Bio 2 Exam Notes

Characteristics of Living Systems

On Study Guide

Levels of Biological Organization

A cell is the smallest, most basic unit of life
Evolution explains diversity and unity of life.
- Results in heritable traits that promote surivial and reproductive success.
Biology: the scientific study of living organisms and how they evolve.

Metabolism

All the chemical reactions in a cell
- Requires energy to maintain order
- Photosynthesis & Cellular Respiration(ATP)
Homeostasis: maintenance of internal conditions within certain boundaries

Reproduction and Development

DNA- defined set of characteristics
- Everyone’s cell has the same DNA, it’s just ordered differently.
- Genetic offspring have traits like their parents.
Reproduction

Adaptation

Any modification that makes an organism suited to its way of life
- Better adapted organisms tend to survive and produce more offspring
Over time, organisms become modified by the process of natural selection
All organisms descended from a common ancestor

Not on study guide

Structure determines function

How individuals Interact with the functions is how the species will change overtime.
Function: how the body is used for benefit
- human hand (grabbing and fine control)

Vertical descent w/ mutation

Between same species
Horizontal gene transfer (non-offspring)
- Swaping genetic material between 2 different species
- Seen in the beginning

Not on study guide

Origin and History of Life

On Study Guide

Overlapping stages

For life to occur…
- Nucleotides and a.a.’s produced prior to the existence of cells
- Nucleotides and a.a.’s became polymerized to form DNA, RNA, and proteins
- Polymers became enclosed in membranes
- separate living molecules
- polymers encoded in membranes evolved cellular properties.

Primitive earth

Reducing atmosphere hypothesis (abiotic synthesis)
- Oparin/Haldane Hypothesis
- Basically unlivable
- Components: H2O vapor, N2,CO2
- Too hot for liquid water ( earth cooled →oceans formed)
- Called “reducing” because there was little free oxygen
- Primordial soup: very energetic/thick
- Volcanoes and lightning
- cause of spontaneous formation of organic molecules

Miller/Urey’s experiment

Showed that biochemicals could be produced from simple, nonbiological sources
Simulated early life ==(ask which part of life I.e. primitive Earth?)==
- Very small organic molecules can turn into very big molecules
First to use scientific method
Found amino acids after experiment
Using glass apparatus was crucial
- Simulated elements found in the environment during this time periods.
Recent studies found more amino acids and sugars than the original experiment.
- Organics can be made under a variety of different conditions

Extra-terrestrial hypothesis

Organic carbond from asteroids and comets stocked in prebiotic soup

Deep-sea vent hypothesis

Key organics arose at deep-sea vents

Clay hypothesis

Hypothesis of the origins of the 1st cell
Monomer (simple organics) polymerize on solid surface (clay, mud, inorganic crystals) into more complex organics
- Stromatolites: mats of mineralized cyanobacteria
- “living fossils”
Protobiont
- Cell-like structures
- Had boundaries (membrane)
- Polymers on the inside contained information
- and had enzymatic function
- self-replication
Chemical Selection
- Why we know RNA was first because
- It can store information
- Capacity for replication
- Enzyme functions (Ribozymes)

Advantages of DNA/RNA/Protein world

Information Storage
- DNA takes on informational role, so RNA can do other things
- DNA is less likely to suffer mutation
- more stable for DNA storage
Metabolism
- Proteins have greater catalytic potential and efficiency
- can also perform other tasks (cytoskeleton, transport, etc)
- ==better for __?==
  - DNA in our cells is transcribed to RNa, etc
  - may not be how it started (chicken and egg story)
  - Chances are it was RNA, can do what DNA and proteins can do
    - can store info like DNA, and enzymes like proteins can do (metabolism)
    - RNA mutates faster, so when DNA came into existence, it would’ve taken over bc of double helix and can store information
    - Proteins are more effective

