6AP Review Evolution.pdf

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Evolutionary Biology

Question #51: What are the current biological models for the origins of biological macromolecules?

–Most popular hypothesis is that chemical and physical processes on early Earth produced very simple cells through a sequence of four main stages

1. Abiotic synthesis of small organic molecules 2. Joining of monomers into polymers 3. Packaging of molecules into protobionts 4. Formation of self-replicating molecules

Electrode

Condenser

Cooled water containing organic molecules H2O

Sample for chemical analysis

Cold water

Water vapor CH4

• Oparin-Haldane Hypothesis tested by Miller-Urey

• Laboratory experiments simulating a potential early Earth atmosphere have produced organic molecules from inorganic precursors

• More likely to have occurred at deep sea

• Some organic compounds extraterrestrial?

Abiotic Synthesis of Polymers

• Small organic molecules

–Polymerize when they are concentrated on hot sand, clay, or rock

• Protobionts: aggregates of abiotically produced molecules surrounded by a membrane or membrane-like structure

• The first genetic material was probably RNA, not DNA

–RNA ribozymes show catalytic activity, self-splice, self-replicate, and bind with amino acids

• Liposomes:

–Membranes selectively permeable, undergo osmosis, maintain a membrane potential (energy storage)

–Provide protective environment for macromolecule synthesis

20 m

(a) Simple reproduction. This lipo-some is “giving birth” to smaller liposomes (LM).

(b) Simple metabolism. If enzymes—in this case, phosphorylase and amylase—are included in the solution from which the droplets self-assemble, some liposomes can carry out simple metabolic reactions and export the products.

Glucose-phosphate

Glucose-phosphate Phosphorylase

Starch

Amylase

Maltose

Maltose Phosphate

• Prokaryotic Heterotroph: 1st, then 3rd

• Chemosynthetic Autotroph 2nd

• Photosynthetic Autotroph 4th

• Aerobic Cellular Respiration 5th

• Colonial organisms with specialization 6th_{or 7}th

• Eukaryotic organism 6thor 7th

• Macroscopic multicellular organisms 8th

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• The theory of endosymbiosis

–Proposes that mitochondria and plastids were formerly small prokaryotes living within larger host cells

• The evidence supporting an endosymbiotic origin of mitochondria and plastids includes

–Similarities in inner membrane structures and functions

–Replicate similar to binary fission

–Both have their own circular DNA

–Similar enzymes and metabolism

–Similarity in ribosomes

Figure 26.13

Cytoplasm DNA

Plasma membrane

Ancestral prokaryote

Infolding of plasma membrane

Endoplasmic reticulum Nuclear envelope

Nucleus

Engulfing of aerobic heterotrophic

prokaryote Cell with nucleus

and endomembrane system

Mitochondrion

Ancestral heterotrophic

eukaryote Plastid

Mitochondrion

Engulfing of photosynthetic prokaryote in some cells

Ancestral Photosynthetic eukaryote Interdependence of host and

endosymbionts led to a single organism

Question #53: What types of evidence support an evolutionary view of life? • Homology: similarity resulting from common ancestry

• Homologous structures: represent variations on a structural theme that was present in a common ancestor

Figure 22.14 Human Cat Whale Bat

Embryology

• Comparative embryology reveals additional anatomical homologies not visible in adult organisms

–All vertebrates have a tail post-anal tail and pharyngeal pouches that develop differently

Figure 22.15

Pharyngeal pouches

Post-anal tail

Chick embryo Human embryo

• Vestigial organs: remnants of structures that served important functions in the organism’s ancestors

Molecular Homologies

• Biologists also observe homologies among organisms at the molecular level

–Genetic Code is universal to all life

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Biogeography

• Biogeography: geographic distribution of species

• Islands are hotbeds of evolution resulting in endemic species (found nowhere else)

• Species living in close proximity tend to be more closely related.

