DESCENT WITH MODIFICATION: A DARWINIAN VIEW OF LIFE

CHAPTER 22

Fossils of trilobites, animals that lived in the seas hundreds of millions of years ago

HISTORICAL CONTEXT

Carl Linnaeus (1707-1778) – founder of taxonomy (scientific name) grouped similar species into same genus

Georges Cuvier (1769-1832) – catastrophism – different species in layered rock due to catastrophic events like floods

James Hutton (1726-1797) – gradualism – profound change is a cumulative product of slow but continuous process; ex. Rivers making canyons

Charles Lyell (1797-1875) – uniformitarianism – geological process have not changed throughout Earth’s history

Jean Baptiste Lamarck (1744-1829)- thought acquired characteristics can be passes on to offspring

Formation of sedimentary rock and deposition of fossils from different time periods

Strata of sedimentary rock at the Grand Canyon

Charles Darwin in 1859, the year The Origin of Species was published

CHARLES DARWIN (1809-1882)

Worked on the HMS Beagle in 1830’s

Observed and collected thousands of different species

Galapagos Islands (west of S. America) most interesting

The Voyage of HMS Beagle

Galápagos finches

“The Galápagos tortoise (or Galápagos giant tortoise), is the largest living tortoise, endemic to nine islands of the Galápagos archipelago. Adults of large subspecies can weigh over 300 kilograms (660lb) and measure 1.2 meters (4 ft) long. Although the maximum life expectancy of a wild tortoise is unknown, the average life expectancy is estimated to be 150-200 years.”Source: en.wikipedia.org/wiki/Gal%C3%A1pagos_tortoise

Darwin read Lyell’s Principles of Geology and felt age of earth was much older than previously thought

1844 Darwin wrote essay on the origin of species

1858 – Alfred Wallace sends manuscript to Darwin about Natural Selection

Lyell presented Wallace’s paper as well as Darwin’s 1844 essay to scientists

1859 The Origin of Species published by DarwinDescent with modificationNatural selection (the

mechanism)

Descent with modification

DARWIN’S OBSERVATIONS

Individuals vary within a population Traits inherited All species are capable of

overproduction Many offspring do not survive

DARWIN’S INFERENCES

Individuals with inherited traits that give them a better chance of surviving and reproducing tend to leave more offspring than those without those traits

Unequal ability of individuals to survive will lead to favorable traits in populations over generations.

NATURAL SELECTION

A population evolves, not an individual!

Acquired characteristics may be adaptable but are not inherited!**

The environment does not create a best fit characteristic, but selects for it!

A few of the color variations in a population of Asian lady beetles

Artificial selection: diverse vegetables derived from wild mustard

AP:April. 29, 2005 ST. THOMAS, Barbados - It's male.  But what is it?  A zonkey? A deebra?  That's the debate in Barbados since a zebra gave birth to a foal sired by a donkey.

Goldendoodle and a liger

EVIDENCE OF EVOLUTION Biogeography – geographical

distribution of speciesEx. Islands with similar species to

mainland Fossil record – transitional forms Comparative Anatomy –

homologous structures among different organisms

Vestigial organs –marginal, if any importance, remnants of structures that once served a function Whale pelvis and leg bones and human appendix

Comparative Embryology – most vertebrates share common early development (gill slits)

Molecular Biology – similar overall DNA, similar proteins (ex. Cytochrome c)

Evolution of insecticide resistance in insect populations

Evolution of drug resistance in HIV

Homologous structures: anatomical signs of descent with modification

Molecular Data and the Evolutionary Relationships of Vertebrates

Different geographic regions, different mammalian “brands”

The evolution of fruit fly (Drosophila) species on the Hawaiian archipelago

A transitional fossil linking past and present

Left: Trilobite evolution Right: Whale evolution

THE EVOLUTION OF POPULATIONS

Chapter 23

GENETIC VARIATION

Genetic variation that makes evolution possibleMutations

Change in DNA sequences Average 1 in 100,000 genes per generation

Sexual reproduction Crossing over Independent assortment Fertilization

POPULATION GENETICS Population – localized group of

individuals belonging to the same species Species – organisms that can interbreed

and produce fertile offspring Gene pool – total genes in a population If all members of a population are

homozygous for the same allele, that allele is fixed.

