evolution exam notes

8/11/2019 Evolution Exam Notes

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Lamarcks Ideas:1) Pattern

a. Living world made up of many separate lineages with independent origins- simpler organisms havent had much time to evolve as those that are more complex

b. Each lineage progresses (strives) towards greater complexity/perfection2) Process/Mechanism

a. Use-and- disuse, and Inheritance of acquired characters ( Lamarckism )- If you use a body part more than other parts, this part will become more developed than otherpart

- Features that you acquire during your lifestyle will be passed onto your offspring- Note that the INDIVIDUALS EVOLVE

Darwins Ideas:1) Pattern- Living things united in a single branching tree of relationships- The history of life on earth is a branching tree, species changing into species over time- A point where one lineage divides into two divisions happen more than once in a tree- Look at the fork closest to the end Most recent Common Ancestor of the two divisions (A + B)- Descent with modification Species A and B are similar because of their shared history prior to

their last common ancestor- But species A and B also differ because of independent changes in their lineages after divergence

from their last common ancestor- This fits with Linnaean classification Tree of Life fits well to hierarchical classification

2) Process- Evolution occurs primarily because of the action of Natural Selection- Key point: individuals of a species belong to populations- Note that populations evolve, not individuals

Natural Selection Ingredients:1) Heritable Variation- Individuals in a population are born differing in many traits (many features)- Many traits can be passed on from parents to offspring (i.e. are heritable )

- Ex: shells that are all belonging to snails, shell patterns are heritable

2) Excess Production- In any population, more offspring are produced than needed to maintain it (usually many more)- When resources are limited, many of the offspring do not survive (or at least, dont reproduce

successfully)- Excess production leads to competition: the struggle for existence some will succeed, some

will not- But because of their differing traits, some individuals have an advantage i.e. will produce more

viable offspring on average- This is the concept of fitness

Then advantageous traits increase in frequency- Heritable traits that helped individuals to have more viable offspring on average will tend to be

passed on to those more numerous offspring- With time, these traits will tend to become more frequent in the population (& disadvantageous

traits will become less frequent)- This is evolution (the population has evolved)- Prevalence of a trail increases, the physical traits represent this in a population

Natural selection over time results in adaptive evolution (adaptation) - organisms well suited to their


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environment

Evidence of Natural Selection Warfarin Resistance in Rats

- Only a few rats that had mutations with warfarin resistance- Once warfarin was introduced, the rats with resistance were more successful and this mutation

was passed on- Over the next couple of years, they stopped poisoning with warfarin, the frequency of warfarinresistance declined

- Shows: Editing rather than creative mechanism needs variation to act on- Shows: Contingent on time and place - happen to be disadvantageous when poison not used

Evidence for Tree-of-life and descent with modificationsHomologySimilarity resulting from common ancestry

a) Standard anatomical structures structures with different functions but the same form

b) Vestigial Structures structures with little or no function derived from more complex structures ex: human appendix, remnant hind-limb bones in whales (later)

c) Embryological Homologies Organs that share a common function during development, buthave a very different form/function once developed

E.g. pharyngeal pouches in vertebrate embryos Comes gills in fishes Become Eustachian tubes in mammals

d) Molecular Homologies Homologies at the biological level- e.g. The universal genetic cods


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- reflects evolutionary events that take place over time

Analogous Structures (converse of homology) similar functions but very different structures (similaritynot from common ancestry)

convergent evolution: feature evolved in two different times and places on the tree of life

Biogeography- The geographic distribution of organisms- Some taxa (groups of similar species) are restricted to certain locations ( endemic, not

ubiquitous )

- Explanation: descent from a common ancestor that lived in that location

Fossil Record- Descent with modification predicts transitional forms - Order of appearance in fossil record- Examples: whales (fully aquatic mammals)

o Dorsal fin, blowhole, tale adaptation to a fully aquatic lifestyleo Lack hind-limbso Forelimbs lack distinct fingerso Dorsal fin, caudal flukeso Nostrils on top of head etc.

