Topic 5.3: Classification of Biodiversity

Binomial system

• All animal names differ from language to language (ex: dog, gos, perro, hund, inu, etc…) creating a need for a system of consistency amongst biologists.

  • In the 18th century Carl Linnaeus (Father of modern taxonomy), developed the binomial nomenclature system to solve this need

  • The binomial nomenclature system ensures consistency among biologists by giving all organisms a universally established name.

    • Binomial = two names

    • Examples: Dog - Canis familiaris, Human - Homo sapiens

  • Congresses were created to help officially name new species as they are discovered

  • What are the rules in Binomial Nomenclature?

    1. Genus name begins with an upper-case letter and the species name with a lower-case letter

       • Rana pipiens (Northern leopard frog) → Rana (Genus) pipens (species)

       • Can also abbreviate to R. pipiens

    2. A binomial is Italicized when typed or Underlined when handwritten

Taxonomy

• Taxonomy - the branch of science concerned with the classification of organisms.

• Domains - the name for the three major categories in which All organisms on earth are

organized in

• The three domains:

  • Bacteria

    • Characteristics: absent histones associated with DNA, rare/absent presence of introns, the structure of cell walls made out of peptidoglycan, cell membrane differences: Glycerol-ester lipids; unbranched side chains; d-form of glycerol

  • Archaea

    • Characteristics: Proteins similar to histones bound to DNA, Presence of introns in some genes, the structure of cell walls not made of peptidoglycan, cell membrane differences: Glycerol-ester lipids; unbranched side chains; l-form of glycerol

  • Eukaryota:

    • Characteristics: present histones associated with DNA, the frequent presence of introns, the structure of cell walls not made of peptidoglycan; not always present, cell membrane differences: Glycerol-ester lipids; unbranched side chains; d-form of glycerol

• Eukaryota Classification:

  • Kingdom → Phylum → Class → Order → Family → Genus → Species

    • Examples:

      • Panther: Kingdom (Animalia) → Phylum *(Chordata)*→ Class *(Mammalia)*→ Order *(Carnivora)*→ Family *(Felidae)*→ Genus *(Panthera)*→ Species (Panthera pardus)

    • Pomegranate Tree: Kingdom (Plantae) → Phylum *(Magnoliophyta)*→ Class *(Magnoliopsida)*→ Order *(Myrtales)*→ Family *(Punicaceae)*→ Genus *(Punica L.)*→ Species (Punica granatum)

The Phyla that IB wants us to know:

• Additional vocab:

  • Types of Symmetry:

    • Asymmetry

    • Radial symmetry – divided along any plane.

    • Bilateral symmetry – divided along only 1 plane.

• The 6 Phyla for Animalia:

  • Porifera, Cnidaria, Platyhelminthes, Mollusca, Annelida, Arthropoda

    • all invertebrates

• How to identify them:

  • Porifera (sponges, etc.)

    • Asymmetrical

    • "Pore-bearer”, cannot move

    • Filter feed: no mouth/anus

    • Internal spicules (needles) as skeleton

    • They lack true tissues, such as muscles, nerves and organs.

      • Examples: Glass sponges, Sponge

  • Cnidaria (jellyfish, corals)

    • Radial symmetry

    • Mouth only

    • Soft skeleton (some corals secrete hard skeleton: CaCO3)

    • Have stinging cells

      • Examples: Coral, Sea Anemones and Jelly Fish

  • Platyhelminthes (flatworms/tapeworms)

    • Bilaterally symmetrical

    • Mouth only

    • Soft, no skeleton

    • No circulatory system but definite body organs including eyespots

    • Body flat like a ribbon

      • Examples: Tapeworms and Marine Flatworms, Planaria

  • Mollusca (squid, snails, etc.)

    • Bilateral symmetry

    • Mouth and Anus (rapula for feeding)

    • Soft bodies, usually have a shell present for the skeleton

    • Open circulatory system

    • Have a head with eyes or tentacles

      • Examples: Clams, Squids, and Snails

  • Annelida (bristleworms, leeches)

    • Bilateral Symmetry

    • Mouth and Anus

    • No bony skeleton; fluids in the body cavity under high pressure maintain shape

    • Segmented Worms, Circulatory system present

    • Can be mutualistic or parasitic.

      • Examples: Earthworms, Leeches, and marine worms

  • Arthropoda (insects, arachnids, crustaceans)

    • Bilateral Symmetry

    • Mouth and Anus

    • Covered by a hard exoskeleton

    • Segmented bodies with jointed appendages

    • Antennae, claws, wings, mouth parts, eyes, etc.

