, or naming system, each of these levels is called a taxon (plural: taxa), or taxonomic category. The two smallest categories, genus and species, were discussed in the previous example of bears and again with the two animals below.
Ursus maritimus
Ailuropoda melanoleuca
Linnaeus's System
Genera that share many characteristics, such as Ursus and Ailuropoda, are grouped into a larger category, the family - in this case, Ursidae. These bears, together with six other families of animals, such as dogs (Canidae) and cats (Felidae), are grouped together in the order Carnivora. An order is a broad taxonomic category composed of similar families. The next larger category, the class, is composed of similar orders. For example, order Carnivora is placed in the class Mammalia, which includes animals that are warm-blooded, have body hair, and produce milk for their young.
Linnaeus's System
Several different classes make up a phylum (plural: phyla). A phylum includes many different organisms that nevertheless share important characteristics. The class Mammalia is grouped with birds (Aves), reptiles (Reptilia), amphibians (amphibia), and all classes of fishes into the phylum Chordata. Finally, all animals are placed in the kingdom Animalia. The kingdom is the largest and most inclusive of categories. Linnaeus named two kingdoms: Animalia and Plantae.

How do we group these guys?
In a sense, organisms determine who belongs to their species by choosing with whom they will mate! Taxonomic groups above the level of species are "invented" by researchers who decide how to distinguish between one genus, family, or phylum, and another. Linnaeus and other taxonomists have always tried to group organisms according to biologically important characteristics. Like any other system, this system had limitations and problems.
Linnaeus grouped species into larger taxa, such as genus and family, mainly according to visible similarities and differences. One of the first problems to be encountered was determining which similarities and differences are most important. For example, where would you classify a dolphin? Would you call them fish because they live in water and have fin-like limbs? Or would you call them mammals because they breathe air and feed their young with milk?
Evolutionary Classification
Darwin's ideas about descent with modification have given rise to the study of phylogeny, or evolutionary relationships among organisms. Biologists now group organisms into categories that represent lines of evolutionary descent, or phylogeny, not just physical similarities. The strategy of grouping organisms together based on their evolutionary history is called evolutionary classification.
Evolutionary Classification
Species within one genus are more closely related to one another than to species in another genus. According to evolutionary classification, that is because all members of a genus share a recent common ancestor. Similarly, all genera in a family share a common ancestor. This ancestor is further in the past than any ancestor of any genus in the family but more recent than the ancestor of the entire order. The higher the level of the taxon, the further back in time is the common ancestor of all the organisms in the taxon.
Not just looks.....
Consider the barnacle and limpet pictured below. Superficial similarities once led the barnacle and limpet to be grouped together. However, barnacles and limpets are different in important ways. For example, their free-swimming larvae are unlike one another, and the adults exhibit different characteristics as well (barnacles shed their exoskeleton). These characteristics make barnacles more similar to crabs than to limpets. Limpets, in turn, have an internal anatomy that is closer to that of snails, which are mollusks. This means that barnacles and crabs share an evolutionary ancestor that is more recent than the ancestor shared by barnacles and limpets.
Cladistic Analysis
To refine the process of evolutionary classification, many biologists now prefer a method called cladistic analysis. Cladistic analysis identifies and considers only those characteristics of organisms that are evolutionary innovations - new characteristics that arise as lineages evolve over time. Characteristics that appear in recent part of a lineage but not in its older members are called derived characteristics.
Cladistic Analysis
Derived characters can be used to construct a cladogram, a diagram that shows the evolutionary relationships among a group of organisms. You can see two examples of cladograms below. Notice how derived characteristics, such as "amniotic membrane" and "bony skeleton", appear at certain locations along the branches of the cladogram. These locations are the points at which these characteristics arose.
Cladistic Analysis
In the cladogram below, you can see that crabs and barnacles share some derived characteristics that barnacles and limpets do not. One such characteristic is a segmented body and another is molting of external skeleton. Thus, this cladogram groups crabs and barnacles together as crustaceans and separates them from limpets, which are classified as a type of mollusk. Cladograms are useful tools that help scientists understand how one lineage branched from another in the course of evolution.
DNA & RNA...AGAIN!?!?!
All of the classification methods discussed so far are based primarily on physical similarities and differences. All organisms use DNA and RNA to pass on information and to control growth and development. Hidden in the genetic code of all organisms are remarkably similar genes. The genes of many organisms show important similarities at the molecular level. Similarities in DNA can be used to help determine classification and evolutionary relationships.
Similar Genes
Even the genes of diverse organisms such as humans and yeasts show many surprising similarities. For example, humans have a gene that codes for myosin, a protein found in our muscles. Researchers have found a gene in yeast that codes for a myosin protein. As it turns out, myosin in yeast helps enable internal cell parts to move. Myosin is just one example of similarities at the molecular level - an indicator that humans and yeasts share a common ancestry.
DNA Evidence
DNA evidence can also help show the evolutionary relationships of species and how species have changed. The more similar the DNA sequences of two species, the more recently they shared a common ancestor, and the more closely they are related in evolutionary terms. The more two species have diverged from each other, or changed in comparison to each other during evolution, the less similar their DNA will be.
Back to Vultures & Storks
Consider the birds below. The bird on the left looks very much like the one in the middle. Both birds have traditionally been classified together as "vultures". American vultures, however, have a very peculiar behavior: when they get overheated, they urinate on their legs to cool off. Storks are the only other bird known to do this. Scientists analyzed the DNA of all three birds and discovered that the DNA sequences of the American vulture and stork were more similar than the DNA of the African vulture. This similarity indicates that the stork and American vulture share a more recent ancestor than do the two vultures.