Fossils

Remains and traces of past life
Somewhat biases process, soft shells don’t show up as often as hard bones
- I.e. vertebrates vs Insects and stools
Sedimentation
- When the animals dies, the sediment converted to rock
- these are recognizable in the rock, called strata
  - starta of the same age have similar fossil assemblages

Paleontology

study of fossil records

==macroevolution==

Evolution of whole taxonomic groups over long periods of time

Dating of fossils

Relative dating: age based on surround fossils and rock at the same time
Index fossils : assigned age of the rock by the fossils found in it
- Both were popular in 18th and 19th century

Absolute Fossil Dating

More concrete, know exactly when the fossil/strata was alive
Radioisotopes - radioactive elements (more neutrons than protons, so they are excitatory)
- Half-life
- unstable but decay in a constant time

Absolute Fossil dating

More concrete, know exactly when the fossil/strata was alive
Radioisotopes - radioactive elements (more neutrons than protons, so they are excitatory)
- Half-life
  - unstable but decay in a constant time

Geological (biological) time scale - factors influencing patterns

Climate/temp (temperature at artic and equator)
Atmosphere (lack of oxygen)
land masses (continental drift)
floods/flaciation, volcanic eruptions/meteorite impacts

Precambrian Time: prokaryotes, stromatolites, eukaryotes, multicellularity (Ediacaran)

87% of Geologic time with little or no atmospheric oxygen
Lack of ozone shield allowed UV radiation to bombard Earth
First cells came into existence in aquatic environments
- Prokaryotes
- Cyanobacteria (left fossils) & added oxygen to atmosphere
- Eukaryotic cells arose (2 bya)
  - Endosymbiotic Hypothesis: two different species being dependent on one another
- Rise of aerobic species
- Cells are half bacterial and half archaean
Eons: Hadean -> Archaeon -> Proterozoic (when life begins)

Paleozoic era - Cambrian, Ordoviciian, Sulurian, Devonian, Carboniferous, Permian

Overview

“Well displayed life”
3 major mass extinction events

Important periods

Cambrian
- Warm, wet with oxygen, no ice at poles
- Existent phyla developed
- First vertebrates (520 mya)
  - Evidence of soft and hard shell animals
High diversity of Cambrian due to:
- Favorable environment (oxygen)
- Evolution of hox genes
  - Genes that determine body patterning
- Predator/prey “Arms Race”
  - Predators had to find new ways to hunt
All species can be pointed to one of these as their ancestors, no other species has been identified from other eras.
Ordovician*
- Warm temp and moist atmosphere
- Diverse marine invertebrates: trilobites(3 body part animals) and brachiopods(shelled animals i.e clams)
- Primitive plants and arthropods first invade land
- End: abrupt climate change (large glaciers) resulted in mass extinction (60% marine inverts)
Silurian
- Stable climate, glaciers melted
- Significant vertebrates (fishes, plants, coral reefs)
- Large colonization by terrestrial plants (seedless vascular) and animals (arthropods)
- Mainly plants on the land
Devonian*
- N dry; S wet is wet due to oceans
- Terrestrial species
- Gymnosperms(seeds for dispersal) emerge insects emerge
- Tetrapods - amphibians emerge
- Invertebrates in oceans
- Age of fishes
- Coral reefs
Carboniferous Period
- Rich coal deposits formed
- Cooler w/land covered by swamps
- Organisms further diversified
- Large plants
- First flying insects
- Amphibians
- Amniotic egg emerges: Reptiles
Permian
- Continental drift formed supercontinent Pangaea
- Regions dry w seasonal fluctuations
- Forests -> gymnosperms
- Amphibians prevalent but reptiles dominant
- First mammal-like reptiles
- End: largest known mass extinction event
  - Cause: Global warming and too much carbon
  - 95% of marine species killed

Mesozoic era(Age of the Reptiles) - Triassic, Jurrasic, Cretaceous

Consistently hot climate, dry terrestrial environments, little if any ice at poles

