5.3: Classification and Biodiversity

*List the three domains of life.* Understanding: All organisms are classified into three domains.

A domain is the broadest taxonomic grouping of organisms. The three-domain system was proposed by Carl Woese et al. in 1990. It divides cellular life forms into three domains, the archaea, eubacteria, and eukaryota.

*Define "taxonomist."* Understanding: Taxonomists classify species using a hierarchy of taxa.​

A taxonomist is a biologist that groups organisms into categories.

*Outline the characteristics of the angiospermatophyta.* Application: Recognition features of bryophyte, filicinophyta, coniferophyta, and angiospermophyta.

Angiospermatophyta are the *flowering* plants, such as grasses, daisies, lilies, roses, tulips. Have roots, stem and leaves. Have vascular tissue that conduct water and nutrients (xylem and phloem). Can grow tall. Reproduce by seeds produced in ovules within flowers. Produce seeds in fruits.

*Outline the characteristics of the phylum annelida.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Annelida are the segmented worms, like earthworms and leeches. May be aquatic or terrestrial. Body is bilaterally symmetrical. May have chaetae, bristles projecting from the skin which function in locomotion. Have a complete digestive system with seperate in and out openings. Gas exchange takes place by diffusion of oxygen from the environment directly into the body; no cell can be too far from the outside. Excretion of nitrogenous waste (ammonia and urea), takes place through nephridia (a tube that opens to the exterior). Have a closed circulatory system, blood is always contained within blood vessels. Asexual reproduction occurs through budding or fission and regeneration (a single organism splits up into smaller fragments which each regenerates). Sexual reproduction occurs through cross fertilization with another individual (internal or external fertilization depending on the species). Some hermaphroditic reproduction occurs.

*State seven major animal phyla.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Some of the major phyla of the animal kingdom are: Porifera Cnidarian Platyhelminthes Annelida Mollusca Arthropoda Chordata

*Define "binomial nomenclature."* Understanding: The binomial system of names for species is universal among biologists and has been agreed and developed at a series of congresses.

Species are named with two name (binomial). The first name is for the genus and the second name is for the species. Together the two names make a unique combination that designate a species.

*Define "taxa"*. Understanding: Taxonomists classify species using a hierarchy of taxa.​

Taxon, plural taxa, is a grouping unit used in biological classification. There are multiple common grouping units of taxa. For example, a "species" is a taxon (group) of all the organisms that can (actually or potentially) interbreed with each other to produce fertile offspring and cannot breed with others.

*Distinguish the archaea domain from the eubacteria domain.* Understanding: All organisms are classified into three domains.

*Archaea* DNA with histone proteins. Usually have intron DNA sequences. Cell walls not made of peptidoglycan. Membrane phospholipids can be branched. Different ribosomes than eubacteria. Not sensitive to antibiotics that affect eubacteria. Can live in extreme environments (hot springs, salt lakes, marshlands, oceans, gut of ruminants and humans). *Eubacteria* DNA without histone proteins. Usually do no have intron DNA sequences. Cell walls made of peptidoglycan. Membrane phospholipids not branched. Different ribosomes than archaea. Sensitive to antibiotics that do not affect archaea. Most do not live in extreme environments.

*State the classification of an animal, from domain to species.* Application: Classification of one plant and one animal species from domain to species level.

*Domain:* Eukaryota (all eukaryotic celled organisms) *Kingdom:* Animalia (all animals) *Phylum:* Chordata (all animals with a hollow nerve cord) *Class:* Mammalia (all animals the nurse their young) *Order:* Carnivora (animals with teeth for tearing meat) *Family:* Felidae (cats with retractable claws) *Genus:* Felis (non-roaring cats) *Species:* domesticus (domesticated pet cats)

*State the classification of a plant, from domain to species.* Application: Classification of one plant and one animal species from domain to species level.

