bio 221: genetics. modern biology: what life is and how it works i. overview - darwin (1859) origin...

BIO 221: GENETICS

Modern Biology: What Life Is and How It Works

I. Overview - Darwin (1859) Origin of Species - Mendel (1865) Experiments in Plant Hybridization - Flemming (1878) Describes chromatin and mitosis

II. Darwin’s Contributions

A. Life

- Born Feb 12, 1809

- Graduated Cambridge, intending to join the clergy

- 1831-36, Naturalist on H.M.S. Beagle

- 1859: The Origin of Species

- Died April 19, 1882, interred in Westminster Abbey


B. His Theories

1.Evolution ‘proper’ – species change

2.Evidence:

a. Change in domesticated animals and plants over time


B. His Theories

1.Evolution ‘proper’ – species change

Evidence:

b. Changes in lineages in the fossil record


B. His Theories

2.Common Ancestry - Species are “related by descent” and have diverged from one another

From his second notebook on the transmutation of species - 1837 From The Origin of Species - 1859


B. His Theories

2.Common Ancestry – Species are “related by descent” and have diverged from one another

Evidence:

Homologous Structures Vestigial Structures

Whale embryo w/leg buds

photo

Haeckel


B. His Theories

2.Common Ancestry – Species are “related by descent” and have diverged from one another

Evidence:

Embryology

The historical fact of evolution – that organisms are biologically related to one another - is the foundational theory of all biological sciences… including medicine:

Dr. Neil Shubin, Department of Anatomy, University of Chicago

http://facweb.furman.edu/~wworthen/bio221/audio/shubin2/shubin2.html


B. His Theories

3. Natural Selection – HOW species change

P1: All populations have the capacity to ‘over-reproduce’

P2: Resources are finite

C: There will be a “struggle for existence”… most offspring born will die before reaching reproductive age.

P3: Organisms in a population vary, and some of this variation is heritable C2: As a result of this variation, some organisms will be more likely to survive and reproduce than others – there will be differential reproductive success.C3: The population change through time, as adaptive traits accumulate in the population.Corollary: Two populations, isolated in different environments, will diverge from one another as they adapt to their own environments. Eventually, these populations may become so different from one another that they are different species.


B. His Theories


Evidence:

1. Divergence in domesticated animals, with humans acting as the selective agent - deciding who gets to breed (“artificial selection”)


B. His Theories


Evidence:

2. Divergence in wild animals, with differences related to different roles in the environment (adaptations).

"Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.“ – Charles Darwin, The Voyage of the Beagle (1839)


B. His Theories


Evidence:

3. Convergence in traits for organisms experiencing the same environment.

Homologous bones are color-coded, but the wing is made from different parts, and thus, while similar functionally, the wings are analogous.


B. His Theories


Evidence:

3. Convergence in traits for organisms experiencing the same environment.

South America (Placentals)

Australia (Marsupials)


C. His Dilemmas

“Long before having arrived at this part of my work, a crowd of difficulties will have occurred to the reader. Some of them are so grave that to this day I can never reflect on them without being staggered; but, to the best of my judgment, the greater number are only apparent, and those that are real are not, I think, fatal to my theory.” – Charles Darwin, The Origin of Species (1859), “Chapter VI: Difficulties of the Theory”.

“Can we believe that natural selection could produce, on the one hand, organs of trifling importance, such as the tail of a giraffe, which serves as a fly-flapper, and, on the other hand, organs of such wonderful structure, as the eye, of which we hardly as yet fully understand the inimitable perfection?”– Charles Darwin, The Origin of Species (1859).


C. His Dilemmas

1. The evolution of complex structures

“To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree…”


C. His Dilemmas


“To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. Charles Darwin, The Origin of Species (1859).


C. His Dilemmas



C. His Dilemmas


Dawkins: Evolution of the Camera Eye

http://www.youtube.com/watch?v=lEKyqIJkuDQ&feature=related

“…why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined? … as by this theory innumerable transitional forms must have existed, why do we not find them embedded in countless numbers in the crust of the earth?” – Charles Darwin, The Origin of Species (1859)


C. His Dilemmas

2. The lack of intermediates between living species, and the lack of complete transitional sequences in the fossil record

XX

X

XX

X

?

