1. Phylogeny & systematics
IB BIO II
Van Roekel
4/17/14

2. Classification
Use binomial nomenclature to name and classify organisms
1st word refers to the genus, 2nd word to the species, i.e. Homo Sapiens.
Carolus (Carl) Linnaeus consolidated and popularized binomial nomenclature
Reasons:
Make sense of biosphere
Identify unknown organisms
Show evolutionary links
Predict characteristics shared by members of a group

3. Biochemical Evidence of Evolution
DNA is universal source of genetic information in all living organisms
Any gene can be mixed and match with DNA from other organisms and generate a certain protein
All proteins use same 20 amino acids to form polypeptide chains
Can have 2 possible orientations, left-handed & right-handed, all proteins are based on left- handed orientation
Chemical similarities suggest common ancestry for all life

4. Phylogeny Study of the evolutionary past of a species
Species that are most similar are closely related
Species with more differences are less likely to be closely related
Traditionally done with morphological characteristics
More recently done by comparing similarities in polypeptide sequences in proteins such as hemoglobin, cytochrome C, and cholrophyll
Also done by examining DNA base sequences

6. Variations and Phylogeny
AAAATTTTCCCCGGGG
AAAATTTACCCCGGGG
AAAATTTACCCGCGGG
AACATCTTCCACGCTG
1 & 2 most similar/closely related
1 & 4 most differences/less related
Use biochemical phylogenies to confirm/contradict work done by paleontologists

7. The Evolutionary Clock
Differences in DNA & polypeptide sequences occur over time through mutations and sexual reproduction
Changes can be used as a “clock” to estimate how far back the species split
Compare homologous molecules and count the number of base pairs that don’t match
3 organisms: A,B,C
A&B 23 differences, A&C 83 differences
A&B more closely related than A&C
Split between A&C occurred roughly three times further in the past than A&B

8. Hybridization Technique that measures differences in DNA sequences
Take sample of DNA from one species (A) and fuse it with sample from another species (B)
Where connections occur, base pairs match
Where no connections, base pairs repel and there is a difference

10. Cladistics
Cladistics is a system of classification which groups taxa together according to characteristics which have most recently evolved
Examine primitive (plesiomorphic) traits and derived (apomorphic) traits
Primitive traits have same structure and function, and evolved early on in organisms being studied (leaves with vascular tissue in plants)
Derived traits also have same structure and function but evolved more recently as modifications of previous traits occurred (flowers with vascular tissue which evolved more recently than leaves)

11. Clades
When groups are split into two parts, one having derived characteristics and the other does not, the groups form two separate clades
Monophyletic groups, composed of the most recent common ancestor and all its descendants
Usually made up of several species

13. Homologous & Analogous Structures
Used to help separate individuals in to different clades
Homologous Structures are derived from the same part of a common ancestor
Pentadactyl limb in animals such as humans, whales, and bats
Analogous Structures have same function but do not necessarily have same structure and are not derived from a common ancestor
Wings in birds, bats, and insects

14. Cladograms
Cladograms are diagrams that visually represent the findings of cladistics
Shows evolutionary relationships with bottom branches showing earliest evolved organisms and top branches most recently evolved
Basic idea is parsimony, meaning the least complicated explanation is preferred
Each time a branch forks into two, a split between species occurred creating two lineages, each split is called a node
Each node shows speciation
Can be made using biochemical and morphological examples

18. BILL
The simplified cladogram of vertebrata is shown with synapomorphies indicated. 
What organisms have bony ribs and shoulder girdles?
Ray-finned fish, lungfish, amphibians, and land vertebrates
What is the oldest creature in this cladogram? They youngest?
Lampreys, landvertebrates
What feature is shared by amphibians and land vertebrates?
Have fingers and toes
What feature did the common ancestor of lungfish and lampreys have?
Vertebrae
What creature is most closely related to land vertebrates? Lampreys?
Amphibians, Sharks

19. Cladogram construction
Construction of Cladograms
Make a list of included organisms
List as many characteristic each organisms posses
From established list, find a characteristic common to all organisms (primitive characteristic)
Make a table with derived characteristics on top row and organisms in first column. (shows derived characteristics in each organism
Construct cladogram from table, organism with least derived traits is on first branch, organism with most derived characteristics is on top branch

