“The longer you live the longer you should live” –Wiley
“Evolution’s a bitch” –Wiley
“Suckers are good to eat” –Wiley

WHAT HAS EVOLUTION DONE FOR ME
What has evolution done for me • Agricultural crops and animal breeding for the past 8,000 years • With the discovery of methods to reconstruct evolutionary relationships there is been a vast increase in the relevance of evolutionary biology to human society.

Reconstructing Phylogenies • 1859-1950- No coherent empirical methods • 1950-1966- Emergence of Phylogenetic Systematics • Phylogeny by discovery of the order of evolutionary innovation

Ribotyping • Fingerprinting or sequencing RNA • Many diseases have unknown causes • However, diseased tissues can be ribotyped. (Wiley Death Fish) • This process involves extracting DNA from diseased tissues and then sequencing the DNA that codes for rRNA. • If a disease agent such as a bacteria is present, then we will get ribosomal DNA sequences from the host (you) and the bacteria (the infection agent).

Ribotyping: Phylogeny matching • Once we have the rDNA sequences, we can plug them into a sequence matrix of all life and see where our unknowns appear on the tree of life.

Our Food Chain • Some products are easy to identify, but others are not. • A slab of fish fillet from a sea bass looks like a slab of sih fillet from a farmed Asian catfish. • But the sea bass costs $10/pound while the Asian catfish costs $4/pound. • Yet, a simple phylogenetic analysis can sort out the sea bass from the catfish, giving regulatory agencies a new weapon to protect consumers from fraud.

Directed Synthetic Evolution • Enzymes for industry. Example, using evolutionary principles to increased enzyme activity of cellulose so that yields of ethanol from corn stalks can be industrially viable. • Designing enzymes that assist in patient recovery: Short DNA molecules with enzyme function designed to leave specific mRNA. • Egr-1 expression causes proliferation of cells in the arterial wall in response to angioplasty. • Mouse models show that a synthetic DNA enzyme cleaves the mRNA, shopping proliferation.

Poliomyelitis • RNA virus • Humans are the only host known • Three strains of native virus • Thousands of cases of polio in the 1950’s (including me!) • Two decades of immunization has largely wiped out the disease on the NA continent. 95% effective against all 3 strains.

Poliomyelitis • Problem: Sporadic outbreaks • Hypothesis 1: The live attenuated vaccine has mutated • Hypothesis 2: Polio virus from another part of the world has been introduced. • Hypothesis 3: An undetected native strain has emerged from carriers. • Discrimination of the three hypotheses has consequences for public health.

Poliomyelitis • Hypothesis 1: The live attenuated vaccine (OPV) has mutated. • Potential serious consequences if it spreads, but OPV effectively protects others immunized. • Hypothesis 2: Polio virus from another part of the world has been introduced. • Vaccination and good hygiene should prevent the spread. • Hypothesis 3: An undetected native strain has emerged from carriers. • Worse-case as only 1% of humans develop the disease—possibility of wide-spread pandemic.
THE ORIGIN OF LIFE, VIRUSES, & PROKARYOTES
The Big Bang Theory (Not the TV Show) -12-15 billion years ago -Sudden expansion -Temperature drops -Atoms and reactions -The universe continues to expand to this day -Gravity takes over

Origin of Earth -4,600 – 3,800 million years ago -Heavy/Dense materials formed the core -Lighter materials formed the outer layers/crust

First Atmosphere -Hydrogen -Ammonia -Methane -Hydrogen Sulfide -Nitrogen -Carbon Monoxide -Carbon Dioxide -NO Gaseous Oxygen -enabled organic compounds to assemble

Stanley Miller’s Experiment -Mixed methane, hydrogen, & water -Simulated lightning by running an electrical current through the mixture -Amino acids and other small molecules formed from organic compounds

Other Experiments and Hypotheses for Early Organic Compounds -Sugars and nucleotides form from formaldehyde -There are many ways for amino acids to form – on clay templates and the heat of hydrothermal vents -But…amino acids are not the molecules of replication

How Did Cells Originate? No complex molecules Our evolved enzymes and DNA will not do Our cell membranes are too selective Molecules must be able to replicate

RNA 1) Can self replicate 2) Has enzymatic properties 3) Can store information RNA was one candidate for the first genetic material Some DNA can also self replicate

Origin of the Plasma Membrane Fatty acids and alcohol Proto-cells Purely physical Self replication

Jack W. Szostak Won the nobel prize in physiology or medicine 2009 Came up with a possible sequence

First Cells 3.8 bybp. Were prokaryotic and anaerobic No oxygen in atmosphere Fermentation metabolism Chemosynthesis

Origin of Photosynthetic Eubacteria 2.7 byp – stromatolites: Use sunlight for respiration. Oxygen atmosphere Aerobic respiration

Origin of the Eukaryotic Cell 2.1 billion years ago organelles

Eukaryotes Evolved from Prokaryotes Membrane infolding – Cytomembrane system Endosymbiosis – Mitochondria and chloroplasts

Theory of Endosymbiosis Lynn Margulis Mitochondria and chloroplasts are the descendents of free-living prokaryotic organisms Prokaryotes were engulfed by early eukaryotes and became permanent internal symbionts

