Midterm 1

Topic 1:

Extinction - when no living individuals of a species remain in Earth, completely wiped out

Extirpation - when a species is no longer found in a specific geographic area but exists in other areas, regional species lost

Endangered - species facing imminent extinction

Threatened - likely to become endangered species

Threats to Populations

• Human activity reducing ecosystem diversity (coral reefs and Aral Sea ecosystem)

• Habitat loss from human destruction (deforestation, forest fires), extirpation of swift fox, black-footed ferret and greater prairie chicken

• Invasive species that have been accidentally or deliberately introduced into non native areas (brown tree snake in Guam or mussels in the Great Lakes)

• Overexploitation, overharvesting of plants and animals (overfishing Atlantic Cod and overhunting the passenger pigeon)

• Climate change, the climate is changing more rapidly than ecosystems can adjust to

Topic 2

Differentiate Scientific Theories vs Hypotheses

• Scientific theories are broad, fact-supported explanations for phenomena that are widely accepted

• Hypotheses are proposed explanations for a set of observations based on the data available and guided by inductive reasoning, need to be testable and falsifiable

Describe the steps of the scientific method

1. Making observations and collecting data, can be qualitative and quantitative

2. Use inductive reasoning to make generalizations 

3. Forming hypotheses 

4. Testing Hypotheses using deductive reasoning and controlled experiments to differentiate between correlation (relationships) and causation (one variable directly affecting another)

Differentiate between inductive reasoning and deductive reasoning

Inductive reasoning - making generalizations from repeated observations

Deductive reasoning - uses generalizations to make specific predictions for testing hypotheses

Interpret example data using the scientific method

Topic 3

1. Describe binomial nomenclature and hierarchical classification

Binomial nomenclature (Linnaeus) - two part scientific name for a species (genus and specific epithet), genus is capitalized and the whole thing is italicized

Hierarchal classification - species are put into broad categories (ranks) based on their similar structures and functions 

2. Differentiate between taxonomic ranks

(Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species)

• Higher level taxa are not directly comparable across lineages

• Classification does not give information about evolutionary relationships 

3. Classify organisms based on taxonomic ranks

3 Main Domains - Bacteria, Archea and Eukarya

3 Main Kingdoms of multicellular organisms - Plantae, Fungi and Animalia

Topic 4

Phylogeny 

• Phylogenies show hypotheses for evolutionary relationships with common ancestors

• Uses morphological (physical traits) and molecular data to make trees

• Consists of clades that are nested hierarchies grouped with an ancestor and all its descendants

Interpreting Phylogenies

• Cladograms show relationships where only branching pattern (topology) is important, only establishes an order of descent of organisms from an ancestor (human and chimps are considered sisters)

• Phylograms show relationships where branch lengths represent evolutionary change, the branching pattern shows relatedness but not evolutionary progress

• Definitions:

1. Branch Point/Node - represents a common ancestor that two lineages descended from

2. Polotomy - branches show where more than two groups emerged and typically is representative of unresolved patterns of divergence

3. Sister taxa - 2 descendants from the same node

4. Basal taxon - diverges the earliest in the group and originates near the common ancestor

5. Homologous - the similarity between organisms due to shared ancestry, shared traits because of a common ancestor

6. Analogous - the similarity of organisms because of convergent evolution, traits that evolved independently due to similar environmental conditions or selected pressures (streamlined body for swimming)

7. Cladistics - infers evolutionary relationships using homologous characteristics to group taxa based on shared derived characteristics

8. Clade - nested hierarchies grouped with an ancestor and all its descendants

9. Ingroup - taxa being studied for evolution

10. Outgroup - taxa related to the ingroup but diverged earlier and used as a reference point

11. Monophyletic - the same thing as a clad and consists of an ancestor taxon and all its descendants

12. Paraphyletic - contains a common ancestor but not all descendants

13. Polyphyletic - includes distantly related taxa but not the common ancestor of all group members

14. Synapomorphy - shared derived characteristics that evolved in the most recent common ancestor of a clade and are unique to that group 

15. Symplesiomorphy - shared ancestral characteristics that are shared by taxa of a clade and also represented in taxa of earlier clades

Homologous Traits

• Homology is the similarity between organisms due to shared ancestry, shared traits because of a common ancestor

• Example is the forelimbs of mammals that are adapted for different functions

• Homologous traits have similar anatomy, similar development and genetic similarities, evolutionary similarities

• More complex structures are more likely to be homologous

Derived vs Ancestral Traits

• Derived traits are characteristics that evolved in the most recent common ancestor of a clade and are unique to that group 

• Ancestral traits are  characteristics that are shared by taxa of a clade and also represented in taxa of earlier clades

Comparison of Phylogenic Trees

• Reading common ancestors goes down a tree not up

How to Build Phylogenetic Trees

1. Select the ingroup and outgroup taxa

2. Identify homologous traits shared among the taxa

3. Construct a tree by grouping taxa with their shared derived characteristics

• Compare the ingroup and outgroup

• Group the taxa with shared derived characteristics and select the one with the fewest evolutionary changed called maximum parsimony

4. Validate the tree with data

Topic 5

Describe the theory of evolution by natural selection

1. Observation 1 - individuals in a population vary in their inherited traits (genetic diversity)

2. Observation 2 - populations can produce more offspring than the environment can support, many of the offspring fail to survive and reproduce

3. Inference 1 - individuals with inherited traits that give them an advantage in their environment are more likely to survive and reproduce, leaving more offspring

4. Inference 2 - the unequal ability of individuals to survive and reproduce will lead to the accumulation of advantageous traits in the population over generations

5. How does this relate to the ground finch example of natural selection

Explain the principles of natural selection using biological examples

1. There is variation within a population of organisms and this variation can be inherited

2. Individuals with inherited traits are advantageous for survival and reproduction in a given environment contribute disproportionately to the next generation (natural selection), natural selection results in the adaptation of populations to their environment

Explain how selective agents influence natural selection by creating selection pressures

• Selective agents are environmental factors that affect the survival and/or reproduction of populations

• When they occur consistently they become a selection pressure 

• Consistent selection pressure causes a directional change in the population

• Selection pressures that change will change the direction of natural selection

Explain why variation in populations is essential for natural selection

• Only genotypic variation is heritable but an individual’s genotype must be expressed in their phenotype to be subject to natural selection

• Genetic variation in populations arises randomly but natural selection is not a random process 

Evolutionary Fitness

• Natural selection allows those with higher evolutionary fitness to pass on their genes to the next generation

Natural Selection Events

• Selective agents influence natural selection by creating selection pressures that can cause a directional change in the population

Natural Selection Characteristics

• Select traits that are more advantageous for survival and reproduction

Descent of Modification of Galapagos Finches

• Finch species on different islands had distinct differences with beak size variation that are adapted based on their feeding needs

Medium Ground Finch

• A drought led to insufficient food for the overproduction of offspring and caused competition for limited resources

• Only the birds with large beaks could open the large, hard seeds survived to reproduce causing differences in reproductive success of individuals

• Beak depth increased as individuals with beneficial traits could produce more offspring

Populations - individuals of the same species that live in the same area and interbreed to produce fertile offspring

Topic 6

Evidence for Evolution

1. Use examples to describe the key types of evidence supporting the theory of evolution

2. Explain how homologies, including anatomical, molecular, and embryonic similarities provide evidence for shared ancestry.

Four Types of Evidence for Evolution

1. Direct observations of evolutionary change

• Galapagos medium ground finch

• Natural selection of soapberry bug beak size

• Artificial selection

• Drug resistance in viruses and bacteria

2. Homologies are similarities that arise from a shared evolutionary ancestor 

• Morphological homologies (tetrapod forelimb bone structure in mammals)

• Homologous embryonic structures (embryos of fish, birds and humans all have gill slits and tail-like structures)

• Vestigial structures (human appendix or pelvic bones in whales)

• Molecular homologies (all living organisms share a universal genetic code)

3. Fossil records provide evidence for the extinction of species

• Transitional fossils shows the changes in groups overtime, documenting intermediate forms appearing to be ancestors of living species

• Chronological fossils order how groups of taxa appear in fossil records, the origin and diversification of new groups

4. Biogeography

• How species are distributed across the globe

• Geographic isolation and environmental factors shape species diversity

• Isolated populations undergo adaptive radiation forming endemic species that are only found in one area 

• Continental patterns of species distribution reflecting evolutionary histories (marsupials are mainly found in Australia from one immigration event)

Topic 7

Evolutionary Fitness

• Variation makes evolution possible

• Balancing selection

• Relative fitness

• Selective agents

Natural selection characteristics

• Favouring individuals with advantageous traits 

• Variation within a population

• Environmental pressures exert selective pressures favouring organisms with certain traits

• Differential reproduction

How do populations maintain genetic variation?

1. Neutral Variation - genetic variation that does not have a selective advantage or disadvantage, does not affect phenotype

2. Balancing Selection - maintains genetic diversity by favouring stable frequencies of multiple alleles in a gene pool population

1. Temporal or spatial variation

• Environmental conditions may change over time or vary in different geographic locations, different alleles can be favoured at different times in different locations

2. Heterozygote advantage

• When an organism with two different alleles of a particular gene has a fitness advantage over an organism with identical copies of either allele 

• Can result from stabilizing or directional selection

• Example is sickle cell disease

3. Frequency-dependent selection

• The fitness of an allele depends on its frequency in the population

4. Negative frequency-dependent selection

• The fitness of an allele declines if it becomes too abundant in the population

• Selection favours rarer alleles 

Natural selection outcomes

1. Directional Selection

• Favours individuals that differ from the mean phenotype in one direction

• Variance stays the same but the mean will shift

• Beak depth in the medium ground finch population during the drought

2. Disruptive Selection

• Favours individuals at extremes of the phenotypic range

• Maintains variation

• Beak size in black bellied seedcracker

3. Stabilizing Selection

• Favours intermediate or common phenotypes, selecting against extremes

• Common to remove deleterious mutations and maintains genetic fitness

• Human birth weight

Modes of evolutionary change 

• Mutation

• Genetic drift

• Gene flow

• Non-random mating

• Natural selection

Properties of populations 

• Localized group of individuals of a single species that share alleles and produce fertile offspring

• Individuals of a population represent different combinations of alleles drawn from the gene pool

Modes of selection

1. Directional selection

2. Stabilizing selection

3. Disruptive selection

Threats to populations 

• Extirpation

• Global extinction

Allele frequencies in populations

1. Natural Selection - adaptive

• Directional, disruptive or stabilizing

2. Genetic Drift - non-adaptive

• Random changes in allele frequencies in a population that causes evolutionary change

• Has the largest effect on small populations as harmful alleles can become fixed

• Leads to a loss of genetic variation within populations, especially for rare alleles

• Bottleneck Effect - sudden reduction in population due to an environmental change and the allele frequency changes in the next generation, greater prairie chicken populations followed a bottleneck effect

• Founder Effect - a few individuals from a larger population become isolated, the small sample is not representative of the population and is genetically diverse while the original population is not affected  

3. Gene flow - non-adaptive

• Movement of alleles throughout populations 

• Can increase or reduce variation 

• Can increase genetic variation in the receiving population 

• Decreases variation population as the population becomes more homogenous

• Can decrease or increase the fitness of receiving populations 

Genetic variation in populations

• Heterozygote advantage

• Disruptive selection

• Gene flow

• Balancing selection

1. Mutations 

• Occur randomly and create new alleles

• Can be deleterious, neutral or advantageous

• Neutral mutations can become harmful for advantageous in the future depending on environmental changes

• Chromosomal mutations are often harmful

• Whole genome duplication us an important driver for evolution by supplying genetic material and increasing genetic complexity

2. Sexual Reproduction

• Allows for recombination that shuffles alleles during meiosis, independent assortment of homologous chromosomes and random mating/fertilization

• Recombination is important for short term diversity

Definitions

1. Alleles - different forms of a gene

2. Gene pool - all alleles possible in a population

3. Adaptation - trait selected through natural selection that provides an advantage to an individual possessing it

4. Relative fitness - measure of reproductive sucess

5. Directional selection - Favours individuals that differ from the mean phenotype in one direction

6. Disruptive selection - Favours individuals at extremes of the phenotypic range

7. Stabilizing selection - Favours intermediate or common phenotypes, selecting against extremes

8. Genetic drift - Random changes in allele frequencies in a population that causes evolutionary change

9. Bottleneck Effect - sudden reduction in population due to an environmental change and the allele frequency changes in the next generation

10. Founder effect - a few individuals from a larger population become isolated, the small sample is not representative of the population and is genetically diverse while the original population is not affected 

11. Gene flow - Movement of alleles throughout populations 

12. Balancing selection - maintains genetic diversity by favouring stable frequencies of multiple alleles in a gene pool population

13. Heterozygote advantage - When an organism with two different alleles of a particular gene has a fitness advantage over an organism with identical copies of either allele 

14. Frequency-dependent selection - The fitness of an allele depends on its frequency in the population

15. Microevolution - change in allele frequencies in populations over generations

Topic 8

Biological species concept 

• A species consists of a group of fully or potentially interbreeding individuals that are reproductively isolated and exchange genes

• Not applicable to fossils or asexual reproduction

• Does not account for gene flow between species

1. Prezygotic Reproductive Barriers Prevent Fertilization

• Habitat isolation 

• Temporal isolation (species breed at different times of the year/day like skunks)

• Behavioural isolation (blue-footed boobies)

• Mechanical isolation (snails)

• Gametic isolation (sea urchins)

2. Postzygotic Reproductive Barriers

• Reduced hybrid viability

• Reduced hybrid fertility

• Hybrid breakdown over generations

Hybrids 

• Interbreeding between two related species and can lead to polyploid species, the doubling of the number of chromosome sets compared to the parent species

• Often have reduced fertility or survival

• Occurs when species with incomplete reproductive barriers interbreed

• Stability continues the formation of hybrid species, fusion weakens reproductive barriers

Allopatric vs sympatric speciation 

1. Allopatric Speciation

• Gene flow is interrupted when a population is divided into geographically isolated subpopulations

• Separated populations may evolve independently through mutation, natural selection and genetic drift

• Seen in snapping shrimp

• Caused by

1. Dispersal - a small population is isolated at the edge of a larger population 

2. Vicariance - range of a species is split by a change in the environment creating two subpopulations

2. Sympatric Speciation

• A reproductive barrier isolates a subset of a population without geographic separation from parent species

• Occurs when gene flow is reduced by polyploidy and hybridization, habitat differentiation (maggot flies) and sexual selection (non-random mating)

Mechanisms of speciation 

• Allopatric or sympatric speciation