Evolution

Chapter 11

Organisms and Environment

• Populations of organisms adapt through time to the environment in which they live

• Environment “selects” adaptations that better able an organism to survive and reproduce

• Environment does not create the adaptations in an individual (a common misconception)

• Thus the ecology and evolution are linked in the lives of organisms

Evolution - change in the allele frequency of a population through time

• Why did scientists ever come up with this idea of evolution?• noted significant changes in earth’s

structure and in living organisms• wondered why there are so many

different species; some resembling each other more closely than others

• Any scientific explanation must work through natural processes“The purpose of science is to search out

and build explanations of the natural world that are based on natural mechanisms.” (Perspectives in Biology)

often seen as changes in

morphology in populations

Interesting book….Evolution's Captain by Nichols Peter

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Un-Fig. 03.3

Large ground finch(seeds)

Cactus ground finch(cactus fruits and flowers)

Vegetarian finch(buds)

40 km (25 mi)

GALÁPAGOSISLANDS

Woodpecker finch(insects)

Evolution

• Role of evolution in science:• central tenet in biological science

• biology doesn’t make sense without evolution

• the occurrence of evolution is not questioned in science

evolution is to biology as gravity is to physics

• Only the mechanisms of HOW it works is discussed and debated in the scientific community

• Lamarck, Wallace, Darwin all provided the mechanisms.

• Wallace’s and Darwin’s explanation of mechanism has survived scientific scrutiny and is called natural selection.

Theory of Natural Selection1. Variation exists among organisms in a

population2. Some of these variations are hereditary3. Populations produce more offspring than

environment can support4. Individuals best adapted (better fitness) to

environment will leave more offspring than those that are not as well adapted (less fit)

• Populations of organisms adapt through time to the environment in which they live

• Environment “selects” adaptations that better able an organism to survive and reproduce

Result of Natural Selection

• This can produce a change in allele frequency in a population over time

…our definition of evolution.

• How much change is necessary before the change is recognize as real, and not due to chance?

• Sounds like a question answerable via statistics?...well hang on partner and lets see about that

Understanding Genetic Function

• What is the genetic material?• What is a gene?• What does a gene do specifically?• What is an allele?• How are the diploid and haploid

conditions reflected in your genetics?• How does inheritance actually work?

DNA structure

Genetic Material• DNA

• organic macromolecule• nucleotides are the

building blocks• nucleotides contain

• sugar• phosphate• base (only variable

portion): ATCG• nucleotides connected to

form a strand

strands connected to each other to form a double stranded molecule

Genetic Material

• genetic information• encoded by the order of nucleotide bases

• gene• piece of DNA• instructs the cell to make an protein

• structural• enzyme

• allele• different forms of a gene

• Example: gene for pea pod color• green pod allele• yellow pod allele

Alleles

Genetic Material• alleles occur in pairs WHY?

• chromosome contains like genes• chromosomes arranged in pairs

• egg donor’s chromosome• sperm donor’s chromosome

• Example: gene for pea pod color• green pod allele (G)• yellow pod allele (g)

• GENOTYPE = allele arrangement• How many genotypes for one gene if only two

alleles?• GG (homozygous)• gg (homozygous)• Gg (heterozygous)

• alleles inherited singly WHY?• gametes (through meiosis) reduce diploid to

haploid

Genetic Material• Possible combinations in offspring

• GG X GG• GG X gg• gg X gg• Gg X GG• Gg X gg• Gg X Gg

• Can we predict genotypes of offspring?

G g

G

g

GG Gg

ggGg

Population Genetics• Hardy-Weinberg Principle

• allele frequency tends to remain constant in a population (thus in equilibrium)

• Population a localized group of potentially interbreeding individuals

belonging to the same species

• Speciesa group of population that potentially can interbreed

• Gene poolsum of all the alleles of all the genes of all the individuals in the

population

Hardy-Weinberg Law (also known as HW Equilibrium) assumes allele equilibrium if the population has the following five conditions:1. random mating within population2. no selection for or against any specific allele,

which would alter gene pool (natural selection)3. no genetic drift (the population is large enough

not to be influenced by chance)4. no gene flow into or out of the population

(population is isolated from other populations)5. no mutations are occurring (mutations alter gene

pool by changing one allele into another)If one or more if these conditions are NOT occurring, then what?