Evidence for Endosymbiosis Mitochondria & chloroplasts have own DNA DNA of organelles circular and lack histones Organelles reproduce by binary fission-like process Ribosome structure like bacterial ones

Viruses & Prokaryotes Viruses are infectious particles of packaged genes Viruses are comprised of nucleic acids, protein coat, membranous envelope

Are viruses alive? HECK NO!!! On own, cannot carry out activities of life e.g., metabolism, reproduction

Viral reproduction has two routes: Lytic cycle: Kills host cell Examples: Herpes simplex, Human papillomavirus, Flu, Small pox, Mumps, Rubella (measles), Filovirus – viral hemorrhagic fever, Ebola Lysogenic cycle: Doesn’t Kill host cell, Can change the host, diphtheria

Retroviruses: RNA virus reproduces via DNA

Virus versus organism
Innate immune response: Antibodies and cell mediated immunity via T-cells. Antibodies bind to virus T-cells mediate killing virus

Vaccines: artificial induction of immunity – stimulating the immune response Live attenuated (Examples: polio, rabies) Dead - protein coat stimulates the immune response. (Example Flu) Subunit - only part of the virus. (trying to develops an AIDS vaccine)

Emerging viruses can refer to virus or threat Three sources: –mutation –host jumping –spreading

Viroids & Prions Viroids –tiny, naked circular RNA molecules -Infect plants with stunted/distorted growth -One form of hepatitis (D) in humans Prions – misfolded, infectious proteins -mad cow, scrapie, Creutzfeldt-Jakob disease

Prokaryotes
First cells prokaryotic dominated from 3.5–2 Ga includes: –Domain Eubacteria –Domain Archaea

Prokaryote Structure Flagella Cell Wall Capsule Pili Nucleoid Region

Basic Prokaryote Shapes Cocci – Spherical Bacilli – Rod-like Spirilla – Spiral

Prokaryotic Reproduction
[pic]
[pic]
[pic]

Endospores Bacterial “resting” cells Resist harsh conditions Wait for conditions to improve

Modes of Nutrition 1) Energy Source 2) Carbon Source

Bacteria
Most prokaryotic diversity in terms of species
All pathogenic prokaryotes known
First to evolve photosynthesis
Found in most environments
Beneficial – includes digestion and nitrogen fixation.

Bacteria versus humans Examples: gonorrhea and syphilis, peptic ulcers, dysentery, typhus, tuberculosus, pneumonia, tetanus

Humans versus bacteria Examples: Antibiotics, Prevent cell wall formation, Damage the cytoplasmic membrane, Interfering with either protein or DNA, synthesis, Immunization (diptheria, tetnus are examples)

Archaea Look like bacteria Transcription and translation of DNA like eukaryotes No known pathogenic or parasitic “extremophiles” Common in oceans, important in carbon and nitrogen cycling “methogenic” important to digestion in humans and cows (and probably other vertebrates)

Bacteria as Weapons Long history of biological weapons Weaponized bacteria –plague –2001 anthrax attack

Bacteria as “partners” food chemical cycling decomposers bioremediation

PROTISTS, PLANTS, & FUNGI
Protists
-eukaryotes -most unicellular -mostly aquatic habitats -classification in flux currently -(don’t memorize the protists tree)

Giardai lamblia – a diplomonad -the most famous diplomonad -“backpacker’s diarrhea” -infects about 200 million people each year -the most common cause of non-lethal diarrhea

Trypanosoma brucei – a euglenozoan -infamous euglenozoan -African sleeping sickness -Toxic metabolic waste -50,000 – 70,000 currently infected in Ugandan epidemic -Sub Saharan African has a large problem with euglenozoan

Alveolates -Dinoflagellates -Apicomplexans -Ciliates

Dinoflagellates -Second largest group of marine algae -Red tides are caused by blooms (or rapid reproductions and high concentrations of dinoflagellate marine algae) -Because they have toxic metabolic waste, a lot of fish and sea animals die -Other Dinoflagellates are a part of coral endosymbiosis -Dinoflagellates can sometimes cause the water of the ocean to light up

Ciguatera -a dinoflagellate that causes a disease -Bioaccumulation – plankton eats dinoflagellate ( fish eats plankton ( large predator eats fish ( the toxic metabolic waste of the dinoflagellate increases in the age and size of the fish -Cooking does not get rid of the metabolic waste -The disease ciguatera causes your senses of hot and cold to reverse

Other Dinoflagellates – zooxanthellae -Endosymbionts of corals –corals cannot make enough sugars for themselves and zooxanthellae help corals meet their energy needs -Warming waters cause corals to expel their zooxanthellae ( this causes them to die because the waters are too warm and die due to lack of nutrition -“Coral bleaching” – coral becomes white when it dies

Apicomplexan – plasmodium (200+ species) -Infamous apicompexan genus that causes malaria -Anopheles mosquito spreads this disease -Closest relatives of this plasmodium infects chimpanzees -250 million cases per year -1 million deaths per year

Apicomplexan – coccidans -Apocomplexans that cause a variety of diseases -Dogs – coccidiosis common if kennels are not kept clean -Cats – toxoplasmosis -About 10% of people are carriers of toxoplasmosis…it is not a problem for humans but it is for the fetuses of pregnant women

Alceolates – Ciliates Paramecium – most are free living Stramenopiles – water molds & downy mildews, diatoms, brown algae