Triassic*
- Gymnosperms dominant
- Reptiles abundant (1st dinosaurs appeared)
- 1st true mammals (looked like mice)
Jurassic
- Dinosaurs achieved enormous size
- Mammals remained small and insignificant
- 1st bird
Cretaceous*
- Dinosaurs began precipitous decline (extinction: meteorite and volcanism)
- Mammals:
  - Began an adaptive radiation
  - Moved into habitats left by dinosaurs
- 76% marine species extinct (needed heat but meteorites covered sun)
- 75% of all plant species died

Cenozoic era

Age of mammals

Tropical conditions replaced by a colder, drier climate
Mammals continued adaptive radiation (birds, fishes, insects diversified)
Flowering plants already diverse and plentiful
Tertiary Period (Paleogene and Neogene) - Older humans, nethanderals
Primate evolution began
- Quaternary Period: Where we as humans (and other primates) are today
- Age of man
- Homo sapiens appear

Mass Extinctions - the importance of them, 1-5, 6+

6th mass extinction (Holocene, Anthropocene)
- Humans= Global Superpredators
- Vanished after Human Civilization
  - 83% of wild mammals
  - 80% of marine mammals
  - 50% of plants
  - 15% of fish
Avg 68% decline in monitor pops (21,000) of mammals, birds, amphibians, reptiles, and fish
Significant declines in tropical subregions of the Americans (94%) and AFrica (65%)
Freshwater biodiversity declining fastest
Megafauna particularly vulnerable
⅕ of wild species are at risk this century due to climate change alone

Not on the Study Guide

How life comes to exist
- Life requires interplay between DNA, RNA and proteins
- Living cells come from pre-exisiting cells

Darwin and Evolution

History of Evolutionary Thought - Plato, Aristotle, Scale of Nature, Christianity and Divine

Pre-Darwinian (1831)
- Influenced by Theology, Myth and Superstition; leading back to ancient Greece
Anaximander: organisms evolve over time
Plato
- Follows socrates
- Objects are temporary reflections of ideal forms
- “Essentialism”: ideal forms that live somewhere else
- Theory of forms
Aristotle
- All living things can be arranged in a linear hierarchy- Scala naturae
- Creationism: a god is absolute creator of heaven and earth, out of nothing, by act of free will
- Includes Christians, Jews, and Muslims
- Spontaneous Generation
- “Living coming from the nonliving”
- I.e Rotting meat produces maggots
- Father of Classic Taxonomy
Scala Naturae
- Great Chain of being
- Establishes man as dominate and perfect form of life
- Sets man above and Apart from nature
- Incorporated into belief that earth and its creatures are the result of special creation,that they

have not changed since they were created

*Insert scale*

Creation, Ray, Linnaeus and Taxonomy, Count Buffon,

Taxonomy matured during lath 17th to mid 18th century

Science of naming organisms

John Ray
- 1st thorough study of natural world
Carolus Linneaeus
- Fixity of species
- Each species had
- Ideal structure and function
- Place in the scala naturae
- Binomial system of nomenclature
Count George Buffon
- Wrote 44-volume catalog of all known plants and animals
- Suggested life forms and change over time
Erasmus Darwin (grandfather of Charles)
- Suggests common descent
- Evidence in developmental patterns, artificial selection, vestigial organs

Cuvier - comparative anatomy, paleontology, Catastrophism

First to use comparative anatomy to develop a system of classification
Founded Paleontology: fossils
Proposed Catastrophism
- Past local catastrophes in past had caused strata to have new fossils
- After each catastrophe; region was repopulated
- Had evidence that organisms because extinct

Lamarck - inheritance of acquired characteristics

First biologist to propose evolution and link diversity with environmental adaptation
Concluded more complex organisms are descended from less complex organisms
Proposed Inheritance of Acquired Characteristics: Lamarckianism
Childhood trauma: can change gene expression

Geology - Charles Lyell, uniformitarianism

Earth is subject to slow but continuous cycles of erosion and uplift
- Long slow change
Proposed Uniformitarianism: rates and processes of change are constant
Principles of Geology: connects to Darwin