Molecular Clocks
Comparisons of DNA can also be used to mark the passage of evolutionary time. A model known as a molecular clock uses DNA comparisons to estimate the length of time that two species have been evolving independently. To understand a molecular clock, think about a pendulum clock. It marks time with a periodically swinging pendulum. A molecular clock also relies on a repeating process to mark time - mutation.
Molecular Clocks
Some mutations have a major positive or negative effect on an organism's phenotype. Other mutations have no effect on phenotype. These neutral mutations accumulate in the DNA of different species at about the same rate. A comparison of such DNA sequences in two species can reveal how dissimilar the genes are. The degree of dissimilarity is, in turn, an indication of how long ago the two species shared a common ancestor.
Baby got Back!!!!!
The Tree of Life
As in all areas of science, systems of classification adapt to new discoveries. Ideas and models change as new information arises. Some ideas have been discarded, while others have been upheld and refined. So, it should not be surprising that early attempts at drawing life's universal tree were based on misguided assumptions.
The Tree of Life Evolves
Some of the earliest trees of life were dominated by humans. These models represented vertebrates as the most important and abundant animals. The scientific view of life was simpler in Linnaeus's time. The only known differences among living things were the fundamental traits that separated animals from plants. Animals were mobile organisms that used food for energy. Plants were green, photosynthetic organisms that used energy from the sun.
Five Kingdoms
As biologists learned more about the natural world, they realized that Linnaeus's two kingdoms, Animalia and Plantae, did not adequately represent the full diversity of life. First, microorganisms, such as protists and bacteria were recognized as being significantly different from plants and animals, so they deserved their own kingdom (Protista). Next, the mushrooms, yeast, and molds were placed in their own kingdom, Fungi. Later still, scientists realized that bacteria lacked the nuclei, mitochondria, and chloroplasts found in other life forms. Therefore, they were placed in a new kingdom, Monera.
Six Kingdoms
In recent years, as evidence about microorganisms continued to accumulate, biologists came to recognize that the Monera were composed of two distinct groups. Some biologists consider the differences between these two groups to be as great as those between animals and plants. As a result, the Monera have been separated into two kingdoms, Eubacteria and Archaebacteria, bringing the total number of kingdoms to six.
Molecular Analyses
Some of the most recent evolutionary trees have been produced using comparative studies of a small subunit of ribosomal RNA that occurs in all living things. Using a molecular clock model, scientists have grouped modern organisms according to how long they have been evolving independently. Molecular analyses have given rise to a new taxonomic category that is now recognized by many scientists - the domain. The domain a more inclusive category than any other.
Three Domains
The three domains are the domain Eukarya, which is composed of protists, fungi, plants, and animals; the domain bacteria, which corresponds to the kingdom Eubacteria; and the domain Archaea, which corresponds to the kingdom Archaebacteria. As scientists continue to accumulate new information about organisms in the domain Bacteria and Archaea, these domains may be subdivided into additional kingdoms.
Domain Bacteria
The members of the domain Bacteria are unicellular and prokaryotic. Their cells have thick, rigid cell walls that surround a cell membrane. The cell walls contain a substance known as peptidoglycan. The domain Bacteria corresponds to the kingdom Eubacteria. These bacteria are ecologically diverse, ranging from free-living soil organisms to deadly parasites. Some photosynthesize, while others do not. Some need oxygen, while others are killed by it.
Domain Archaea
Also unicellular and prokaryotic, members of the domain Archaea live in some of the most extreme environments you can imagine - volcanic hot springs, brine pools, and black organic mud totally devoid of oxygen. Indeed, many of these bacteria can survive only in the absence of oxygen. Their cell walls lack peptidoglycan, and their cell membranes contain unusual lipids that are not found in any other organism. The domain Archaea corresponds to the kingdom Archaebacteria.
Brine Pools?
Domain Eukarya
The domain Eukarya consists of all organisms that have a nucleus. It is organized into the four remaining kingdoms of the six-kingdom system: Protista, Fungi, Plantae, and Animalia.
The kingdom Protista is composed of eukaryotic organisms that cannot be classified as animals, plants, or fungi. Of the 6 kingdoms, Protista is the least satisfying classification, because its members display the greatest variety. Most are unicellular, but some, such as multi-cellular algae, are not. Some are photosynthetic, while others are heterotrophic. Some are more like plants, others are more like fungi, and some are more like animals.
Members of the kingdom Fungi are heterotrophs. Most feed on dead or decaying organic matter. Unlike other heterotrophs, these fungi secrete digestive enzymes into their food source. They then absorb the smaller food molecules into their bodies. The most recognizable fungi, including mushrooms, are multicellular. Some fungi, such as yeasts, are unicellular.
Members of the kingdom Plantae are multicellular organisms that are photosynthetic autotrophs. Plants are nonmotile - they cannot move from place to place. They also have cell walls that contain cellulose. The plant kingdom contains cone-bearing and flowering plants as well as mosses and ferns. Although older classification systems regard multicellular algae as plants, your text groups algae with the protists.
Members of the kingdom Animalia are multicellular and heterotrophic. The cells of animals do not have cell walls. Most animals can move about, at least for some part of their life cycle. As you will discover, there is incredible diversity within the animal kingdom, and many species of animals exist in nearly every part of the planet.
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