?


C. His Dilemmas

2. The lack of intermediates

“As natural selection acts solely by the preservation of profitable modifications, each new form will tend in a fully-stocked country to take the place of, and finally to exterminate, its own less improved parent or other less-favoured forms with which it comes into competition. Thus extinction and natural selection will, as we have seen, go hand in hand. Hence, if we look at each species as descended from some other unknown form, both the parent and all the transitional varieties will generally have been exterminated by the very process of formation and perfection of the new form.” –The Origin of Species (Darwin 1859)


C. His Dilemmas


X

X

Better adapted descendant outcompetes ancestral type


C. His Dilemmas


XX

XX



C. His Dilemmas


XX

X

XX

X



C. His Dilemmas


XX

X

XX

X

?

“I believe the answer mainly lies in the record being incomparably less perfect than is generally supposed.” The Origin of Species (Darwin 1859)


C. His Dilemmas


1861 – Archaeopteryx lithographica

“…and still more recently, that strange bird, the Archeopteryx, with a long lizardlike tail, bearing a pair of feathers on each joint, and with its wings furnished with two free claws, has been discovered in the oolitic slates of Solenhofen. Hardly any recent discovery shows more forcibly than this, how little we as yet know of the former inhabitants of the world.” – Charles Darwin, The Origin of Species, 6th ed. (1876)


C. His Dilemmas



C. His Dilemmas

3. What is the source of heritable variation?

- Inheritance of acquired characters – (wrong)

- Use and disuse – (sort of, but not as he envisioned it)


C. His Dilemmas


Jean Baptiste Lamarck (1744-1829)

"It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved". - The Origin of Species (Darwin 1859).

?Natural Selection


D. Darwin’s Model of Evolution


SOURCES OF VARIATION AGENTS OF CHANGE

Modern BiologyI. OverviewII. Darwin’s ContributionsIII. Mendel's Contributions

III. Mendel's Contributions

A. Mendel’s Life:

- Born July 20, 1822 in Czech Rep.

- Entered Augustinian Abbey in Brno – 1843


A. Mendel’s Life:

- 1856-63: tested 29,000 pea plants

- 1866: Published “Experiments on Plant Hybridization”, which was only cited 3 times in 35 yrs

- Died Jan 6, 1884 in Brno.


A. Mendel’s Life:

B. Pre-Mendelian Ideas About Heredity

Traits run in families….


A. Mendel’s Life:


1. Preformationist Ideas

OVIST

HOMUNCULAN


A. Mendel’s Life:



2. Epigenetic Ideas

?


A. Mendel’s Life:



2.Epigenetic Ideas

3.Blending Heredity


A. Mendel’s Life:


C. Mendel’s Experiments

C. Mendel’s Experiments1. Monohybrid Experiments

Pollen (purple) Ovule (white) Ovule (purple) Pollen (white)

WHY??


a. reciprocal crosses

Results falsified both the ovist and homunculan schools – hereditary information must come from both parents….

Pollen (purple) Ovule (white) Ovule (purple) Pollen (white)PARENTAL CROSS


a. reciprocal crosses

Decided to cross the offspring in an F1 x F1 cross:

Got a 3:1 ratio of purple to white…. (705:224)

SO, the F1 Purple flowered plant had particles for white that were not expressed, but could be passed on.


a. reciprocal crossesb. crossing the F1 hybrids

- Proposed 4 ‘postulates’ (hypotheses) to explain his data:

1) hereditary material is “particulate”


1) hereditary material is “particulate”…. and each organism has 2 particles governing each trait



2) if the particles differ, only one (‘dominant’) is expressed as the trait; the other is not expressed (‘recessive’).




3) during gamete formation, the two particles governing a trait SEPARATE and go into DIFFERENT gametes…




3) during gamete formation, the two particles governing a trait SEPARATE and go into DIFFERENT gametes. Subsequent fertilization is RANDOM (these gametes are equally likely to meet with either gamete type of the other parent…and vice-versa). This is Mendel’s Principle of Segregation


a. reciprocal crossesb. crossing the F1 hybridsc. Proposed four postulates

2. Monohybrid Test Cross

Mendel’s ideas rested on the hypothesis that the F1 plants were hiding a gene for ‘white’Hypothesized Genotype = Ww





Ww

½ W

½ w

Based on his hypotheses (postulates), the plant should produce two types of gametes at equal frequency.

