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Organismal Biology Notes, Study Guides, Projects, Research of Biology

Ottawa University (OU) - Kansas City Biology

that are a good notes for students which can help them to understand some deffecult notes in organismal biology

Typology: Study Guides, Projects, Research

2016/2017

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Chapter 1: The Scientific Method

Inductive Reasoning:

- Specific observations lead to generalizations

- Description based approach

- Particular → General

Scientific Process

- Observation: Orange is sweet

- Hypothesis: All oranges are sweet

- Prediction: If I taste all kinds of oranges, then they will all be sweet

- Test: Tasting all kind of oranges

- Travel to Madagascar oranges there are not sweet ⇒

- Hypothesis is falsified

Contract between science and knowledge:

- Initial skepticism on facts

- We ask honest questions, re-test what has been found

- Realism

- Acknowledge that the world is older and exists independently from my perception of it

- Realm of ideas < Real World

- Notions we have need to be realistic

- Rationality

- Deductive and inductive approach → Logic demonstrations from a scientist must be the result of

coherent steps

- Parsimony

- Methodological principle which states that acceptable theories are hypothetically the

most economical in assumptions

- Simplest option is usually true

- Methodological Materialism

- All that is experimentally accessible in the real world is material or has material origin

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Chapter 1: The Scientific Method

Inductive Reasoning:

Specific observations lead to generalizations
Description based approach
Particular → General

Scientific Process

Observation: Orange is sweet
Hypothesis: All oranges are sweet
Prediction: If I taste all kinds of oranges, then they will all be sweet
Test: Tasting all kind of oranges
- Travel to Madagascar ⇒oranges there are not sweet
Hypothesis is falsified

Contract between science and knowledge:

Initial skepticism on facts
- We ask honest questions, re-test what has been found
Realism
- Acknowledge that the world is older and exists independently from my perception of it
- Realm of ideas < Real World
- Notions we have need to be realistic
Rationality
- Deductive and inductive approach → Logic demonstrations from a scientist must be the result of coherent steps
- Parsimony
  - Methodological principle which states that acceptable theories are hypothetically the most economical in assumptions - Simplest option is usually true
Methodological Materialism
- All that is experimentally accessible in the real world is material or has material origin

Chapter 3: Charles Darwin and Evolution

Evolution and Natural Selection

Species resemble themselves because they share a common ancestor (not common environment)
- Rejects fixity of species and accepts concept of descent with modifications (evolution)
- Contradicts religious dogma of the time
- Rejects Lamarck’s evolutionary mechanism (environmental determinism)
Finches are similar because they share a common ancestor → Finches of Galapagos Island
Rock Hyrax Example
Dugong Example
African Elephant
99% of species that have lived on Earth are extinct
Most of the evolutionary branches finish in a dead-end (extinction) → Due to natural selection
Every human population has a tendency to increase geometrically, whereas the available resources to feed these populations increase arithmetically - Human population increases faster than its capacity to feed itself ⇒chaos (famine, sickness, war, etc.) & reduction in population size

Darwin’s First Observation:

All species can produce more offspring than their environment can sustain and many of these fail to survive and reproduce - Examples: - Mola mola (Ocean sunfish) - Maple tree and its samaras) - Puffball (spore cloud)

Darwin’s Second Observation

Members of a population often vary in their inherited traits
High variability in inherited traits
- In our genes → transmitted to offspring
Examples
- Amphidormus adamsii
- Asian ladybird beetles
Natural Selection
- Traits passed down that are favored while reproducing
- Comes to the advantage of those being reproduced = reproductive success
- Enables the emergence of adaptations

Important notions linked w/ natural selection:

Individuals don’t evolve, populations evolve
Only hereditary traits are subject to natural selection
For evolution to occur, we need genetic variability
Natural selection corresponds to differential reproductive success within a population from generation to generation
Natural selection enables individuals to become better adapted to their environment

Increased blood flow

Many regions in high altitudes were independently colonized by humans.

ANDES QINGHAI-TIBET

PLATEAU

Increase in hemoglobin concentration (RBC) - Increased blood flow
Natural selection keeps the individuals with the genetic traits that allow adaptation to high altitude
Individuals that have the mutation are at an advantage for survival and reproduction (production of offspring)

In three cases (moth, finch, humans) that hereditary traits that give a reproductive advantage to individuals in a population will be favoured

There will be a higher percentage of individuals carrying the adaptation
- = natural selection
These adaptations can sometimes redefine a species and can occasionally define a new species

Chapter 4: Genetics, Neo-Darwinism, & Modern Synthesis

Modern additions to Mendel’s laws

Dominance

Incomplete Dominance:

Red is not TOTALLY dominant = mix
Example → Snapdragon

Incomplete Dominance

Example --> Palomino horse (Cc)

Codominance:

Example → Checkered chicken

Three concepts to use:

Polygenism
- When a phenotypic trait is under combined action of two or multiple genes (very common)
- All characterized by continuous traits (height, skin color)
- Eyes → Discrete; Skin color ⇒Parents
Epistasis
- When the effect of a gene hides or blocks the expression of another gene
Pleiotropy
- When a gene affects more than one trait
- Manx cat →> M gene
- Incomplete dominance compared to normal gene
- Gene responsible for no tail = lethal (embryo reabsorbed) when homozygous ( ⇒death)
- Heterozygous ⇒short tail (or no tail), only affects part of vertebral column

Chapter 5: Evolution of Populations

-images in notebook- -genotypic and phenotypic frequencies-

Hardy-Weinberg’s Principle

Population is in HW Equilibrium when:
- Frequencies of alleles and genotype within a population will remain constant (according to p2+2pq+q2=1) from generation to generation as long as: - There are no mutations - Mating is done randomly - Size of the population is really large - There is no genetic (gene) flow (no migration of alleles between populations) - No natural selection
HW Principle describes a hypothetical population that does not evolve

Mutation

Changes in the DNA sequence of an organism
This is the source of genetic variability
Mutations are:
- Random not directed
- Transmissible (only in the gametes) to the next generation if it touches sex cells
- Frequent throughout the gene pool but rare at each locus
- Will influence allele frequencies but is a weak evolutionary force from generation to generation, espc in large population

Point Mutation

Additions, deletions, substitution of a base (A-C, instead of A-T)
Negative effect (Ehlers-Danlos Syndrome → fabrication of CT)
- Linked with Dwarfism → Achondroplasia
Lethal effect (will cause death)

Found black guppies BUT died because they lost all genetic variability → deformed vertebral column, etc.

Choice of partners in relation to the phenotype (modifies HW)

Positive Assortative Mating Negative Assortative Mating

Autogamy or selfish of plants (pure lineage of Mendel) - Self-fertilization
Geographical proximity of individuals (population of mice in a barn)
In humans: mating according to height and skin color (not random)
Between individuals that look similar thus increasing homozygosity - Don’t look alike, and mate - Plants: Little change of self-fertilization, stamen and carpel = baby - Histocompatibility → female rejects own pollen therefore no SF - One species, two genders

Gene Flow

Migration: exchange of genes between populations
- One species: gene flow is not possible with one population
Tends to standardize the genetic pool of the populations involved
- Make it similar v quickly
- Ex. Bass
- Population ⇒Each lake does not interact with each other
- Species ⇒Bass in general
Can play a similar role as mutations by introducing new genes in one of the populations

Example of Gene Flow → Parus major (Great Tit)

Mainland → Island migration
Central part survived, Eastern part was very different

Genetic Drift

Result of chance
Chance will have increasingly more impact on a population as the size of the population gets smaller

Small population
- Genetic drift triggers decrease in genetic variability & decrease in heterozygosity
Large population
- Cause little changes in allelic or genotypic frequency of a population
Larger the pop, less sampling error between expected and observed frequencies
If nothing affects allele frequencies, genetic drift will eventually result in the fixation of an allele and the elimination of all others for this locus
Probability that an allele will become fixed is equal to its frequency
Population bottleneck
- Small populations → genetic drift = fixation of deleterious alleles and loss of genetic variability
- This can correspond to an increase in rise of extinction
- Cheetah → All of them are the same, when an epidemic occurs, most of them will die because all of them had the same alleles that were affected
- Greater prairie chicken
  - Still some population left in the US
  - Average # of allele/locus

Selection for a continuously variable trait

Directional Selection

DDT and Mosquito Example
- DDT → insecticide
- MQ became resistant to DDT
- High mortality, then very low mortality after 2 years
Medium Ground Finch example

Disruptive Selection

Birds and width of their lower jaw example → Pyrogentes ponceau
- Measure width of lower jaw → correlated with seed they eat
- Selection against average value
- Intermediate size seed was not available
- Extreme value is favored
- Maybe important in speciation

Stabilizing Selection

Newborns that weighed 8lbs had a higher rate of survival than smaller or larger newborns
- This stabilizing selection has diminished in many wealthy countries
All mammals have seven cervical vertebrae
- Pleiotropic effect: one gene has many effects on the body

Not a standard habitat

Sexual Selection

Formulation of Darwin’s concept

Intersexual Selection

Individuals possess some specific hereditary traits are more susceptible than others to find partners
Ex. Widow bird
- Do females birds prefer longer tails?
- Females choose the male in this species
- Very popular male → longer tails
Ex. Male stalk eyed flies
- Longer eye stalk > shorter eye stalk
  - Healthier
Ex. Central American Birds
- Moonwalk when they want to mate

Intrasexual Selection

Selection between individuals of same sex
- Fight over who has sex
Confrontational behavior = ritualized combat
Ex. Kangaroos fighting

Penis Bone or Baculum → Walrus

Quick copulation
Also in dogs and cats
Facilitate penetration, lock penis inside their mate

Chapter 6: Adaptation

Evolutionary Compromise

Why are humans the only Primates choking on food?
- Pay a price for something
Snout of a chimp (longer tongue) is longer than a humans
- Reduces spaces between throat and tip of mouth
Back of mouth: Soft palate separates nasal area from mouth
- Epiglottis: Cartilage shuts trachea

CHIMP HUMANS

Can swallow and the food is automatically blocked by epiglottis and trachea, there is not space for the food to go down the wrong pipe - Space between tip of palate and epiglottis - Swallow food and mechanism for epiglottis doesn’t work automatically - Space in between makes us vulnerable

Why only humans?

No a lot of space between palate

When can increase or decrease space, space between vocal cord is bigger in humans
Chimps can emit sound but not at the same capacity as humans
Humans tube allows for fast and clear pronunciation
- Allows us to pronounce vowels clearly
Old adaptation

Studying Adaptations

Initial function of fins was to stabilize the fish body in its environment → adaptation
In terrestrial animals (tetrapods) the limbs (that evolved from fins) are used to support the body in an aerial environment - Limbs are exaptations for terrestrial mobility (locomotion)
Exaptation allows us to have a historical outlook to adaptation
- Current function is not what it initially was Ex. Hair
Adaptation → thermoregulation
Exaptation → to dissipate heat for elephants
They have thinner skin in some areas
Trunk, ears, these random patches have hot spots
Origin of hair was not to preserve heat, it was to get rid of it, but NOW it preserves heat

Ex. Feathers

Preservation of heat
Dinosaurs were not endotherms, they accumulated hear with feathers
Origin is not known, but it’s for sure that it wasn’t for flight, possibly sexual selection

Chapter 7: Geographic Variation and Speciation

Evolution of the loss of fur and skin color in humans

6-8 million years ago, the hominins (all human species) shared a common ancestor with the chimpanzee (pale skin covered of a dark fur)
Sahelanthropus tchadensis → oldest hominin known

A. afarensis

Lived in tropical forests
- A lot of hair
Bipedal, and arboreal
- Long arms, feet with capacity to climb attachment of VC, under the cranium
Diet of fruits, tubers, and leaves
- Frugivores
Sedentary way of life
- Limited movement
Australopithecus afarensis → 3.7-3 Myr

Skin of all hominis species (including Homo sapiens ) was dark
Hypothesis:
Find an inherited trait that gave those who had it a positive survival and reproduction differential (adaptation) from generation → generation compared to other members of the population
Fur
Protection from abrasion to skin
Hair reacts to cold and strong emotion
Loss of hair = facial expressions became important
Dark skin
For over 1 Myr
The skin of ALL hominins species was dark
Including homo sapiens

Vitamin D and Pale Skin 3 

Synthesized in skin by UV rays
Helps absorption of Ca 2+^ in the gut
- Deficiency of Calcium ⇒rickets, other diseases
Direct impact on reproductive success of affected individuals
Pale skin in low UV radiation → maximize absorption of UV rays and the survival of the human population in areas of UV deficiency (adaptation)
More North = paler skin
Migration = 100 000 years ago
- Humans invade northern habitats more recently →. 40 000 years ago
- Evolve paler skin to maximize UV absorption in areas where UV radiation is weak for adequate synthesis of Vitamin D by the skin 3 
Humans can compensate for this (10-15 000 years ago) through diet (hunting, fishing, domestication)

Conclusion

Loss of fur in hominins linked to lifestyle
- Due to climate change → 1.2 Myr
Skin = dark after loss of fur → 1 Myr
Colonization up north = paler skin → maximize D absorption 3 
- Dark skin = synthesize D at a slower rate 3 
Selective advantage of darker skin on high UV intensity areas = minimize degradation of folic acid by UV rays

Color of Skin

Variable polygenic trait, explains pigment intensity variability
Adaptation to UV radiation
Indicator of environment in which population has lived

Origin of Species

Eastern Meadowlark ( Sturnella Magna) and Western Meadowlark ( Sturnella

neglecta )

Minimal phenotypic differences (except for their song and behavior that are very distinct)

Sympatric speciation:

New species appears within population (speciation without geographic isolation):
Polyploidy (30-40% of plants): multiplying the normal number of chromosomes

Can happen when the chromosomes do not separate during meiosis → produces diploid games instead of haploids
Rare in animals
Ex. Apple maggot v. Thornapple maggot
Two morphs of Rhagoletis pomonella in the process of sympatric speciation

Hybrid Zone

Ex. Toads
- Yellow bellied toad → Bombina variegata
  - Lives at higher altitudes
- Fire bellied toad → Bombina bombina
  - Lives at lower altitudes
- Both came to the middle altitude or the hybridzone and more of them survived there than in either of the altitudes
Ex. Grolar bear
- Rupture of reproductive isolation between grizzly and polar bear
- Exception? Consequence of global warming?
Enhancement of reproductive barriers in the contact area (hybrid zone)
- Character displacement
  - Differences between two related species are often greater in sympatric areas
    - 2 species of Galapagos finches
Enhancement of reproductive barriers in flycatchers

3500 Myr since LUCA
Human species is the only one terminal twig in the bush of life
Luca is at the center of things, with 3 branches of life around it
Some branches will stop meaning they dies (extinction)
All species share a common ancestor that is at the center of the bush
WE ARE ALL THE SAME → we make have a different way of life, but we are all equal in terms of evolution of species because we all share 3500 million years of history

Homology and Homoplasy

Homologous structures

Indicative of a common ancestor and the data that is used to reconnect phylogenies
Ex. Humerus in a human vs humerus in cat, whale, and bat
Limb of species have different functions and can be found in different species, but they are homologous structures that indicate a common ancestor

Homoplasy

NO HOMOPLASIES IN PHYLOGENY

Convergent Evolution
- Ability to hover in sugar gliders v flying squirrels → might be related in terms of phylogeny but they might have evolved the gliding trait independently
- Convergent evolution is a problem when you describe phylogeny because not all characters that look alike have common ancestors
Evolutionary Reversion
- Absence of fur in whales

Taxonomy and Classification

Biologists use binomial system to identify living organisms
Homo = name of genus
- Signifies “man”
Sapiens = name of species
- Signifies: intelligent, wise and reasonable

Classification
- System of words used to group species into increasingly generalized categories
- Hierarchical system
  - Sequential and orderly arrangement of categories
Taxonomic rank → taxon
The classification needs to reflect on the phylogeny

Phylogenetics

Tree with dichotomous branches (cladogram)
Bifurcation point (branching point)
- Common ancestor denotes related groups
Cladogram indicates the sequence of appearance of taxa
No time frame incorporated in cladogram
Classification reflects ramifications of the cladogram, homologous characters help define the order of sequence

Branching point and polytomy

Taxon D, E, F → Unresolved Basal Taxon: defines relationship in A-F

Basis to compare evolution within our group

Cladistics:

Taxa should be based on shared derived characters aka
- Synapomorphy
- Homology
  - Material upon we build classification
Not shared ancestral characters aka
- Symplesiomorphy
  - Do not want this!
  - A character might be either derived or ancestral character → distinguish this!
Only valid group
- Monophyletic group

Monophyletic groups → contains all and only the descendants from a common ancestor NON MONOPHYLETIC GROUPS: (WE DON’T WANT THIS) Paraphyletic groups → does not contain all the descendants from a common ancestor Polyphyletic groups → contains descendants from several ancestors

Only way to find an answer is to look at birds and crocodilians → birds came from dinosaurs and crocodiles came before dinosaurs
Hypothesis based on cladogram: birds and crocs take care of their young → if oldest and most derived groups related to dinos take care of their young, it's safe to assume that based on historical data that dinos took care of their young too

Chapter 9: Biosphere and Ecology

Ecology: Definitions, Concepts, and Issues

Ecology

Scientific study of interactions between organisms and between organisms and their environment
Environment:
- Abiotic Factors → interactions between organism and environment
- Biotic Factors → interactions between organisms

Scope of Ecology

Organism ecology
- Interactions between organism and environment
  - Physiology, behavior
  - Main example = evolution
Population ecology
- Groups of organisms of one species living in the same age (dynamics of population size fluctuations)
Community ecology
- Groups of populations of different species in an area
  - How interactions between species (predation, competition) affect the structure and organization of communities
Ecosystem ecology
- Community of organisms in an area and the interaction of organisms with physical factors (study of energy flow, chemical cycling)
- How animals interact with their environment
- ecosystem approach is more important and prioritize ecosystems with endangered species
Landscape ecology
- Mosaic of connected ecosystems (study of factors controlling of energy, materials and organisms across multiple ecosystems)
- Ex: Ottawa has a green belt, conscious attempt to keep a belt of forest around the city, important for fauna and flora (helps maintain), have corridors to connect ecosystems
Global ecology
- Study of the biosphere
- Sum of all ecosystems (study of regional exchange of energy and materials its global impact on the biosphere)
- Activity done in one part of the ecosystem and affects the entire planet ( global warming)

Precautionary Principles

Strategy to cope with possible risks where scientific understanding is yet incomplete
- Better to be safe than sorry
Earth’s climate is warming up due to human activity
Interaction between society and ecology
Always uncertainty with science doesn't matter what kind of science

Scientists might give warning → ex: climate change, scientific evidence indicated that ifwe keep emitting the amount of carbon we are, temperature will rise
We have to find a way to come with it ( summits that are put together between countries)
It's going to cost more to repair things than prevent it

Ex: lack of cod in the Maritimes, there was a limited supply due to all the fishing done. Government warned that if people didn’t stop fishing the cod, there would be none left à ultimately no one took the precaution seriously, overfished cod, Maritimes fishing business collapsed

MAYBE if precautionary principle was applied, we might still have cod

Climate

Abiotic Factors

Light, Temperature, Wind, Precipitation
In polar regions:
- Solar rays are slanted whereas they are vertical in equatorial regions
- Solar energy spreads over a large surface area
- Temperature varies depending on where you are on the planet
Earth is tilted on its axis at 23.5 degrees angle
- Extratropical regions have seasons
- Tropical regions have little differences between seasons and days
- Angles of the earth has an effect on our climate à makes seasons because the fact of what part of the earth is closer or farther away from the sun determines the weather
- If the earth became flat, we would lose our seasons
- Angles also determine how much light we get (winter and summer equinox)
- All facts are impact on species

Air circulation and precipitations at a global scale

Winds are made with friction between atmosphere and planet → the friction is the cause of win
Wind is not straight
Descending dry air absorbs moisture
Ascending moist air releases moisture
Circulation of surface water in the oceans influence climate
All currents are linked
Combination between warm and cold currents
Currents have an impact on climate on land
Effect of large bodies of water on the climate
- Cool air comes from the ocean
- Land absorbs and emits more heat making the air warm

Organismal Biology Notes, Study Guides, Projects, Research of Biology

Related documents

Partial preview of the text

Download Organismal Biology Notes and more Study Guides, Projects, Research Biology in PDF only on Docsity!

Chapter 1: The Scientific Method

Inductive Reasoning:

Scientific Process

Chapter 3: Charles Darwin and Evolution

Evolution and Natural Selection

Darwin’s First Observation:

Darwin’s Second Observation

Important notions linked w/ natural selection:

ANDES QINGHAI-TIBET

PLATEAU

Chapter 4: Genetics, Neo-Darwinism, & Modern Synthesis

Modern additions to Mendel’s laws

Dominance

Three concepts to use:

Chapter 5: Evolution of Populations

Hardy-Weinberg’s Principle

Mutation

Point Mutation

Choice of partners in relation to the phenotype (modifies HW)

Example of Gene Flow → Parus major (Great Tit)

Sexual Selection

Intersexual Selection

Intrasexual Selection

Penis Bone or Baculum → Walrus

Chapter 6: Adaptation

Evolutionary Compromise

CHIMP HUMANS

Studying Adaptations

Chapter 7: Geographic Variation and Speciation

Evolution of the loss of fur and skin color in humans

A. afarensis

Vitamin D and Pale Skin 3 

Conclusion

Color of Skin

neglecta )

Sympatric speciation:

Homologous structures

Homoplasy

NO HOMOPLASIES IN PHYLOGENY

Branching point and polytomy

Cladistics:

Chapter 9: Biosphere and Ecology

Ecology: Definitions, Concepts, and Issues

Ecology

Scope of Ecology

Precautionary Principles

Abiotic Factors

Air circulation and precipitations at a global scale