–Species living geographically apart, tend to be less related

The Fossil Record

• Evolutionary transitions and branches of descent leave signs in the fossil record

Figure 22.18

The Evolution of Drug-Resistant Bacteria

• The bacterium Staphylococcus aureus is commonly found on people • One strain, methicillin-resistant S. aureus (MRSA) is a dangerous pathogen

–resistant to penicillin in 2 years (1945)

–Resistant to methicillin in 2 years (1961)

–Now resistant to many antibiotics

• Antibiotics do not create mutations, but select for them

Figure 23.1

1976 (similar to the prior 3 years)

1978 (after drought)

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Figure 22.2

Linnaeus (classification) Hutton (gradual geologic change)

Lamarck (species can change) Malthus (population limits)

Cuvier (fossils, extinction) Lyell (modern geology) Darwin (evolution, nutural selection)

Mendel (inheritance) Wallace (evolution, natural selection) 1750

American Revolution French Revolution U.S. Civil War

1800 1850 1900

1795 Hutton proposes his theory of gradualism. 1798Malthus publishes “Essay on the Principle of Population.”

1809 Lamarck publishes his theory of evolution. 1830 Lyell publishes Principles of Geology.

1831–1836 Darwin travels around the world on HMS Beagle.

Darwin begins his notebooks on the origin of species. 1837

Darwin writes his essay on the origin of species. 1844

Wallace sends his theory to Darwin. 1858

The Origin of Speciesis published. 1859

Mendel publishes inheritance papers. 1865

• The historical context of Darwin’s life and ideas Question #54: What is the role of natural selection in the process of evolution?

• Observation #1: For any species, population sizes would increase exponentially if all individuals that are born reproduced successfully

• Observation #2: Nonetheless, populations tend to be stable in size

• Observation #3: Resources are limited

• Inference #1: Production of more individuals than the environment can support leads to a struggle for existence among individuals of a population

• Observation #4: Members of a population vary extensively in their characteristics

• Observation #5: Much of this variation is heritable

• Inference #2: Survival depends in part on inherited traits

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Figure 22.UN02

Observations

Individuals in a population vary in their heritable

characteristics.

Organisms produce more offspring than the environment can support.

Individuals that are well suited to their environment tend to leave more offspring than other individuals.

Inferences

and

Over time, favorable traits accumulate in the population.

Question #5: How are heredity and natural selection involved in the process of evolution?

The Hardy-Weinberg Theorem describes a population that is not evolving

–States that the frequencies of alleles and genotypes in a population’s gene pool remain constant from generation to generation provided that only Mendelian segregation and recombination of alleles are at work

–Mendelian Inheritance preserves allelic frequencies

Preservation of Allele Frequencies

• If mating is random then independent assortment and recombination does not change allele frequencies

Figure 23.4 Generation

1

CRCR genotype

CWCW genotype Plants mate

All CRCW (all pink flowers)

50% CR gametes

50% CW gametes Come together at random Generation

2

Generation 3

Generation 4

25% CRCR50% CRCW25% CWCW 50% CR gametes

50% CW gametes Come together at random

25% CRCR50% CRCW25% CWCW Alleles segregate, and subsequent generations also have three types of flowers in the same proportions

H-W Equilibrium

• A population in Hardy-Weinberg equilibrium

• If 2 possible alleles, then p = frequency of 1 allele and q = frequency of 2ndallele:

P2_{+ 2pq + q}2_{= 1}

P2_{= homozygous frequency}

q2_{= homozygous freq.}

2pq = heterozygous freq.

Gametes for each generation are drawn at random from the gene pool of the previous generation:

80% CR(p = 0.8) 20% CW(q = 0.2)

Sperm CR

(80%) C

W (20%) p2

64% CRCR

16% CRCW

16% CRCW C4%WCW qp

C

R

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0

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Eg

gs

C

W

(2

0

%)

pq

If the gametes come together at random, the genotype frequencies of this generation are in Hardy-Weinberg equilibrium:

q2

64% CRCR, 32% CRCW, and 4% CWCW

Gametes of the next generation: 64% CRfrom

CRCRhomozygotes 16% CRfrom CRCWhomozygotes

+ = 80% CR= 0.8 = p

16% CWfrom CRCWheterozygotes

+ = 20% CW= 0.2 = q

With random mating, these gametes will result in the same mix of plants in the next generation:

64% CRCR, 32% CRCWand 4% CWCWplants p2

4% CWfrom

CWCWhomozygotes

Conditions for Hardy-Weinberg Equilibrium

• The Hardy-Weinberg theorem describes a hypothetical population that rarely exists.