HOW can we see these frequencies, when we can only actually observe the phenotypes of the offspring?





Ww

½ W

½ w

Mate with the recessive parent, which can only give recessive alleles to offspring

ww

w





Ww

½ W

½ w


ww

w

½ Ww

½ ww

Genotypic Ratio of offspring





Ww

½ W

½ w


ww

w

½ Ww

½ ww


½ W

½ w

Phenotypic Ratio of offspring





Ww

½ W

½ w


ww

w

½ Ww

½ ww


½ W

½ w

Phenotypic Ratio of offspring

Same as gamete frequencies of unknown parent

Round and Yellow Peas Wrinkled and Green Peas

C. Mendel’s Experiments1. Monohybrid Experiments2. Monohybrid Test Cross3. Dihybrid Experiments a. Parental cross

Round and Yellow Peas Wrinkled and Green Peas

C. Mendel’s Experiments1. Monohybrid Experiments2. Monohybrid Test Cross3. Dihybrid Experiments

a. Parental cross

RRYY rryy

RY ry

100% F1 = RrYy

C. Mendel’s Experiments1. Monohybrid Experiments2. Monohybrid Test Cross3. Dihybrid Experiments a. Parental cross b. F1 x F1 cross

315 round, yellow (~9/16)

RrYy RrYy

X

108 round, green (~3/16)

101 wrinkled, yellow (~3/16)

32 wrinkled, green (~1/16)



RrYy RrYy

X



32 wrinkled,green(~1/16)

Monohybrid Ratios Preserved

423 Round (~3/4)

133 wrinkled (~1/4)

~ 3:1



RrYy RrYy

X





416 Yellow (~3/4)

140 Green (~1/4)

~ 3:1

C. Mendel’s Experiments1. Monohybrid Experiments2. Monohybrid Test Cross3. Dihybrid Experiments a. Parental cross b. F1 x F1 cross c. His explanation


RrYy RrYy

X





¾ Round x ¾ Yellow =

Product Rule Predicts Combinations

¾ Round x ¼ Green =

¼ Wrinkled x ¾ Yellow =

¼ Wrinkled x ¼ Green =

Mendel's Principle of Independent Assortment: During gamete formation, the way one pair of genes (governing one trait) segregates is not affected by (is independent of) the pattern of segregation of other genes; subsequent fertilization is random.

F1: Round, Yellow: RrYy

Each gamete gets a gene for each trait:

R or r AND Y or y

RY Ry rY ry

R = ½, r = ½

Y = ½, y = ½

So, if R’s and Y’s are inherited independently, THEN each combination should occur ¼ of time.

IF the genes for these traits are allocated to gametes independently of one another, then each F1 parent should produce four types of gametes, in equal frequencies

c. His explanation: (including patterns of dominance)

Independent Assortment occurs HERE




Round Yellow = 9/16




Round Yellow = 9/16

Round Green = 3/16




Round Yellow = 9/16

Round Green = 3/16

Wrinkled Yellow = 3/16




Round Yellow = 9/16(3/4) x (3/4)

Round Green = 3/16(3/4) x (1/4)

Wrinkled Yellow = 3/16(1/4) x (3/4)

Wrinkled Green = 1/16(1/4) x (1/4)

C. Mendel’s Experiments1. Monohybrid Experiments2. Monohybrid Test Cross3. Dihybrid Experiments4. Dihybrid Test Cross

The hypothesis rests on the gametes produced by the F1 individual.How can we determine if they are produced in a 1 : 1 : 1 : 1 ratio?