Phytophthora – A water mold -Major plant parasite genus -Caused the Great Irish Potato Famine (1845-1849) -Major organisms causing root rot of plants when over watered

Amoebozoans -Lobe-shaped pseudopodia -3 Subgoups: Amoebas Two groups of slime mold

Entamoeba Histolytica -Anaerobic amoeba -Amoebic dysentaery -50 million cases a year -Water, soil, and food transmission -Kill you by emptying out all the water in the body…drugs are the best solution

Amoebozoans -cellular slime molds -heterotrophic -eat bacteria -Normally unicellular -No food? Chemical signals attract others to form a slug-like creature that can perform coordinated movements -Fruiting body

Multicellularity -evolved several times -cells must recognize other cells within the same body as the same or “self” -Broadly” two diverging lineages -One to multicellular plants, via red and green algae -One to multicellular fungi & animals, via certain amoebozoans

Two basal lineages Red algae Green algae It is among the green algae that we see the origin of land plants Innovation – alternation of generations

Green algae & land plants Photoauto (photosynthesis) Cell walls and Cellulose Chlorophyll A and Bhlorophyll B

Diversity of the Greens Two major lineages with many branches “typical” greens Major carbon recyclers Major oxygen producers Charophytes and embryophytes (are plants)

Embryophytes (land plants) 300,000 species At least 500 million years old Photoautotrophs Multicellular Alternation of generations Embryophytes – plants that have a multicellular embryo dependent on a parent plant

Plant Structure: Life on Land Needs support Needs nutrients from soil & air Avoid dessication

Alternation of Generations Two multicellular generations: -gametophyte -multicellular -haploid (1n organisms) -produces gametes by mitosis -sporophyte -multicellular -diploid (2n organisms) -produces spores by meiosis -In algae the gametophyte and sporophyte are usually about the same…they have a nearly identical outer appearance -In embryophytes the balance shifts -“primitive embryophytes” sporophyte (2n) lives on the gametopyte (1n) -Seed plants “advanced embryophytes” gametophyte (1n) lives on the sporophyte (2n)

Trees Trees are sporophytes Ovary – meiosis – female gametophyte Anther – meiosis – male gametophyte

Plant diversity 4 major lineages 1) Bryophytes (need a watery environment for reproduction) 2) Seedless vascular plants (can live independent of water, but need water for fertilization) 3) Gymbosperms (pine trees…first seed plants, do not need water for pollination or fertilization) 4) Angiosperms (flowering plants, some produce fruits)

Fungi Chemoheterotrophs….don’t photosynthesize…they eat things Don’t need to know how shrooms reproduce
ANIMAILIA
Animal Origins Come from choanoflagellates Evidence – Morphology and DNA At least 600 million years old

Animals Are: 1) Chemoheterotophs (they eat things) -nutrients via ingestion 2) Multicellular -animal cells have no cell walls -collagen

Animal Trivia Longest animal:180 foot ribbon worm Largest animal: 210 ton blue whale

(on the final there will be a lot of common names with scientific group names…example: a sponge is a….parazoa)

Parazoa Sponges No Tissues Filter Feeders

Eumetazoa True Tissue layers Ectoderm Endoderm Blastula

Body Symmetry Radial symmetry: life form all sides are symmetric (typically lower organisms) Bilateral symmetry: only one plane is symmetric (typically higher up organisms) [pic]Radial [pic]Bilateral

Radiata – Phylum Cnidaria Sea anemones, jellyfish, corals, hydras Cnidocytes – stinging cells that shoot out coils sometimes with a poison…used to help capture prey There are two forms of Phylum Cnidaria 1) Polyp Form – shaped kind of like a flower (corals spend most of their life in this form) 2) Medusa Form – shaped liked a jellyfish (jellyfish spend most of their life in this form)

Jellyfish Trivia -Largest and longest Lions Mane -- diameter of 2.3 m (7 feet 6 inches) and tentacles 36.5 m (120 feet) long -Cubozan jellys- Small Jellyfish with a sting that can be fatal if not promptly treated -For all stings, Vinegar is best instant cure

Bilateria Have bilateral symmetry with a head and tail Beginnings of having an organized brain Three tissue layers Mesoderm added Gastrulation

Protosome and Deutrostome Protostome – blastopore becomes anus, mouth is new…food goes in mouth and comes out butt (Polyp Form Coral) Deutrostome – blastopore becomes mouth, anus is new…food goes in mouth and comes out butt (Humans)

Some Protostome in Phyla II -The phyla that shed their exoskeleton (crabs)

Old and Modern Theories Old: Annelids (earthworms) are related to arthropods (crabs, etc…) and insects. New: Anelida are related to clams and squids (Mollusca) New: Both share a unique larvae (trochosphore) and DNA sequence innovations

Phylum Platyhelminthes Flatworms: planarians, flukes, tapeworms, Schitosomiasis (fluke) 200 million infections…low mortality but chronic illness Tapeworms- over 45 million infections in 2000 Some are beneficial – biological control of exotic snails

Tapeworm trivia -Longest human tapeworm – 37 feet – Removed via mouth 1991 (!) -Whale tapeworms to 120 feet -Common mode of infection- via freshwater fish eaten raw -Sushi? OK if marine - marine parasites rarely invade humans