Darwin and Voyage of the HMS Beagle - Galapagos Islands, Tortoises, Finches

Darwin went to college to be a surgeon but didn’t like it
Went to the military school after, was bad at that
Enjoyed exploring the natural world
Got a job on HMS Beagle: goal was to collect specimen from around the world and bring it back to England
Got seasick, lasted 5 years and was a unpaid trip
Darwin’s theory
- Geological observations consistent with Hutton & Lyell
- Biogeographical observations
- Study of the geographic distribution of life forms on Earth
- Darwin saw similar species in similar habitats
- Reasoned related species could be modified according to environment
Galapagos Islands
- Tortoises
- Darwin observed tortoise neck length varied from island to island
- Proposed that speciation on islands correlated with a difference in vegetation
- Finches
- Darwin observed many different species of finches (13) on various islands
- Speculated they could have descended from a single pair of mainland finch

Natural Selection and Adaptation, Variations, Struggle for Existence

Essay on the Principle of Population: Struggle for Existence
- Written by Thomas Malthus (political economist)
- Each generation has the same reproductive potential as the previous generations
- Reproductive potential is greater than environment can support
- Death, disease, and famine were inevitable if population is to have stability
Alfred Russell Wallace
- Darwin read his manuscript, work was presented at meeting of Linnean Society

*Insert Darwins chart of natural selection*

Survival of the Fittest, Industrial Melanism, Adaptive Melanism (video: Rock Pocket Mice)

Fitness is the relative reproductive success of an individual
- Most-fit individuals in population capture disproportionate share of resources
- Interactions w/environment determine which individuals reproduce the most
Adaptation
- Changes that help a species become more suited to environment
- Product of natural selection
Industrial Melanism
- Before industrial rev.
- Peppered moths: 10% dark colored; 90% light colored
- After industrial rev.
- Soot in atmosphere, tree trunks darkened, etc
- Peppered moths 80% dark colored 20% light colors
Adaptive Melanism
- Moth example from the industrial revolution
- *insert rock pocket notes*

Evidence for Evolution

Morthology: study of structure and design

Comparative Anatomy
- Homologous Structures
- Anatomically similar because they are inherited from a common ancestor
- May be functionally similar or not
- Want to use to construct ancestral trees
- Analogous structures
- Serve the same function
- Not constructed similarly
- Don’t share common ancestor
- Convergent evolution
- Vestigial Structures
- Fully-developed anatomical structures
- Reduced or obsolete function in descendent groups
- We are developed with them as our ancestors needed them but now they have no use to us
  - I.e Human appendix, male breast tissue/nipple
  - Wisdom teeth
- Comparative Development
  - Embryology
  - All vertebrate embryos look similar at an early age, as they all descended

from a common ancestor

All have
- Postanal tail
- Paired pharyngeal (gill) pouches (in parathyroid gland, tubes that run from

Middle ear to throat, still there but a different function)

Dorsal, hollow, nerve cord
Notochord (becomes vertebral column; starts as cartilage)

Fossil Record
- Fossils record history of life from past
- Document a succession of life forms from simple to more complex
- Sometimes record is complete enough to show descent from ancestor
Biogeography
- Geographical evolution of plants and animals
- Consistent with origin in one locale and then spread to accessible regions
- ^Animals more isolated than mainland, different adaptations in the same animals
Continental drift; tectonic plates
Molecular Homologies
- Almost all organisms
- Use same basic biochemical molecules
- Utilize same DNA triplet code
- Utilize same 20 amino acids in proteins
- Utilize ATP as energy source
- Genetic Homologies
- When very similar, suggest recent common descent
- More different, suggest more ancient common descent