      • Examples: Insects, Arachnids and Crustaceans

• The Plantae Phyla IB wants us to Know:

  • Bryophyta (mosses)

    • Have no vascular system (i.e no xylem and phloem)

    • Have no ‘true’ leaves, roots, or stems (are anchored by a root-like structure)

    • Reproduce by releasing spores from sporangia (reproductive stalks)

      • Examples: mosses and liverworts

  • Filicinophyta (Ferns, etc…)

    • Have vascular system (i.e xylem and phloem)

    • Have true leaves, roots, and stems (pinnate leaves – large fronds divided into leaflets)

    • Reproduce by releasing spores from clusters called sori on the underside of the leaves

      • Examples: ferns

  • Coniferophyta (Pines, cedars, etc…)

    • Have vascular system (i.e xylem and phloem)

    • Have waxy needle-like leaves, roots, and woody stems

    • Reproduce through cones

      • Examples: pine trees and conifers

  • Angiospermophyta (roses, grass…)

    • Have vascular system (i.e xylem and phloem)

    • Have true leaves, roots, and stems

    • Reproduce by seeds produced in ovules within flowers (seeds may develop in fruits)

      • Examples: all flowering plants and grasses.

• Phylum Chordata:

  • Bony ray-finned fish

  • Amphibians

  • Reptiles

  • Birds

  • Mammals

Natural Classification vs Artificial Classification

• Natural Classification -

  • A way to classify species in a way that most closely follows the way in which species evolved.

    • All members of a genus or higher taxon should have a common ancestor

  • Can also use DNA technology to determine evolutionary relationships and thus how to classify organisms (ex: looking at amino acid sequences in same protein)

  • Advantages:

    • Allows us to predict characteristics of newly discovered species if we know which families/classes/etc. they belong to.

• Artificial classification-

  • Grouping on superficial characteristics

    • Birds, bats, and insects all in one group because they can fly.  (not good**)**

What is the difference between Natural and Artificial classification methods? (exam review question)

Natural classification is done by classifying species in a way that most closely follow the way in which species evolved., either through DNA technology or anatomical similarities (ex: homologous structures). Which allows grouping on a basis of common ancestry and evolution. On the contrary Artificial classification is based solely on superficial characteristics like if they can fly, breathe underwater, etc... which is highly unreliable and can lead to groupings like birds, bats, and insects just because they can fly.

Dichotomous Keys

• What are Dichotomous Keys?

  • They are keys often constructed to use for identifying species within a group.

• How do Dichotomous Keys work?

  • A dichotomy is a division into two; a dichotomous consists of a numbered series of pairs of descriptions. One of these should clearly match the species and the other should clearly be wrong. The features that the designer of the key chooses to use in the descriptions should therefore be reliable and easily visible. Each pair of descriptions leads either to another of the numbered pairs of descriptions of the key or to an identification.

    • Example: (look at slide 21)

      1. 1. The beak is relatively long and slender…….Bird W

         2. The beak is relatively short and heavy….go to 2

Topic 5.4: Cladistics

Clades

• Clade: a group of organisms that evolve form a common ancestor.

  • including all both living and extinct species

• How can you identify a clade?

  • In its most objective way they can be identified through base sequences of genes or amino acid sequences of proteins

    • Species with a recent common ancestor can be expected to have few differences in sequences, and vice versa.

      • sequence differences accumulate gradually so there is a positive correlation between the # of differences between 2 species and the time since they diverged from a common ancestor.

Homologous vs Analogous structures

• Analogous structures

  • Similar because of convergent evolution

    • The human eye and the octopus eye show similarities in structure and function but they are analogous because they evolved independently

    • Streamline appendages shared found in sharks (fish), penguins (birds), and dolphins (mammals)

• Homologous structures

  • Similar because of common ancestry

    • pentadactyl forelimbs shared btw Humans (mammals), cats (mammals), whales (mammals), and bats (mammals)

Cladograms:

• Cladograms: an evolutionary tree that diagrams the ancestral relationships among organisms.

  • Can show ancestral relationships and reflect how recently two groups share a common ancestry.

  • Can serve as visual representations of clades that allow us to better understand branching points and how closely organisms are related.

• How to read a Cladogram

  • the diagram consists of the organisms being studied, lines, and nodes where those lines cross.

    • The main line represents the passage of time.

    • The branches show when each animal split off from the main line.

    • The nodes represent traits/characteristics.

      • The node, before an animal branches off, is the last characteristic that the animal has in common with the rest of the organisms further up the diagram.