Phylum Mollusca Gastropods (Snails), Bivalves (Clams), Cephalopods (Octopi) 85,000 known species Well-known from about 540 mybp Source of many luxury items (pearls, Tyrian purple dye) Important source of food, but be careful…since they are filter feeders, polluted water can make them bad to eat. A few, such as cone shells and certain octopi, are very poisonous

Phylum Annelida Earthworms, Polychaetes, Leeches They have segmented bodies

Earthworm Trivia (“they are our friends”…yeah right) -If there are 500,000 worms living in an acre of soil, they could make 50 tons of castings. That's like lining up 100,000 one pound coffee cans filled with castings. These same 500,000 worms burrowing into an acre of soil can create a drainage system equal to 2,000 feet of 6-inch pipe. -The first person to study earthworms in detail was…Charles Darwin (surprise, surprise)

Some Protostome in Phyla I -The phyla that have the trochophore larva (snails, earthworms)

Old and Modern Theories Old: Round worms are primitive worms just above flatworms New: Round worms are related to arthropods and insects and have DNA inovation

***Probable Exam Question…what is molting?….All round worms have exoskeletons and shed them in the same way (ecdysis).

Phylum Nematoda
Roundworms
Complete digestive tract Very habitat on earth probably 500,000 species

Nematodes Several species are significant parasites hookworm, filarial worms (the fiery serpent of the Bible), whip worms, roundworms, heartworms, round worms NOT ringworm – that is a fungus that makes a ring that looks like a worm

Phylum Arthropoda Insects, spiders, crabs, lobsters, etc… Have specialized segments

Arthropoda Crustaceans include: crabs, lobsters, shrimps, crayfish, barnacles (almost all aquatic) Arachnids include: spiders, scorpions, ticks, mites (almost all terrestrial, predators/parasites) Insecta Millipedes & Centipedes

Crustaceans in the food chain Crustaceans from a major link in the food chain, both terrestrial and aquatic. Copepods – primary consumers

Krill (Crustacean) Small shrimp Feed on plankton Food for whales and many fishes Large schools

Ticks (Arachnids) Rocky Mountian Spotted Fever bacterium in saliva of American dog ticks and RM ticks non- specific early symptoms effective Lime Disease bacterium in deer ticks saliva

Spider Myths and Truths Most spiders are deadly – not true Brown Recluse spiders are common in house in this area – true Brown recluses are deadly – although there are reports of death, it is very rare. (80% of “bites” are misdiagnosed!) Black widows are deadly – about 5% fatality reported.

Millipedes & centipedes millipedes: •herbivores •two pairs legs/segment centipedes: •carnivores •one pair legs/segment

Insecta
-insects:
Entomology FLIGHT Many w/larvae &metamorphosis

Arthropod trivia
• Largest arthropod – a Devonian “water scorpion”
• Largest insect – a Carboniferous dragonfly (2.5 ft. wingspan)

Some Duetrostomes Major phyla Echinodermata Chordata
[pic]

Anthropods cannot produce twins like humans can

Phylum Echinodermata Sea stars, Sea urchins, Sea cucumbers Living classes have “radial” symmetry – larvae: bilateral Have an endoskeleton Have a water vascular system

Echinoderms and chordates Some of the earliest echinoderms were bilateral, not radial. They had tails like chordates.

Phylum Chordata Tunicates, Lancelets, Craniates (= “vertebrates”)

Agnathans Jawless fishes: – hagfishes – lampreys

Lamprey Economics Great lakes catastrophe Introduced in 1830 Collapse of a $4 billion fishing industry by the 1950s Continuing control has brought back the fisheries. Special toxin that kills only the lampreys was found and is used to fight them. The fishing industry has come back but now we have to worry about Asian silver carp

Class Chondrichthyes Cartilagenous fishes: sharks, skates, rays About 1000 species

Some shark facts Shark attacks are rare but are correlated with amount of water activity. Fatalities form shark attack is relatively rare. Death from shark attack is not the norm, even Great White attacks – 25% fatalities

Class Actinopterygii Ray-finned bony fishes: tuna, guppies, eels, largemouth bass, (normal fish) etc… About 22,000 species

Actinopterygian Economics -In 1987, the unprocessed value of tuna catch in the South Pacific was estimated at around $1.5 billion US. -In 1996, 2,612,000 anglers fished TX waters. The spent $2,869,557,000 in fishing related expenditures with a total expanded economic impact estimated at $ 6,366,579,000.

Class Sarcopterygii Lobe-finned fishes and tetrapods About 25,000 species

Tetrapoda Amphibia: frogs, toads, salamanders (about 3,900 species) Amniota: Reptilia: turtles, snakes lizards, crocodiles, BIRDS (about 15,000 species) Aves: BIRDS (8,000 species) Synapsida: mammal-like reptiles, as ancient as reptilian, differentiated teeth like humans Mammalia: humans, bears, etc

Amniota Fully terrestrial The Amniotic Egg Shelled in basal amniotes

Synapsida - Mammalia Endotherms Hair Mammary glands About 5,400 living species Began in Early Jurassic

Three Groups Monotremes (lay eggs like the platypus) Marsupials (less advanced embryos like kangaroos) Eutherians (more advanced embryos like humans)

Know these phyla for sure and be able to tell what types of animals live in each one:

Phylum Platyhelminthes: Flatworms: planarians, flukes, tapeworms,
Phylum Mollusca: Gastropods (Snails), Bivalves (Clams), Cephalopods (Octopi)
Phylum Annelida: Earthworms, Polychaetes, Leeches
Phylum Nematoda: Roundworms, Nematodes
Phylum Arthropoda: Crabs, lobsters, shrimps, crayfish, barnacles, spiders, scorpions, ticks, insects, etc
Phylum Echinodermata: Sea stars, Sea urchins, Sea cucumbers
Phylum Chordata: Tunicates, Lancelets, Craniates (Vertebrates)….Humans, cats, sloths, ferrets, rats, etc
HUMAN EVOLUTION

Kingdom (Animalia) Phylum (Chordata) Class (Mammalia) Order (Primates) Family (Hominidae) Genus (Homo) Species (Homo sapiens)

Primate Features -Individual mobility of fingers, opposable thumb -Collar bone (clavicle) -Good vision (binocular) -Complex brain, complex behavior -Intensive parental care

Trends in Lineage Leading to Humans -Less reliance on smell, more on vision -Skeletal changes to allow bipedalism -Modifications of hand allow fine movements -Bow-shaped jaw and smaller teeth -Longer lifespan and period of dependency -Larger brains

Hominoids - Humans and other apes • Hominoids diverged from other primates (25-15mya) – Lack tail – Larger brains relative to body size – More erect posture – High degree of social organization

Humans and Chimps • Anatomy – Similar anatomy in teeth, skull and limbs – Delayed sexual maturity • Genetics – >99% identity between gene sequences

Hominids-Humans and extinct relatives • Diverged from the apes 4-6 mya. – Oldest fossil 6-7million years old • Sahelanthropus tchadensis • Diversification of hominids in Africa • Many hominids coexisted temporally and spatially

[pic](CORRECT [pic](WRONG

Australopithecines • Widespread in Africa, ~4.5- 2.5 mya • Bipedal, with relatively large brains • Africa transitioning to semi-arid climate? – Less dependent on the trees for food and shelter and moved upright on the ground

Australopithecus afarensis • 4- 3 mya • Relatively good fossil record, Including “Lucy” • Prognathous face • Definitively bipedal • Knuckle walkers and partially aboreal

Australopithecus africanus • 3.3-2.5 mya • Braincase rounded, relatively larger • Toe and hand morphology suggest arboreality • Phylogenetic position uncertain – Homo-like cranial morphology – Paranthropus-like facial structure

The “robust” australopithecines: Paranthropus spp. • 2.3-1.2 mya • Relatively large body • Massive jaw musculature • Co-existed with the genus Homo • ~ 4.5 feet tall

Early humans -The genus Homo • Homo habilis 2.2-1.6 million years ago -the first human • Less face protrusion – very long arms • Lived in woodlands of eastern and southern Africa • Marks evolution of larger brains and less differences between sexes

Moderns Humans -Homo erectus, Homo neanderthanlensis, and Homo sapiens • Evolved in Africa 2mya • H. erectus migrated into Europe and Asia • H. neanderthanlensis may have evolved in Europe • Larger brain than H. habilis • Creative toolmaker • Built fires and used furs for clothing

Homo floresiensis (Hobbits) • Descendents of H. erectus • 3’3” feet tall, 55 lbs • Discovered in 2003 • Extinct only 12,000 years ago

Homo erectus – Peking Man

Homo neanderthalensis • Early humans that lived in N. Africa, Europe and Middle east • Broader, shorter, more robust body. Larger nasal cavity, brow ridges, larger brains • Physically capable of speach • DNA evidence suggests that they did not contribute to modern European populations • Evidence of cultural interchange • Light skin, red hair • Became extinct 25-30K years ago

Homo sapiens • 160,000 year old fossils in Ethiopia • Associated with abstract material artifacts • Compared to Homo erectus and Neanderthals – More slender – Smaller teeth and jaws – lack heavy brow ridges – Larger-volume brain case

Out of Africa hypothesis of Homo sapiens migration
[pic]

Milestones in human evolution • Upright posture (modification of foot, pelvis and vertebrae). • Enlargement of the brain • Prolonged period of parental care.

Scavenging, gathering and hunting • Homo were scavengers for 100,000 years. • Tool making - became hunters, but continued gathering. • Began to decimate populations of large mammals. • Migrate to follow herds.

Agriculture • 10,000-15,000 years ago. • Depletion of soil nutrients and overgrazing – Desertification of middle east. • Permanent settlements and first cities. • Paved the way for development of industry and technology.

