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Evolution and Taxonomy Bio 2 Wk1 D1

Evolution and Taxonomy Bio 2 Wk1 D1
Assignment Brake down
Select one species of organism that is interesting to you (try to pick something different from your classmates’ choices—you only have about two million to choose from). Show the hierarchy of classification for the organism you choose from Domain through to binomial name (genus and species). Be sure to write the names in correct format and to spell correctly.
What are the nearest relatives of your chosen species? How do the levels of classification for your species trace the major evolutionary steps the ancestors of your species took over time? Be prepared to discuss similarities and differences in the evolution of diversity in the examples chosen by your classmates.
Reading for assignment
Why is Biodiversity Important?
Which plot of land is the most diverse? If you just look at the species’ richness (that is, the number of species present regardless of individual numbers), they are equal. Both plots have four species.
Now reflect on the biodiversity. Plot 1 has an equal number of all species, while plot 2 has nearly all species A and only one member of the remaining three species. Plot 1 is much more diverse in having multiples of each species present.
Can you see the importance of diversity in this simple example? If a big wind were to blow through the plots and uproot four trees, both would lose one tree of each species. Take another look at the species’ richness. Plot 1 still has four species, while plot 2 has only one! This is a very clear example of why biodiversity is important.
Diversity within a community allows it to better handle natural (or more commonly, man-made) disasters and still maintain a richness of species. This is most evident in the tropical regions of our planet. We are losing tracts of rain forests at alarming rates. In fact, we just lost ten-plus acres in the time it took to write this sentence!.
Of course, some of the areas do recover to a degree, but we have no idea how many species are lost due to this rapid decline of habitat. The loss of biodiversity is likely one of the biggest problems the human population will face in the coming century.
We will come back to the concept of biodiversity and what we are doing to preserve it in later weeks of this course.
Our key to understanding or even comprehending biodiversity is the science of taxonomy (the naming and classifying of organisms). Without taxonomy we have no idea of what organisms we are dealing with in our research.
In case you are curious, we currently have close to 2 million identified species on earth. Of those, over 350,000 are from one group of insects, the beetles. This means there are probably more species of beetles on earth than the combined numbers of vertebrate animal and plant species. So, who really is running the show? If number of species is a sign of success, then the beetles have to be the most successful group of organisms on earth!
A great place to explore the diversity of life is the Tree of Life Web Project which is being built by a large number of scientists from around the world. It is a great place just to wander around and explore.

Taxonomy and the Hierarchy of Classification.
In taxonomy, we name organisms then group them with other organisms that are their relatives. This grouping is based on shared homologous characteristics (structures or processes that are derived from a common shared characteristic such as the bones of the wings of a bat and the bones in the arm of a human). These indicate a shared ancestry. Taxonomy is how we keep track of the diversity of life.
As we mentioned, the hierarchy of classification for living things is:
Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.
Whew! That’s going to be a challenge to memorize! However, we’re willing to bet this acronym will help you to keep the order straight:
Dashing King Philip Crossed Over For Good Sex (or Spinach—your choice!)
You may have noticed that the species name for humans—Homo sapiens—appears to be written in some odd foreign language! In fact, it is Latin for “wise one” (a cruel joke, perhaps?).
Why have biologists chosen to use Latin instead of using simple names like “dog” or “oatmeal”? The reason is two-fold:
First, all organisms have one—and only one—scientific name.
Second, regardless of the country we’re in, if we say Homo sapiens to scientists of that country, they will know exactly what we’re talking about!
Latin was chosen because it was the language of science and scholarship at the time that Linnaeus was creating binomial nomenclature. All science was written in Latin at that time. This is rooted in the preservation of earlier writing in Latin in Roman Catholic monasteries during the dark ages. Latin continues to be useful today because it’s a “dead” language—no culture truly uses it in modern times and this means the words do not change in their usage over time. Such is not the case with English and other modern languages. Using Latin we have a single language that transcends all cultures. We have only to assign a single name and everyone will know what organism we are talking about. (A rose is a rose is a rose—unless you are talking about the color red!)