      • All of the animals that branch off at or after a node share the trait/characteristic.

• How can you tell which organisms in a cladogram are more closely related to each other?

  • the closer the organisms are in the cladogram the more closely related they are

Topic 5.1: Evidence for Evolution

• Evolution: the cumulative change in the heritable characteristics of a population

Forms of evidence:

• Fossil Record

  • Fossils are any remains, impressions or traces of a living thing from a former geologic age.

  • What does Fossil Record let us know?

    • Sedimentary layers

      • The sequence in which fossils appear matches the sequence in which they were likely to evolve.

        • The deeper the layer the older the ancestor

      • The sequence of sedimentary layers also fits in with the ecology of the groups:

        • plant fossils appearing before animal, land plants before land animals, etc.

    • Radioisotope dating reveals the ages of rock strata and the fossils within.

    • Transitional fossils

      • Fossils that can link existing organisms with their likely ancestors

• Selective Breeding (artificial selection)

  • the deliberate breeding of a plant or animal species to elicit certain traits in the offspring.

    • Provides evidence for the process of evolution as it allows us to document changes happening to a species through selective breeding

  • Artificial selection vs natural selection

    • Natural selection occurs without human intervention;  Artificial selection is when humans intentionally select organisms with desirable traits to breed. The changes are evident much faster with artificial selection.

• Homologous structures:

  • Similar anatomical structures that result from being inherited from a common ancestor

  • May have different functions and don’t necessarily exist in the same habitat

    • Example:

      • Pentadactyl limb - Same skeletal plan but have slightly different functions. Whale for swimming, a mole for digging, a primate for grasping, a bat for flying, etc

Topic 5.2: Natural Selection

Natural selection: the mechanism by which evolution occurs…AKA, it explains how species evolve

The 4 components of natural selection

1. There is variation within a population

2. Variations are Inherited

3. Due to the overproduction of offspring, there is competition.

   1. Some survive and reproduce; some don’t.

4. Over time, the frequency of traits in a population can change.

1. Variation

• Natural selection can only occur if there is variation amongst members of the same species.

• Sources of variation:

  1. Gene mutation - New alleles can enlarge the gene pool (not always bad)

  2. Meiosis - Traits differ from generation to generation

  3. Sexual reproduction - Mutations/traits that occur in different individuals can be brought together

2. Overproduction of Offspring

• The number of offspring varies from species to species, but overall, living organisms produce more offspring than the environment can support which leads to competition for survival.

  • Survival of the Fittest.

3. Survival of the Fittest (Darwin)

• Variations that give an advantage are selected for

• The individual which can best compete and live longer will pass those traits on to the next generation

• Variations that give a disadvantage are selected against

  • Less suited to its environment, making it more difficult to survive, thrive, and pass that trait onto the next generation

4. Progressive Change

• Over many generations, the characteristics (allele frequencies) of a population will gradually change such that favorable traits will become more common in the population.

Examples of adaptations as a result of Natural Selection

Industrial Melanism (Peppered Moths)

• Dark varieties of light-colored insects are called melanistic.

• The peppered moth Biston betularia showed that as pollution increased in industrial areas, the soot and pollution killed the lichen on the trees making them darker.

• In polluted areas, the melanistic (darker) moth variation increased in frequency as it gave them an advantage over light-colored ones as they now stood out more to predators while the dark ones could hide better.

Antibiotic Resistance

• Bacteria have a very rapid rate of reproduction

  • Generation period of sometimes less than 1 hr

• Exist in huge populations, increasing the chance of a resistant gene formed by random mutation

• Many different ways to pass this gene on to the next generations

Galapagos Finches

Three forms of selection

1. Stabilizing selection - pressures act to remove extreme varieties. (All phenotypic extremes are selected against.)

   1. How to identify it in a graph:

   2. Examples: Birth weight in humans, size of clutch (number of eggs laid)

2. Disruptive selection - pressures act to remove intermediate varieties, favoring the extremes. Often more dependent on the environment (Two or more different phenotypic extremes are selected for at the same time.)

   1. How to identify it in a graph:

      1. The bell curve is not typical in shape when exhibiting disruptive selection. In fact, it looks almost like two separate bell curves. There are peaks at both extremes and a very deep valley in the middle, where the average individuals are represented

   2. Examples:

3. Directional selection - pressures act to shift population towards one extreme or the other. (One phenotypic extreme is selected.)

   1. How to identify it in a graph:

      1. the slope the bell shifts forward or back.

   2. Examples: Pepper moths