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Lab 06: Classification and Dichotomous Keys Once again, there is an unbelievable amount of diversity of life on Earth. From the smallest single-celled bacterium to the worlds largest creatures: blue whales, redwoods, and a fungus that spans many acres. How can we keep track of all of it?

Organizing the Diversity of Life: Taxonomy Scientists like to divide things into categories. They put things into boxes and give those boxes names. Despite the diversity, they are quite good at it. Taxonomy is the field of biology that seeks to classify this diversity. The father of modern biological taxonomy was Carl Linnaeus who published his Systema Naturae describing his taxonomic system in 1735. Although Linnaeus' system has been modified over the years, the modern taxonomic system maintains a number of its features, including the following: Division of organisms into named hierarchical groups, known as taxa (singular:

taxon). Examples include (in order of increasing specificity): o Kingdom (plural: kingdoms)

Phylum (also known as "division" in plants) (plural: phyla) Class (plural: classes)

o Order (plural: orders) Family (plural: families)

Genus (plural: genera) o species (plural: species)

Each taxon delineation is based on a set of particular morphological,

biochemical, or genetic characteristics, known as characters, that are shared by members of the group. Linnaeus' system was innovative because in many cases it focused on reproductive characteristics rather than the overall form and habits. (This emphasis caused some of his contemporaries to consider him a pervert, but it was probably more accurate given the BSC.) Thus Linnaeus ultimately correctly classified whales as mammals rather than fish.

Identification of a particular type of organism by a TWO-PART scientific name (= binomial nomenclature).

o Never write the species name without the genus name in front of it. This means that each type of organism gets called by its generic AND specific name:

GENUS + SPECIES.

o It is always italicized (or underlined if hand-written).

Twelve species in the genus Drosophila

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o It is Latinized, which avoids bias towards one particular country, since no country speaks Latin.

o The Genus is Capitalized (as are all higher levels), while species is never capitalized. o On first mention, the genus name is written in full (e.g. Escherichia coli) and on

subsequent references within a work it is usually abbreviated using the first letter (e.g. E. coli).

In total:

Binomial nomenclature is important because it is the same throughout time and space. Common names, like dragonfly in English, which is libellule in French or in Chinese or mosquito hawk in Bubbabonics, vary wildly from place to place, but as long as you know the scientific nomenclature, you can talk about it with any scientist the world over (assuming you understand the other words they are saying).

Naming species Most of the higher levels of taxonomy are set; it is rare that a new family or even genus is discovered. Sometimes the highest levels are reworked as new genetic data are introduced, but this comes with a storm of discussion. Quite often however, new species are discovered. In this case, the person who discovered it gets to name it. This does not mean that anything goes. There are many rules he/she must follow. Usually the name reflects some attribute of the specimen or its location. For instance, mockingbirds are in the family Mimidae, which means mimic, because they mimic the calls of other birds. The American black bear is Ursus americanus which is Latin for American bear. Some of the codes stipulate that a scientist cannot name a species after him or herself, however if you have a friend that also just found a new species, there can be some back scratching. If you like long lists of rules here are some of the International Codes of Nomenclature: Bacteria: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=icnb&part=A185 Plants: http://www.bgbm.fu-berlin.de/iapt/nomenclature/code/SaintLouis/0001ICSLContents.htm Animals: http://www.iczn.org/iczn/index.jsp A note on taxonomic divisions. The levels of hierarchy are not necessarily created equally. For instance one family, like Hominidae, only contains 1 species: humans. However another family, like Curculionidae, the weevils, can contain 60,000 species and may show more genetic and phenotypic diversity than some classes. Sometimes the credentials for putting something into a given category work all the time, sometimes they dont. For example, Pluto used to be a planet. Now that more objects in space have been found, if Pluto qualifies as a planet, then many other space-objects must be considered planets too. Taxonomic subdivisions work something like that. One definition of a species works for some taxa, but not others. What separates two genera (plural for genus) of leafhoppers is not necessarily what separates two genera of deer. This can be even more confusing when you consider that evolution can change phenotypes gradually and in a continuum, so what works now might not work in the future or for their ancestors.

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An example of the characters used to define taxonomy Lets follow the taxonomy of the Grizzly Bear and explore the characters used to define each of its taxonomic levels.

The Grizzly Bear was given the species epithet Ursus arctos, which in Latin and Greek mean

bear respectively, in 1815 by George Ord (ironically, an ornithologist) after specimens were sent to him for scientific description by the Lewis and Clark expedition. It is not specific to grizzlies, which are distinguished as a subspecies called U. arctos horribilis, because Ord misunderstood the description grizzly which refers to the bears rough gray hairs for something more sinister.

Ursus is the genus that includes mostly northern hemispheric bears such as polar bears, black

bears, and other brown bears. Ursidae is a family that includes all 8 living bear species, including pandas. Bears are

distinguished as being large dog-like mammals with a typically carnivorous dentition (although all but the polar bear and panda are omnivorous). They have stocky legs, a long snout, shaggy hair, plantigrade paws with five nonretractile claws, and a short tail.

