1. Lecture #1
Chapter 22~ Descent with Modification: A Darwinian View of Life

2. Evolution
Evolution: the change over time of the genetic composition of populations
Natural selection: populations of organisms can change over the generations if individuals having certain heritable traits leave more offspring than others (differential reproductive success)
Evolutionary adaptations: a prevalence of inherited characteristics that enhance organisms’ survival and reproduction
November 24, 1859

3. Evolutionary history Georges Cuvier (1769-1832)
Paleontology: The study of fossils
Charles Lyell ( )
Uniformitarianism: Geological processes have not changed throughout history
Charles Darwin ( )
Evolution: Organisms adapt to their environment and these changes are inherited by offspring
Gregor Mendel ( )
Inheritance: Genetic inheritance through pea plants
Alfred Wallace ( )
Evolution: Natural Selection is how evolution occurs.
Carolus Linnaeus ( )
Taxonomy: the naming and classification of organisms
James Hutton ( )
Gradualism: Geological changes occur slowly over a long period of time
Jean Baptist Lamarck ( )
Evolution: Organisms have specific adaptations
Thomas Malthus ( )
Populations: Economic paper on the population growth in England

4. Evolution Time Line

5. Descent with Modification
5 observations:
1- Exponential fertility
2- Stable population size
3- Limited resources
4- Individuals vary
5- Heritable variation

6. Observations
Exponential fertility:
Organisms have the ability to produce such a large number of offspring they would increase exponentially if all organisms in the population reproduced.
Stable Population Size:
The population of a organism is stable. It is neither increasing or decreasing with the exception of seasonal changes.
Limited Resources: There are not enough environmental resources for all, the organisms must compete for available resources.
Individual Variation: Individuals have different traits and phenotypes.
Heritable Variation: The phenotypic traits and variation is inherited by offspring.

7. Descent with Modification
3 Inferences:
1- Struggle for existence
2- Non-random survival
3- Natural selection (differential success in reproduction)

8. Inferences Struggle for existence: Non-random mating:
Organisms fight to survive through competition for resources (ex: food, shelter, predators, etc.)
Non-random mating:
Those that are the most fit are the most likely to mate
Natural selection:
Predators, nature, etc. select those that are better suited to the environment leading to a gradual change toward favorable characteristics .

9. Achieving Descent with Modification
Artificial Selection: an external force selects which mating events occur
Occurs in domesticated plants and animals
How Mendel discovered genetics
How animals produce greater amounts of milk, etc.
Natural Selection: random mating events
The effects of predator/prey relationships
Mates chosen upon organisms will

10. Artificial Selection Animals: Plants:
Humans have used artificial selection to create specific types of animal food products
Plants:
Humans have used artificial selection to produce more resilient plants
Plants produced through artificial selection include hybrid plants

11. Natural Selection Predator/Prey relationships: Environmental factors:
Predators determine which organisms are the most fit
Organisms that are the most able to avoid predators, find food, shelter, etc. survive to reproduce
Environmental factors:
Availability of food and shelter, as well as weather determines which organisms survive to preproduce

12. Evolution evidence: Biogeography
Geographical distribution of species
Physical barriers such as lakes, rivers, mountains, oceans, etc.
Examples:
Islands vs. Mainland Australia Continents

13. Evolution evidence: The Fossil Record
Succession of forms over time
Transitional links
Vertebrate descent

14. Evolution evidence: Comparative Anatomy
Homologous structures (homology)
Descent from a common ancestor
Vestigial organs Ex: whale/snake hindlimbs; wings on flightless birds

15. Evolution evidence: Comparative Embryology
Pharyngeal pouches, ‘tails’ as embryos

16. Comparative Embryology
Evolutionary evidence:
Embryology : the study of embryonic development; comparison of the development of fetal development
Scientists compare the development of various organisms to determine how similar the organisms are
Similarity in embryonic development suggests evolutionary links

17. Evolution evidence: Molecular Biology
Similarities in DNA, proteins, genes, and gene products
Common genetic code

18. Final words…...
“Absence of evidence is not evidence of absence.”

19. Lecture #2
Chapter 23~ The Evolution of Populations

20. Population genetics
Population: a localized group of individuals belonging to the same species
Species: a group of populations whose individuals have the potential to interbreed and produce fertile offspring
Gene pool: the total aggregate of genes in a population at any one time
Population genetics: the study of genetic changes in populations

21. Modern synthesis/neo-Darwinism:
formed in the 1940’s it states that the population is the unit of evolution and natural selection has significant role as the most important mechanism
“Individuals are selected, but populations evolve.”
The selection of individuals in a population allows certain traits to be passed from one generation to the next and the overall population changes