Cultural Evolution • With the evolution of language, accumulation of knowledge, customs, beliefs, arts…. • Makes humans unique in the history of life

POPULATION ECOLOGY
What is ecology? The scientific study of interactions between organisms & their environments

“The environment” has two types of components…
1) Abiotic Components Sunlight Water Temperature Wind Rocks & Soil Periodic Disturbances
2) Biotic Components Other organisms 2 Different types of Interactions between…Same Species and Different Species

Fields of Ecology -Organismal Ecology -Population Ecology (composed of all the members of a species at a particular place & time) -Community Ecology (composed of all the populations in a particular place & time) -Ecosystem Ecology

Population Ecology
Study factors influencing a population’s: size, density, growth rate, structure Size: total number of individuals in a population Density: number of individuals per unit area

Population Size & Density Measurable by… -counting everyone in population -statistical sample plots -mark & recapture

Dispersion Patterns – the way individuals are spaced Clumped: most common, resources are distributed unevenly and the population density increases around the resources Uniform: result of interactions within the population, due to social interactions (emperor penguins, desert plants) Random: absence of strong attractors (like food) and repulsions (like predators) so there is nothing making a species uniform or clumped

Population Growth–Two Major Models:
1) Exponential Growth Model Rate of growth under ideal conditions Growth unregulated No limiting factors

Typical exponential growth seen in… Early stages of disease epidemics Plankton blooms Successful invasive species Human growth and consumption

2) Logistic Growth Model Limiting Factors slow growth as population gets bigger Idealized growth slowed Place where it levels off is the Carrying Capacity

Examples of Population Limiting Factors Density dependent Effects increase as population size increases -Limited food -Limited space -Waste build up Density independent Effects independent of population size Abiotic factors: -Freezes -Droughts -Fires Density independent factors usually kick in first Most population are a mix of factors

Population cycles Many populations are fairly steady Others: “boom and bust”

Human Population Growth Exponential Growth Age Structure: proportion of individuals in different age groups -helps predict population growth

Life Histories (check online notes here) Made up of traits affecting schedule of: Reproduction Death Survival and death tracked via life tables which is used to predict life expectancy Survivorship Curves – graphs that show the life expectancy, infant mortality, etc… of a species

Life Histories are Subject to natural selection (Example: Egg clutch size) Territorial birds – magpies – size of clutch varies with the size of their territory Colonial birds – frigate birds – less variable and smaller and there is no particular selection

Two extreme life histories 1) opportunistic life histories(goes through a long exponential growth period potentially overshooting the carrying capacity and then crashing) Unpredictable Environments Conditions good ( Exponential Quantity over quality

2) equilibrial life histories (goes through a relatively short exponential growth period and then levels off) Predictable Environments Quality over quantity

What morphological feature is unique to humans and great apes?
Answer: The lack of a tail
COMMUNITY ECOLOGY
Community Ecology
Community: all organisms in area at the same time

4 key properties of communities 1) Biodiversity 2) Prevalent vegetation 3) Have a fairly predictable response to disturbance and environmental change 4) Trophic structure

[pic]

Biodiversity: Community’s variety of species
Two components -Species richness -Relative abundance

Richness vs. Abundance
A) Both communities have the same species richness
B) They differ in relative abundance

[pic][pic]

Interspecific Interactions: Interactions between individuals of different species…three main types: 1) Competition (Members of different species compete for limited resources, too (food, shelter)) 2) Predation (see on next page) 3) Symbiosis (see on next page)

Competitive exclusion – two species with the same limiting resources cannot co-exist – If species’ needs too similar…Then…inferior competitor may go extinct

Ecological niche – use of biotic and abiotic factors (habitat + occupation)

Fundamental vs Realized Niche
Resource Partitioning – Stable communities are composed of species that partition resources

Predation – kill and eat • Parasitism – don’t kill but do eat • Parasitoidism – let your children do the eating • Herbivory – only eat part and leave the rest.

Predator and Prey •Co-evolutionary dance •exerts strong natural selective pressure

“Classic Predators” •sharp senses •speed & agility •camouflage •special powers

Parasites – Predators that are smaller than the prey and do not kill them, at least immediately.
Parasitoids -- In essence, the young predate other organisms.

Prey Adaptations: Plants Physical (thorns, tough bark, etc…) Chemical (Please note: many of these chemical defenses are medicinal) -strychnine -morphine -nicotine -mescaline

Prey Adaptations: Animals Flee (run for your freaking life) Mechanical Defenses Chemical Defenses (warning coloration, poisonous) Camouflage Mimicry (predators can also mimic – Batesian mimicry (harmless animal mimics harmful one) – Müllerian mimicry (harmful species mimic each other)

Predation & Diversity •predator-prey relationships maintain diversity •keystone predator– strongest competitors

Symbiosis “living together” Symbiont lives in/on the host organism Symbiont → always benefits – host → may/may not Symbiont examples: mosquito, tape worm

Parasitism – only symbiont benefits
Mutualism – both benefit

BIOLOGY 100- EXAM IV

Fall 2007
Version A

1. What version of the Test do you have? a. A c. C b. B d. D

2. Who was the economist who wrote “Essay on the Principle of Population” whose conclusion formed part of the theory of evolution? a. Malthus c. Darwin b. Hutton d. Emory

3. Which of the following were Darwin’s observations during his voyage on the Beagle? a. Groups of fossil and living species resembled each other b. Species near each other often resembled each other, but with differences c. Some of these differences seemed to suit their particular environment d. all the above

4. An inherited trait that enhances an organism’s ability to survive and reproduce is a. a mutation. b. natural selection. c. spontaneous generation. d. an adaptation.

5. Which of these was NOT part of Darwin’s and Wallace’s theory of natural selection? a. Variation is found within species. b. Populations tend to increase over time unless checked. c. Mutations occur in DNA. d. Individuals with favorable traits will leave more offspring than those without favorable traits.

6. A population is a. all the alleles in a species that live in the same place and time. b. a group of individuals of the same species that live in the same place and time. c. all the species living in the same place and time. d. a basic unit of macroevolution.