The order Carnivora contains historically carnivorous mammals and includes dogs, cats,

raccoons, seals, and the weasel family. As such they have a carnivores skull that contains large canines, forward-facing eyes (giving them binocular vision) and strong jaw muscle attachments. They also have clawed toes.

Mammals are vertebrate animals that have fur, a four-chambered heart, feed their young with

milk, have three middle ear bones, a diaphragm, and heterodont dentition.

Chordates are animals with a notochord, dorsal nerve cord, endostyle, phanryngeal pouches and arches, and a post-anal tail (at least as embryos).

The kingdom Animalia is distinguished as undergoing a blastula stage during development, and

typically being multicellular, mobile, and cute.

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Merging taxonomy and phylogeny: The shape of the Tree of Life Linnaean taxonomy was not originally intended to show evolutionary relationships. However, this view of taxonomy has changed dramatically with increased knowledge of evolutionary patterns. All life on earth is now thought to be related (i.e., descended from a common ancestor) and much evidence, such as carbon-based molecules, cells, and DNA, support this hypothesis. In the almost unimaginable span of time since the first organisms arose (about 3.5 billion years) life has gradually diversified into the myriad forms we see today. Darwin believed that evolutionary patterns could be described by a "tree of life" that showed how descendants of a common ancestor diverged to form separate taxonomic groups over time. However, Linnaean taxonomy is still used for most groups and so we will be exploring it today. Linnaeus divided all life into two kingdoms: plants and animals. When microorganisms were discovered in the 19th century, a third taxon was created by Ernst Haeckel to include them: the kingdom Protista. As more was learned about the biochemistry and microscopic structure of cells, it became clear that certain groups of microorganisms should be grouped separately or placed in the plant and animal kingdoms. Single-celled organisms that lacked nuclei (prokaryotes) were spun off into the kingdom Monera and the other microorganisms were left in Protista. Fungi, which didn't fit in as either plants or animals were put into their own kingdom. This "five kingdom" system prevailed for decades. When the creation of molecular phylogenies became possible in the 1990's, systematists sought to reorganize taxa into groups that better reflected the phylogenetic patterns they inferred from their data. Below is phylogeny of all life on Earth as far as we know. It also includes the characters that define and distinguish each group and where they might have evolved.

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The branching pattern (the bush of three main branches) near the "root" of the tree above was determined by Woese et al. (1990) and based on molecular data. They showed that several groups of unusual prokaryotes that had previously been considered bacteria were actually more closely related to eukaryotes than bacteria. Based on this pattern, they proposed dividing all life into three groups at a taxonomic level higher than kingdom which is now called domain (or superkingdom). The organization of the domains Archaea and Eubacteria at the kingdom levels is somewhat unclear - they are not usually divided into kingdoms, although taxa within the domains are organized into definite phyla. This part of the tree is still unresolved. In fact a very intriguing paper by Rivera and Lake (2004) hypothesizes that Eukaryotes evolved out of a hybridization of Archaea and Eubacteria in what they termed the ring of life. See the pic on the right. At any rate, the organization of the domain Eukaryota is more clear-cut. Eukaryotes are divided into the traditional Plantae, Fungi, and Animalia (or Metazoa) kingdoms as well as two or more kingdoms of what have traditionally been called protists (the Kingdom Protista is no longer accepted as a monophyletic group). Each of those kingdoms is then subdivided into phyla and lower taxonomic groups as in the traditional Linnaean system. Comparison of taxonomic ranks

Taxonomic rank Human Gorilla Longleaf Pine Anthrax Domain Eukaryota Eukaryota Eukaryota Eubacteria

Kingdom Animalia Animalia Plantae Bacteria Phylum Chordata Chordata Coniferophyta Firmicutes

Class Mammalia Mammalia Pinopsida Bacilli Order Primates Primates Pinales Bacillales

Family Hominidae Hominidae Pinaceae Bacillacae Genus Homo Gorilla Pinus Bacillus

Species H. sapiens G. gorilla P. palustris B. anthracis You can see that those organisms that are more closely related, such as humans and gorillas, share more ranks in common. In other words, they fit into more of the same boxes. Many of these groups are divided even further into subgroups, for example: subphylum, superfamily, subspecies, tribe, but we will mostly stick with the basics. How To Tell A Klotz From A Glotz

Well, the Glotz, you will notice, has lots of black spots. The Klotz is quite different with lots of black dots. But the big problem is that the spots on a Glotz are about the same size as the dots on a Klotz. So you first have to spot who the one with the dots is. Then its easy to tell who the Klotz or the Glotz is.

Dr. Suess. 1979. Oh Say Can You Say?

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Dichotomous keys When identifying taxa, taxonomists look very closely at many traits and their different forms, or characters. Once identified and distinguished, they create a key to these characters so that other scientists can separate the groups later. Often these keys contain steps to follow that lead you to ever finer categorization. If only 2 steps are provided at a time, sort of an if-then this/if not-then that, rule it is called a dichotomous key. This is very much like a flow chart or the old Choose Your Own Adventure books.

Here is a very basic example. Say we found this creature: and had no idea what it was. We could use a dichotomous key to find out.