• In order to maintain H-W Equilibrium, a non-evolving population must have:

–Extremely large population size: avoid genetic drift

–No gene flow: no transfer of alleles between populations (migrations)

–No mutations

–Random mating

–No natural selection

• Genetic drift

–Describes how allele frequencies can fluctuate unpredictably from one generation to the next

–Tends to reduce genetic variation

Figure 23.7

CRCR

CRCW

CRCR

CWCW CRCR

CRCW

CRCR

Only 5 of 10 plants leave offspring

CWCW CRCR

CRCW

CRCR CWCW

CRCW

CWCW CRCR

CRCW CRCW Only 2 of 10 plants leave offspring

CRCR

CRCR CRCR

CRCR

CRCR Generation 2

p= 0.5

q= 0.5

Generation 3

p= 1.0

q= 0.0 Generation 1

p (frequency of CR) = 0.7

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The Bottleneck Effect

• In the bottleneck effect

– A sudden change in the environment may drastically reduce the size of a population

– The gene pool may no longer be reflective of the original population’s gene pool

Original population

Bottlenecking event

Surviving population

Figure 23.8 A

(a)

Shaking just a few marbles through the narrow neck of a bottle is analogous to a drastic reduction in the size of a population after some environmental disaster. By chance, blue marbles are over-represented in the new population and gold marbles are absent.

• The founder effect

– Occurs when a few individuals become isolated from a larger population

– Can affect allele frequencies in a population

• Gene flow

–Causes a population to gain or lose alleles

–Results from the movement of fertile individuals or gametes

–Tends to reduce differences between populations over time

• Some examples of geographic variation occur as a cline, which is a graded change in a trait along a geographic axis

Figure 23.11

EXPERIMENTResearchers observed that the average size of yarrow plants (Achillea) growing on the slopes of the Sierra Nevada mountains gradually decreases with increasing elevation. To eliminate the effect of environmental differences at different elevations, researchers collected seeds from various altitudes and planted them in a common garden. They then measured the heights of the resulting plants.

RESULTSThe average plant sizes in the common garden were inversely correlated with the altitudes at which the seeds were collected, although the height differences were less than in the plants’ natural environments.

CONCLUSIONThe lesser but still measurable clinal variation in yarrow plants grown at a common elevation demonstrates the role of genetic as well as environmental differences.

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Heights of yarrow plants grown in common garden

Seed collection sites Sierra Nevada

Range

Great Basin Plateau

• Discrete characters can be classified on an either-or basis (simple

inheritance)

• Quantitative characters vary along a continuum within a population

(complex, polygenic inheritance)

• Genetic variation can be measured at:

–Nucleotide level (PCR, fingerprints, sequencing)

–Gene level-average heterozygosity:the average percent of loci that are heterozygous in a population

Variation Within a Population

• The three modes of selection

Fig 23.12 A–C

(a) Directional selectionshifts the overall makeup of the population by favoring variants at one extreme of the distribution. In this case, darker mice are favored because they live among dark rocks and a darker fur color conceals them from predators.

(b) Disruptive selectionfavors variants at both ends of the distribution. These mice have colonized a patchy habitat made up of light and dark rocks, with the result that mice of an intermediate color are at a disadvantage.

(c) Stabilizing selectionremoves extreme variants from the population and preserves intermediate types. If the environment consists of rocks of an intermediate color, both light and dark mice will be selected against. Phenotypes (fur color)

Original population

Evolved population

Sexual Selection

• Sexual selection is natural selection for mating success

• It can result in sexual dimorphism, marked differences between the

sexes in secondary sexual characteristics

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• Intrasexual selection is competition among individuals of one sex (often males) for mates of the opposite sex

• Intersexual selection, (mate choice) occurs when individuals of one sex (usually females) are choosy in selecting their mates

–Male showiness a balance between attracting female and survival

–Females choose “good genes” for male health

• Heterozygote advantage occurs when heterozygotes have a higher fitness than both homozygotes, maintaining >2 alleles

–The sickle-cell allele causes mutations in hemoglobin but also confers

malaria resistance

Distribution of malaria caused by Plasmodium falciparum (a parasitic unicellular eukaryote)

Key Frequencies of the sickle-cell allele

0–2.5% 2.5–5.0% 5.0–7.5% 7.5–10.0% 10.0–12.5% >12.5%

• Frequency-dependent selection, the fitness of a phenotype declines if it becomes too common in the population, selection favors less common phenotype

“Left-mouthed” P. microlepis

“Right-mouthed” P. microlepis 1.0

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Sample year ’82 ’83 ’84 ’85 ’86 ’87 ’88 ’89 ’90

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Why Natural Selection Cannot Fashion Perfect Organisms

• Evolution is limited by historical constraints

• Adaptations are often compromises (human limb joints)

• Chance and natural selection interact

• Selection can only edit existing variations

Question #56: What mechanisms account for speciation and macroevolution?

• Reproductive isolation: the existence of biological factors that impede members of two species from producing viable, fertile hybrids

–Prezygotic barriers: impede mating between species or hinder the fertilization of ova if members of different species attempt to mate

–Postzygotic barriers: Often prevent the hybrid zygote from developing into a viable, fertile adult

• Prezygotic barriers

Figure 24.4

Prezygotic barriers impede mating or hinder fertilization if mating does occur

Individuals of different species

Mating attempt Habitat

isolation Temporal

isolation Behavioral

isolation Mechanical isolation

HABITAT ISOLATION TEMPORAL ISOLATION BEHAVIORAL ISOLATION MECHANICAL ISOLATION (b)

(a)

(c) (d)

(e)

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Prezygotic Postzygotic barrier

Viable fertile offspring Reduce

hybrid viability

Reduce hybrid fertility

Hybrid breakdown

Fertilization Gametic isolation

GAMETIC ISOLATION REDUCED HYBRID

VIABILITY REDUCED HYBRID FERTILITY HYBRID BREAKDOWN

(h) (i)

(j) (k)

(l) (m)

(a) Allopatric speciation.A population forms a new species while geographically isolated from its parent population.

(b) Sympatric speciation.A small population becomes a new species without geographic separation.

Figure 24.5 A, B

• Speciation can take place with or without geographic separation

• Speciation can occur in two ways –Allopatric speciation

–Sympatric speciation

Allopatric (“Other Country”) Speciation

• In allopatric speciation, gene flow is interrupted or reduced when a population is divided into geographically isolated subpopulations

–Why Islands are hot spots of biodiversity

–What is a barrier depends on ability of population to disperse (Fly? Swim? Climb?)

A. harrisii A. leucurus

Sympatric (“Same Country”) Speciation

• In sympatric speciation, speciation takes place in geographically overlapping populations

–Results from

•Polyploidy

•Habitat Differentiation (Niche divergence)

•Sexual selection

Polyploidy

• Polyploidy: the presence of extra sets of chromosomes in cells due to accidents during cell division

–Has caused the evolution of some plant species due to gametic isolation

•Ex: oats, cotton, potatoes, tobacco, wheat

Sexual Selection

• Sexual selection can drive sympatric speciation

–Sexual selection for mates of different colors has likely contributed to speciation in cichlid fish in Lake Victoria

Normal light

Monochromatic orange light

P. pundamilia

P. nyererei

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Habitat Differentiation

• Sympatric speciation can also result from the appearance of new ecological

niches (habitat, temporal, behavioral)

– Example: the North American maggot fly can live on native hawthorn trees as well as more recently introduced apple trees

– Example: Anoles niche divergence

Question #57: What different patterns of evolution have been identified and what mechanisms are responsible for each of these patterns?

• Adaptive radiation (Divergent)

–Is the evolution of diversely adapted species from a common ancestor upon introduction to new environmental opportunities

• The punctuated equilibrium model

–Contrasts with a model of gradual change throughout a species’ existence

Figure 24.13

Gradualism model.Species

descended from a common ancestor gradually diverge more and more in their morphology as they acquire unique adaptations.

Time

(a) Punctuated equilibrium

model.A new species

changes most as it buds from a parent species and then changes little for the rest of its existence. (b)

• Anagenesis: long-term microevolution

• Cladogenesis: macroevolution, increases biodiversity

Sugar glider

AUSTRALIA NORTH AMERICA

Flying squirrel

Figure 22.17

• Convergent Evolution: species become more similar due to similar habitats and niche

–They are still evolutionarily distant, evolving independently from separate ancestors

–Evidence for Natural Selection

–Produces Analogous structures

Coevolution

: cases where two (or more) species reciprocally affect each

other’s evolution Examples may include: Predator/Prey relationships Competitive Species Mutualistic Species

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Evolutionary Patterns

Question #58: What are the major body plans of plants and animals?

• Parazoa= lack tissue

• Eumetazoa= have tissue layers –Radiata= diploblastic (2 germ layers)

–Bilateria = triploblastic (3 germ layers) • Acoelomate

• Pseudocoelomate

• Coelomate

• Cephalization (gathering of sensory and

Integration cells at anterior end, only in bilaterals)

• Protostome

• Deuterostome

• Root System, Shoot System

• Monocot or Dicot

Survey of the Diversity of Life:

Question #59: What are the distinguishing characteristics of the three domains? 3 Domain System

Bacteria Archaea Eukarya

6 Kingdom System

Eubacteria Archaebacteria Protista Plant Fungi Animal

2 Kingdom System (1700s)

Plant Animal

3 Kingdom System (late 1800s)

Protista Plant Animal

5 Kingdom System (1950s)

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Figure 26.21 Archaea Bacteria Eukarya COMMON ANCESTOR OF ALL LIFE Land plants Green algae Red algae Forams Ciliates Dinoflagellates

Cellular slime moldsAmoebas

Animals Fungi Euglena Trypanosomes Leishmania Sulfolobus Thermophiles Halophiles Methanobacterium Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia Cyanobacteria Green sulfur bacteria (Plastids, including chloroplasts) Diatoms

• One current view of biological diversity

P ro te o b a c te ria C h la m y d ia s S p ir o c he te s C y an o b a c te ria G ra m -p o s itiv e b ac te ri a K o ra rc h a e o te s E u ry arc h a e o te s, cre n a rc h a e ote s , n a n o arc h a e o te s D ip lo m o n a d s , p a ra b a s alid s E ug le n o zo a n s A lv e o la te s ( d in ofl a g e lla te s , a p ic o m p le xa n s , c ili ate s ) S tr am e n o p ile s ( w a te r m o ld s , d ia to m s , g o ld e n a lg a e , b ro w n a lg a e ) C e rc o zo a n s , ra d io la ria n s R e d a lg a e C h lo ro p hy te s C h a ro p h yc e a n s

Domain Archaea Domain Eukarya

Universal ancestor Domain Bacteria

Chapter 27 Chapter 28

B ry o p h yte s ( m o s se s , liv e rw o rt s , h o rn w o rt s ) Plants Fungi Animals S e e dle s s v a s cu la r p la n ts ( fe rn s ) G y m no s p e rm s A n g io s p e rm s A m o e b o z o an s ( a m o e b a s , s lim e m o ld s ) C h y tr id s Z yg o te f u n g i A rb u s c u la r m y c o rr h iz a l fu n g i S a c f u n g i C lu b f u n g i C ho a n o fl a g ella te s S p o n g e s C nid a ri a ns ( je lli e s, c o ra l) B ila te ra lly s ym m e tr ic al a n im als ( a n n e lid s , a rt h ro p o d s , mo llu s c s, e c h in o d e rms , v e rt e b ra te s )