22. Hardy-Weinberg Theorem
Serves as a model for the genetic structure of a nonevolving population (equilibrium)
5 conditions:
1- Very large population size
2- No migration
3- No net mutations
4- Random mating
5- No natural selection

23. Hardy-Weinberg Theorem
Very large population size
In small populations, genetic drift can can alter allele frequencies
No migration
There must be no transfer of alleles between two populations
No net mutations
A mutation alters the gene pool
Random mating
The selection of mates for particular characteristics does not allow for the necessary random mating
No natural selection
Differential survival and selection favor the transmission of some alleles but not others

24. Hardy-Weinberg Equation
p=frequency of one allele (A)
q=frequency of the other allele (a);
p+q= (p=1-q & q=1-p)
P2=frequency of AA genotype
2pq=frequency of Aa plus aA genotype
q2=frequency of aa genotype;
p 2 + 2pq + q 2 = 1.0

25. Microevolution, I
A change in the gene pool of a population over a succession of generations
Genetic drift: changes in the gene pool of a small population due to chance (usually reduces genetic variability)

26. Microevolution, II
The Bottleneck Effect: type of genetic drift resulting from a reduction in population such that the surviving population is no longer genetically representative of the original population
Usually a result of natural disaster

27. Microevolution, III
Founder Effect: a cause of genetic drift attributable to colonization by a limited number of individuals from a parent population
Seen on the various Galapagos Islands

28. Microevolution, IV
Gene Flow: genetic exchange due to the migration of fertile individuals or gametes between populations
reduces differences between populations

29. Microevolution, V
Mutations: a change in an organism’s DNA (gametes; many generations); original source of genetic variation
raw material for natural selection

30. Microevolution, VI Nonrandom mating: inbreeding and assortive mating
both shift frequencies of different genotypes
Selection for specific characteristics

31. Microevolution, VII
Natural Selection: differential success in reproduction; only form of microevolution that adapts a population to its environment

32. Population variation
Polymorphism: coexistence of 2 or more distinct forms of individuals (morphs) within the same population
Geographical variation: differences in genetic structure between populations (cline)

33. Variation preservation
Prevention of natural selection’s reduction of variation
Diploidy nd set of chromosomes hides variation in the heterozygote
Balanced polymorphism
1- heterozygote advantage: hybrid vigor i.e., malaria/sickle-cell anemia
2- frequency dependent selection: survival & reproduction of any 1 morph declines if it becomes too common i.e., parasite/host

34. Natural selection
Fitness: contribution an individual makes to the gene pool of the next generation
3 types:
A. Directional
B. Diversifying
C. Stabilizing

35. Natural selection Directional Selection Diversifying Selection
Shifts the overall makeup of the population to favor one extreme or the other
Ex: Dark snails are selected over light or medium snails
Diversifying Selection
Selection favors both extreme over the intermediate individuals.
Ex: Light and Dark snails are selected over the medium
Stabilizing Selection
The intermediate phenotype is selected over either of the extremes
Ex: The medium snail is selected over the light or the dark snail

36. Sexual selection
Sexual dimorphism: secondary sex characteristic distinction
Ex: Physical size or plumage
Sexual selection: selection towards secondary sex characteristics that leads to sexual reproduction
Ex: The use of feathers to attract a mate

37. “Perfect” Organisms Organisms are locked into historical constraints.
Adaptations are often compromises.
Not all evolution is adaptive.
Selection can only edit variation that exists.
- Evolution cannot create perfect organisms

38. Lecture #3
Chapter 24 ~ The Origin of Species

39. Macroevolution: the origin of new taxonomic groups
Speciation: the origin of new species
1- Anagenesis (phyletic evolution): accumulation of heritable changes
2- Cladogenesis (branching evolution): budding of new species from a parent species that continues to exist (basis of biological diversity)

40. What is a species?
Biological species concept (Mayr): a population or group of populations whose members have the potential to interbreed and produce viable, fertile offspring (genetic exchange is possible and that is genetically isolated from other populations)

41. Reproductive Isolation (isolation of gene pools), I
Prezygotic barriers: impede mating between species or hinder the fertilization of the ova
Habitat (snakes; water/terrestrial)
Behavioral (fireflies; mate signaling)
Temporal (salmon; seasonal mating)
Mechanical (flowers; pollination anatomy)
Gametic (frogs; egg coat receptors)

42. Reproductive Isolation, II
Postzygotic barriers: fertilization occurs, but the hybrid zygote does not develop into a viable, fertile adult
Reduced hybrid viability (frogs; zygotes fail to develop or reach sexual maturity)
Reduced hybrid fertility (mule; horse x donkey; cannot backbreed)
Hybrid breakdown (cotton; 2nd generation hybrids are sterile)