RrYy

¼ RY

¼ Ry

¼ rY

¼ ry


Cross with a recessive individual that can only give recessive alleles for both traits to all offspring

RrYy

¼ RY

¼ Ry

¼ rY

¼ ry

rryy

¼ RrYy

¼ Rryy

¼ rrYy

¼ rryy

All gametes = ry

Genotypic Frequencies in offspring


Cross with a recessive individual that can only give recessive alleles for both traits to all offspring

RrYy

¼ RY

¼ Ry

¼ rY

¼ ry

rryy

¼ RrYy

¼ Rryy

¼ rrYy

¼ rryy

All gametes = ry

Genotypic Frequencies in offspring

¼ RY

¼ Ry

¼ rY

¼ ry

And the phenotypes of the offspring reflect the gametes donated by the RrYy parent.

1) Hereditary information is unitary and ‘particulate’, not blending

2) First Principle – SEGREGATION: During gamete formation, the two particles governing a trait separate and go into different gametes; subsequent fertilization is random.

3) Second Principle – INDEPENDENT ASSORTMENT: The way genes for one trait separate and go into gametes does not affect the way other genes for other traits separate and go into gametes; so all gene combinations in gametes occur as probability dictates. Subsequent fertilization is random.

C. Mendel’s ExperimentsD. Summary

E. The Power of Independent Assortment

1. If you can assume that the genes assort independently, then you can calculate ‘single gene’ outcomes and multiply results together…

For Example: AaBb x Aabb

- what is the probability of an Aabb offspring?

- What is the probability of an offspring expressing Ab?

- How many genotypes are possible in the offspring?

- how many phenotypes are possible in the offspring?





Do the Punnett Squares for each gene separately:

For A: For B:

A a

A AA Aa

a Aa aa






For A: For B:

A a

A AA Aa

a Aa aa

b b

B Bb Bb

b bb bb






For A: For B:

Answer the question for each gene, then multiply:

P(Aa) = ½ x P(bb) = ½ = 1/4

A a

A AA Aa

a Aa aa

b b

B Bb Bb

b bb bb






For A: For B:


P(A) = 3/4 x P(b) = ½ = 3/8

A a

A AA Aa

a Aa aa

b b

B Bb Bb

b bb bb







For A: For B:


(AA, Aa, aa) = 3 x (Bb, bb) = 2 = 6

A a

A AA Aa

a Aa aa

b b

B Bb Bb

b bb bb








For A: For B:


(A, a) = 2 x (B, b) = 2 = 4

A a

A AA Aa

a Aa aa

b b

B Bb Bb

b bb bb



2. You can easily address more difficult multigene problems:

(female) AaBbCcdd x AABbccDD (male)





- how many types of gametes can each parent produce?

- What is the probability of an offspring expressing ABCD?








For Female: For Male:

2 x 2 x 2 x 1 = 8 1 x 2 x 1 x 1 = 2

Aa Bb Cc dd

A, a B, b C, c d

2 2 2 1

AA Bb cc DD

A B, b c D

1 2 1 1







At A: At B: At C: At D:

P(A) = 1 x p(B) = ¾ x p(C) = ½ x p(D) = 1 = 3/8

A A

A AA AA

a Aa Aa

B b

B BB Bb

b Bb bb

c

C Cc

c cc

D

d Dd









At A: At B: At C: At D:A A

A AA AA

a Aa Aa

B b

B BB Bb

b Bb bb

c

C Cc

c cc

D

d Dd







- How many genotypes are possible in the offspring? 2 x 3 x 2 x 1= 12

- how many phenotypes are possible in the offspring? 1 x 2 x 2 x 1 = 4

At A: At B: At C: At D:A A

A AA AA

a Aa Aa

B b

B BB Bb

b Bb bb

c

C Cc

c cc

D

d Dd



2. You can easily address more difficult multigene problems.

As you can see, IA produces lots of variation, because of the multiplicative effect of combining genes from different loci together in gametes, and then combining them together during fertilization… we’ll look at this again; especially with respect to Darwin’s 3rd dilemma.

Natural Selection

III. Mendel’s Contributions

F. Evolution after Rediscovering Mendel (1903)

SOURCES OF VARIATION AGENTS OF CHANGE

IndependentAssortment

bio 221: genetics. modern biology: what life is and how it works i. overview - darwin (1859) origin...

Documents

different species

darwins contributionsb

origin of species

transmutation of species

darwins contributionsa

different environments

different roles

different ends