- and birds (powered flight)- A series of many transitional forms link modern whales to land -dwelling mammals

Modes of Selection


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Oscillating directional selection in fluctuating environments- does not need to go in one direction- ex: rainfall in Galapagos Islands, seed size, and finches- Seeds that are big and hard, you need a large beak to get food- Seeds that are small, you need a smaller beak to get food- In rainy years, increase in small beaks- In dry years, need a more robust beaks- Because the environment is changing, the distribution of a phenotype is constantly changing

directions- Fitness is more than survival- Can have a longer life time, but less offspring if behaviour doesnt allow it to mate

Sexual Selection- Effectively a special case of natural selection- Competition for mating opportunities-

Results in adaptations that increase mating successo But can actually reduce change of survival

Intrasexual selection- Competition within one sex (usually males) for mating opportunities- Adaptations: Armaments physically competing

Intersexual selection- One sex (usually females) chooses mate from (competing members of) other sex- Ornaments visually competing

Evolution of populationsFixed alleles: Whole population is homozygous at locusPolymorphic loci: two or more alleles in population, each present at some frequency

Microevolution: Change in the frequencies of different alleles in the gene pool over generations At the extreme, change can mea n fixation of an allele, or loss (extinction) of an allele.

Hardy-Weinberg Principle: describes expected relationships between allele and genotype frequencieswhen there is no evolution

p + q = 1 p2 + 2 pq + q2 = 1


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e.g. High prevalence of particular normally rare genetic diseases in isolated human populations- Ellis-van Creveld Syndrom- ~1000x more common in a particular Amish group than in general population

Endangered populations/species- Genetic diversity (gene pool) can be increased by adding individuals from other populations

(enforced gene flow)- Captive breeding programs manage matings to preserve remaining genetic diversityPreserving Allelic Variation

Diploidy hides recessive alleles from selection when they are rare .- e.g. earlier cystic fibrosis example: q =~0.02; ~1 in 25 Europeans are carriers; Only 1 in 2500 arehomozygous.

Natural Selection can sometimes favour allelic variation: Balanced Polymorphisms, e.g.: Frequency-dependent selection Heterozygote advantage (= overdominance)

Inverse Frequency-Dependent Selection: Rarity increases relative fitness of a variant e.g. the scale-eating fish left and right mouthed scale eating fish tend to eat scales off the plank of a fish

Sickle-cell anemia (a case of Heterozygote advantage) Single locus recessive genetic disease ss homozygotes - severe illness, high mortality while young: Fitness of ss much lower

than SS or Ss But, Ss confers resistance to malaria (deadly) Malaria absent: SS, Ss similar fitness Malaria prevalent: Ss confers higher fitness than SS ** learn this as an example

What is a species?Morphological Species Concept: based on morphological similarity. (Molecular sequencing is now alsoused)Biological Species Concept:

Inter-fertility: populations that interbreed to produce fertile offspring

Reproductive Isolation: Do not normally successfully interbreed in nature with other species

Speciation- Reproductive barriers inhibit gene flow between populations, allowing evolutionary divergence- Prezygotic barriers: act before fertilization- Postzygotic barriers: act after fertilization

Prezygotic Barriers Postzygotic Barriers1. Habitat isolation2. Temporal isolation3. Behavioural isolation

4.

Mechanical isolation5. Gametic isolation (gameteincompatibility)

1. Hybrid Inviability2. Hybrid Infertility3. Hybrid Breakdown

(pages 490-491)


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Geographic Barriers:(Mountain ranges, rivers, open water, lakeformation, land bridges)

- Either barrier forms during history ofspecies or rare migrants cross existingbarrier.

- Ex: Isthmus of Panama: formed 10-3million years ago, isolating populationof many species

Evolution after separation:- Natural selection to different

environments (adaptive evolution)- Genetic drift (especially in small isolated

populations)- Migrants found new small population in

peripheral habitat

SpeciationAllopatric speciation: geographic barrier blocks geneflow between populationsSympatric speciation: new species arise within rangeof parent population

Requires a barrier to gene flow within a geographic

region Host switching by specialist herbivores or

parasites (habitat/behavioural isolation) Disruptive selection, favouring evolution of

reproductive barriers between individualswith different phenotypes?