43. Modes of speciation (based on how gene flow is interrupted)
Allopatric: populations segregated by a geographical barrier; can result in adaptive radiation (island species)
Sympatric: reproductively isolated subpopulation in the midst of its parent population (change in genome); polyploidy in plants; cichlid fishes

44. Adaptive Radiation
Adaptation from a common ancestor when placed into varied ecological systems.
Caused by migration
New ecological niches

45. Examples of Adaptive Radiation
Hawaii – Hawaiian archipelago illustrates diversity and adaptation
Kauai: oldest and most humid island
Maui: some vegetation grows even on dry side
Hawaii: active volcano, very dry, very wet side of island
Most organisms are found only on the archipelago

46. Punctuated equilibria
Tempo of speciation: gradual vs. divergence in rapid bursts; Niles Eldredge and Stephen Jay Gould (1972); helped explain the non-gradual appearance of species in the fossil record

47. Punctuated equilibria
Species change most as they arise from ancestral species
Relatively little change occurs after
Eldredge & Gould’s model contrasts with the model of gradualism

48. Growth & Development
Heterochrony: change in the rate or timing of developmental events
Can change physical features as well as timing of reproductive development
Allometric Growth: Proportioning that helps give a body its specific form
Small changes in these rates changes the adult form substantially

49. Evolution Continued Evolution is not goal oriented
Bushes do not grow toward only one point, organisms do not evolve along a single lineage.
Speciation creates several branches, many which become extinct
The species that survives the longest and produces the most offspring determines the direction of major evolutionary trends “Species Selection”

50. Lecture #4
Chapter 25 ~ Phylogeny & Systematics

51. Phylogeny: the evolutionary history of a species
Systematics: the study of biological diversity in an evolutionary context
The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock
Paleontologists

52. The fossil record
Sedimentary rock: rock formed from sand and mud that once settled on the bottom of seas, lakes, and marshes
Dating:
1- Relative ~ geologic time scale; sequence of species
2- Absolute ~ radiometric dating; age using half-lives of radioactive isotopes

53. Homology vs. Analogy
Homology – similar characteristics due to common ancestry
Hawaiian silversword plants
Analogy – similar characteristics due to environmental pressures and natural selection
Australian and North American burrowing moles

55. Biogeography: the study of the past and present distribution of species
Pangaea-250 mya √ Permian extinction
Geographic isolation-180 mya √ African/South American reptile fossil similarities √ Australian marsupials

56. Mass extinction
Permian (250 million years ago): 90% of marine animals; Pangea merge
Cretaceous (65 million years ago): death of dinosaurs, 50% of marine species; low angle comet

57. Phylogenetics
The tracing of evolutionary relationships (phylogenetic tree)
Linnaeus
Binomial
Genus, specific epithet
Homo sapiens
Taxon (taxa)

58. Phylogenetic Trees
Cladistic Analysis: taxonomic approach that classifies organisms according to the order in time at which branches arise along a phylogenetic tree (cladogram)
Clade: each evolutionary branch in a cladogram
Types:
1- Monophyletic single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram

59. Phylogenetic Trees
2- Polyphyletic members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion
3- Paraphyletic lacks the common ancestor that would unite the species; does not meet cladistic criterion

60. Constructing a Cladogram
Sorting homology vs. analogy...
Homology: likenesses attributed to common ancestry
Analogy: likenesses attributed to similar ecological roles and natural selection
Convergent evolution: species from different evolutionary branches that resemble one another due to similar ecological roles

61. A Cladogram

62. Phylogram
Branch length – represents the number of changes that have taken place (DNA Sequence)
The greater the length the greater the change in the DNA

64. Ultrametric Trees
All organisms from a common ancestor have survived for the same number of years
Equal chronological amounts of time are represented by equal lengths on the tree

66. Phylogeny as Hypothesis
Phylogenic Trees give rise to evolutionary hypotheses
Using maximum parsimony and maximum likelihood, scientists develop evolutionary hypotheses
Occam’s razor
Assumptions
Molecular comparison

67. Genomes
Orthologous genes – homologous genes in different gene pools due to speciation
Paralogous genes – gene duplication creating multiple copies in the same genome

68. Genome Evolution Orthologous genes are widespread
50% of genes are traceably orthologous between humans and yeast
Paralogous genes do not appear at the same rate as phenotypic complexity
Humans have 5x as many genes as yeast despite complexity differences

69. Universal Tree of life
1960’s – DNA is universal in all organisms, therefore, all organisms must have a common ancestor
DNA identifies branching patterns
Region must be sequenced
Must have evolved slowly