Chapter 29 Chapter 30Chapter 28 Chapter 31 Chapter 32Chapters 33, 34

• The phylogeny of fungi

Chytrids Zygote fungi Arbuscular mycorrhizal fungi Sac fungi Club fungi C hy tridiom y c ot a Z y gom y c ot a Glom erom y c ot a As c om y c ot a Bas idiom y c ot a Figure 31.9 Uncertainty, Paraphyletic?

Question #60: What are representative members of the major animal phyla and plant divisions and what are the distinguishing characteristics of each group?

Highlights of plant evolution

Bryophytes

(nonvascular plants) Seedless vascular plants Seed plants

Vascular plants Land plants

Origin of seed plants (about 360 mya)

Origin of vascular plants (about 420 mya)

Origin of land plants (about 475 mya)

Ancestral green alga

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Fig. 32.4

Traditional Anatomy-based Phylogenetic Tree

• Phylogenetic tree

based on nucleotide sequences from the small subunit ribosomal RNA.

Fig. 32.8

• The phylum Chordata includes three subphyla, the vertebrates and two phyla of invertebrates, the urochordates (tunicates) and the cephalochordates (lancelets).

Fig. 34.1

Gnathostomes, have true jaws and also two sets of paired appendages

Tetrapods, the appendages are modified as legs to support movements on land

Amniotes, producing shelled, water-retaining eggs which allow these organisms to complete their life cycles entirely on land

Evolutionary Relationships

Question #61: What evidence is used to determine evolutionary relationships between organisms and how is this used in classification?

• Currently, systematists use

–Morphological, biochemical, and molecular comparisons to infer evolutionary relationships

Figure 25.2

Morphological and Molecular Homologies

• In addition to fossil organisms

–Phylogenetic history can be inferred from certain morphological and molecular similarities among living organisms

• In general, organisms that share very similar morphologies or similar DNA sequences

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Evaluating Molecular Homologies

• Analyzing comparable DNA segments from different organisms

• Go with most parsimonious solution

Figure 25.6

C C A T C A G A G T C C

C C A T C A G A G T C C C C A T C A G A G T C C

C C A T C A G A G T C C G T A

Deletion

Insertion

C C A T C A A G T C C C C A T G T A C A G A G T C C

C C A T C A A G T C C C C A T G T A C A G A G T C C 1Ancestral homologous

DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor.

2Deletion and insertion mutations shift what had been matching sequences in the two species.

3Homologous regions (yellow) do not all align because of these mutations.

4Homologous regions realign after a computer program adds gaps in sequence 1.

1 2

1 2 1 2

A C G G A T A G T C C A C T A G G C A C T A

T C A C C G A C A G G T C T T T G A C T A G

Figure 25.7

Homologous

Analogous

Hierarchical Classification

• Linnaeus also introduced a system for grouping species in increasingly broad categories

–Binomial Nomenclature: latinized 2-part name genus + species

Figure 25.8

Panthera pardus

Panthera

Felidae

Carnivora

Mammalia

Chordata

Animalia

Eukarya Domain

Kingdom Phylum

Class Order

Family Genus

Species

• A valid clade is monophyletic

–Signifying that it consists of the ancestor species and all its descendants

Figure 25.10a

(a) Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A mono-phyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics.

Grouping 1

D

C

E G

F

B

A J

I K

H _{The most}_parsimonious

tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters

The Universal Tree of Life

• The tree of life

–Is divided into three great clades called domains: Bacteria, Archaea, and Eukarya

• The early history of these domains is not yet clear

Figure 25.18

Bacteria EukaryaArchaea

4Symbiosis of chloroplast ancestor with ancestor of green plants

3Symbiosis of mitochondrial ancestor with ancestor of eukaryotes

2Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells

1Last common

ancestor of all living things

4 3

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