Polyploid speciation in plants

- mutation- Having more than two sets ofchromosomes

- Can cause speciation in sympatric plantpopulations, gene flow is reducedbetween polypoloid and normalindividuals

- Reproductive isolation, genetic isolationoccurs


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If contact re-establishd between evolved allopatric populations:1) Complete reproductive barriers evolved:

populations now classic biological species OR

Fusion: Dont undergo sympatric speciation eventhough they have separated, failure to speciation Reinforcement: Have a reproductive barrier less likely to make the disasterous choice, number ofhybrids being produced declines - Speciation can be favoured further

Evolution of complex features(Darwin proposed evolution through many small steps, every step should improve fitness)

1) Functioning Intermediates- In many cases, simpler forms of complex structures are potentially functional

o Evidence: Organs of different complexity in related specieso Tep-wise evolution plausibleo Ex: Functional eyes of different complexity in different living molluscs

2) Modification of existing structurs- Exaptation: Structures adapted for one function are coincidently used for another function

o Ex: Birds are related to dinosaurs. The original function of the feather was not for flight.

Feathers in non-flying dinosaurs were used foro thermoregulation or display 3) Larger steps than imagined by Darwin- Changes in developmental regualtion- Origin of novel genes (gene duplication)

o Evolution of developmental regulation: mutations affecting genes that controldevelopment small genetic change can result in lage coordinated changes inphenotype

o Homeotic genes genes that are involved in embryologic development which specifiywhich segments of the ebryo develop into

Hox genes: control indentity of segments along developing animal bodyo Evolutionary modification of rates of growth during development


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Phylogenies and SystematicsSystematics: study the diversity of life

two componentsTaxonomy: naming andidentification of taxa species and groups of speciesPhylogenetics: ofevolutionary trees(phylogenetictrees/phylogenies)

Binomial Names Genus species

Different groups on trees Monophyletic group (Clade):

An ancestor and all of itsdescendants

Paraphyletic group: An ancestor and some, but not all , of its descendants Polyphyletic group: A group that does not include its own most recent common ancestor (= 2+

branches artificially grouped together)


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How do we infer phylogenies? Character states (possible homologies)

Morphological features, etc. Identities in DNA / protein sequences

Distribution of character states amongorganisms reflect evolutionary relationships (see next

slides)

What if there is a conflict? i.e. character state distributions are not all consistent with the same tree

Convergent evolution (analogy not homology - see lecture 2) Reversals (e.g. loss) Compare many (all) possible trees

Parsimony criterion: best tree is the one that implies fewest evolutionary changes.

Molecular Sequence Data Phylogenies usually constructed by comparing molecular sequences (e.g. DNA, proteins). A site in a set of aligned DNA sequences is a character: Different bases at site are the states


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Phylogenies of genes Evolution of genes themselves is often of interest e.g. tracing history of gene duplication, or of

gene transfer between genomes One of many aspects of the disciplines of

molecular evolution and genome evolution Aligned molecular sequences (DNA, proteins) can

be used to infer relationships among organisms, Genes themselves have evolutionary trees, which

can be studied to understand their history, (e.g. genetransfer)

MacroevolutionSedimentary rock is where most fossils arefound.

Relative dating Order of appearance in strata Index fossils to compare locations

Absolute dating Radiometric (Isotopic decay) Ancient sedimentary rock and

organic material hard to date directly Radiometric dating used to directly

date volcanic (igneous) rock. e.g. Potassium-40 Argon-40

dating

Indirect dating of sedimentary rock and fossils associated with datable volcanic layers


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End-Permian Mass Extinction

~250 million years ago Most devastating mass extinction. Extinction of ~90% of species on earth Many large taxa went totally extinct

(e.g. ~50% of Families) Ultimate Cause:

Volcanic activity??End-Cretaceous mass extinction

~65 million years ago Most recent big mass -extinction Extinction of ~50% of species on earth

e.g. dinosaurs (other thanbirds)

Several marine invertebrategroups

Cause Asteroid impact (probably)

Adaptive Radiations: is the evolution of ecological and phenotypic diversity within a rapidly multiplyinglineage.