*Domain:* Eukaryota (all eukaryotic celled organisms) *Kingdom:* Plantae (all plants) *Phylum:* Angiospermatophyta (all flowering plants) *Class:* Dicotyledonae (plants two to seed cotyledons) *Order:* Rosales (all roses and rose like plants) *Family:* Rosaceae (all roses) *Genus:* Rosa *Species:* gallica

*Outline why the binomial naming system is used in science rather than local or common names.* Nature of Science: Cooperation and collaboration between groups of scientists- scientists use the binomial system to identify a species rather than the many different local names.

1. Binomial names are standardized, allowing people throughout the world to communicate unambiguously about species even when they speak different primary languages. 2. Each binomial name refers to only one species. The same species can have many different local names. 3. Binomial names provide clues to the evolutionary relationships between species. Members of the same genus are more related to each other than to members of a different genus. Local names do not give clues to relationships between species.

*Explain the use of a dichotomous key in the identification of a specimen.* Application: Construction of dichotomous keys for use in identifying specimens.

1. Observing the specimen you want to identify. 2. Look for distinguishing features. 3. Follow the pairs of “either-or” choices to the next pair of choices to the point of identification.

*List difficulties in determining the natural classification of species.* Understanding: In a natural classification, the genus and accompanying higher taxa consist of all the species that have evolved from one common ancestral species.

1. Species and their distinctive attributes are not fixed and eternal, rather species are continually changing. As a consequence, any current classification is essentially a somewhat arbitrarily defined point along an evolutionary line. 2. Species are physically and genetically diverse. What may appear to be very different are actually variations within the same species (for example, spotted and black jaguars). 3. There is debate among researchers over defining new species because it is not obvious what the most important traits are for determining classification. 4. Due to convergent evolution, distantly related organisms appear superficially similar. Likewise, adaptive radiation may make make closely related organisms appear different.

*Outline the role of botanical and zoological congresses in the naming of plants and animals.* Understanding: The binomial system of names for species is universal among biologists and has been agreed and developed at a series of congresses.

A "congress" is a regularly occurring meeting of taxonomists attended by delegates from all over the world. At these meeting, the biologist modify the rules for naming and classifying species and approve the names of any new species that have been discovered.

*Define "dichotomous key."* Application: Construction of dichotomous keys for use in identifying specimens.

A dichotomous key is a tool for identification of unknown organisms. Sets of statements act as clues leading to the identification of an organism or group.

*Outline the characteristics of the phylum arthropoda.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Arthropods have jointed appendages/legs. Body is bilaterally symmetrical. Body is divisible into head, thorax and abdomen. Head bears a pair of compound eyes and antenna. Body is covered with chitinous exoskeleton. Occur in almost every habitat found on Earth. Digestive system is complete and well developed. Gas exchange takes place by general body surface or gills (in crustaceans) or trachea (in insects) or book-lungs (in arachnids). Circulatory system is open (do not have blood vessels and enters directly into the body chambers). Excretion of nitrogenous waste (uric acid) takes place through Malpighian tubules. Sexual reproduction (fertilization is internal or external).

*Compare artificial and natural classification systems of taxonomy."* Understanding: In a natural classification, the genus and accompanying higher taxa consist of all the species that have evolved from one common ancestral species.

Artificial classification is the grouping of organisms into groups on the basis of observable structural features (e.g. the grouping together of plants according to the number and situation of their stamens, styles, and stigmas rather than their evolutionary relationships). As knowledge of homologous structures, genetics and evolutionary relationships has grown, artificial systems have been superseded by systems of natural classification, which considers evolutionary relationships for groupings.

*State the role of Carl Linnaeus in naming species.* Nature of Science: Cooperation and collaboration between groups of scientists- scientists use the binomial system to identify a species rather than the many different local names.

Binomial nomenclature that was originally codified in the writing of Linnaeus (Systema Naturae, 1758). In addition to a consistent binomial system of naming, Linnaeus also developed a system of organizing the diversity of life in a hierarchical classification.