Usually though, dichotomous keys are written out in long hand, using many long-winded and inane names for characters, as in my description of bears above. During this lab, you will use and create keys to distinguish organisms of various sorts. If you notice, dichotomous keys share a lot in common with phylogenies. Basically, species are organized by their shared and unshared characters. In a key, we group species according to features they share. In a phylogeny, we think they are related because they share features. Each description has two choices, called couplets. For example,

1 Description 1.2 1 Description 2.3

One of the pair is the number (1) and the other is the number prime (1). To use the key, begin by deciding which description in the first couplet is most appropriate for the specimen you are identifying. Be sure to examine all of the traits mentioned in the couplet. When you have decided which description is a better match, go to the next numbered couplet as indicated at the end of the description. Continue going to subsequent couplets until the description ends with the name of an insect order. If you get lost or get to a name that doesnt seem to make sense, go back and start again. Each couplet past 1 tells you which couplet led you to this one. For example, 1 says to go to 2. If you go to 2, it says 2 (1), meaning you got there from 1. Use these to retrace your steps. Use the key below, and a dissecting microscope if necessary, to identify the insect specimens to their various orders.

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A dichotomous key to selected insect orders.

1 Mouthparts consist of two mandibles adapted for chewing (they are pincer-like) (Fig. 1A) .............................................................................................................................. 2

1 Mouthparts are adapted for sucking (they are sharp/pointy, coiled into a tube, or spongelike) (Fig. 1B-D) ....................................................................................................... 6

2 (1) Four venous wings are very obvious and held out to sides of body.

Eyes large, longer than antennae, and touching each other on the top of the head. Skinny abdomen nearly the same length as wings. ........................... Odonata

2 Abdomen usually shorter than wings. Antennae are longer than eyes .............................................. 3 3 (2) Hindlegs adapted for jumping, with thick femora and two rows of

spines running the length of the tibia (Fig. 2) ......................................................................... Orthoptera 3 All legs similar in shape. No spines or spines not running length of leg. ........................................... 4 4 (3) Thick waist with no distinction between thorax and abdomen

when viewed from above (Fig. 3A). Wings folded and/or covering abdomen closely ........................................................................................................................................... 5

4 Waist pinches in the middle when viewed from above and side (Fig. 3B). Wings from opposites sides are not touching and not contoured to the body. Abdomen oval shaped with point at posterior ................................................ Hymenoptera

5 (4) Flat wings with visible veins crossed over each other on abdomen,

usually brown. Long skinny antennae. One pair of cerci on posterior of abdomen (Fig.4) ......................................................................................................................... Blattodea

5 Front wings hard and opaque, look like a shell (they dont look like wings). These hard wings form a single straight line down the center of the back (Fig.5) ....................................................................................................................... Coleoptera

6 (1) Wings transparent. Antennae are relatively short. ................................................................................. 7 6 Wings opaque. Antennae may be long or short ....................................................................................... 8 7 (6) Mouthparts are blunt (adapted for sponging up liquid) (Fig. 1D).

Body is hairy. ..................................................................................................................................... Diptera 7 Mouthparts are sharp and point posteriorly (Fig. 1B). Body is

Smooth (not hairy). .............................................................................................. Hemiptera (Homoptera) 8 (6) Mouthparts are coiled into long tube (Fig. 1C). Wings are stretched

to sides and covered in scales. Typically with hairy thorax ............................................... Lepidoptera 8 Mouthparts are sharp. Wings are crossed over abdomen, partially

venous (posterior) and partially leathery (anterior) .................................... Hemiptera (Heteroptera)

DO NOT TOUCH THE INSECTS! THEY ARE VERY FRAGILE!!!! Hold the pin instead.

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Figure 1. A

B C D

Figure 2.

Figure 3. A B

Figure 4.

Figure 5.

Femur

Tibia

To view the side or underside of insects without touching them, use a Styrofoam block:

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BIOL 1108 Lab 06 Classification Postlab Name ___________________________________ 1. Do some research and provide one fact that you find interesting about Carolus Linnaeus. Be honest.

Use good sources; cite them.

2. Using the dichotomous key, correctly identify your INSECT specimens to order. Also, look up the common name of this insects order. Check with your instructor before moving on.

Group # Unknown

Insect Insect order Common name A

B

C

D

E

3. Use the characters and the pattern from the dichotomous key, to draw a phylogeny depicting the

evolutionary relationships of these insects. Remember that a good phylogeny is bifurcating (meaning that each node splits into exactly two branches) just like the dichotomous key has two choices each time. Add the characters to the tree as you think they evolved.

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4. Create a dichotomous key to 5 MOLLUSK specimens from your bag so that someone else can distinguish them. Be specific about the characters you use. Use the terminology in the figure. Remember: these are just representative individuals of a presumably much more varied species, so slight differences in color and size are probably not the best characters to use.

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5. Draw a phylogeny to depict those relationships. Add characters to the tree to indicate how you think they evolved.

6. Ask someone else to key out your specimens using your key. Have them describe here how well your key worked and how easy it is to use. Have them print and sign here: