Exam 3 ( 12,18,19 )

Who was Gregor Mendel and what was his contribution to science?

Johann Gregor Mendel (1822–1884) was a lifelong learner, teacher, scientist, and man of faith. ( Austrian Monk/Teacher )

•  Developed true-breeding strains of peas 

• Performed specific crosses between plants

• Followed crosses through several generations

• Followed crosses through several generations

• Disregarded traits that didn’t show simple patterns

• Later tried second round of experiments with Red Runner Beans 

How did Mendel’s approach differ from previous approaches?

Disregarded traits that didn’t show simple patterns

What did Mendel not understand about genetics?

No knowledge of :

• Genes or genetics 

• Chromosomes

• Meiosis

• Evolution

What study organism did Mendel do most of his research with?

Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance.

What is a true‐breeding strain? 

highly inbred, or “true-breeding,” .These are plants ( A generation) that always produce offspring that look like the parent.

What is the P, F1, F2 generation (etc.)?

Plants used in first-generation crosses were called P0, or parental generation one

called the F1, or the first filial (filial = offspring, daughter or son) generation.

F2, or second filial, generation.

What does it mean that alleles remain discrete in a heterozygote?

No blending or contamination 

The presence of an allele doesn't guarantee that the trait will be expressed 

( Some alleles may be dominant over others ) 

How does dominance work in simple dominant/recessive alleles?

1. One allele masks the other allele 

2. Generally due to one allele not producing a functional product 

( Gene that doesn’t work ) 

What causes an allele to be recessive? 

• incomplete dominance

  -heterozygote is intermediate 

  e.g. red/white/pink flower

• codominance

  - both alleles produce their product 

  - heterozygote shows both traits 

  e.g. AB blood types

What is the term: Locus?

Region of the chromosome containing a particular gene 

What is the term: Allele?

Gene variations that arise by mutation and exist at the same relative locations on homologous chromosomes

What is the term: Homozygous?

having two identical alleles for a given gene on the homologous chromosome

What is the term: Heterozygous?

having two different alleles for a given gene on the homologous chromosome

What is the term: Genotype?

 Genetic makeup of the individual at a locus 

• Which alleles the individual processes 

What is the term: Phenotype?

“ Appearance” of the individual for the trait 

• Which alleles are expressed 

What is incomplete dominance?

• Heterozygote is intermediate 

“ in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype “

What is codominance?

• Both alleles produce their product 

• Heterozygote shows both traits 

“ in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic “

( i.e. AB Blood type ) 

Be able to use a Punnett square to calculate the outcomes of a cross.

alleles are abbreviated by letters 

• usually first letter of trait 

• capital letters for dominant traits, small letters for recessive

 Be able to use the rules of simple probability to calculate the outcome of an event.

Rules used to predict likelihood of events 

- expressed as fraction or decimal 

- ranges from 0 to 1 - 0 means no chance

- 1 means certain to occur 

e.g. ¾ or 0.75 - an event should happen 3 times out of 4

What is a monohybrid cross?

result of a cross between two true-breeding parents that express different traits for only one characteristic

What is a dihybrid cross? 

 result of a cross between two true-breeding parents that express different traits for two characteristics

Be familiar with common genotype/phenotype ratios and their implications for inheritance. 

What are Mendel’s laws and how do they apply to studying genetics?

Law of Segregation ( Mendel’s 1st Law ) 

1. When producing gametes, alleles segregate 

I.e. only 1 allele for a locus goes to each gamete

2. Recessive alleles which are hidden by dominant alleles can still be passed on to the next generation 

Law of Independent Assortment ( Mendel’s 2nd Law)

1. Alleles at different loci segregate independently 

• The result is a random mixture of alleles in gametes 

2. The behavior of alleles at one locus should not affect the behavior of alleles at other loci 

• Comes into play when you're working with another locus.

How is sex/gender determined in mammals? 

Chromosomal sex determination 

XY system 

• Female has two X chromosomes 

• Genotype = XX 

• The homogametic sex

• Male has one x and one Y chromosome 

• Genotype = XY

• The heterogametic sex

What other sex determination systems did we discuss?

1. Temperature-dependent determination 

   Gender is determined by the incubation temperature of the egg ( Some reptiles) 

2. Hermaphroditism 

   All individuals have both sex organs 

What is sex‐linked inheritance?

characteristics (or traits) that are influenced by genes carried on the sex chromosomes.

• There are two types of sex linked inheritance x linked and y linked

What is sex‐influenced inheritance?

the traits which are controlled by genes present on autosomes but whose expression is influenced by the sex of individual 

 What is dosage compensation?

 female gets two X chromosomes

•  double the number of X genes 

2. during development, one X is turned off

• random (in placental mammals) 

• inactive X becomes Barr Body

• attached to the nuclear membrane

3. variegation 

• if a female is heterozygous at an X locus

•  different alleles may be shut off in different cells

What is variegation of X‐linked genes?

If female is heterozygous at an X locus 

• different alleles may be shut off in different cells

What is linkage?

phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited together

How do linked loci violate Mendel’s 2nd Law?

linked alleles are not independent

•  tend to be inherited together

• can be separated by crossing over

What is epistasis? 

“one gene interferes with expression of another”

antagonistic interaction between genes such that one gene masks or interferes with the expression of another

What other complicating factors make understanding inheritance more complex?

Linkage

• linked alleles are not independent ( tend to be inherited together, can be separated by crossing over )

polygenic traits

• many traits are controlled by multiple genes, Quantitative traits ( E.g. phenotype is the result of additive effect of alleles )

Epistasis

• One gene interferes with expression of another

epigenetic effects

• Changes in gene expression not related to changes in DNA sequence, environment can affect expression

Pleiotropy

• one locus has multiple phenotypic effects

How is evolution a unifying principle for biology? 

“It is the framework within which biologists ask questions about the living world.”

1. A scientific explanation of biological processes 

2. Groundwork on which to base scientific hypotheses 

3.  Fundamental force governing species over time.

What were the main bases for the explanation of biological diversity prior to the 19th century? 

Diversity was static 

A. Various hypotheses regarding origins, often supernatural 

B. Changes were the result of catastrophism ( There was a flood, there was a huge hurricane ) 

• Remaining species spread/reproduced to fill gaps

• Fossils were the results of these events (  or geological curiosities

C. No good scientific explanation for the mechanisms of change  

• Most revolved around a supernatural guiding hand or plan

D. Middle ages

1. Theocratic rule 

1. Biblical explanation becomes a tenet of faith 

2. Independent thought discouraged 

• Even considered heretical

2. Young earth theories dominate 

1. Archbishop Ussher ( 1600s )

E. 18th  and 19th centuries 

1. Enlightenment and industrial revolution 

2. Increased freedom for academic thought 

3. Natural philosophers started to examine the world scientifically 

1. Changes are governed 

2. Questioning the status quo 

• Leads to discoveries and revolutions

4. Begin to propose an old and changing earth 

5. Progressivism 

What is meant the idea that the diversity was static?

No good scientific explanation for the mechanisms of change 

• Most revolved around a supernatural guiding hand or plan 

What was Archbishop Ussher’s contribution to the understanding of the age of the earth? 

Archbishop Ussher ( 1600s ) 

• Well-educated, respected religious figure 

• Studied biblical accounts and compared them with other writings from other available cultures 

• Made meticulous calculations of the earth’s age based on these rights 

• Calculated earth was created in 4004 BC. 

What was the contribution of Jean Baptiste de Lamarck to our understanding of biological diversity? 

1. First truly scientific explanation for the mechanism of evolution (1809) 

2. Fossils were evidence of extinction 

3. Inheritance of acquired characteristics drove evolutionary change 

4. Evolution was progressive 

 According to Lamarck, what was the mechanism of evolutionary change? 

Evolution was progressive, creatures were evolving in a particular direction

What was meant by the term progressive evolution?

Evolutionary progress is gradual directional change embodying improvement.

I.e The human condition should improve via evolution.

What were the contributions of the following individuals to Darwin’s formulation of his theory of evolution by modification through descent? Thomas Malthus

Essays on the principles of population ( 1838 ) 

• Sociological examination of humans in modern industrial England 

• Humans have the capacity to produce more children than they can support 

• Some factors must lead to the inevitable death of some children 

What were the contributions of the following individuals to Darwin’s formulation of his theory of evolution by modification through descent? Alfred Russell Wallace

Came up with the idea of modification through descent independently of Darwin 

• Wrote to darwin to have Darwin review his manuscript on the theory 

• Darwin and Wallace essays were presented together to meeting a royal academy of science in london 

What is uniformitarianism (in respect to geological processes)? 

The principle that states that geologic processes that occur today are similar to those that have occurred in the past. Theory. the earth works almost exactly the same today as it did in the past.

What are the 5 basic steps in Darwin’s theory of Natural Selection?

1. There is variation in species 

2. Species produce more offspring than can survive 

3. Individuals who survive must survive because of the advantage 

4. Only the survivors pass on their characteristics to the next generation 

5. Over many generations, those variations become more common, and the species changes 

When did Darwin publish his manuscript and what was it called? 

Darwin finishes “The Origin of Species” and published in 1859

Why was Darwin’s theory not widely accepted during the latter part of the 19th century? 

1. Non-progressive evolution 

• Changes affected by random factors 

2. Contradicted thousands of years of religious doctrine 

• No need for “The hand of God”

3. Eliminates the anthropocentric universe 

4. Small variations would be swamped by “average” individuals 

What scientific discoveries lead to widespread acceptance of Darwin’s ideas? 

1. Multiplication Of Species 

2. Biogeography 

3. Evolution Observed 

4. Resistance in organisms responding to human chemical treatments 

5. Genetics

6. Modern molecular Biology 

What is the raw material upon which evolution works? 

Natural selection works on variation

• No Variation = no raw materials 

 Why must the variation discussed by Charles Darwin be heritable?

• Maintained by mutation and genetic recombination 

• Variation  must affect phenotype to affect the survival of the individual 

What is evolutionary fitness?

• Fitness = ability to survive and successfully reproduce 

Success is determined by the fitness of individual 

What is adaptation?

• A characteristic that has been changed to fit the environment by the process of natural selection 

• The process of becoming better suited to your environment

How does divergence support Darwin’s model?

• Species that used to be similar can become very dissimilar due to the build-up of differences over time.

EX : Lizards from across west of America to Mexico

What is convergence?

• Species that evolve under similar selective pressures develop similar adaptations even if they are not closely related. 

EX : Shark and Dolphins

How has the fossil record supported Darwin’s model?

Fossils are evidence of change over time

• Fossils should show intermediate characteristics

Why are fossils rare? ( Remember Cartoon !)

Most species leave no fossils 

• Hard tissues ( Vertebrate skeletons and invertebrates with shells )

• Soft-bodied animals leave fossils only in exceptional conditions 

Most individuals leave no fossils 

Fossils need a place where it's not broken down by fungi or bacteria.

• The fossil record will always be incomplete and require interpretation 

What is meant by the principle of common descent?

1. All plants and animals descended from a common ancestor

2. We can trace backward forming a phylogeny 

3. All forms of life connect to this tree somewhere 

4.  Phylogenetic research attempts to reconstruct this history of life 

What are homologous structures?

The same structure is seen in different organisms but may have different functions 

e.g. Vertebrate limbs 

What are analogous structures?

Different structures that have acquired the same function

How has antibiotic resistance in microorganisms supported Darwin’s model?

Resistance in organisms responding to human chemical treatments

“Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic. They simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time.”

How has the advent of modern molecular biology supported Darwin’s model?

Modern molecular Biology 

• Can see homology in the molecular structure of organisms

• Protein structure and DNA structure/sequences 

Why did Darwin not understand the genetic basis for the inheritance of the traits he was discussing?

1. Phyletic Gradualism

2. Punctuated equilibrium 
   

What is wrong with the criticism “Evolution is just a theory”?

• Argument based on a misunderstanding of the process of science 

• The implication is that there isn't sufficient evidence 

  •  A gross mischaracterization of the truth 

  •  there is an extraordinary amount of evidence supporting evolution and none supporting alternate theories.

• Evolution is an explanation for the diversity of life we see today and the changes that have occurred in the past 

• There is no “Evolutionary” explanation for the origins of life because that isn't the question it answers

What is teleology?

• The assignment of design or purpose to natural events 

• The implication that these natural processes have “Goals”

• Evolution is a random series of changes driven by natural selection, it isn't working “Toward” anything 

• Species aren’t “Improving” over time.

What is taxonomy?

“The Science of Naming Organisms”

What was the contribution of Carolus Linneaus?

• Danish Systematist ( We should come up with a set of names, like Latin or Greek and name that species ) 

  • Each Species gets a double name  (Ex : last name, who we belong to)

What are the correct names for the two parts of a scientific name? 

• Genus + Specific epithet 

Ex: Canis familaris , Canis latrans , Canis lupus 

ALWAYS CAPTILIZE GENUS ( Never Epithet)

What are the hierarchical categories used to classify organisms?

“ Dear King Philip Came Over For Good Soup “

• KINGDOM                                EX: Animalia 

• Includes all animals ( 800,000 species - mostly beetles )

• PHYLUM ( DIVISION)            EX: Chordata

• Includes all vertebrates, protochordate ( 60,000 species )

• CLASS                                       EX:

• Includes all mammals (5800 species ~ mostly bats and rats)

  
  

• ORDER                                      EX: Carnivora

• Includes dogs, cats, seals, weasels, etc (270 species)

• FAMILY                                     EX: Canidae 

• Includes all genera of dogs, foxes, etc (35 species)

• GENUS                                      EX:   Canis 

•  Includes related dogs, like coyote, and wolf (6 species)

• 
  

• SPECIES ( Specific epithet)       EX:  Canis lupus

Why is the species the only taxonomic category with any biological meaning?

A species is a group of populations that can breed

What are prezygotic reproductive isolating mechanisms?

- Prevent species from actually mating 

• Temporal Isolation 

  • Different breeding seasons or time of day

• Mechanical Isolation

  • Incompatible anatomical structures

• Gametic isolation 

  • Gametes incompatible

• Behavioral Isolation

What are postzygotic reproductive isolating mechanisms?

Post-zygotic barriers ( EX: whooping crane, Zebra, and Horses mix )

• Hybrid inviability 

  • Physiological

  • Behavioral 

  - Parent species won’t mate with hybrid

• Hybrid sterility (EX: Mule)

 How does the biological species concept define species?

Group of populations that are reproductively isolated from other populations

What are the strengths and weaknesses of the BSC?

Strengths: Fits most people’s “model” , seems easy to define 

Problems: How isolated? , What about isolation through time ( Fossil species ) ? what about asexual species? 

What is phyletic gradualism?

• Species evolve at a constant rate 

• Species have been continually evolving 

• This was Darwin’s Belief 

• Not supported by the fossil record

What is punctuated equilibrium? How does this happen?

1. Rates of species are not constant 

2. Species evolve rapidly after major environmental changes 

   • Often after extinction events 

   • The rate of speciation slows during intervening times

What is the modern synthesis?

The combined understanding of inheritance, genetics, and natural selection

What is microevolution?

1. Changes within the genetic structure of a population 

2. Usually only impacts that population or species 

3. Changes can occur rapidly from one generation to the next 

What is macroevolution?

1. Large scale environmental ( Geologic ) changes

2. Change many species within the affected area

3. Can result in major changes of higher-level taxa

Why would it be reasonable to expect that natural selection would reduce variation in species?

1. Promotes traits and behaviors that increase the change of successful reproduction 

2. Selects against traits that are maladaptive or less adaptive 

3. Does not create the variation we observe in populations 

   • Selection should reduce variation 

   • But populations maintain variation despite selection

Why must variations be heritable to be acted upon by natural selection?

• Sources of phenotypic variation 

  • The environmental derived variations 

  • Generally not heritable 

• Environmentally triggered variations

  • Heritable traits that are influenced by environment

How do the following contribute to the variation we observe in natural populations? Mutation

• Changes in genetic structure

  • Changes in nucleotide sequence 

  • Errors in DNA duplication,

  • Damage to DNA by environmental factors 

  • Random events 

How do the following contribute to the variation we observe in natural populations? Mating Systems and Behavior

• endogenous mechanisms

• exogenous mechanisms

How do the following contribute to the variation we observe in natural populations? Segregation during meiosis

• independent assortment of alleles during meiosis

How do the following contribute to the variation we observe in natural populations? Sexual Reproduction

inbreeding avoidance 

- temporal and spatial isolation of related gametes

What is the gene pool?

combination of all alleles at all loci within a population

What are the mechanisms we can use to measure variation?

1. Phenotype distribution/frequency 

2. Allele distribution/frequency

3. Gene flow

How do we calculate phenotype frequencies?

counting the number of times a particular phenotype appears in a population and dividing it by the total number of individuals in the population.

• Can hide variation represented by dominant or codominant traits

How do we calculate allele frequencies?

dividing the number of times the allele of interest is observed in a population by the total number of copies of all the alleles at that particular genetic locus in the population

• A more accurate measure of genetic variation in a population

• More discrete values than measuring phenotype variation. 

Why is the advantage of measure allele frequencies over measuring phenotype frequencies?

• A more accurate measure of genetic variation in a population

• More discrete values than measuring phenotype variation.

How does evolution by natural selection change allele frequencies in a population?

• Can be used as a measure of evolution rates 

• The distribution of alleles changed in separate locations 

changes in phenotype actually reflect changes in allele frequency ∴ evolution acts by changing allele frequencies in populations

What is the difference between clinal and abrupt distribution of variation?

Clinal

• Change occurs gradually across a cline 

• Indicates gene flow across the contact zone between the populations 

Abrupt 

• Indication of limited gene flow between populations 

  • may indicate the populations represent different species

• Biologists may search for the barrier to gene flow

How does measuring the distribution of variation help us understand gene flow between populations?

showed that a stable population that is not undergoing evolution should have a genotype distribution.

What types of barriers to gene flow exist in wild populations?

Mutation

Nonrandom Mating

Environmental Variation

What is directional selection? How does it alter allele frequencies?

Selection for one of the extremes 

- Increases frequency of favorable alleles by decreasing unfavorable allele frequencies 

- Selection works against less favorable traits, not for favorable traits 

What is stabilizing selection? How does it alter allele frequencies?

Keeps allele frequencies the same by selecting against extremes 

• May be due to heterozygote advantage 

• Birth weights

What is disruptive selection? How does it alter allele frequencies?

(Diversifying) Selection

• selection against the intermediate 

• for the extremes 

e.g. - Peppered Moths