*Outline an example of a species (or group of species) which were reclassified when new evidence was discovered.* Understanding: Taxonomists sometimes reclassify groups of species when new evidence shows that a previous taxon contains species that have evolved from different ancestral species.

Birds were categorized in the biological class Aves in Linnaean taxonomic hierarchy, and both snakes and crocodiles were part of class Reptilia. Under this scheme, snakes and crocodiles are more similar to each other than either is to birds. However we now understand that the bird lineage shares a more recent ancestor with some modern reptiles (crocodiles) than with others (snakes). Natural classification places birds in the same taxa as crocodiles (theropoda).

*Outline the characteristics of the phylum chordata.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Body is bilaterally symmetrical. At some point in their life, all chordates have a notochord, a flexible rod made out of a material similar to cartilage providing skeletal support through the length of the body. Have a dorsal hollow nerve cord, which in most chordates develops into the brain and spinal cord. Have pharyngeal slits, openings in the pharynx that extend to the outside environment. May be present only during embryonic development. Have a post-anal tail, an elongation of the body, extending beyond the anus. In humans, the tail is present during embryonic development and is vestigial as an adult. Digestive system is complete and well developed. Gas exchange takes place through skin, in gills or in lungs. Have a closed circulatory system, blood is always contained within blood vessels. Excretion of nitrogenous waste (ammonia, urea or uric acid) takes place through a kidney. Primarily sexual reproduction (internal or external fertilization).

*Outline the characteristics of the bryophyta.* Application: Recognition features of bryophyte, filicinophyta, coniferophyta, and angiospermophyta.

Bryophyta are the liverworts, hornworts and mosses. No roots, only simple, hair-like projections called rhizoids that grow directly out of the photosynthetic tissue. Simple leaves (or flattened leaf like structures called a thallus). Leaves do not have a cuticle layer. Reproduce via spores. Spores are single-cells that can develop into a new organism using mitotic division. No vascular tissue (no xylem or phloem), so have no way to transport water and nutrients. Very short plants, since the only way to move substances through the plant body is by osmosis and diffusion from surface moisture. Must live in moist habitats.

*List two situations in which the reclassification of a species may be necessary.* Understanding: Taxonomists sometimes reclassify groups of species when new evidence shows that a previous taxon contains species that have evolved from different ancestral species.

Changes to classification occurs as new discoveries are made and better methods of classification are found. 1. Sometimes new evidence indicates that members of a taxa do not share a common ancestor and therefore should not be grouped together in a natural classification scheme. 2. Sometimes new evidence indicates that species that were not thought to be related actually do share a common ancestor and therefore should grouped together in a natural classification scheme.

*State the major classes of chordata.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

Class Agnatha (jawless fishes) Class Chondrichthyes (cartilaginous fishes) Class Osteichthyes (bony fishes) Class Amphibia (amphibians) Class Reptilia (reptiles) Class Aves (birds) Class Mammalia (mammals)

*Outline the characteristics of the phylum cnidarian.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Cnidaria are the anemones, jellyfish, and corals. Two distinct morphological body plans: polyp, which are sessile as adults, and medusa, which are mobile. Some species exhibit both body plans in their lifecycle. Predominantly marine. Body is radially symmetrical. Have an incomplete digestive system with only one opening; the gastrovascular cavity serves as both a mouth and an anus. Have tentacles with stinging cells called nematocysts that they use to capture food. Gas exchange takes place by diffusion of oxygen from water the flowing into the body. Excretion of nitrogenous waste (mainly ammonia) directly from the body with outgoing water current. Most polyps reproduce asexually (budding). Medusa usually reproduce sexually using eggs and sperm. Depending on the species, fertilization is either internal or external.

*Outline the characteristics of the coniferophyta.* Application: Recognition features of bryophyte, filicinophyta, coniferophyta, and angiospermophyta.

Coniferophyta are the conifers, such as cedars, firs, cypresses, junipers, pines, hemlocks, and redwoods. Have roots, stem and leaves. The leaves are usually evergreen (do not seasonally drop) Leaves are often needle shaped and have a waxy cuticle to limit water evaporation. Have vascular tissue that conduct water and nutrients (xylem and phloem). Can grow tall. Have woody stems. Produce seeds in *cones*.

*Outline the characteristics of mammals.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

Dogs, whales, sloths and humans are members of the class Mammalia. All mammals have internal fertilization and after birth feed the babies milk produced by the mammary glands. Mammals are heterodonts (they have a variety of specialized teeth) which allows them to chew their food into small pieces before swallowing it. Subsequently, they can eat any size plant or animal.

*Outline the characteristics of the filicinophyta.* Application: Recognition features of bryophyte, filicinophyta, coniferophyta, and angiospermophyta.

Filicinophyta are the ferns and horsetails. Have roots, stem and leaves. The leaves are often pinnate (fronds with leaflets on each side of a common axis). Have vascular tissue that conduct water and nutrients (xylem and phloem). Produce spores which may be visible in clusters called sori on the underside of the leaves. Do not have flowers, fruits or seeds.

*Outline the characteristics of amphibians.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

Frogs, toads, and salamanders are amphibians. Amphibia spend part of their lives under water and part on land. Many of these species must keep their skin moist by periodically returning to wet areas. All of them must return to water in order to reproduce because their eggs would dry out otherwise. They start life with gills, like fish, and later develop lungs to breathe air.

*Summarize the evidence that supports a three domain classification of life.* Understanding: All organisms are classified into three domains.

Genetic sequencing provided researchers a new way of analyzing relationships between organisms. The three domain system groups organisms primarily based on differences in ribosomal RNA (rRNA) structure. Ribosomal RNA is a molecular building block for ribosomes. Each of these three domains contains unique rRNA.

*Outline the characteristics of the phylum mollusca.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Mollusca are the slugs, squid, snails, octopus and clams. Have soft, unsegmented bodies with a head, a muscular foot and a visceral mass. This is all covered with a mantle that typically secretes a hard shell. Occur in almost every habitat found on Earth. Body is bilaterally symmetrical. Have a complete digestive system with seperate in and out openings. Circulatory system is open (do not have blood vessels and enters directly into the body chambers). Gas exchange via gills. Excretion of nitrogenous waste (ammonia and urea), takes place through nephridia organized as kidneys, that collect liquid wastes from the coelom and dump them in the mantle cavity. Primarily sexual reproduction with external fertilization. Some use internal fertilization and/or are hermaphrodites.

*Explain an advantage of natural classification.* Understanding: Natural classification helps in identification of species and allows the prediction of characteristics shared by species within a group.

Natural classification allows for the prediction of homologous characteristics shared by species within a group since all members of a taxa in a natural classification will have evolved from a common ancestral species.

*Define "natural classification."* Understanding: In a natural classification, the genus and accompanying higher taxa consist of all the species that have evolved from one common ancestral species.

Natural classification is the grouping of organisms into taxa on the basis of their evolutionary relationships.

*Outline the characteristics of the phylum platyhelminthes.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Platyhelminthes are the flatworms. May be marine, terrestrial or parasitic. Body is bilaterally symmetrical. Have an incomplete digestive system with only one opening serving as both a mouth and an anus. Body is flat and not segmented. Gas exchange takes place by diffusion of oxygen from the environment directly into the body; no cell can be too far from the outside, making a flattened shape advantageous. Excretion of nitrogenous waste (mainly ammonia) directly from the body. Most flatworms are hermaphrodites, having both male and female sex organs. As a result, platyhelminthes can reproduce sexually on its own or through cross fertilization with another individual (with internal fertilization). Asexual reproduction occurs through fission and regeneration (a single organism splits up into smaller fragments which each regenerates).

*Outline the characteristics of the phylum porifera.* Application: Recognition features of porifera, cnidarian platyhelminthes, annelida, mollusca, arthropoda and chordata.

Porifera are the sponges. Are multicellular organisms which are sessile (fixed in one place). Predominantly marine. Body is cylindrical and usually asymmetrical. Feed on small organisms and organic particles which enter the body through water current. Gas exchange takes place by diffusion of oxygen from water the flowing into the body. Excretion of nitrogenous waste (mainly ammonia) directly from the body with outgoing water current. Reproduction may be asexual (budding) or sexual (involves internal fertilization).

*Outline the characteristics of reptiles.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

Reptilia includes turtles, snakes, lizards, and alligators. All of them have lungs to breathe on land and skin that does not need to be kept wet. They produce an amniote egg which usually has a leathery shell that protects the embryo from drying out. After internal fertilization the the amniote egg can be laid on land.

*State rules of binomial nomenclature formatting.* Understanding: When species are discovered they are given scientific names using the binomial system.

Scientific names are Latin or latinized names that are standardized by a series of rules that are applicable worldwide. 1. The Genus name is capitalized. 2. The species names is lower case. 3. The binomial is shown underlined if printed or italicized if typed.

*Outline the benefits of using a system of binomial nomenclature.* Understanding: The binomial system of names for species is universal among biologists and has been agreed and developed at a series of congresses.

The binomial system has been a successful system because it is functional, has been the only system that is recognized worldwide, and has been used over the last 250+ years of naming species. Having an internationally recognized system of naming species facilitates communication between people with a different language.

*Outline the characteristics of birds.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

The class Aves includes all the birds. They produce an amniote egg which usually has a hard shell that protects the embryo from drying out. After internal fertilization the the amniote egg can be laid on land. Birds are descendents of theropod dinosaurs (two-legged mostly carnivorous dinosaurs).

*List the four kingdoms of eukaryotes.* Understanding: The principal taxa for classifying eukaryotes are kingdom, phylum, class, order, family and genus and species.

The four eukaryotic kingdoms are animalia, plantae, fungi, and protista.

*List the hierarchy of biological taxa, from largest to smallest.* Understanding: Taxonomists classify species using a hierarchy of taxa.​

The hierarchy of taxa from largest to smallest is: 1. Domain 2. Kingdom 3. Phylum 4. Class 5. Order 6. Family 7. Genus 8. Species

*State the four major plant phyla.* Application: Recognition features of bryophyte, filicinophyta, coniferophyta, and angiospermophyta.

The major phyla (divisions) of the plant kingdom are: Bryophyta (mosses) Filicinophyta (ferns) Coniferophyta (conifers) Angiospermatophyta (flowering plants)

*Define "vertebrate" as related to classification of chordata.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

The vertebrate animals are all the members of the phylum chordata that possess a backbone that runs from head to tail and surrounds and protects the main nerve cord. In vertebrates the notochord becomes part of the back bone during embryonic development.

*Draw a tree diagram to illustrate the evolutionary relationship between the three domains.* Understanding: All organisms are classified into three domains.

There is ongoing debate about the early evolution of life on Earth and the placement of the three domains on a tree diagram. The current consensus places the last universal common ancestor (LUCA) at the root of the tree with two branches, one leading to the eubacteria (B) and the other two the archaea (A) and eukaryota (E).

*Outline the characteristics of fish.* Application: Recognition of features of birds, mammals, amphibians, reptiles and fish.​

Three of the vertebrate classes are fish. The most primitive of these is Agnatha, jawless fish that do not have scales (lampreys and hagfish). Fish that have skeletons consisting of cartilage rather than bone are members of the class Chondrichthyes (sharks and rays). All of the bony fish are members of the class Osteichthyes (tuna, bass, salmon, and trout).

*State the two prokaryotic domains.* Understanding: All organisms are classified into three domains.

Two domains consist of prokaryotic organisms, single-celled microorganisms whose cells have no nucleus or internal membrane bound compartments. 1. Archaea 2. Eubacteria