Binomial Naming of Species
The science of taxonomy dates back to the ancient Greeks. Aristotle was one of the first people to attempt a classification of living things. His system was simple: If they moved, they were animals; if they didn’t move, they were plants!
Scientists consider Carl Linnaeus to be the “father of taxonomy” as we know it today. Linnaeus is famous for being the first scientist to use binomial (two-part) names for species. One example of a binomial name is Homo sapiens; the genus is Homo and the specific epithet is sapiens. The genus name indicates a group of close relatives. The specific epithet identifies the individual species within that genus. This particular example suggests that we may not be the only member of the genus Homo!
There several important things to keep in mind when writing scientific binomial names. They must be correctly spelled and in correct format or they are not correct. Relative to format, Latin is a foreign language. When we include a foreign language in English writing, it is a rule that the word should be set in italic type. Classically, this was indicated when typing or writing by underlining the word. This told a typesetter to put the word in italic type. So… all binomial names including the genus and species should be in italic type! Second, genera are typically nouns and specific epithets are adjectives describing the noun. In Latin, all nouns begin with a capital letter and adjectives never start with a capital letter. This means for the scientific binomial name to be correct, the genus should start with a capital letter, the species should start with a lowercase letter and both names must be either set in italic type or underlined. And, don’t forget to spell the name correctly. It is amazing how many people write our name as Homo sapien. It is not only incorrect, it is like not knowing how to spell your own name!
Linnaeus was the first scientist to use only binomial names in his writings. Others used binomials interspersed with “phrase names.” These people might have called us Homo sapiensis north americanius inhabitus houseous in the yardious all dayious.
Of course, this is a joke. But you do get the idea—using phrase names for species could have been very confusing! The Evolution of Biodiversity
The Evolution of Biodiversity
We need to examine just how biodiversity came about and where it is going. This requires a review of major events in the origin and history of life on earth. We will then come back and take a little closer look at some of the major groups of organisms around today.
According to our best scientific explanations to date, the universe came into existence about 13.7 billion years ago as a result of something we call the Big Bang. As the universe expanded and started to cool, matter came into existence and then was pulled together into gas clouds that went through a series of compressions and explosions until fairly stable galaxies including billions of stars and possible solar systems came into existence. Around 4.5 billion years ago, our Sun, solar system and Earth formed. After the crust of the Earth cooled considerably, life came about through chemical reactions and things have not been the same since!
The first forms of life were probably much simpler than the prokaryotic and eukaryotic cells that we see today. As life progressed, the Bacteria and the Archaea (both prokaryotic organisms) evolved and diverged and invented processes we call cellular respiration and photosynthesis. We think the Eukarya (eukaryotic organisms) arose out of the Archaea.
About 2.4 billion years ago, oxygen produced by early prokaryote autotrophs (photosynthetic organisms) was no longer absorbed by minerals in the soil and water at a fast enough rate to keep it from escaping into the atmosphere. For many organisms, the oxygen built up to a poisonous level in the atmosphere. This was called the Great Oxidation. Some species sought out low oxygen refugia to survive in (their descendants still live in areas with little or no oxygen today). Others found ways to adapt to this poison. One way was to learn to use oxygen as part of the cellular respiration process.
About 1.5 to 2 billion years ago, we start to see evidence of eukaryotic cells in the fossil record. There is a good chance they arose long before this but we have to go with what we see in the evidence. The eukaryotes were characterized by much larger cells and folded cell membranes that both increased the surface area of the cells and helped to form the first membranous organelles within the cells. Something else was going on as well. It appears that eukarotic cells first picked up some bacterial cells that were capable of doing the new kind of respiration using oxygen as hitchhikers. The eukaryotic cells provided food to these bacteria and protected them while the bacteria broke the food down more efficiently and shared the released ATP energy with the surrounding eukaryotic cell material. Mitochondria were born!
Following this, some eukarotic cells also took on photosynthetic bacteria as hitchhikers that could capture sunlight and turn carbon dioxide and water into food molecules that stored that energy. Chloroplasts were born!
At this point the stage was set for the later development of animals whose cells only had the mitochondria and plants whose cells had both mitochondria and chloroplasts. These early eukarotic cells formed the first protists which still exist today in the form of protozoa, algae, etc. Another major change started to happen and evidently happened several times. That was the evolution of multicellularity.
Single celled organisms were dependent on one cell to do all the work of life. This put some limitations on how these organisms could change and adapt to the changing world around them. Some however first formed colonies then made the long march to forming sophisticated multicellular organisms which had many kinds of cells specializing for specific jobs and sharing the work of life. Organisms became larger and more complex and began developing the many structural and physiological changes that have led to the wide diversity of life on Earth today.
Multicellularity evolved at least three times. Once to become the fungi, once to become the plants and once to become the animals.
Let’s now take a closer look at the different kinds of life on earth today: Bacteria, Archaea, Protists, Fungi, Plants and Animals.

Bacteria: They are Everywhere!
This may seem like an odd statement, but it’s true! Wherever you find life on this planet, there will always be bacteria. In fact, there are many places such as deep ocean hydrothermal vents, hot sulfur springs, and high saline environments, like the Great Salt Lake where the only organisms you will find are bacteria or Archaea. We do not discuss Archaea in these lecture notes, but you will read about them in your textbook assignment this week.
Remember that bacteria are usually extremely small single-celled organisms. Bacteria are quite simple in structure; they do not have cellular organelles and their means of reproduction (binary fission) is relatively simple. Each individual cell is capable of producing millions of copies of itself!
Consider that literally millions of cells can fit into the space of the period at the end of this sentence—you’ll never look at punctuation the same way again!
Why are the bacteria so successful in invading every aspect of the environment?
Bacteria have adopted every means of meeting nutritional requirements imaginable! Some bacteria obtain energy via photosynthesis. The mechanisms and basic chemistry are quite similar to those of plants. This has led to certain researchers suggesting that the chloroplasts of plants are actually modified bacteria – they’ve been able to form a very intimate relationship with the plant cells in which they live!
On the other hand, some types of bacteria must meet their nutritional needs in the total absence of light. How do they do this? Recall the process of photosynthesis. The main function of photosynthesis is to convert radiant energy (light) into chemical bond energy (food for the cell).
Some bacteria (the chemoautotrophs) take inorganic chemicals and convert them into organic molecules—the bond energy that can be used by living things. Of course, other bacteria depend on organic molecules produced by other organisms (the heterotrophs). Take note: human beings fall into this category!
As you can see, bacteria are able to obtain nutrition in many different ways. This is one explanation why they are found everywhere. Another factor is that bacteria are capable of withstanding extreme temperatures. You may live in an area where boil-water advisories or boil-water orders have been issued in the past—usually due to a water main break and repair.
Years ago, most people thought that boiling water for five minutes would be enough to take care of any “critters” found in the water. The time was then extended to ten minutes, fifteen minutes, twenty minutes—at last count in some towns, thirty minutes.
Why do you think this number keeps rising? As it turns out, many bacteria produce specialized structures called endospores (internal spores). These structures are capable of withstanding extreme temperatures and quickly grow into new bacterial cells. In other cases, the capsule of the bacteria is such that it can live in extremely caustic conditions (such as the hot sulfur springs).
Bacteria: The Vital Roles They Play in Life
Why do bacteria exist in this world? There must be a reason! It’s like wondering why the sky is blue. (For your information, the sky is blue because of the light refraction in the upper atmosphere.) Bacteria are everywhere because they are capable of serving several distinct roles in the environment.
One of the most important roles of bacteria is decomposition. We just mentioned that if it weren’t for bacteria and fungi, we’d be swimming in our own waste. Bacteria are a vital part of our sewage treatment facilities. Consider the concept of a “settling pond”—this settling allows the bacteria to do their work. They break down our waste products into useful and harmless chemical components. The next time you flush the toilet, remember the bacteria!