Rapid speciation and evolutionary change in underexploited habitats Regional:

e.g. colonisation of new island chains World-wide: Following mass extinction events. Replacement in fossil record.
http://en.wikipedia.org/wiki/Evolutionhttp://en.wikipedia.org/wiki/Ecologyhttp://en.wikipedia.org/wiki/Phenotypichttp://en.wikipedia.org/wiki/Lineage_(evolution)http://en.wikipedia.org/wiki/Lineage_(evolution)http://en.wikipedia.org/wiki/Phenotypichttp://en.wikipedia.org/wiki/Ecologyhttp://en.wikipedia.org/wiki/Evolution


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The major lineages of life(page 515)

- Since ancient times: 2 kingdoms:animals and plants

- In 1970: five -kingdom scheme: o Animaliao Plantaeo Fungio Protistao Monera (prokaryotes)

Some problems with the five-kingdom scheme- Imperfect fit to phylogeny

o Protista and Monera are paraphyletic groups, not monophyletic (lecture 5)- No formal taxon for Eukaryotes

Importance of Prokaryotic Life On Earth for >3 billion years Most of biological activity in many ecosystems

Ocean Soil More prokaryotes than human cells in body Cause many major diseases & infections Biotechnology

Typical prokaryotes Small, simple in structure

Single cells, sometimes simple colonies Little compartmentalisation of cell

Compact genome Usually one chromosome (plus plasmids) Most of DNA is coding: usually 1-6000 genes

Efficient Growth when resources are scarce, and/or ..very rapid growth and reproduction when resources plentiful

Some species can reproduce every 20 mins under ideal conditions (by binary fission )

Metabolic diversity (examples) Photoautotrophy (photosynthesis) in some groups:

Harvest light energy; Convert CO 2 into new organic carbon - as in plantsBut also


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Chemoautotrophy : Obtain energy from oxidising inorganic chemicals; Convert CO 2 into neworganic carbon

e.g. Sulfide (H 2S) oxidisers

Evolution by acquisition gene transfer: Some Plasmids Lateral (Horizontal) gene transfer between genomes

Now recognised as extremely important evolutionary process in prokaryotes

Bacteria Most diverse Domain Most of the well-known prokaryotes Includes all known disease-causing prokaryotes- Cell Surface- Usually two bounding membranes : Plasma membrane and outer membrane- Peptidoglycan layer between (complex polymer of sugars and amino acids)- Some instead have plasma membrane only- Usually with thick peptidoglycan wall

A few important types of bacteria- Spirochetes- Gram-positive bacteria- Cyanobacteria (photoautotrophs)- Proteobacteria

Archaea Some (many) are extremophiles

Some are extreme thermophiles (some grow at 110C; usually also chemautotrophs) Some are extreme halophiles (salt-loving)

Many are methanogens - produce methane as a waste product of (anaerobic) energymetabolism.

Dominant biological source of methane.

Archaea Cell surface No outer membrane; no peptidoglycan Membrane lipids chemically different from those of both Bacteria and eukaryotes


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Archaeal membrane lipids

(Branched chains, Ether-linked) Bacterial or Eukaryotic membrane lipids


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Some prokaryote-cell-like features of mitochondria and plastids Similar size Divide by binary fission Have ribosomes (Prokaryotic-like) Have their own genomes!

Encode some RNAs, and proteins that are translated on the organelle ribosomes

Protists: The first eukaryotes were single cells Most of the major lineages of eukaryotes alive today are still single- celled protists Very abundant in most ecosystems

Important photosynthesisers (algae) The major predators of prokaryotes Parasitic protists cause some major diseases

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