\n \n

Evolution in a Genetic Context - Microevolution

Population Genetics: study of genes and genotypes in population
- Helps us understand how genetic variation is related to phenotypic variation
Genes in Natural Populations
- Genes can be monomorphic (99% = 1 allele) or polymorphic ( 2 or more alleles)(more likely)
- Polymorphism comes from
- Duplication of gene region
- Deletion of significant region of gene ( disease & death)
- Change in a single nucleotide (SNP)(smallest and most common change in gene)
- Allele frequency: # of copies of a specific allele in pop/total # of individuals in a pop
- Genotype frequency: # of individuals with a particular genotype/total # of individuals in a pop

Hardy-Weinberg Principle

Genes remain in equilibrium (constant frequency) over time (in each succeeding generation of a

sexually reproducing pop) as long as 5 conditions met

Equation
- p + q = 1
- p^2 + 2pq + q^2 = 1
Allele freq
- p = freq. of dominant allele
- q = freq. of recessive allele
Genotype freq
- p2 = freq of homozygous dominant genotypes
- q2 = freq of homozygous recessive genotypes
- 2pq = freq of heterozygotes
Conditions to be met( will never occur, natural selection will always happen)
- No mutations
- Allelic changes do not occur, or changes in one direction are balanced by changes in

opposite direction(no gene dup, exon shuffling or horizontal gene transfer

No gene flow
- Migration of alleles into or out of pop does not occur
Random mating
- Individuals pair by chance and not according to genotypes
No genetic drift
- Pop is very large and changes in allele frequencies due to change alone are insignificant
No selection
- No selective agent favors one genotype over another; all are equal adapted

Causes of Microevolution

Genetic Mutations
- Raw material for evolutionary change; source of genetic variability
- Source of new alleles; new combinations of alleles; source on which other evolutionary forces

can act

Not goal-directed; not result of environmental necessity
Random events depending on environmental conditions
Other forces acting
Gene Flow- Gene Migration
- Movement of alleles between pops when
- Gametes or seeds (plants) are carried into another pop
- Breeding individuals migrate into or out of pop
- Continual gene flow reduces genetic divergence between pops & typically increases genetic

diversity within pop

Nonrandom mating: when individuals do not choose mates randomly
- Assortative mating
- Individuals select mates with their phenotype and reject opposites
- Increase # of homozygotes
- DIsassortative mating
- Dissimilar phenotypes mate preferentially
- Increase # of heterozygotes
- Inbreeding
- Mating of 2 genetically related individuals
- Chose a mate from same genetic lineage
Genetic Drift
- Changes allele frequency due to random chance
- Can cause gene pools of two isolated pops to become dissimilar
- Some alleles lost and some fixed
- Bottleneck effect
- Species is wiped out and created based on new genetics
Founder effect
- New pop is started from just a few individuals
- Alleles carried by pop founders are dictated by chance
- Formerly rare alleles will either
- Occur at higher frequency
- Be absent in pop

Same principal(genetic drift)

Random, effect will be greater on smaller pop
Bottle neck:
- Only 10 survive, they will be the only to reproduce
- Baby’s will have the genes that those 10 have
- Disease, volcano ash,
Founder effect:
- population that is good size, but other members go somewhere else
- Think of pilgrims
- The Amish
  - Mutations occur at higher freq. Because they only reproduce with each other

Natural Selection - directional selection, stabilizing selection, disruptive selection

Abiotic
- Climate, water availability, minerals
Biotic
- Competition, predation, sexual selection
Directional Selection
- Individuals at one extreme of a phenotypic range have greater reproductive success in environment
- Curve shifts in that direction
Stabilizing selection
- Intermediate phenotype is favored
- Peak of curve increases and tails decrease
- I.e human babies with low or birth weight less likely to survive
Disruptive (Diversifying) Selection
- Two or more extreme phenotypes are favored over intermediates; bimodal distribution
Balancing Selection
- Maintains genetic diversity
- Balanced polymorphism
- 2 or more allele are kept balance, and therefore maintained in a population over the cour