You should think about bacteria the next time you sit down to your favorite meal, too. Primary digestion is a function of the stomach and small intestine. Secondary digestion and water reabsorption take place in the large intestine, thanks to bacteria such as E. coli.
Bacteria are pivotal in the lives of plants as well. Plants can’t process nitrogen as it exists in the environment so they turn to bacteria. Bacteria have the natural ability to convert nitrogen into compounds that are usable by plants. This planet would not have its lush vegetation if bacteria didn’t carry out this important procedure. Instead, plants would be forced to rely on lightning and volcanic reactions.
As you can see, the bacteria serve many vital roles in the world around us. The next time you hear the word “bacteria” mentioned with distaste, recall that most are beneficial; very few cause disease. In fact, bacteria don’t set out to cause disease! Rather, it is caused by proteins in the capsule wall of the bacteria, or by the waste products of the bacteria.
Next, we’ll step into the realm of the eukaryotes and learn about the science of taxonomy!
Classifying the Protists
What is a protist? Simply put, if we don’t know what it is, we group it in the phylum Protista!
To give you a few facts about protists, they are:
Unicellular (at least for part of their life cycle)
Most exhibit motile cells at some point in their life cycle
In addition, protists can be:
Fungus-like (slime molds, for example)
Plant-like (the algae)

Animal-like (the good old paramecium that most of you have heard of)
What do you think of when you hear the word “fungus”? Much like with bacteria, we often take a negative view of these guys! At best, we might think of the mushrooms on our favorite pizza. However, the kingdom of the fungi is much more varied and interesting (even if you’re really fond of pizza with mushrooms!). Fungi are a diverse bunch, comprised of six major groups that vary in form and type of reproduction.
All fungi are eukaryotic and heterotrophic, with external digestion. Most fungi are multicellular. The fungal body is composed of hyphae (filaments), and some with groups of hyphae matted together to form a structure called a mycelium.
One group of fungi, the lichens, is one of the most intriguing. Lichens are unique in the organismal world because they are actually a composite organism. What’s a composite organism? It’s an organism that is composed of two separate organisms. In the case of the lichens, there is a fungus and an alga (a member of the Protista) that make up the lichen body. Each serves a specific purpose:
Algae are photosynthetic, and hence, the primary producers.
Fungal hyphae provide the structure to the lichen body and protection for the fragile algal cells. This association is so well-developed that the fungus and algae may not be able to survive outside of the lichen body.
Lichens may be foliose (leaf-like), fruticose (stem-like branches), or crustose (crust-forming). The lichens are capable of growing on such things as bare rock. In fact, they are able to break down rock into soil particles, due to the excretion of acids that destroy the rock. The lichens are some of the first organisms to colonize bare rock. They grow on soil, tree bark, leaves, and many other substrates as well.
Lichens are also some of the best pollution indicators on this planet. This means that they are among the first kinds of life to leave an area if pollution levels become too high. This leads us to our next topic: fungi and the environment.
Fungi and the Environment
Like the bacteria, many fungi are involved in decomposition of the Earth’s wastes. When a fish goes bad, we are actually smelling the by-products of the bacteria. While we cringe at the smell, the fungi sneak in and quietly digest the fish away (and they tend not to smell as bad!).
Fungi also break down the things that the bacteria do not, or cannot, touch. The next time you pass a rotten log, think of the fungi—they are helping the wood to decay. And fungi are not just decomposers, they are also fermenters.
Fermentation is one process that we utilize in many different forms. For example, many things are products of fermentation, such as alcohol, turpentine, cheese, bread—even chocolate. Fermentation naturally occurs in the absence of oxygen. If the layers of decomposing stuff get too deep, the lowest levels will not have any oxygen available. Therefore, it’s a good thing the fungi and bacteria can “keep on trucking” when there is no oxygen in the vicinity!