Gene frequency - two or more alleles for a gene, each having a relative frequency (proportion) in the gene pool

Example:A = pinka = white 1000 plants = 200 white + 800 pink800 pink = 340(AA) + 460(Aa)

Find A’s frequency From AA: 340 x 2 = 680From Aa: 460 x 1 = 460680 + 460 = 11401140/2000 = .57 = .6The 2000 is total number of alleles for 1000

plants

Find a’s frequency From aa: 200 x 2 = 400From Aa: 460 x 1 = 460400 + 460 = 860860/2000 = .43 = .4

Find A’s frequency1- .4 = .6

HARDY-WEINBERG THEOREM

Frequencies of alleles and genotypes in a population’s gene pool remain constant over the generations unless acted upon by agents other than random sexual recombination

Hardy-Weinberg tells us what to expect if a population is NOT evolving!!

The Hardy-Weinberg Theorem

Random Gamete production

The Hardy-Weinberg theorem

EXAMPLE USING FLOWER POPULATION

Probability of picking 2 A from example.6 x .6 = .36

Probability of picking 2 a from example.4 x .4 = .16

Probability of picking Aa from example (aA or Aa)(.4 x .6) + (.6 x .4 ) = .48

HARDY-WEINBERG EQULIBRIUM

The sexual process of meiosis and random fertilization maintain the same allele and genotype frequencies over generations.

In the example:p = .6 = Aq = .4 = a

p + q = 1p = 1 - q and q = 1 - p

p2 + 2pq + q2 = 1(AA)+ (2Aa) + (aa) = 1

FIVE CONDITIONS FOR H-W

1. Very large population size2. No gene flow (genes entering or

leaving a population)3. No net mutations4. Random mating5. No natural selection

These mean NO EVOLUTION!

MICROEVOLUTION

Microevolution – generational change in a population’s frequencies of alleles or genotypes

FIVE AGENTS OF MICROEVOLUTION

1. Genetic Drift – rapid changes in a gene pool of a small, isolated population due to chance

Flip coin 10 times: may get 7 heads and 3 tails

Flip coin 1000 times: unlikely to get 700 head and 300 tails

Genetic drift

Two conditions that lead to genetic drift

a. Bottleneck Effect – genetic makeup of a small surviving population is unlikely to be representative of original population Northern elephant seals nearly

extinct due to hunting in late 1890’s which caused little genetic variation at 24 different loci

The bottleneck effect: an analogy

Cheetahs, the bottleneck effect (only 3 small populations in the wild)

b.The Founder Effect – occurs when a few individuals colonize a new habitat; the smaller the sample size, the less the genetic makeup of the colonists will represent the gene pool of the large population they left

2. Gene Flow – a population may gain or lose alleles through genetic exchange due to immigration and/or emigration

Example: wind blowing pollen

Bent grass grows on abandoned mine and is more copper tolerant that grass not near mine. Ongoing gene flow

makes hard for either population to fully adapt.

Gene flow and human evolution

3. Mutations- change in an organism’s DNA For any one gene locus,

mutation does not have much effect on population unless mutation is a benefit and allows for more offspring

Example: bacteria resistant to antibiotics

Mutations – can only be passed on to offspring when they occur in cells that produce gametesOn rare occasions, a mutant allele

may be beneficial Ex. Houseflies resistant to DDT A single bacterium can make a billion cells in 10 hours so mutations can change whole populations quickly.

4. Nonrandom mating – individuals choosing mates

Inbreeding – mating between closely related partners (extreme example is self-fertilization) Increases homozygous offspring, decreases heterozygous offspring

Assortive mating – individuals select partners like themselves

5. Natural Selection – populations consist of varied individuals and some of these variants leave more offspring then others

White flowers easily seen by herbivorous insects so more pink survive to make more pink plants

Of all the agents of microevolution that change gene pools, only natural selection is likely to adapt a population to its environment.

Figure 23.7 A nonheritable differences within a population (Map butterflies that emerge in spring are orange and brown and those that emerge in late

summer are black and white.)