Se of many generations

Two common ways
- For a single gene, heterozygous is favored
- Negative frequency dependent reaction
- Rare individuals have high fitness
Keeping allele that may be dangerous in pop, to confer an advantage (in certain population)
- Keeping one good allele and one bad allele
- Sickle gene and other gene, so that you aren’t going to be effected if you are both
Predators recognize prey by having a general idea in their head
- Rabbit and fox example
- Fox will look for white and small thing, so dog can look like one.
- Brown rabbit will survive

Speciation

Two types
- Anagenesis
- The transformation of the one species into a new species over time
- Cladogenesis
- The splitting of one species into two
Definitions of species
- Typographical(Morphological): Species is defined by fixed, essential features.
- Each species has a unique structure that makes it distinct.
- Based on unchanging features
- Pre Darwin
- Biological Species Concept: Species is a reproductive community of populations
- Reproductively isolated from others
- Occupies a specific niche in nature, interbreeding with a common gene pool.
- Ecological Species Concept
- Using the ability of organisms to successfully occupy their own ecological niche or habit
  - Including their use of resources and impact on the environment, to distinguish

Species

Many similar organisms that use the environment in similar ways
Phylogenetic (Evolutionary) Species Concept
- A species is an irreducible group of organisms diagnosably distinct from other such groupings and which there is a parental pattern of ancestry and descent.
morphological(anatomical), chromosomal, molecular characters used.

Reproductive Isolating Mechanisms

Inhibit gene flow between species and maintain distinctiveness of species

Prezygotic: discouraged attempts to mate
- Habitat isolation
- Temporal (monthly difference) isolation
- Behavioral (mating difference) Isolation
- Mechanical (anatomy) Isolation
- Gamete(sperm/egg don’t match) Isolation
Postzygotic: Prevent hybrid offspring from developing of breeding
- Hybrid Inviability (Zygote Mortality) - hybrid won't be accessible
- Hybrid Sterility - hybrid can’t mate with hybrids
- Hybrid Breakdown - offspring of offspring doesn’t reproduce

Modes of Speciation

Allopatric speciation: Natural phenotype that disrupts flow
- Two geographically isolated populations of one species → become different species over time
- May be due to differing selection pressures in differing environment
- Most common
- Adaptive Radiation
- Members of a species invade several new geographically separate environments
- Population become adapted to the different environments
- From one ancestral species
Sympatric speciation
- One population develops into two or more reproductively isolated groups
- No prior geographic isolation (no physical barriers to interbreeding)
- Autoploidy: 2n plant -> 2 gamete (+n) = triploid (sterile, seedless)
- Alloploidy: tetraploid hybridization in plants
  - Results in self fertile species
  - Reproductively isolated from either parental species

Not on Study Guide

Special Case of Natural Selection

Sexual selection
- Directed at certain traits of sexually reproducing species that make it more likely individuals to find of choose a mate and/or engage in successful mating
- Males are affected more
- Sexual selection =/ good overall
- Intrasexual - same sex (males compete for mating opportunities or territories)
- Intersexual - opposite sex (females choose with males possessing a particular phenotype)

Maintenance of Variations

Genetic variability
- Populations with limited variation may not be able to adapt
- Exposed allele(phenotypes) are subject to natural selection

Pace of Evolution

Phyletic Gradualism: speciation occurs gradually
- “Living fossils”: sharks, crocodiles, etc
- Statis (stable condition) is apparent, not real
- Transational link found
- Ancestral spp. transformed into new species
Punctuated Equilibrium: speciation occurs rapidly
- Species experiences stasis
- Transitional links not found
- Subpopulation becomes new spp.