Certain plants rely on fungi to survive. Many trees depend on fungi to help with water absorption and nutrient uptake. Fungi are in close association with the roots of these trees, either growing around the roots or inside the root tissue. This allows them to take in the extra water and nutrients—acting like a super-absorbent paper towel! During bulk tree plantings, it’s common practice to add a fungal culture (either a liquid dip or powder) to promote early seedling growth and establishment.
Some of the root-associate fungi are prized as delicacies. Truffles are a group of fungi that typically grow in association with oak roots. We have trained both pigs and dogs to “sniff” out these tasty morsels, which sell for a premium (refer to the advertisement to the right).
Effects of Mold and Rot
We use many fungi to our advantage, but some forms cause an opposite effect on the economy each year. We lose millions of dollars in crops due to “mold and rot” before they can be processed into foodstuffs. We also lose millions due to spoilage after the raw materials are treated. Remember that moldy bread? How about that long-forgotten container of what used to be chicken noodle soup?
Consider that we are talking about biology—there is often good in the bad. The good old green mold gave us penicillin. And we’ve developed other drugs from fungi, including other antibiotics and hormone treatments.
As you can see, the fungi are major decomposers and they serve many other equally important roles in the world around us!

A plant is a plant is a plant? Seems like a simple concept, but consider that botanists do not classify large algae as plants.
Algae, similar to plants, are multicellular, eukaryotic, and photosynthetic. However, botanists have classified them as protists. But why take a set of organisms that so clearly appear to be plants and group them with the Protista? The answer is simple: these organisms didn’t dry off their feet and become “land plants”!
As we just pointed out, most land plants have roots, stems, and leaves. Each of these structures serves a specific function in land plants:
Roots provide anchorage and water uptake as the plants are no longer floating in water.
Stems provide support for the plants in the aerial environment.
Leaves are usually the specific area where photosynthesis takes place (as opposed to the entire algal body).
How Plants Absorb and Retain Water
Another important development in the land plants is a structure called a cuticle. The cuticle is a waxy layer directly outside of the epidermal cells. What happens if you add water to wax? Of course, it quickly runs off, since wax repels water.
Plants absorb water from the soil by the roots. The vascular tissue (specifically the xylem) then routes the water throughout the plant body. The cuticle helps the plant body to retain its water.
Why don’t plants just take the water they need from the air? But how constant is the amount of water in the air, compared to that in the soil? Besides holding much more water than air, soil has a level of liquid water often referred to as the water table.
Thus, plants have developed a way to extract the water and then keep it inside the plant body. Water is needed both as a liquid in the plant cells and as a means of cooling the plant during photosynthesis, when water is released as a vapor from the leaves.
Interestingly, after having evolved on land, some plants have returned to the water and had to develop new adaptations to handle the challenges of living in the aquatic environment.

Plants and Reproduction
Another issue plants dealt with during their transition to dry land had to do with sex! Consider that algae release their gametes in water. In some cases, both the male and female gametes swim; in others, it’s just the male gametes, or sperm.
What happens when gametes that are used to water are dumped into the air? Of course, they don’t survive. Land plants had to form a means of getting the males and females together. As a result, they developed specialized structures to accommodate the gametes. In the most developed cases, the gametophytes are housed within protective structures found on the sporophyte: the pistil (egg) and anther (sperm) of the flower.
To recap, land plants are a group defined by being multicellular autotrophs. As autotrophs, they have:
The ability to produce their own food by the process of photosynthesis
Structures of support in the absence of a liquid support medium (water)
A cuticle and internal routing system of water
Measures to assure fertilization in the absence of liquid water.
The Major Groups of Plants

Much as with the fungi, land plants are divided into major groups based on various characteristics. Most biologists recognize the following six plant groups:
Ferns and fern allies
Flowering plants
Many biologists consider the bryophyte and fern/fern ally groups to be the most primitive. Why would this be? Think back to the typical plant life cycle covered in the first section of this class.