20. Constructing a Cladogram
Use the following information to construct a cladogram
Organisms: Paramecium, flatworm, shark, hawk, koala, camel, human
Characteristics: Eukaryotic, multicellular, vertebral column, produces amniotic egg, has hair, has placenta, has one opposable thumb on each forelimb

21. Eukaryotic
Multicellular
Vertebral Column
Amniotic Egg
Hair
Placenta
Opposable thumb
Totals
Paramecium + X 1
Flatworm 2
Shark 3
Hawk 4
Koala 5
Camel 6
Human 7

22. Paramecium
Flatworm
Shark
Hawk
Koala
Camel
Human
Hair
Multicellular

23. Cladograms and Classification
Cladistics attempts to find most logical and natural connections between organisms by using morphological or biochemical data
Classification shows connections by groupings organisms into different taxa
Each time a derived characteristic is added to a cladogram, it is similar to moving up one taxa in Linnaean System
Differences occur in organisms such as birds,
Cladistics says birds share characteristics with dinosaurs and thus are in the same clade
Linnaean Classification have birds in a class of their own
Cladistics, rules are always the same concerning derived and primitive characteristics
Classification definitions such as species, classes, and phyla can be challenged

24. Classification
Use binomial nomenclature to name and classify organisms
1st word refers to the genus, 2nd word to the species, i.e. Homo Sapiens.
Carolus (Carl) Linnaeus consolidated and popularized binomial nomenclature
Reasons:
Make sense of biosphere
Identify unknown organisms
Show evolutionary links
Predict characteristics shared by members of a group

25. Hierarchy of classification
Five Kingdoms
Kingdom Plantae (plants)
Kingdom Animalia (animals)
Kingdom Fungi (fungi and molds)
Kingdom Protoctista (protozoa and algae)
Kingdom Prokaryote (bacteria)

27. Hierarchy of Classification
Within each kingdom, there are several subdivisions, called taxa
Seven-level hierarchy of taxa:
Kingdom
Phylum
Class
Order
Family
Genus
Species
King Phillip Came Over For Good Soup

28. Examples Taxa Human Garden Pea Kingdom Animalia Plantae Phylum
Chordata
Angiospermae
Class
Mammalia
Dicotyledoneae
Order
Primate
Rosales
Family
Hominidae
Papilionaceae
Genus
Homo
Pisum
Species
sapiens
sativum

29. Other Means of Classification
Feeding Habits (carnivore/herbivore)
Habitat (land dwelling/aquatic)
Daily activity (nocturnal/diurnal)
Risk (harmless/venomous)
Anatomy (vertebrates/invertebrates)
System of classification must be clear, consistent, easily implemented and a general consensus to apply it.

30. Plant Phyla Bryophyta: short in stature such as moss
Four of the several types of plant phyla include:
Bryophyta: short in stature such as moss
Filicinophyta: ferns and horsetails
Coniferophyta: coniferous, pine trees cedar, juniper, fir
Angiospermophyta: all plants that make flowers and have seeds surrounded by fruit

32. Distinguish plant phylas
Vegetative Characteristics such as leave types and stems
Bryophytes: non-vascular, lack vascular transport tissue such as xylem or phloem
Filicinophyta: vascular plants, small leaves
Conifers: vascular, all produce woody stems and leaves are needles or scales
Angiosperms: vascular and have flowers and fruit

33. Distinguish plant phylas
Reproductive characteristics
Bryophytes: produce spores (microscopic reproductive structures) transported by rain water
Filicinophytes: produce using spores in a similar manner
Conifer: use wind to help reproduce by pollination, produce seed cones with seed scales
Angiosperms: produce seeds, rely on birds, insects, and mammals to transport pollen. Sexual organ is flower, fruit is enlarged ovary

35. Animal Phyla Six of many animal phyla include:
Proifera: sponges
Cnidaria: sea jellies (jellyfish), coral polyps, and others
Platyhelminthes: flatworms
Annelida: segmented worms
Mollusca: snails, clams, octopi, etc…
Atrhtropoda: insects, spiders, crustaceans, etc…
All listed phyla are invertebrates

