Bio 192 Notes

The Scientific Method

• Observation

• Types of questions:

  • Correlational: Examine natural variation in A to correlate with variation in B.

• Hypothesis

• Prediction: "If…then…"

• Experiment: Manipulate A and record response in B.

• Results

  • Physiology, neurobiology, evolution, ecology

  • Descriptive statistics: mean, SD (standard deviation), median, range

  • Inferential statistics: t-test (numeric vs. categorical)

• Fail: Find a new mechanism

• Key Components:

  • Ask good questions that can be answered.

  • Define your variables well.

  • Be aware of assumptions you are making.

Evolution

• Change over time

• Biological/Organic (in person/organism)

• Change in the genetic composition of a population over time; examples include: eye membrane and vestigial structures like gills, tails, and homologous structures.

• Narrow Sense Evolution

• Broad Sense Evolution: Change in the genetic composition of a population over time.

• Descent with modification

• P(m)

• Ancestors

• Character states due to shared ancestry.

• Vestigial, non-functional characters inherited from ancestors become non-functional. (e.g., eye membrane, appendix)

• Fossil Record: Shows patterns of evolution

• Artificial Selection: Selective breeding of other species by humans to promote the occurrence of desired traits (e.g., dogs, plants, horses).

• Natural Selection

• Mutation, Genetic Drift, Gene Flow

Adaptation & Natural Selection

• Adaptation: A favorable trait.

Natural Selection

• Evolution: Change in the genetic composition of a population over time; due to nonrandom survival and reproduction

• Evolution

Artificial Selection

• Evolution

• Antibiotic resistance is a result of:

  • Patient noncompliance

  • Overuse of antibiotics

• Fitness: Success of a genotype relative to other genotypes, often measured using reproductive success (matings and offspring).

• Successful genotypes have higher fitness.

• Modes of Selection:

Directional Selection

• Selection for one extreme.

• Fitness is highest at one extreme; positive selection for the high extreme or negative selection for the low extreme.

• Time is a measure used in evolutionary graphs.

Stabilizing Selection

• Selection for intermediate forms.

• Fitness is highest for the middle forms.

Disruptive Selection

• Selection for both extremes.

• Fitness is highest at both extremes.

• Other Types of Natural Selection

  • Frequency Dependent Selection

  • Sexual Selection: Natural selection for mating-related traits

    • Fitness depends on the relative frequency of each traits

• Two major trait categories:

  • Female choice

  • Male choice

Mate Choice Mechanisms

• Good Genes: Payoff to females through increased genetic quality of offspring.

• Direct Material Benefits: Payoff to females through access to resources; females would avoid if not

• Sneaker Males: Some males do not display; instead, they sneak mating events, maintained through frequency-dependent selection. They must be in low frequency relative to displaying males; otherwise, females would avoid them.

Other Mechanisms of Evolution

• Mutation: Generates random variation; can be positive, neutral, or negative. Most are neutral; positive changes tend to be favored by selection.

• Gene Flow: Transfer of alleles into or out of a population due to movements of individuals or gametes (e.g., frogs move between ponds that differ in local selection pressures).

  • Frogs differ in traits among ponds and carry differences into other ponds when they move

• Genetic Drift: Change in genetic composition of population - unpredictable fluctuations in allele frequencies from one generation

Two Mechanisms

• Population Bottleneck

  • Original population is large, but a drastic environmental event occurs, causing the death of most of the population. Death is random, not due to natural selection.

  • New population differs genetically from the original population.

• Founder Effect

  • Original population has a large size, but a subgroup moves away to colonize a new area.

  • Genetic composition of the new population differs from old population.

  • In some cases, can increase speciation rates.

Population Genetics

• Determine if evolution is occurring in a population over time.

• Genetic Composition of population

Three estimates of interest

• Genotype frequency

• Phenotype frequency

• Allele frequency

Genotype Frequency

• Proportion of each genotype in a population

• Total of values must equal 1.0

• AA = \frac{100}{200} = 0.5

• Aa = \frac{50}{200} = 0.25

• aa = \frac{50}{200} = 0.25

• Total = 200

Phenotype Frequency

• Proportion of each phenotype in a population

• Total of values must equal ~1.0

• Example of Complete Dominance:

  • Black (AA) = 100

  • Blue (Aa) = 50

  • Red (aa) = 50

• Example of Incomplete Dominance:

  • Black (AA) = 100

    • \frac{100}{200} = 0.5

  • Black (Aa) = 50

    • \frac{50}{200} = 0.25

  • Red (aa) = 50

    • \frac{50}{200} = 0.25

    • Total = 200

Allele Frequency

• 2 \text{ alleles in each organism}

• A = 2N{AA} + 1N{Aa}

• a = 2N{aa} + 1N{Aa}

• 2n

• n = \text{number of organisms}

• p + q = 1

• Population genetics and evolution test if evolution is occurring by comparing genotypes frequencies to those expected if evolution is NOT occurring; use a null model similar to a null hypothesis

Hardy-Weinberg Equilibrium Model (HW)

• HW Approach

Assumptions for No Evolution

• Use existing genotype frequencies to calculate allele frequencies

  • No mutation

  • No natural selection

  • Random mating (no sexual selection)

  • Large population size (no genetic drift)

  • No migration (no gene flow)

  • p^2 + 2pq + q^2

    • p^2 = homozygous dominant genotype (AA)

    • 2pq = heterozygous genotype (Aa)

    • q^2 = homozygous recessive genotype (aa)

• Compare observed genotypes to predicted genotypes under HW equilibrium

Deviations Indication

• Example: Flowers (Red [RR] = 300, Pink [Rr] = 100, White [rr] = 100); Total = 500

  • Genotype:

    • Red: \frac{300}{500} = 0.6

    • Pink: \frac{100}{500} = 0.2

    • White: \frac{100}{500} = 0.2

• Observed and Expected Frequencies Compared (assuming p = 0.7 and q = 0.3):

  • RR: Observed = 0.6, Expected = (0.7)^2 = 0.49

  • Rr: Observed = 0.2, Expected = 2(0.7)(0.3) = 0.42

  • rr: Observed = 0.2, Expected = (0.3)^2 = 0.09
    If p<0.05 = reject Ho

0.05 = fail to reject Ho
= 0.05 = fail to reject Ho
Table

• Example:

  • Red (RR) = 320

  • Pink (Rr) = 160

  • white (rr) = 20

    • A = 2(320) + 160 = 800

    • N = 2(20) + 160 = 200

• p = \frac{800}{1000} = 0.8

• q = \frac{200}{1000} = 0.2

• p^2 + 2pq + q^2 = 1

• (0.8)^2 + 2(0.8)(0.2)+(0.2)^2

• 0.64+0.32+0.04

Micro vs Macro Evolution

• Microevolution:

  • Evolution of populations

  • Evolution below the species level

• Macroevolution:

  • Evolution above the species level

  • Speciation: Origin of new species

• Microevolution is the mechanism while Macroevolution is the pattern

Species - Definitions

• Biological Species Concept

  • Population/group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring with members of other populations

  • Exceptions:

    • Asexual organisms (no sexual reproduction)

    • Extinct organisms in the fossil record

• Morphological Species Concept

  • Species are grouped by structural similarities

  • Does not require reproduction within species

  • Exception:

    • Unrelated organisms can appear similar in traits

    • Convergent evolution: Evolution of similar traits in unrelated organisms

    • Homoplasy: Similar traits that have evolved independently (e.g., wings in eagles and bats)

Speciation: Origin of New Species

• Allopatric Speciation: "Other Country"

• Sympatric Speciation: "Same Country"

Allopatric Speciation

• Original population becomes geographically isolated

• Subdivided into subpopulations (e.g., river redirects and separates original population)

• Once isolated, gene flow is decreased between subpopulations

• Each subpopulation responds to local selection pressures (natural selection)

• The subpopulations diverge

• Reproductive isolation occurs

• Members of subpopulations can not interbreed, forming two separate daughter species
  *Illustration: Homoplasy: Wings (morphology), Traits: flight (behavior)

Sympatric Speciation

• Speciation occurs in geographically overlapping populations

• Subgroups diverge in a trait, such as feeding in different regions of the habitat

• Other traits also vary (e.g., coloration)

• Mating is linked to feeding/color differences

• Genetic divergence occurs

• Two separate daughter species are formed

Reproductive Barriers

• Biological barriers that prevent members of different species from producing hybrids

  • Hybrids often have reduced fitness

  • Favored by natural selection against hybrids

Two Major Types

• Pre-zygotic

• Post-zygotic

Pre-zygotic Barriers

• Habitat Isolation:

  • Species occupy different habitats

  • Decreased probability of encountering other species (e.g., Garter Snakes - Water vs. Land)

• Temporal Isolation:

  • Breed at different times of day or year

  • Decreased probability of encounter while reproductively active (e.g., Skunks -Summer vs. Winter)

• Behavioral Isolation:

  • Courtship rituals that are species-specific

  • Not recognized by other species (e.g., Blue-footed boobies)

• Mechanical Isolation:

  • Morphological differences prevent successful mating

  • Differences in Size and Shape in Snails

• Gametic Isolation:

  • Sperm and eggs are not compatible

  • Sea urchins release sperm into the water

Post-zygotic Barriers

• Reduced Hybrid Viability:

  • Hybrid forms, but alleles interact and impede development

  • Hybrids are frail and cannot compete (e.g., Salamanders)

• Reduced Hybrid Fertility:

  • Hybrid forms but is sterile (e.g., Donkey + Horse = Mule)

• Hybrid Breakdown:

  • First generation is viable and fertile, but 2nd generation is weak and sterile

  • Due to accumulation of recessive alleles (e.g., Cultivated rice)

Genetic Drift and Speciation

• Increasing divergence among populations due to the Founder effect increases speciation

• Colonization of Islands

• Genetic Drift: Mainland Vs Island

Taxonomy

• Theory and practice of classifying organisms.

• Taxon: Group of organisms treated as a unit for classification.

Classification System

• Linnaean System

• Hierarchical inclusiveness changes with levels

  • Species Name composed of two parts: Genus (1st) and Species (2nd)

    • ex: Ambystoma opacum (italicized or underlined) with first letter of genus capitalized and all other letters lower case

Classification groups

• Domain- most inclusive

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species- Least Inclusive

Phylogenetic Reconstruction

• Hypothesis of evolutionary relationships

• Cladogram: Shared derived character states'

Definitions

• Character: Wing

• Character State: Present or absent

• Character State Assigned in two ways:

  • Present: 0 (ancestral), Absent: 1 (derived) OR

  • Absent: 0 (ancestral), Present: 1 (derived)

• Outgroup: Group used for comparison

  • Possesses all ancestral character states

• Ingroup: Group whose evolutionary relationships you are trying to explain

Phylogenies

*Define

• outgroup,

• ingroup,

• characters,

• character states (ancestral: 0, derived: 1).

• Construct Character Table (Matrix)

  • Matrix of 0 values and 1 values for each character taxa

• Use Character Matrix to construct phylogeny based on shared derived character states.

Phylogeny of 3 Domains

• Bacteria (B)

• Archaea (A)

• Eukarya (E)

Choosing Among Phylogenies

• Use principle of parsimony: Assume the fewest evolutionary events occurred

• Phylogeny with the fewest evolutionary events is more likely.

Key Terms

• Sister Taxa: Group of organisms that share an immediate common ancestor

• Uniquely Derived Character State:

  • Derived character state only present in one taxa

  • Does not help resolve phylogenetic relationships

  • Phylogenetically uninformative

• Clade: Group that contains an ancestral species and all of its descendants. Can be:

  • Monophyletic group (clade): An ancestral species and all of its descendants

  • Paraphyletic group: An ancestral species and some, but not all, of its descendants

  • Polyphyletic Group: A group which includes distantly related species but not a recent common ancestor

Scientific Method

• Random sampling

• Sample

• Inference

• Population

• Optimal Sample Size:

  • Large enough to represent true value of population,

  • Not so costly (financially and in time)
    Context-dependent questions

Control Group

• Group used for comparison (e.g., predators absent vs. predators present)

• Drug Trail

Experimental set up

• Double-blind (patient and doctor don't know)

• Replicate: Independent experimental unit (EU)

• Unit used for analysis: e.g., each patient in a treatment group

• Pseudoreplicate: False replicate: Non-independent units treated as independent units

Benefits of Paired Designs

• Increased replication

• Remove additional 'noise' due to variation among individuals included in the study

• Ex: twins, morning vs. afternoon, same vs. different location

Paired vs. Unpaired Analysis

• Experiment to examine if drug X influences blood pressure levels (BPL)

• 2 treatment groups

Set up of test groups

*Experimental (drug X)
*Control (placebo)
*Variables

Scientific Method - Results: Data Collection & Analysis

• Why use statistics? To describe data and test hypotheses to reveal general patterns

Definitions

• Variable: Characteristic that can be assigned a number or a category

  • Categorical Variable: A variable that is assigned to a category (e.g., blood type, eye color)

  • Numerical Variable: A variable that is recorded as an amount (e.g., human weight, number of bacterial colonies)

Descriptive and Inferential Statistics

• Descriptive

  • Describes data (for the sample)

    • Graphs, tables

  • Central tendency:

    • Mean

    • Median

  • Dispersion:

    • Standard deviation

    • Interquartile range

Inferential tools

• Analysis of sample data. Tests: t-test (numeric),

• X² test (categorical),

• Make decision about statistical hypothesis (null for sample data)

• Interpret overall hypothesis.

• Make inferences about Population

General Approach

• Generate hypothesis

• Define Ho (null) and Ha (alternative)

• Set critical value level (α), typically at 0.05

• Collect sample data

• Calculate test statistic

• Obtain critical value and p-value (Table)

• Make decision about Ho

• Interpret original hypothesis

Definitions

• P-value: Probability that the results obtained are due to chance

• α Value (critical value): Threshold used to determine if results obtained are likely due to chance

Statistical Hypotheses

• Ho: There is no difference in DV (dependent values) between experimental and control groups

• Ha: There is a difference in DV between experimental and control groups

• Decision rule (Ho)

• Error analysis

  • Type 1 error: false positive ( rejecting the null hypothesis when it is actually true)

  • Type 2 error: false negative (failing to reject the null hypothesis when it is actually false.)

Evrov Table

Ho rejected = Type 1 error (false positive)
Ho not rejected = No error

If Ho is false

Ho rejected = NO error
Ho not rejected = Type 11 error (false negative)

Ecology

• Scientific study of the interactions between organisms and their environment

Environemental Factors

• Abiotic Factor: Non-living (e.g., soil, weather, pH, temperature, wind, salinity)

• Biotic Factor: Living (e.g., organisms of the same or different species, competition, predation, parasitism)

Levels of Organization in Ecology

• Individuals: Behavior, physiology, morphology

• Populations: (of the same species) #'s in nature, patterns in space and time

• Community: (interacting populations) Multiple species: species diversity, food webs

• Ecosystem: nutrient cycling, energy flow, human impacts

Research in Ecology

• Factors that determine the distribution and abundance of organisms (Where are we finding organisms?)

• related disciplines

• factors of the habitat and animals
  Factors to make a choice: ex Diet? mate?
  survival?
  2 two catergories:
  Intra Sexual Selection
  competition between members of the same sex
  Intersexed Selection

Mating Systems and Behavior

Mating Systems

• Male and female monogamy =for life

• examples are given

• Male and female polygamy

• Even Fights

• Uneven fights retreate
  Social manogamy
  molecular appears

Parental care

• needs of young are most important factor is evolution of parental

Cases of parental care

• If young can care for themselves

• If not
  *Octopus
  *Strawberry poison dart frog

Certainty of Paternity and the Role of Paternal Cave in Males

Conditions

Fertilization of sperm and eggs at the same time female. Fish and amphibians need eggs stirred during fertilisation.
Paternal cave in 7% of species. Paternal cave,70% of species.

Communication

*Signals by sending
*Legitimate receiver
*Illegitimate receiver

Signal types

• honest signal's

Signal's honest

• Dishonest Signal.
  *Agnastic Behavior.

Definitions

*Displays: Symbolic actor
Information of fighting potential
Hones Signal
Hones Signal Example:
Response will
Chemicals are released into the environment following
with the response on each species
Time
Distractions

Innate & Learned Behavior

• voluntary

• Stimulus trigger response
  Vesponse:
  Models vs response

Types of Learning

• Learning in the first 24

• Associations base

• Learning from Solving

• watching individual behavior
  *Examples and behaviors

Altruism

• type of behavior is and definition

types

• Reciprocal Altruism

• Kin Selection
  *act Altruism is

Reciprocal Altruism

*Requirements
*Must be present time
*must not internet
*Punishment

Altruism

*Kin Selection.
*teaching sibling by teaching

Fitness

*Components:
Selection can
Kin teaching behavior

Populations

• influence on each other

Population Dispersion

Population patterns

*categories
Patterns for social and resources
Water patterns
Penguins interact
Unpredictable and Influence paterns
Wind,water patterns

The population over time and rates in

Survivorship

Summarizing population summary
Column groups
Survival is
There are patterns to groups
III mortality rate
Each group is labeled

Survivorship Cumes

Mortality rates each of the patterns
investment in parents
throughout of
*Growth of population
*Capacity of pattern or type to have food and Shelter
resources available
Model can not have limits to resource
unrealistic pattern