7-9. Background information for questions 7, 8, and 9. Consider the case of squirrels. The “B” allele is dominant and squirrels with the “B” allele are bold squirrels. The “b” allele is recessive and “bb” squirrels are shy. So, shy squirrels hide (bb) and bold squirrels (BB, Bb) are always running about in the open, not attempting to hide. We start the population out with equal number of bold and shy squirrels.

7. In an environment with many squirrel predators, you would predict a. The frequency of bold squirrels would decrease. b. The frequency of bold squirrels would increase. c. The frequency of bold squirrels would stay the same. d. Bold squirrels would first increased and then decrease in numbers.

8. The kind of natural selection described in #7 is a. sexual. c. directional. b. stabilizing. d. disruptive.

9. What would you predict if a bunch of bold squirrels migrated from Eudora? a. The number of shy squirrels would decrease. b. The frequency of shy squirrels would decrease. c. The frequency of shy squirrels would stay the same. d. The frequency of bold squirrels would stay the same.

10. The kind of natural selection that weeds out extremes and harmful mutations is a. directional b. disruptive c. sexual d. stabilizing

11. Genetic drift a. is one form of natural selection. b. is change due to chance events c. is caused by recombination d. is caused by mutation

12. The high incidence of retinitis pigmentosa among inhabitants of the island of Tristan de Cunda and the fact that northern elephant seals have almost no genetic variation are due to: a. the founder effect or bottlenecks b. stabilizing selection c. mutation d. migration

13. Sexual dimorphism may result from _______________ selection. a. directional b. disruptive c. sexual d. stabilizing

14. The study of biological diversity is the area of a. natural selection c. taxonomy b. biogeography d. geology

15. One of the reasons macroevolution is considered the best explanation for the evolution of species is that a. independent sources of information tell the same story b. genetic drift is operating to create all the patterns c. organisms alive today are found in the earliest rocks d. mutations are always beneficial

16. Archaeopteryx a. has all the features typical of modern birds b. has some features of “reptiles” and some of modern birds c. is exactly intermediate in all its characters between “reptiles” and modern birds. d. is a crocodile

17 Feathers a. first appeared in Archaeopteryx. b. first appeared in crocodiles. c. first appeared in dinosaurs. d. provide no evidence that birds are related to dinosaurs.

18. The “modern” view of macroevolution a. is a complex branching pattern b. is a straight line between intermediate forms c. considers only molecular evidence d. is a process in which microevolution does not operate.

19. Ballpark estimate: the earliest evidence of life on Earth is from about a. 100 million years ago b. 500 million years ago c. 4 billion years ago d. 14 billion years ago

20. The best scientific explanation of why we see fossils of the same species in South America and Africa is a. continental drift c. parallel evolution b. ocean dispersal` d. special creation

21. Structures that descend from a common ancestor are termed _______ structures. a. parallel c. convergent b. common d. homologous

22. In development among vertebrates we expect a. that embryos will resemble each other more in later development. b. that embryos will resemble each other earlier in development. c. that there will be no correlation between how embryos look and how the organisms are related. d. “lower form” to have bigger embryos at each stage of development.

23. If we compare the amino acid sequence of cytochrome C among fungi, turtles, rhesus monkeys, chimpanzees and humans, we would predict that a. Rhesus monkeys and humans would share more common amino acids. b. Rhesus monkeys and chimpanzees would share more common amino acids. c. Chimpanzees and humans would share more common amino acids. d. there would be about the same number of common amino acids shared between each organism.

24. Relationships within sexual species form a. a hierarchy c. a vicariance b. a network d. a blob

25. Hybrids between species a. tend to be fertile b. never occur c. are very frequent d. tend to be sterile

26. Species that live in different regions are said to have _______ distributions. a. allopatric b. parapatric c. sympatric d. hierarchical

27. Which of the following is a premating isolating mechanism a. behavioral differences b. ecological isolation c. gamete mortality d. hybrid sterility

28. The common mode of speciation in animals is a. behavioral isolation b. sympatric speciation c. gradual evolution d. allopatric speciation

29. Our common varieties of wheat are thought to have originated via a. behavioral isolation b. sympatric speciation c. gradual evolution d. allopatric speciation
30. The idea that evolution occurs in spurts centered around speciation, with little change between speciation events is termed a. allopatric speciation b. sympatric speciation c. the gradualist model of speciation d. punctuated equilibrium

31. Ribotyping is most useful for a. explaining the origin of eukaryotes b. identifying unknown disease bacteria c. identifying unknown food products d. testing the theory of punctuated equilibrium

32. The original atmosphere of earth contained high amounts of all of these molecules EXCEPT a. hydrogen c. nitrogen b. oxygen d. carbon dioxide

33. The Theory of Endosymbiosis asserts that a. mitochondria and chloroplasts are descended from free-living prokaryotes. b. mitochondria and chloroplasts are descended from free-living eukaryotes. c. mitochondrial and chloroplasts are independent evolutionary novelties. d. mitochondria and chloroplasts are the result of membrane infolding.