Classification of Living Things

Taxonomy, Phylogeny, naming, identifying, classifying

Systematics: study of the biological diversity and evolutionary history of life on earth
Taxonomy: Branch of biology concerned with identifying, naming, and classifying organisms (both living and extinct)
Name: Only 1 scientist gets to “name” a species
Identify: anyone can with a key
Classify: groups a species with its closest relatives
- Began with the ancient Greeks and Romans
- Aristotle classified organisms into groups such as horses, birds, and oaks
- John Ray: believed that each organism have set name based on anatomy & physiology

Binomial nomenclature: Genus + specific epithet

First word: Genus
Second word: specific epithet
- One species within its genus
- Species is referred to by full name (genus species)
- Genus name can be used alone to refer to a group of related species

Classification, gets more specific as you go down

Domain: one or more supergroups
Supergroup: one or more kingdoms
Kingdom: one or more phyla
Class: one or more orders
Order: one or more families
Family: one or more genera
Genus: one or more species
Species

Higher the category, more inclusive
Same domain: general characteristics in common
Classification categories can be subdivided into more categories:
- Superorder
- Suborder
- Infraorder
DIstinguishing species on the basis of structure

Goal of Systematics

Discover all species (impossible)
Reconstruct phylogeny (evolutionary history of a group)
Classify accordingly

Phylogenetic Tree

Diagram indicating lines of descent
Each branching point
- Divergence from common ancestor
- Represents an organism that gives rise to two new groups

Primitive characters

Present in all members of a group, and present in the common ancestor

Derived characters

Present in the some members of a group but absent in common ancestor

Tracing Phylogeny

Fossil Record
- Better to find hard fossils rather than soft fossils
- Fossil record is incomplete
- Often difficult to determine the phylogeny of a fossil
Homology
- Refers to features that stem from a common ancestor
- Homologous structures are related to each other through common descent
- Same underlying anatomy
Convergent Evolution - Analogy(look similar but not related, have similar environmental pressures)
- Acquisition of a feature in distantly related lines of descent
- Feature is not present in common ancestor
Parallel Evolution
- Independent evolution of similar traits, starting from similar ancestral condition
- Several species respond to similar challenges in a similar way
- Following parallel paths w/out common ancestors, species deal with similar things

Molecular data:

Protein Comparison

Immunological techniques
Degree of cross reaction used to judge relationship

- Amino acid sequencing

Similar sequence in same protein indicates close relationship

RNA and DNA Comparisons

Systematics assumes:
- Two species with similar base pair sequences are assumed to be closely related
- Two species with differing base-pair sequences are assumed to be only distantly related

Molecular clocks

Change is slow because sequences are rare
Use non adaptive nucleotide sequences
Assumed constant rate of (neutral) mutations over time
Favorable mutations are rare
Detrimental mutations are quickly eliminated
Most mutations are neutral

Traditional Evolutionary Systematics

Classifying organisms using assumed phylogeny with emphasis on phenotype

Mainly uses anatomical data
Common ancestry and degree of structural difference
Phylogenetic trees by applying evolutionary principles
Not strict in making sure all taxa are monophyletic

Grouping

Monophyletic groups
- Taxon whose units all evolved from a single parent stock; most recent common ancestry and all
- Descenednts
Paraphyletic groups
- Sometimes okay
- Some structure that makes it distinct
- All ancestors common but not all descendants
Polyphyletic groups
- Never okay
- All descendants none of the ancestors are in the same group.
*insert picture*

Cladistic Systematics

Traces evolutionary history of the group under study

Synapomorphies
- Shared derived characteristics
- Arranges taxa into cladogram(special type of phylogenetic tree)
- Clade: Evolutionary branch that includes a common ancestor with all its descendant species

Classification systems

5-kingdom system
- Was a plants(plantae), animals(animalia), protists(protista), fungi and monera(prokaryotes)
3 domain system
- Turned into Domain Eukarya, Bacteria and Archaea
- Bacteria and Archaea were so different that they had their own domains.
  - Difference in rNA base sequences, plasma membrane and cell wall chemistry.
- Eukarya
  - Un- and multicellular organisms, cells with a membrane bound nucleus
  - Sexually reproduction
  - Kingdoms:
  - Fungi, Plantae and, ANimalia
    - NEW: Protists and Hemimastigotes

Not in Study Guide

Parsimony

Cladist guided by this principal
Arrangement requiring the fewest assumptions is preferred
- Simplest reasoning is accepted (not always the best answer though)