The typical plant life cycle is that of a “flowering plant”—those plants that develop a flower as part of their reproductive cycle. More importantly, the flower will lead to the production of seeds (if the egg is fertilized). The bryophytes and fern/fern allies do not develop seeds; they have only spores to help them circulate.

The Importance of Seeds to Plant Diversity
The plants discussed from this point on are distinct in that they all produce seeds. What is so important about a seed? First, we need to define the seed: a seed is simply a tough outer coat surrounding an embryonic plant and a food source.
The seed represents a giant leap in the plant’s adaptation to dry land. Not convinced? Then consider which of these two plant types has a better chance at establishment and survival:
A spore, devoid of any food, that must develop from a single cell into a gametophyte plant.
A multicelled sporophyte embryo containing an intact food source within its protective coat.
It’s pretty easy to see the advantage of a seed!
Flowering Plants: The Fruit
It seems only appropriate to end the plant section with the most diverse group. The flowering plants are more precisely referred to as angiosperms (Greek for “seed in a vase”). The “vase” refers to the structure developed by the ovary and possibly certain accessory parts that form the fruit.
What’s the big deal about the fruit? Look at it this way: if it wasn’t for fruits, you’d have very little to eat! Of course, we have vegetables—any edible non-fruit part of a plant. But it’s probably safe to say that most of us enjoy the fruits of the plants’ labor more than we enjoy the vegetables! And this is by design.
One purpose of a fruit is to entice organisms to take a bite. Sounds pretty masochistic, but it serves a purpose. Remember that a seed, or seeds, is found inside of the fruit. If we take a bite, we stand a good chance of ingesting a seed. Where does this seed go? Well, as the old saying goes, “What goes in must come out.” Sooner or later, the seed will pass through the digestive tract and land in a nice pile of… fertilizer! So, the main purpose of a fruit is dispersal of the seed.
Not all fruits are meant to be eaten—for instance, the lowly dandelion. Dandelions don’t produce a tasty fruit; instead, they create a seed with a built-in parachute. The dandelion’s fruit is the downy pappas that allows the seed to float on air currents until it reaches a new location.
Another purpose of the fruit is to keep the seeds from sprouting before their time. In fact, hormones are produced in the fleshy fruits that keep the seeds from germinating. Why would you want to keep a seed from growing – isn’t that the whole point of a seed? Well, consider what will happen if the seed sprouts beside the parent plant. This spells competition and the offspring will likely lose the fight. The reproductive effort of the parent is wasted.

Flowering Plants: The Flower
We’ve discussed the importance of the fruit; now it’s time to look at the structure that develops prior to the fruit: the flower. The flower also serves to attract critters, but for a very different reason.
Two things have to happen before we get a seed, pollination, and fertilization. Recall that fertilization is the union of gametes (sperm and egg) to form a diploid, a single-celled zygote. This zygote will continue to grow, producing the embryo and the future adult planat is pollination?
If we recollect from our discussion on the bryophytes and fern/fern allies, no pollination occurs. The sperm swims directly to the egg via liquid water. Pollen was a major step in a plant’s ability to survive on land. A pollen grain is a structure that contains sperm cells. The pollen can be moved around without needing liquid water for fertilization. This opens up numerous areas for plant growth.
How does pollen circulate? There are two ways: by air and by flowers. With conifers and many of the flowering trees, the pollen is moved around by the air. If you have a black car that sits out in the spring, you know about airborne pollen – your car turns yellow-green! As you can guess, this is not a very efficient way to move pollen around. It is random at best; the pollen doesn’t hit a wind current that always goes directly to another plant (either cone or flower).
Lots of flowers offer something that animals can use. The reward may be in the form of nectar, or simply an abundance of pollen for critters to eat. The flowering plant produces much less than the wind-dispersed pollen plant does. In more interesting cases, the flower may resemble a female insect to entice the male to attempt copulation, but all he gets out of it is pollen! Or, the flower may look and smell like rotten meat (guess what insect pollinates them?).
In any case, the flower is often an instrument to move pollen from one like flower to another.

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