Geographic variation between isolated populations of house mice (on Madeira island which was settled by Portuguese who

brought mice with them in 15th century)

Neutral Variation – variation that appears to have no selective advantage Example: fingerprints

NATURAL SELECTION: Natural selection is the mechanism for

adaptive evolution. Darwinian fitness – the relative contribution

that an individual makes to the gene pool of the next generation

Relative fitness – the contribution of a genotype to the next generation compared to other alternative genotypes for same locus The highest relative fitness a genotype can

have is 1 If plants with white flowers average 80% as

many offspring as pink flowered plants, their relative fitness is 0.8

NATURAL SELECTION EFFECTS

Stabilizing selection– acts against both of the extreme phenotypes and favors intermediatesExamples:

human birth weight in 3-4Kg range

horseshoe crab

Directional selection– shifts towards one extreme phenotype (often during periods of environmental change)Examples:

bacteria resistant to antibiotics light vs. dark moths in England

Directional selection for beak size in a Galápagos population of the medium ground finch

Diversifying (disruptive) selection – when environmental conditions favors both extremes of a phenotypic rangeExamples:

finch population with 2 bill sizes butterfly with 2 distinct morphs

Diversifying selection in a finch population

Modes of selection

Sexual dimorphism – distinction between the secondary characteristics of male and females

Sexual selection – selection process leading to sexual dimorphism

Sexual selection and the evolution of male appearance

Male peacock

DIPLOIDY

Recessive alleles persist in environment due to heterozygotes

The rarer a recessive allele, the greater degree of protection a hybrid offers (especially if recessive allele is harmful)

Heterozygote advantage – when a heterozygote has greater survivorship and reproductive success than any homozygoteExample: those who are carriers for

sickle cell anemia are resistant to malaria

Inbreeding can cause excessive homozygous conditions

Normal and sickle cells

Mapping malaria and the sickle-cell allele

Frequency-dependent selection – the reproductive success of any one morph declines if that phenotypic form becomes too commonFemale African swallowtail

butterflies mimic several noxious species This would be less effective if only one species was imitated.

Right and left mouthed fish (cichlids) have different shaped mouths for approaching prey and eating scales

THE ORIGIN OF SPECIES

Chapter 24

Origin of Species

Macroevolution – the origin of new taxonomic groups

Speciation – the origin of new species

How does one species split into two?????

A Galápagos Islands tortoise

SPECIES Species - population(s) whose

members interbreed in nature and produce fertile offspring

The biological species concept is based on interfertility rather than physical similarity

Diversity within species

Reproductive isolation – barriers that prevent two species from producing viable, fertile offspring

1. Prezygotic – impede mating between species by hindering the fertilization of ova

2. Postzygotic – impede mating between species by preventing the zygote from developing into a viable, fertile adult

Barriers that prevent different species from interbreeding:

A summary of reproductive barriers between closely related species

PREZYGOTIC BARRIERS

a. Habitat Isolation – living in different habitats within same area • Example: snakes in water vs.

landb. Behavioral Isolation – special

signals to attract mates (probably most important barrier)

• Example: fireflies using different blinking signals

Blue-footed boobies: Males high step as part of a courtship ritual. This creates a behavioral barrier between species.

c. Temporal Isolation – breeding during different seasons or years• Example: skunks mating in summer vs.

late winterd. Mechanical Isolation – cannot mate due to

anatomical differences• Example: flowers with different

structures for different pollinatorse. Gametic Isolation – gametes unable to fuse

together to make zygote• Example: sperm not surviving vaginal

environment

POSTZYGOTIC BARRIERSa. Reduced Hybrid Viability – zygotes/embryos

aborted (miscarriage)• Example: frogs (Ranus)

b. Reduced Hybrid Fertility – offspring end up being mostly sterile

• Example: horses mating with donkeys to make sterile mules

c. Hybrid Breakdown – offspring are fertile, but next generation is sterile

• Example: cotton

FAULTS WITH THE BIOLOGICAL SPECIES CONCEPT

Extinct organisms Asexual organisms Too rigid: dogs and coyotes Gene flow through

subspecies

OTHER SPECIES CONCEPTS

Morphological – physical features

Recognition – mating adaptations

Cohesion –phenotype (genes and adaptations)

Ecological – live and do (niches)

Evolutionary – sequence of ancestral and descendant populations

SPECIATION

1. Allopatric – a geographic barrier isolates populations blocking gene flow

2. Sympatric – intrinsic factors alter gene flow (like nonrandom mating)

Figure 24.6 Two modes of speciation

ALLOPATRIC SPECIATION

Geographical barriers – mountains forming, canyons forming, climate changing landExample: pupfishes (Cyprinodon) in springs of Death Valley CA and OR (drying caused separated “pools” in which speciation occurred)

Allopatric speciation of squirrels in the Grand Canyon. On left is Antelope squirrel (A. harris) and on right White-tailed antelope squirrel (A. leucurus)

Has speciation occurred during geographic isolation?

Conditions Favoring Allopatric Speciation

Peripheral isolate already different from original population (ex. phenotypic extremes)

Genetic drift at work because smaller population size

Different natural selection in new environment

SYMPATRIC SPECIATION

Mate choice in two species of Lake Victoria cichlids: females chose mates that have same color as themselves. Under monochromatic light, females chose both colors equally because they look the same. (Nonrandom mating causes sympatric speciation)

POPULATION GENETICS LEADING TO SPECIATION

Adaptive divergence – when 2 populations adapt to different environments, they accumulate differences in their gene poolsReproductive barriers may evolve coincidentally causing the populations to differentiate into 2 species

OUTCOMES OF DIVERGENCE

Two populations get back together and interbreed = no new species

Two populations get back together and do not interbreed = 2 new species

Hybrid Zone = where 2 populations get back together and interbreed to make hybrids only around the region where they overlap

Alleles specific to yellow-bellied toads decrease from 100% in areas where only they are found, to 50% in hybrid area, to almost 0% in fire-bellied area.

Speciation can occur rapidly or slowly and can result from changes in few or many genes

Punctuated equilibrium – describes periods of apparent stasis “punctuated” by sudden change

THE HISTORY OF LIFE ON EARTH

CHAPTER 25

A painting of early Earth showing volcanic activity and photosynthetic prokaryotes in dense mats

Volcanic activity and lightning associated with the birth of the island of Surtsey near Iceland; terrestrial life began colonizing Surtsey soon after its birth

INTRODUCTION

Life originated between 3.5 and 4 billion years agoStromatolites – fossilized mats

that contain banded domes of sedimentary rock (3.5 bya) and contain prokaryotes

Oldest rocks are 3.9 billion (Greenland)

Bacterial mats and stromatolites

Stromatolites in Northern Canada

Early Life

To produce simple cells via chemical/physical processes and natural selection:

1. Abiotic synthesis of small organic molecules (ex. amino acids)

2. Joining of smaller molecules into macromolecules (ex. proteins)

3. Packaging macromolecules into protobionts where internal and external environments are different

4. Origin of self-replicating molecules that lead to inheritance

ABIOTOIC SYNTHESIS OF ORGANIC MONOMERS

A.I. Oparin and J.B.S. Haldane (1920’s) – early atmosphere of earth favored chemical reactions that could produce organic compounds

Low oxygen = a reducing (electron adding) atmosphere

Energy from lightning and higher UV radiation needed to make bonds

Stanley Miller and Harold Urey (1953) – made amino acids from H20, CH4, NH3, H2 and electricity

Now we wonder where this occurred – atmosphere or deep sea vents?

Lightning

Proteinoids – proteins formed from abiotic means (no enzymes)Need a substratum like hot

sand, clay, or rockVaporization would concentrate

monomers on substratumMetals in substratum act as

catalysts to bind monomers together

PROTOBIONTS

Aggregates of abiotically produced molecules

Not capable of precise reproduction, but maintain different internal conditions than external environmentLiposomes – found to form

spontaneously and are made of lipids Can have membrane potential and undergo osmotic pressure

Laboratory versions of protobionts

RNA FIRST GENETIC MATERIAL

When a RNA strand is added to a solution of RNA nucleotides, small sequences can be made using strand as template and base pairing

Thomas Cech (1980s) found ribozyme (enzyme that is not a protein) which catalyzes RNA synthesis

Abiotic replication of RNA

RNA can make a variety of shapes due to different sequences

This could lead to natural selection of certain shapes (sequences)

Weak binding of amino acids to strand of RNA allows protein to be made (this happens today in rRNA/protein interactions)

Packaging of RNA genes and their products within a membrane a great milestone!

Origin of life debate

Laboratory experiments prove that life could have evolved in the “primordial soup”, but cannot prove that it did.

First bacteria able to survive extreme heat so life could have evolved near deep sea vents and volcanoes

Extraterrestrial source? Line between protobionts and live cells

blurry

Radiometric dating – absolute datingHalf-life – the amount of time that it

takes for 50% of the original sample to decay

Carbon-14 has a half life of 5,730 years so its used for younger fossils

Uranium-238 has a half-life is 4.5 billion years so its used for older fossils

Not temperature sensitive

Radiometric dating

The Geologic Time Scale

Clock analogy for some key events in evolutionary history

GEOLOGIC TIME SCALE

Earth is approximately 4,600,000,000 years old

Precambrian – (4.6 bya to 542 mya) Only bacteria for a billion years Towards end of era there were some

eukaryotes which included algae and soft-bodied invertebrates (some multicellular)

Gradual increase of oxygen caused by photosynthetic bacteria (2.7 – 2.2 bya)

Oxygen revolution followed with great increase in O2. Why? Maybe chloroplasts???

Endosymbiotic Origin of Mitochondria and Chloroplasts

Larger prokaryotes engulfed smaller prokaryotes (ancestor of mitochondria and chloroplasts) for origin of eukaryotes

Evidence for endosymbiosis Inner membranes of both organelles have ETC

like prokaryotes Both organelles replicate like binary fission,

have ribosomes, and circular DNA like prokaryotes

Many genes move to nucleus (transposons)Eukaryote genome “chimera” like – mixture of

prokaryotic genes and cell parts

Endosymbiosis

Paleozoic – (542 – 245 mya) Cambrian explosion of animals

Mostly marine lifeColonization of land by plants

and later animalsFirst amphibians, reptiles and

insectsShallow seasExtinction of marine life at endPangaea formed at end

Mesozoic – (245 – 65 mya)Flowering plants appearPangaea breaks upSmall mammals appearExtinction of dinosaurs as well as

many other organisms (65mya) Cenozoic – (65 mya – present)

Major radiation of mammalsHumans appear 500,000 years

ago

HISTORY OF LIFE

Long periods of slow change punctuated by briefer intervals when turnover of species was extensiveMass extinctionsExplosive adaptive radiation

Survivors became adapted to vacant niches left by extinctions

MASS EXTINCTIONS

Examples: dozen or more in fossil record

Two most studied Permian Extinctions (end of

Paleozoic)Cretaceous Extinctions (end

of Mesozoic)

Diversity of life and periods of mass extinction

PERMIAN EXTINCTIONS

Claimed 90% of marine life Occurred in less than 5 million years Possible causes:

Pangaea forming, Siberian volcanoes caused global warming, reduced temperature differences causing low O2 in oceans

Earth’s crustal plates and plate tectonics (geologic processes resulting from plate movements)

Crustal plate boundaries

San Andreas fault

The history of continental drift

CRETACEOUS EXTINCTIONS

Claimed half of marine species and most dinosaurs

Possible causes:Continental drift (volcanoes etc.)Asteroid hitting earth on the

Yucatan coast of Mexico Chicxulub crater approximately 180 km in diameter

Trauma for planet Earth and its Cretaceous life

Evidence supporting Chicxulub:Thin layer of iridium in rock

layers (from ET debris)Dust cloud blocks sun and

makes acid rainExtinction rates in N. America

more severe and occurred fasterExtinction rates not uniform

across the globe

Adaptive Radiation

MAJOR EPISODES 4.6 bya – Origin of earth 4 bya – first prokaryotes Oxygen increases due to

photosynthesis by cyanobacteria (2.7 billion)

2.1 bya - first eukaryotes 1.2 bya – first multicellular

organisms Snowball earth – possible severe

ice age that ended ~570 mya which allowed explosion of life

570 mya – oldest animal fossils

Some major episodes in the history of life

Filamentous cyanobacteria from the Bitter Springs Chert

Fossilized animal embryos from Chinese sediments 570 million years old

500 mya – plants and symbiotic fungi colonize land

66 mya – dinosaurs extinct 5 mya – apelike humans 500,000 years ago – first

“humans” Animals more like fungi than

plants Most of life on earth has been

aquatic

Evolution is NOT goal oriented! Evolution is like tinkering—it is a

process in which new forms arise by the slight modification of existing forms

Fig. 25-25

Recent(11,500 ya)

NeohipparionPliocene(5.3 mya)

Pleistocene(1.8 mya)

Hipparion

Nannippus

Equus

Pliohippus

Hippidion and other genera

Callippus

Merychippus

Archaeohippus

Megahippus

Hypohippus

Parahippus

Anchitherium

Sinohippus

Miocene(23 mya)

Oligocene(33.9 mya)

Eocene(55.8 mya)

Miohippus

Paleotherium

Propalaeotherium

Pachynolophus

Hyracotherium

Orohippus

Mesohippus

Epihippus

Browsers

Grazers

Key

PHYLOGENY AND THE TREE OF LIFE

CHAPTER 26

Fossil of a fish: perch

A gallery of fossils

Figure 25.1b Skulls of Australopithecus and Homo erectus

Ammonite

Figure 25.1f Dinosaur tracks

Mammoth tusks

Barosaurus

VOCABULARY

Phylogeny – evolutionary history of a species or related species

FOSSIL RECORD Incomplete record Minerals replace organic

material Hard parts leave fossils Some tissues preserved Molds made Relative dating (older

fossils in bottom layers of rock)

CLASSIFICATION

DomainKingdomPhylumClassOrderFamily

GenusSpecies

Hierarchical classification

The connection between classification and phylogeny

PHYLOGENY V. CLASSIFICATION

Scientific Name = Genus speciesHomo sapiens

Any level is a taxon (pl. taxa)Example: phyla and order etc.

EVOLUTIONARY HISTORY OF TAXA

Monophyletic – when a single common ancestor gave rise to all species within that taxon (ideal)

Polyphyletic – members of a taxa are derived from 2 or more common ancestors

Paraphyletic – when a taxon excludes species that share a common ancestor

Monophyletic versus paraphyletic and polyphyletic groups

Homology – shared likeness due to common ancestry

Analogy – shared likeness due to convergent evolution

Convergent evolution – species from different evolutionary branches may come to resemble each other due to similar ecological roles and natural selection

Parsimony and the analogy-versus-homology pitfall

Convergent evolution and analogous structures

The ocotillo of southwestern N. America (left) looks like Alluaudia of Madagascar (right).

MOLECULAR BIOLOGY AND SYSTEMATICS

Species diverge only when changes occur in nucleotide sequences

Species that are phylogenetically closely related have more similar nucleotide sequences

MOLECULAR CLOCKS The number of differences in

nucleotide bases between homologous sequences is a measure of evolutionary distance

Clocks calibrated by graphing differences in sequences against known events in fossil recordAssumes constant mutation ratesNatural selection would alter mutation rates

Dating the origin of HIV-1 M with a molecular clock

• Most widespread strain of HIV

• Estimated to jump to humans in 1930’s

• Based on DNA sequences from 1980 – 1990’s

FOSSILIZED DNA

Use PCR DNA may be contaminated

with bacterial DNA or other DNA

Even with DNA cloned, cannot make dinosaurs until we understand the developmental steps involved

PHYLOGENETIC SYSTEMATICS

Phenetics – based on measurable similarities and makes no phylogenetic assumptions

Cladistics – classifies according to the order in time that branches arose along a dichotomous treeClade – an evolutionary branchOutgroup – a species that is

relatively closely related to the group of species being studied, but is clearly not as closely related as any study group members are to each other

Synapomorphies – shared derived characteristicsCharacteristics that are homologous and evolved in an ancestor that is common to all species on one branch of a fork, but not common to other branch

Parsimony – find the simplest explanation

Constructing a cladogram

Cladistics and taxonomy

Branch lengths can indicate time

Cladistics accepts only monophyletic taxa Example: birds are more closely related to

crocodiles than snakes and lizard are to crocodiles (birds and crocodiles have synapomorphies not present in snakes and lizards)Class Aves and Class Reptilia wrong

cladistically because birds should be in same group as crocodiles

On other hand both mammals and birds have 4-chambered hearts and yet birds are more closely related to reptiles (not mammals)Four chambered heart evolved more than

once

Figure 25.18 Modern systematics is shaking some phylogenetic trees (this means class Reptilia in its traditional form is paraphyletic, not monophyletic)

Figure 25.19 When did most major mammalian orders originate?