• no allele equilibrium, thus alleles change in frequency through time…evolution

Population Genetics…• Hardy-Weinberg Principle

• assumes 2 alleles for each gene• where frequencies of G + g = 1• if alleles remain constant…

• since genotype of diploid contains 2 alleles for each gene…

• then (G + g)2 = genotype frequency in population

• and expanding binomial gives G2 + 2Gg + g2

• hard to keep G separate from g so lets use p=G and q=g; thus….

p2 + 2pq + q2 = 1• where p2 = GG, 2pq = Gg, and q2 = gg

• tests to evaluate if results (observed) differ from what was expected• one must know expected values

Chi-square analysis

χ2 = (observed – expected )2

expectedΣ

Determining HW Equilibrium

• A scientist has studied the amount of polymorphism in the alleles controlling the enzyme phosphoglucomutase (PGM) in a desert fern.

• From one population, 520 individuals were sampled. The scientist found the following genotypes represented:

• AA = 42• Aa = 145• aa = 333

• From these data calculate the diploid genotype frequencies and allele frequencies for PGM in this population.

• Use the appropriate statistical test (Chi-square) to determine if this population is in Hardy-Weinberg equilibrium

• What is your strategy?• 1. calculate allele frequency• 2. plug frequencies into HW binomial to obtain expected #’s• 3. Chi-square analysis to determine if observed differ from expected

Determining if HWE ExistsAA = 42 Aa = 145 aa = 3331. Determine genotype frequencies

AA (p2) = 42/520 = 0.080Aa (2pq) = 145/520 = 0.279aa (q2) = 333/520 = 0.640

2. Determine allele frequency Total #of PGM alleles in population

= 520 X 2 since individuals are diploid = 1040Number of A alleles in population:

2X42 + 145 = 229Frequency of A

A (p) = 229/1040 = 0.220Number of a alleles in population:

2X333 + 145 = 811Frequency of a

a (q) = 811/1040 = 0.780

Determining if HWE ExistsA (p) = 0.220 a (q) = 0.7803. Determine Expected Genotype Frequencies (under HWE)

AA = p2 = (0.220)2 = 0.0484

Aa = 2pq = 2 X 0.220 X 0.780 = 0.343

aa = q2 = (0.780)2 = 0.608

4. Determine expected # individuals (under HWE)AA

= 0.0484 X 520 = 25Aa

= 0.343 X 520 = 178aa

= 0.608 X 520 = 316

Determining HW Equilibrium5. Test HWE with Chi-square analysis

compare #’s (not frequencies)

χ2 = (observed – expected )2

expectedΣ

Genotype

Observed (O)

Expected (E)

O-E (O-E)2 (O-E)2/E

AA

Aa

aa

Sum

Determining HW Equilibrium5. Test HWE with Chi-square analysis

compare #’s (not frequencies)

Genotype

Observed (O)

Expected (E)

O-E (O-E)2 (O-E)2/E

AA 42 25 17 289 11.560

Aa 145 178 -33 1089 6.118

aa 333 316 17 289 0.915

X2calculated =

18.593

χ2 = (observed – expected )2

expectedΣ

Determining HW Equilibrium6. Evaluate X2 and draw conclusion

• A statistical analysis tests the null hypothesis• Null hypothesis is that no difference occurs between

compared groups (HWE)• To do this:

• a statistic is calculated (called the X2calculated in our example)

• the calculated statistic (called the X2critical in our example) is compared

to a critical statistic which is found on a table• if X2

calculated is less than X2critical

• Null hypothesis is supported; thus the differences that appear are simply due to chance and are not real (not statistically different groups)

• HWE exists, in our example

• if X2calculated is greater than X2

critical

• Null hypothesis is rejected; thus the differences that appear are real (statistically different groups)

• HWE does not exist, in our example

critical value

Determining HW Equilibrium

Genotype

Observed (O)

Expected (E)

O-E (O-E)2 (O-E)2/E

AA 42 25 17 289 11.560

Aa 145 178 -33 1089 6.118

aa 333 316 17 289 0.915

X2calculated =

18.593

6. Evaluate X2 and draw conclusion

X2calculated = 18.593

X2critical = 5.99

Accept or Reject Null Hypothesis? REJECT

Is population in Hardy Weinberg Equilibrium? NO

So what has caused the difference?

If population is NOT in Hardy-Weinberg Equilibrium, what five processes are responsible? 1. non-random mating within population2. selection for or against any specific allele, which

would alter gene pool (natural selection)3. genetic drift (the population is large enough not to

be influenced by chance)4. gene flow into or out of the population (population

is isolated from other populations)5. mutations are occurring (mutations alter gene

pool by changing one allele into another)

Practice ProblemA botanist is investigating a population of plants whose petal color is controlled by a single gene whose two alleles (B & B1) are codominant. She finds 170 plants that are homozygous brown, 340 plants that are homozygous purple and 21 plants whose petals are purple-brown. Is this population in HWE? (don’t forget to do the proper statistical test)

Gen FreqAllele Freq

HW Gen Freq HW #

BB 170 0.320 B 0.340 0.116 61

BB1 21 0.040 B1 0.660 0.449 238

B1B1 340 0.640 0.436 231

sum 531 1.000 1.000 1 531

Practice ProblemA botanist is investigating a population of plants whose petal color is controlled by a single gene whose two alleles (B & B1) are codominant. She finds 170 plants that are homozygous brown, 340 plants that are homozygous purple and 21 plants whose petals are purple-brown. Is this population in HWE? (don’t forget to do the proper statistical test)

Genotype

Observed (O)

Expected (E)

O-E (O-E)2 (O-E)2/E

BB ( brown) 170 61 109 11803 192

BB1 (purple-brown) 21 238 -217 47214 198

B1B1 (purple) 340 231 109 11803 51X2

calculated 441.531

X2calculated = 441.531

X2critical = 5.99

Accept or Reject Null Hypothesis? Is population in Hardy Weinberg Equilibrium?

Effects of Natural Selection on the population

Stabilizing selection

Directional selection

Disruptive selection

What is the source of variation?

Mutation• chemicals and radiation (UV) are mutagens

• incorrect copying• change base pair sequence• bonds between DNA bases, repair leads to change in

sequence

Recombination• viruses transfer DNA from one host to another• sexual reproduction

• different DNA from two parents• crossing over• independent assortment of homologous pairs

The joint action of mutation and recombination and selection is sufficient to explain evolution!

Natural Selection

• Variation that is heritable is genetic• Source of variation is

• random mutation of nucleotide base sequence

• recombination (meiosis)• independent assortment (meiosis)

• Natural selection can lead to the appearance of new species given enough time and acting upon enough traits

Natural Selection• Nature selects those that survive and reproduce - this is

natural selection• Natural selection is THE major force in changing allele

frequencies• Artificial selection - used by Darwin to clarify natural selection

Major Evolutionary Advances

• Flowers - 140 mya

5,000mya

4,000mya

3,000mya

2,000mya

1,000mya

EarthForms

ProkaryoticCells

EukaryoticCells

MulticellularPlants

Vascular

tissue

Seeds

Flowers

• Life - 3,800 mya• Prokaryotic cell/autotrophic

• Eukaryotic cell - 1,400 mya• Multicellar plants - 1,000 mya• Vascular tissue - 430 mya

• Needed on land - why?

• Seeds - 350 mya

Place on the time scale, the following events:

1. Earth2. Prokaryotes3. Eukaryotes4. Multicellular life5. Vascular tissue6. Seeds7. Flowers

Numbers of Species on Earth

0

5,000,000

10,000,000

15,000,000

number of species

total identified

total estimated to exist

however, this number could be as high as 112,000,000

14 mil

1.75 mil

Species Diversity on Earth

0

250,000

500,000

750,000

1,000,000

number of species

insects other animals

higher plants fungi

protistsbacteria

viruses

Where are these species?

• Tropics• 7% of land mass• 50% of species

Species Concepts1. Morphological species

• the smallest groups that are consistently distinct by their morphology

• practical approach• useful with paleontological specimens

2. Biological species• groups of actually or potentially interbreeding natural

populations which are reproductively isolated from other such populations

• more useful with animals than plants • genetic isolation (reproductive isolation) critical• prevent gene flow….

• given enough time the two populations may become distinct from one another - so distinct...

• that when the populations come back into contact, reproduction is not possible

Species Concepts

Geographic Isolation = Reproductive Isolation

Eastern Redbud (Cercis canadensis L.)

California Redbud (Cercis occidentalis Torr. ex Gray)

Redbud - a small shrub that has attractive flowers (early spring) and produces nice shade

Continental Drift

• The continents are moving, along with the sea floor, at about 2 inches/year. They don't travel very far over a human life span, but the distance adds up over millions of years.

• This animation shows the movement of the continents over the past 250 million years. It starts when dinosaurs roamed the earth. At that time, the continents were all together, forming one land mass called Pangaea.

• http://www.tectonics.caltech.edu/outreach/animations/drift.html

Continental Drift• The continents are moving, the sea floor as well, at

about 2 inches/year. They don't travel very far over a human life span, but the distance adds up over millions of years.

• This simulation, which is based on current data, shows the movement of the continents over the past 140 million years. (Note that time is given in the units "Ma," which means "millions of years ago.")

• 140 million years ago, dinosaurs roamed the earth. At that time, the continents were all together, forming one land mass called Pangaea. Over the next 140 million years, this land mass broke apart and the pieces travelled to their current positions.

• http://www.tectonics.caltech.edu/outreach/animations/drift2.html

Species Concepts

3. Phylogenetic species concepts• Based upon reconstructing the evolutionary

history of populations• character-based concepts• history-based concepts

Hybrids• Combining unlike gene

sets• Why can’t two unlike

species form fertile offspring?

• Problem arises at meiosis (gamete formation)

• Doubling of chromomsomes can solve this problem• Haploid - N• Diploid – 2N• Polyploidy – 3 or more sets

• Triploid – 3N• Tetraploid - 4N• Pentaploid – 5N• Hexaploid – 6N • etc

Hybrids

Allopolyploidy• hybrid between two

different species (interspecific hybrid)

• sterile because meiosis does not occur

• doubling of chromosomes (autopolyploidy) can cure this problem

• how common is this?• 70% flowering plants• 80% of grasses• read about origin of wheat

(Triticum aestivum) in text

Widespread sterile hybrid• Horsetail Equisetum X ferrissii• reproduces by vegetative propagation

Origin of species – how?

1. Allopatric Speciation• geographically isolated

populations• gene flow prevented

Origin of species - how?

2. Sympatric speciation• geographic isolation

NOT required• polyploidy is

mechanism• autopolyploids• allopolyploids

Plant Evolution: a case study in

Astrolepisdesert ferns• an odd place for

ferns, it would seem!• several genera

representing a few hundred species worldwide

Astrolepis distribution

• in most deserts of the New World

• concentrated in North America

Astrolepis morphology

• pinnately compound leaves

• species distinguished by:• leaflet

• size• lobing• scale covering

Number of species?

Weatherby (1943)Tryon (1956)

Notholaena sinuata var. sinuataNotholaena sinuata var.

integerrimaNotholaena sinuata var.

cochisensis

Hevly (1963)

Notholaena sinuata ssp. sinuata var. sinuataNotholaena sinuata ssp. sinuata var. robustaNotholaena sinuata ssp. madriensis var.

madriensisNotholaena sinuata ssp. madriensis var.

madriensisNotholaena integerrimaNotholaena cochisensis

Mickel (1979, 1988)

Cheilanthes sinuataCheilanthes crassifoliaCheilanthes integerrimaCheilanthes cochisensisCheilanthes beitelii

Techniques in study

1. chromosome counts• during prophase I• determine levels

of polyploidy

Meiosis

Diploid spore

mother cell

Tetrad of haploid homospores

Squash of cell in prophase I

Squash allows chromosome number to be determined!

Count the X & O

Techniques in study cont’d

2. allozyme electrophoresis

origin (where plants

are placed)

starch gel

direction of migration when

current is applied

parent A

parent B

hybrid?

Techniques in study cont’d

gel, after electrophoresis,

stained for specific enzyme

hybrid?parent

Aparent

B

• after electrophoresis• different forms of

the enzyme (isozymes) migrate at different speeds (due to differences in amino acids and thus electrical charge)

2. allozyme electrophoresis

Techniques in study cont’d

2. allozyme electrophoresis• How many enzymes are

tested?• How many markers do you

need?• Increasing marker number

increases reliability.

• Enzyme systems with good markers for Astrolepis• phosphoglucoisomer

ase PGI

• triosephosphate isomerase

TPI

• phosphogulcomutase

PGM

• shikimate dehydrogenase

SkDH

Data: stained gel

• band patterns additive between proposed parents

• thus the parentage of hybrid is known and can then be named

Results & Conclusions

• hybridization is common in Astrolepis

• hybridization plays prominent role in speciation within Astrolepis

MM

Missing

A. cochisensis

CCCCCCCCC

A. sinuata

SSSSS

A. beitelii

BBBBBA. windhamii

CMS

A. integerrima

CMMCCM

BMS

BBM

A. crassifolia

BMM

Results & Conclusions

• Thus, morphology seems to “fits” genetic species concept once more information about genetics is known

Remember the leaflet morphology?