34. Ballpark estimate: the first evidence for eukaryotes in the fossil record is about a. 2 billion years ago b. 4 billion years ago c. 500 million years ago d. 10,000 years ago

35. The mammalian order Primates is characterized by a. binocular vision b. opposable thumbs c. a collarbone d. all of the above

36. The closest relatives of animals are a. bacteria b. fungi c. ciliates d. plants

37. Humans are chordates, chordates belong to what larger group? a. Protostoma b. Duetrostome c. Mammalia d. Radiata

38. The tree of life is useful to humans because a. we can use it to identify and trace the origins of bacteria and viruses b. we can use it to barcode/identify food c. we can use it to document biodiversity d. all of the above

39. Among living organisms, the closest relatives of Homo sapiens are a. gorillas b. monkeys c. chimpanzees d. gibbons

40. Which of the following species is not considered to be a “modern human?” a. Homo erectus b. Homo neanderthalis c. Homo sapiens d. Homo habilis

41. A group of populations of different species that interact with each other in a given area is known as a a. population b. community c. ecosystem d. guild wars

42. The role individuals of a species play in nature is termed a. the community of the species b. the characteristics of the species c. the dynamics of the species d. the niche of the species

43. Which of the following is a characteristic of mass extinctions? a. speciation rates are much higher than extinction rates. b. extinction rates are much higher than speciation rates. c. allopatric speciation is operating d. allopatric extinction is operating.

44. Ballpark: how many mass extinctions have been documented in the past. a. 5,000 b. 500 c. 50 d. 5

45. What is the current scientific hypothesis about the cause of dinosaur extinctions? a. gamma ray bursts b. climate change c. asteroid hit d. plate tectonic changes

46. What is the major cause for our current biodiversity crisis? a. habitat destruction b. climate change c. plate tectonics d. harvesting of pharmaceutical plants

47. Alternative use of land, especially topical land for sustainable use would include a. gathering pharmaceutical plants for medicine. b. habitat friendly crops such as coffee. c. ecotourism. d. all the above.

48. In the best situation, the exponential growth of a population will stop when the ______________ of the environment is reached. a. carrying capacity b. biotic potential c. habitat capacity d. dynamics

49. Growth in human populations a. is negatively correlated with rates of extinction b. is not correlated with rates of extinction c. is positively correlated with rates of extinction d. in unrelated to rates of extinction

50. What costs the Australian tax payers about 4 billion dollars a year to control? a. kudzu b. exotic weeds c. Nile perch d brown snakes

Quiz Questions

51. Height in humans is an example of what type of trait? a. qualitative b. dimorphic c. quantitative d. polymorphic
52. Why has sickle cell anemia not been eradicated from the human population? a. it is spread by mosquitoes which are very abundant b. sufficient vaccines have not been developed c. people who are heterozygous for sickle cell anemia are more resistant to malaria d. it is not fatal, even people homozygous for the sickle cell anemia are not at a disadvantage

53. What idea did Lamarck propose to explain changes in species? (his idea has since been disproved) a. genetic mutations occur and are passed to offspring b. fittest individuals are more likely to survive c. populations that become separated evolve independently in response to their environments d. individuals strive for perfection and their offspring inherit acquired physical traits

54. Bird wings and bat wings are examples of: a. analogous structures b. homologous structures c. morphological convergence d. both a & c

55. A burst of sudden divergence from a single lineage is called: a. adaptive radiation b. anagenesis c. cladogenesis d. gradual speciation

56. Which has NOT been proposed as a prerequisite for the origin of cells? a. an atmosphere relatively free of oxygen b. the formation of a nucleus containing DNA c. the accumulation of water into seas on the earth’s surface d. the formation of carbohydrates and lipids

57. Which of the following is NOT a characteristic that makes DNA more suitable than RNA for use as the cell’s genetic material? a. DNA can self-replicate b. DNA is more stable c. DNA can carry more information d. DNA double helix shape packs efficiently in the cell
58. A zero in an evolutionary matrix represents traits that a. Evolved earlier than the common ancestor, and therefore CANNOT be used to establish groups of related organisms b. Evolved earlier than the common ancestor, and therefore CAN be used to establish groups of related organisms c. Evolved after the common ancestor, and therefore CANNOT be used to establish groups of related organisms d. Evolved after the common ancestor, and therefore CAN be used to establish groups of related organisms

59. Archaea are most closely related to a. Eukarya c. Rocks b. Bacteria d. None of the above

60. Which of the following scientists believed that speciation occurs gradually? a. Simpson c. Gould b. Eldredge d. All of the above

61. With regards to Cytochrome C, the species listed in lecture differ in a. The sequences of their amino acids b. The number of amino acids they have c. Both the number of amino acids and their sequence d. Cytochrome C is the same among all species

62. There is very little genetic variation among cheetahs because of a. natural selection C. the bottleneck effect b. mutation d. sexual selection.

63. Which of the following is true? a. Feathers originally evolved for flight b. Large amounts of genetic variation make an organism more subject to extinction. c. Disruptive Selection favors extremes in phenotypes. d. None of the above.

64. A frog egg with its nucleus removed a. Will not develop at all b. Will develop just enough for an observer to know that it is a vertebrate c. Will develop into a normal juvenile, but will not be capable of reaching sexual maturity d. Will develop into a normal adult

65. Which of the following is NOT a method of reproductive isolation that prevents the act of reproduction? a. Mechanical c. behavioral b. Temporal d. gamete mortality