1. BIO440: Population Genetics and Evolution

2. I. What is Evolution?

3. I. What is Evolution?
A. Definitions
"descent with modification"

4. I. What is Evolution? A. Definitions
1. Darwin - "descent with modification"
2. Ridley - "change in a lineage of populations between generations"
3. Futuyma - "a change in the properties of populations of organisms, or groups of such populations, over generations"
Freeman and Herron - “changes in allele frequencies over time"
Zimmer and Emlen - “any chance in the inherited traits of a population that occurs from one generation to the next.”

5. I. What is Evolution? A. Definitions B. Key Elements
1. Populations evolve – individuals develop.

6. I. What is Evolution? A. Definitions B. Key Elements
1. Populations evolve – individuals develop.
- Evolution is observable:
heritable change in a population over generations. We might term this "Lineage Evolution".
This may be observed at the genetic level, in the genetic structure of the population, or may also be reflected in the physiological, morphological, or behavioral traits affected by this genetic change.

7. I. What is Evolution? A. Definitions B. Key Elements
1. Populations evolve – individuals develop.
2. - Evolution is observable:
3. - with known, observable causes:
the genetic structure of a population changes as a function of selection, drift, mutation, migration, and non-random mating.

8. I. What is Evolution? A. Definitions B. Key Elements
4. - and known, observable results:
As the genetic structure of a population changes over generations, it can become different (diverge) from other populations.
We term this "Radiational Evolution".
These differences may mean that the populations can no longer breed, and they become biologically distinct entities - different species.

9. I. What is Evolution? A. Definitions B. Key Elements
4. - and known, observable results:
5. “Radiational Evolution” creates nested, hierarchical, patterns of relatedness…. within and between biological entities: phylogenies

10. Genetic Relationships Among Some Human Populations

11. Phylogeny among some Artiodactyls

12. Hominidae NESTED, HIERARCHICAL, PHYLOGENY SUPERFAMILY: FAMILY:
SUBFAMILY:
TRIBE:
GENUS:
SPECIES
15 Gibbon sp.

13. Modern Diversity, Biogeography, and Ecological Relationships
Anatomy, Physiology, Behavior
Genetics and Evolution
“Nothing in biology makes sense except in the light of evolution”
– Theodosius Dobzhansky
History of Life

14. II. The History of Evolutionary Thought
(Mayr, E The Growth of Biological Thought)
At one time, there were no scientists, theologians, or historians. There were just philosophers that studied everything, using one way of thinking. That has changed, as we will see.... “Plato (left) and Aristotle (right), a detail of The School of Athens, a fresco by Raphael. Aristotle gestures to the earth, representing his belief in knowledge through empirical observation and experience, while holding a copy of his Nicomachean Ethics in his hand. Plato holds his Timaeus and gestures to the heavens, representing his belief in The Forms” (Wikipedia).

15. II. The History of Evolutionary Thought
A. Early Greeks
Pantheon of meddlesome gods that controlled every aspect of nature and human experience; even took humans for mating (produced the heroes).
Prometheus fashions humans out of earth and water, and Athena gives humankind a soul

16. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
“I swear by Apollo Physician and Asclepius and Hygieia and Panaceia and all the gods and goddesses, making them my witnesses, that I will fulfill according to my ability and judgment this oath and this covenant…”

17. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
- Valued an empirical approach… “look and see”
- Believed in use and disuse and inheritance of acquired traits
- Close to an evolutionary approach

18. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
2. Plato ( bc)

19. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
2. Plato ( bc)
pure philosopher
UNIVERSAL PHILOSOPHY (four dogmas)

20. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
2. Plato ( bc)
pure philosopher
UNIVERSAL PHILOSOPHY (four dogmas)
Essentialism (unchanging eidos)
Plenitude (harmony)
Demi-Urge (creative force)
Soul (spark of life; most in humans)
The cave

21. trained in Pythagorean School; pure philosopher
UNIVERSAL PHILOSOPHY (four dogmas)
Essentialism (unchanging eidos)
Plenitude (harmony)
Demi-Urge (creative force)
Soul (spark of life; most in humans)
Mayr states: "It took more than 2000 years for biology, under the influence of Darwin, to escape the paralyzing grip of essentialism...the rise of modern biology is, in part, the emancipation from Platonic thinking".

22. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
2. Plato ( bc)
3. Aristotle ( bc)

23. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
2. Plato ( bc)
3. Aristotle ( bc)
Interested in nature
Described 100’s of species
Scala Naturae

25. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
1. Hippocrates ( bc)
2. Plato ( bc)
3. Aristotle ( bc)
Interested in nature
Described 100’s of species
Scala Naturae
Formalized logic, and
accepted empirical observations
as premises in arguments. But
conclusions were drawn from the
internal consistency of the argument; they were not
tested by observation.

26. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity

27. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
1. Constantine the Great
(reign ad - First Holy Roman Emporor)
- conversion to Christianity signaled change from to monotheism in west (middle east monotheistic for millenia).
Platonic Dogma’s meshed with Bible:
Single, perfect, harmonious, unchanging
creation

28. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
1. Constantine the Great
2. Middle Ages
- Fall of Rome (476) to Fall of Constantinople (1453)
- Catholic Church as the Political Power

29. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
1. Constantine the Great
2. Middle Ages
- Fall of Rome (476) to Fall of Constantinople (1453)
- Catholic Church as Political Power
- The Persians ( ce)
- Ibn a-lHaytham (Alhazen)
- al-Biruni
- Ibn Sena (Avicenna)
Aristotelian logic and Empiricism!!

30. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
1. Constantine the Great
2. Middle Ages
- Fall of Rome (476) to Fall of Constantinople (1453)
- Catholic Church as Political Power
- Thomas Aquinas ( ):
- must be an unmoved mover
- must be an initial causality
- must be an initial being
- must be an ultimate good
- the ‘design/purpose’ of nature
implies a designer
...yes…

31. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
1. Constantine the Great
2. Middle Ages
- Fall of Rome (476) to Fall of Constantinople (1453)
- Catholic Church as Political Power
- Thomas Aquinas ( ):
- must be an unmoved mover
- must be an initial causality
- must be an initial being
- must be an ultimate good
- the ‘design/purpose’ of nature
implies a designer
- translating the Persians
(with Grosseteste and Bacon)

32. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
D. The Renaissance ( )

33. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
D. The Renaissance ( )
1. Voyages of Discovery
Dias - Rounds Cape of Good Hope
Columbus - "New World"

34. 2. Scientific Revolution a. Astronomy and Physics
1. Nikoli Copernik ( )
2. Galileo Galilei ( )
3. Johannes Kepler ( )
4. Isaac Newton ( )
Heliocentric solar system
- confirmed by Galileo’s observations
Planets orbit in imperfect ellipses
The motion of planets and other material objects could be explained and predicted based on constant laws of nature

35. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
D. The Renaissance ( )
1. Voyages of Discovery
2. Scientific Revolution
a. Astronomy and Physics
b. The Age of the Earth

36. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
D. The Renaissance ( )
1. Voyages of Discovery
2. Scientific Revolution
a. Astronomy and Physics
b. The Age of the Earth
1. James Ussher ( ):
Bishop who Applied logical rigor to
the History of the Earth as revealed in
the Bible... counted the 'begats'...
- creation began at 9am on October 23, 4004 b.c.

37. 2. Scientific Revolution
a. Astronomy and Physics
b. The Age of the Earth
1. James Ussher ( )
2. Nicolaus Steno ( )
- introduced concept of stratigraphy and superposition
- sedimentary rocks are layered in order deposited
- erosion is continuous and is the primary agent of geology on earth.

38. 2. Scientific Revolution 3. Conclusions of the Revolution
- Mechanics of Physical Universe were de-deified
- Constant, physical laws governed nature.
- God as creator (first cause) of universe and laws by which it operates; requires less intervention.
The Ancient of Days –
William Blake

39. 2. Scientific Revolution
3. Conclusions of the Revolution
4. Counter-intuitive Effects on Biology
a. constant laws implied stasis since creation
b. conflict:
- Deists = secondary laws enough
- Natural theologians = diversity and perfection of life requires a God attending to every detail.
"there is special providence in the fall of a sparrow..."
- Shakespeare ( ) - Hamlet

40. 5. Resolution and Problems
Life was divine and not explicable by natural law
Natural Theology re-emerged
An impressive cataloguing of nature… Botanist John Ray's book (1691) "The Wisdom of God Manifest in the Works of Creation"
How did all these species fit on the ark? Why aren’t they mentioned in the Bible? How did they get to the new world as flood water receded?

41. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
D. The Renaissance ( )
E. The Enlightenment (1700’s)

42. E. The Enlightenment (1700’s)
Cultural Climate
- American, French Revolutions over Monarchy/Authority
- reason as a way to solve humanity’s problems

43. E. The Enlightenment (1700’s)
Cultural Climate
2. Natural Theology
a. Carl Linne ( ) - "Linnaeus"
- the great cataloger
- latin binomen system
group species based on reproductive structures
created higher taxa order, class, phylum (nested)
- Systema Naturae: Creationis telluris est gloria Dei ex opere Naturae per Hominem solum -- "The Earth's creation is the glory of God, as seen from the works of Nature by Man alone." 1758

44. E. The Enlightenment (1700’s)
Cultural Climate
2. Natural Theology
a. Carl Linne ( ) - "Linnaeus"
b. Georges Louis Leclerc, Comte de Buffon ( )
the foremost "biologist" of the 18th century
1749 Histoire Naturelle
emphasized life-history of organisms not their classification Was aware of evolution as a possibility, but…
36 volumes
(if all are independent creations, what does ‘similarity’ represent, anyway?)

45. "Not only the ass and the horse, but also man, the apes, the quadrupeds, and all the animals might be regarded as constituting but a single family... If it were admitted that the ass is of the family of the horse, and different from the horse only because it has varied from the original form, one could equally well say that the ape is of the family of man, that he is a degenerate man, that man and ape have a common origin; that, in fact, all the families, among plants as well as animals, have come from a single stock, and that all the animals are descended from a single animal, from which have sprung in the course of time, as a result of progress or of degeneration, all the other races of animals. For if it were once shown that we are justified in establishing these families; if it were granted that among animals and plants there has been (I do say several species) but even a single one, which has been produced in the course of direct decent from another species; if, for example, it were true that the ass is but a degeneration from the horse - then there would no longer be any limit to the power of nature, and we should not be wrong in supposing that, with sufficient time, she has been able from a single being to derive all the other organized beings. But this is by no means a proper representation of nature. We are assured by the authority of revelation that all animals have participated equally in the grace of direct Creation and that the first pair of every species issued forth fully formed from the hands of the Creator."
Georges Buffon - Histoire Naturelle (1766)

46. E. The Enlightenment (1700’s)
Cultural Climate
2. Natural Theology
a. Carl Linne ( ) - "Linnaeus"
b. Georges Louis Leclerc, Comte de Buffon ( )
"it makes no difference which of the authors of the second half of the 18th century one reads - their discussions are, in the last analysis, merely commentaries on Buffon’s work. Except for Darwin and Aristotle, there has been no other student of organisms who has had as far-reaching an influence." Ernst Mayr - Growth of Biological Thought (1982)

47. E. The Enlightenment (1700’s)
Cultural Climate
2. Natural Theology
a. Carl Linne ( ) - "Linnaeus"
b. Georges Louis Leclerc, Comte de Buffon ( )
c. William Paley ( )
Theologian who restated Aquinas’s “proof of God”, largely using the ‘argument of design’ and the ‘watchmaker’ analogy in his book, Natural Theology (1802).

48. 2. Natural Theology
a. Carl Linne ( ) - "Linnaeus"
b. Georges Louis Leclerc, Comte de Buffon ( )
c. William Paley ( )
d. James Hutton ( )
- Wrote "Theory of the Earth" in 1795; marks the discovery of "deep time" in English science.

49. James Hutton ( )
- Wrote "Theory of the Earth" in 1795; marks the discovery of "deep time" in English science.
- Based on two observations:
- 1. granite is an igneous rock, it infuses itself into other rocks (shists) and can only do that when molten.

50. James Hutton ( )
- Wrote "Theory of the Earth" in 1795; marks the discovery of "deep time" in English science.
- Based on two observations:
2. the proper interpretation of “unconformities” - boundaries between cycles of uplift and erosion

51. Siccar Point unconformity, observed by Hutton

52. Process:
1. Initial depositional cycle

53. Process:
2. uplift (time)

54. Process:
3. erosion (time)

55. Process:
4. second depositional cycle (time)

56. James Hutton ( )
- the crust is recycled - the earth has "no vestige of a beginning - no prospect of an end"

57. James Hutton ( )
- the crust is recycled - the earth has "no vestige of a beginning - no prospect of an end"
Hutton supported the contention that the natural processes of erosion and deposition occur at constant rates over geologic time… so it must take eons for sediments to accumulate to the depth of the cliffs., and natural weathered rock outcrops must be extremely old if rock walls 1500 years old show almost no sign of weathering. =
Hadrian’s Wall – 122 a.d.
White Cliffs of Dover
UNIFORMITARIANISM