36. Details Porifera: Cnidaria:
Simple marina animals that are sessile (stuck)
Feed by pumping water through tissues and filtering out food
No muscle, nerve tissues, or internal organs
Cnidaria:
Very Diverse: Coral, sea anemones, jellyfish, hydra, Portuguese man-of-war
All have stinging cells called nematocysts
Some sessile, some free swimming, some both
Gastric pouch for digestion

38. Details Platyhelminthes: Annelida:
Flatworms with one body cavity, gut with one opening for food to enter and waste to leave
No heart, no lungs
Exchange gas by diffusion
Example: Tapeworms
Annelida:
Segmented worms such as earthworms, leeches, and polychaetes
Bodies divided into sections separated by rings
Have gastric tracts, w/ mouth at one end and anus at opposite

40. Details Mollusca: Arthropoda: Aquatic animals, snails, clams, octopi
Shell produced with calcium
Non-segmented bodies
Arthropoda:
Hard exoskeleton made with chitin, segmented bodies, and limbs (walking, swimming, eating)
Insects, spiders, scorpions, crustaceans such as crab and shrimp
Live in most habitats throughout world
Vary in size

42. Dichotomous Key Example in book, pg. 149
Used to help identify which order, genus, and species an organism is by using observable characteristics
In General:
Look at first section of key which has a pair of sentences
Look at the organism to see if particular characteristics are present
If answer is yes, to go end of line/next section that contain a new pair of statements to examine
If answer is no, go to second statement just below it and follow that one, should it be true
Continue this until the end of the line has a name, not a number and if each question was answered correctly, should be your organism.
Example in book, pg. 149

43. 1. a. Organism is living........................................................go to 4.
1. b. Organism is nonliving go to 2.
2. a. Object is metallic go to 3.
2. b. Object is nonmetallic ROCK.
3. a. Object has wheels BICYCLE.
3. b. Object does not have wheels TIN CAN.
4. a. Organism is microscopic PARAMECIUM.
4. b. Organism is macroscopic go to 5.
5. a. Organism is a plant go to 6.
5. b. Organism is an animal go to 8.
6. a. Plant has a woody stem go to 7.
6. b. Plant has a herbaceous stem DANDELION.
7. a. Tree has needle like leaves PINE TREE.
7. b. Tree has broad leaves OAK TREE.
8. a. Organism lives on land go to 9.
8. b. Organism lives in water CLAM.
9. a. Organism has 4 legs or fewer go to 10.
9. b. Organism has more than 4 legs ANT.
10 a. Organism has fur go to 11.
10 b. Organism has feathers ROBIN.
11 a. Organism has hooves DEER.
11 b. Organism has no hooves MOUSE.

44. Dichotomous Key Vocabulary can be challenging and technical
Make sure using the right key, no key can identify all the species
Making a Dichotomous Key
Start by putting things in groups by identical characteristics
Invent statements that divide things into created groups

45. Practice Problems
List five kingdoms and determine where each organism belongs: algae, hydra, spider, mushroom, yeast, bacterium.
Design a dichotomous key using ten different objects/organisms
In a population of 278 mice, 250 are black, 28 are brown. B=black, b=brown. Identify the allele and genotype frequencies in this generation.
Spots for camouflage exist on many different species, such as butterflies and cheetahs. A student groups all organisms with spots in the same clade. Is this justified? Why or why not?

46. Plantae, Animalia, Fungi, Protoctista, and Prokaryote
List five kingdoms and determine where each organism belongs: algae, hydra, spider, mushroom, yeast, bacterium.
Plantae, Animalia, Fungi, Protoctista, and Prokaryote
Algae – Protoctista
Hydra – Animalia
Spider – Animalia
Mushroom – Fungi
Yeast – Fungi
Bacterium - Prokaryote

47. Design a dichotomous key using ten different objects/organisms
Answers may vary

48. b = q = Square root of .10 = 0.32 = 32% B = p = 1-.32 = 0.68 = 68%
In a population of 278 mice, 250 are black, 28 are brown. B=black, b=brown. Identify the allele and genotype frequencies in this generation.
b = q = Square root of .10 = = 32%
B = p = = 0.68 = 68%
bb = q2 = 28/278 = 0.10 = 10%
Bb = 2pq = 2(.68 x .32) = 0.44 = 44%
BB = q2 = = 0.46 =46%