58. E. The Enlightenment (1700’s)
Cultural Climate
2. Natural Theology
3. Conclusions of the Period
All were creationists, their discoveries had to be reconciled with their Biblical worldview. But there were conflicts and inconsistencies:
- fossils and extinct species vs. plenitude and universal harmony/perfection
- age of earth bc? - uh, not likely...
- The earth has changed...
- How can life remain “harmonious” if earth changes?
...could life change, too?
All were creationists, their discoveries had to be reconciled with their Biblical worldview. But there were conflicts and inconsistencies:
- fossils and extinct species vs. plenitude and universal harmony/perfection
- age of earth bc? - uh, not likely...
- The earth has changed...
- How can life remain adapted if earth changes?
...could life change, too?

59. II. The History of Evolutionary Thought
A. Early Greeks
B. 2nd Greek School
C. The Impact of Christianity
D. The Renaissance ( )
E. The Enlightenment (1700’s)
F. The Battle in France (1780's-1830's)

60. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
a. Early Career
- wrote a four-volume flora of France
- Buffon selected him to be his son's tutor
Buffon got him a position in the Botany Dept. of the Natural History Museum - believed in the fixity of species.

61. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
b Appointed Professor of Invertebrates
- found living molluscs that were similar to fossil forms
- could array some species in nearly continuous lineages from the Tertiary (65 mya) to present
- concluded that species change over time.
c Philosophie Zoologique (culminating work)
- animals: series of perfection towards man (Scala naturae)
- change through time (lineage evolution)

62. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
d. Mechanisms of Change:
“use and disuse”
“inheritance of acquired characteristics”
innate potential, given by Creator, to become
progressively more complex.
- Interactions with the environment
causes a NEED |
Organism uses some organs more
Organism changes during its lifetime
passes modification to offspring

63. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
e. Solves the Extinction Problem
- Previous solutions were:
- all extinct species were killed by Noah's flood
- might live elsewhere (and NOT be extinct)
- it is the work of humans, not God.

64. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
e. Solves the Extinction Problem
change without extinction, or loss of harmony
E F G H
A B C D

65. "May it not be possible that the fossils in question belong to species still existing, but which have changed since that time and have been converted into that similar species that we now actually find?" - Lamarck (1809)
E F G H
A B C D

66. f. Summary of Lamarck’s contributions:
- First to commit to evolution as historical fact
- First to propose a testable mechanism of change
- Uniformitarian approach
- Support for ancient Earth
- Courage to include humans
"Lamarck was the first man whose conclusions on the subject excited much attention. This justly celebrated naturalist first published his views in he first did the eminent service of arousing attention to the probability of all changes in the organic, as well as in the inorganic world, being the result of law, and not of miraculous interposition."

67. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
was vertebrate zoologist at Museum of Natural History with Lamarck.
Invited Georges Cuvier to join him in 1794.
There were 'unities of type' among organisms - homologous structures
form constrains function, but form is malleable
- the form responds to environment

68. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
"The external world is all-powerful in alteration of the form of organized bodies.. . these [modifications] are inherited, and they influence all the rest of the organization of the animal, because if these modifications lead to injurious effects, the animals which exhibit them perish and are replaced by others of a somewhat different form, a form changed so as to be adapted to the new environment."

69. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include the same bones, in the same relative positions? Geoffroy St. Hilaire has insisted strongly on the high importance of relative connexion in homologous organs: the parts may change to almost any extent in form and size, and yet they always remain connected together in the same order.

70. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )

71. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
3. Georges Cuvier ( )

72. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
3. Georges Cuvier ( )
a. Arguments against Lamarckian evolution:
- organisms are functional 'wholes’; change in an organ would stop its function
- and use and disuse were
not heritable
- extinction is real

73. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
3. Georges Cuvier ( )
b. Accomplishments in Biology:
- Founded comparative anatomy as a discipline
- Founded vertebrate paleontology as a discipline
- split the Scala into four embranchments
Vertebrata
Articulata (Arthropoda and Annelida)
"Mollusca" (Molluscs and other bilateral inverts)
Radiata (Cnidaria and Echinodermata)

74. F. The Battle in France (1780's-1830's)
1. Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck ( )
2. Geoffroy Saint-Hilaire ( )
3. Georges Cuvier ( )
4. Conclusions of the Period
Cuvier’s arguments won the day, but evolution was part of the cultural discussion