Lectures 2-8

Lecture 2

“Evolution is just a theory, its not a fact”

• scientific theory is different

  • not a guess or a hunch

  • well-established, well-supported, well-documented explanation for our observations and is supported by facts

• theory > law

Laws of gravity → if you drop something it will fall to the ground

• description, but doesn’t explain why

• theory explains why

Humans and chimpanzees shared a common ancestor 5-7 mya

• example of divergence

• but this is considered recent in evolutionary terms

• but our genomes are still 99% identical

Life started in the water.

Whales are examples of mammals returning to the sea

Blue whale

• largest animal to exist on earth

Virus

• very small

• with relatively less protein-coding genes

Whales are mammals

• share numerous synapomorphies (shared derived traits) with mammals

  • mammary glands → produce milk

  • three middle ear bones

  • hair (in embryos)

• their similarities with fish are convergent evolution → evolved independently

Homoplasy refers to a shared trait between species that did not arise from a common ancestor but rather evolved independently.

Convergent evolution is a specific type of homoplasy where unrelated species evolve similar traits due to similar environmental pressures or ecological niches.

Dordudon has teeth that has a strong resemblance to extinct land animals (synapomorphy)

Pakicetus

• transitional species

• long snout and teeth like dolphin

• share traits with modern relatives

  • involucrum

  • astragalus (within our ankles)

Plantigrade → walk on entire foot (humans)

Digitigrade → walk on fingers (cat/dog)

Unguligrade → walk on one finger (horse)

Terrestrial animals drink freshwater; marine animals drink seawater

• 18 O/16 O ratio is higher in saltwater → higher in teeth of marine animals

• the smaller the ratio → drinking freshwater → spent time outside water

• Pakicetids had a small ratio

Changes in gene expression led to hindlimb loss

• hindlimb begin to form but fail to fully develop

• genes for hindlimb express less

• opening in the bone allows movement by limbs

  • over time, as they shifted from land to water, the bone closed

Mysticetes → Whale → baleen (“comb-like” that traps food)

• completely replaced teeth

• genes for teeth have been disabled

Odontocetes → Dolphin → teeth (for hunting)

Whales and fish have evolved similar body forms (independently)

Replication of genetic material results in mutations

• spike proteins on the Cov-2 virus bind to surface ACE2 receptors

  • spike proteins are proteins found on the surface of viruses that bind to receptors on the surface of the host cell

• the virus hijacks the host’s cellular machinery to express viral proteins and replicate the viral RNA, making new coronavirus

• occasionally a mutation occurs during replication, altering the tip of the spike protein produced

• the new viruses are released. Some of them carry the altered spike protein

• if the mutation is beneficial it will be favored via natural selection

  • no longer recognized by the immune system

  • increase reproduction

  • dominates population

Similar structure of SARS CoV-2 found in bats

Omicron is highly infectious

Viral reassortment → different combinations

• ex. H7N9 influenza genome is derived from 4 different bird strains

Macroevolution → inferring evolution across millions of years (e.g. whales)

Microevolution → observing allele frequencies change across generations (e.g. viruses)

Whales and humans share a common ancestor (both mammals)

Lecture 3

One of the MOST important and central themes in evolutionary biology is that all of life on Earth is related

Cetaceans are mammals with fish-like bodies

• as they returned to the water they evolved fish-life bodies as it is well adapted to an aquatic environment

Dolphins have the same set of genes that regulate the development of hindlimb that land mammals have

• they grow hindlimb but the expression is terminated very early on by a mutation in a regulatory region

Darwin

• all living things are connected in the “tree of life”

• explains how patterns of diversity came to be

• combined his ideas with the work of many others

Special creation

• a common thought was that:

  • species are independent (unrelated)

  • life on Earth is young

  • species are immutable (incapable of change)

Plato:

• God creates every organism

• they were unchanging

• typological thinking → discrete types independent of each other

Aristotle:

• linear great chain of being

• species were fixed types

• increasing size and complexity

• minerals and lower plants to humans

• above us are angels and god

Carolus Linnaeus:

• father of modern taxonomy

• included all of the animals

• didn’t go against typological thinking

• DKPCOFGS → used structural similarities

Georges Buffon

• Earth was formed by chemistry and physics

• started to accept that Earth was older than initially thought

• acceptance of distinct types → transformed when environment changed

Georges Cuvier

• fossils resemble modern species

• extinction

• realized life has changed over periods of time

Mary Anning

• challenged great chain of being by introducing extinction

• found many extinct reptiles

James Hutton

• recognized that small changes occur over time

• Earth must be very old

William Smith

• different layers contain distinct fossils

• extinction insight in rocks below

• created the first geological map where same layers of rock in different parts of England

• strata → layers

Jean-Baptiste Lamarck

• simple to complex

• species change through time

• complex species start off as microbes

• he believed in acquired changes

  • giraffe needs to reach higher branches so it stretches its neck → passed to offspring

Charles Darwin

• unofficial naturalist for HMS Beagle voyage (5 years old)

• finches differ on islands

• received a letter from Wallace

Charles Lyell

• uniformitarianism → same observable natural process today were also responsible for events in the past

• slow process of erosion over long period of time can produce massive canyons

Alfred Russel Wallace

• proposed similar evolutionary ideas

• common ancestor, natural selection

Darwin and Wallace:

• change does not occur linearly

• population → individuals of the same species living in the same area at the same time

• certain traits produce more offspring

• population thinking instead of typological thinking

• branching tree of life

Artificial selection is when humans are selective agents (breeders) and exaggerate traits not seen in nature

Thomas Malthus

• grim proposal

• do not support poor

• only those that can adapt would survive and reproduce

Descent with modification:

• origin of species

• species change through time

• common ancestor relates species

Homologous trait is similar due to inheritance from a common ancestor

Adaption is when traits evolve by natural selection

Lecture 4

Darwin: if erosion was a gradual process, then Earth must be billions of years old

Lord Kelvin

• challenged Darwin’s proposal → argues Earth was younger

• since the Earth is still hot, it must not be that old

• wrong because Earth is not static

Age (radiometric dating)

• extra neutrons means unstable

  • ex. 8 neutrons in carbon mean it is unstable

• unstable carbon-14 will eventually decay to nitrogen-14

• half-life is the time required for half of the radioactive atoms in a sample to become non-radioactive

  • exponential and constant

• for carbon-14, 50% of it will turn into nitrogen-14 in 5730 years

• all radioactive isotopes came to Earth when it was formed and have been decaying since

Earth is 4.56 billion years old

• the line that separates isotopes that will exist on Earth to those that will be decayed is drawn between uranium-238 and uranium-234

  • uranium-234 has a half-life of 245 thousand years, meaning they have all decayed as of now

  • uranium-238 has a half-life of 4.5 billion years, which means that only half of it as decayed as of now

High decay probability → rapidly decay

Low decay probability → slowly decay

Fossil record is incomplete:

• some organisms will erode before becoming fossilized

• invertebrates are challenging

• useless unless we find them

Most organisms do not fossilize

Age of fossils can be estimated by analyzing layers and estimating the position of the fossil

Fossils can also provide clues about behaviour

• fossils of turtles that died while mating

• fossil of organism giving birth

• fossil of organism eating

Trilobite fossils

• provide insight about development

• as the head shield grows longer, it gets wider

• 1:1 ratio

Hadrosaur crest

• connected to the nasal cavity

• hollow and open and sound generated by blowing air

• ears tuned to frequency

• when sound os pushed through, the crest was used to communicate

Biomarkers

• traces of “vanished” life

• presence of okenane → made by purple sulfur bacteria

• distinctive molecules only produced by certain organisms

Inferring diet:

• C3- trees/shrubs

• C4- grasses/rice

• carbon-13 has a higher C4 content than carbon-12

• therefore, if the ratio is higher then C4 plants were the diet

• we have some C3 because the organisms we eat have C3 diets

Three domains:

1. bacteria

   • prokaryotic

2. archaea

   • prokaryotic

3. eukarya

• eukaryotic, membrane-enclosed nucleus and mitochondria

Stromatolites

• living bacteria

• layers of bacteria build-up

• rock-like looking

Multicellularity evolved many times from unicellular ancestors (2.1 bya)

• allow organisms to get larger and more complex

Earliest animal life resembles sponges

• animal, not a plant

• biomarkers also demonstrate existence of sponges early on

Cambrian explosion

• Burgess Shale → thin layer of rock, basically sand

• British Colombia

Early chordates

• organisms that have a notochord

  • hollow nerve cord

  • beginning of spinal cord

• have pharyngeal gill slits and post anal tale

Prokaryotes were the first to colonize terrestrial habitats

First terrestrial plants & fungi:

• 475 million years ago

• had no roots

• Wattieza (very tall tree)

First terrestrial animal life:

• invertebrates (480 mya)

  • likely relatives of insects and spiders

• oldest fully terrestrial animal dates to 428 mya

  • pneumodesmus (like a milipede)

• vertebrates (390 mya)

  • tetrapod (370 mya)

350 mya is when currently existing lineages evolved

Synapsid has one opening for jaw muscles (where we evolved from)

• what early mammal-like organisms evolved from (ex. Dimetrodon)

• first mammals 150 mya

Diapsid had two openings for jaw muscles

Mammals

• diversify after dinosaur extinction

• placental mammals

• whales, bats, primates emerged 50 mya

Birds emerged 150 mya

Flowering plants emerged 132 mya

Insects emerged 400 mya

Humans emerged 300,000 years ago

Lecture 5

Mammals were able to occupy niches left by dinosaurs

Darwin viewed evolution as a branching process

Phylogeny: evolutionary history of a lineage or lineages

• can depict populations, genes, species, or higher taxonomic units

Phylogenetic tree: visual representation of phylogeny

Node: represents common ancestors for all descendant lineages

• free rotation at any node → shapes of trees can change without changing the relationships

Branch: lineage evolving through time; connects successive speciation events or other branching events

Taxa: units of classification

• not linear hierarchy (do not read top to bottom)

Clade: a common ancestor & all descendants

Trees don’t have to include everyone

• they can vary by scale

• without all related species included

Tree of Life: not all species are shown

Polyphyletic group: an unnatural group that does not include the most recent common ancestor

Paraphyletic group: a group that includes an ancestral population and some of its descendants but not all

• fish is a paraphyletic group because it does not include all descendants of the common ancestor of its members

Homoplasy: similarity in organisms due to reasons other than common ancestor

Lecture 6

Tetrapod vertebrates is a monophyletic group because it includes all descendants of the common ancestor.

Characters: identifiable heritable traits

Character state: condition of the character

Ancestral vs. Derived is preferred over Primitive vs. Advanced

• because organisms live as they and adapt with changing environments

Synapomorphies in carnivores

• carnassial → teeth for shearing meat

• synapomorphy in bobcat and Mexican gray wolf

• compared with outgroup (sheep) to infer what is ancestral and what is derived

Ancestral = 0

Derived = 1

Outgroup has all 0

Parsimony: is choosing the topology (tree) depicting the fewest evolutionary steps is often the most accurate

• changes take time, so it is unlikely that traits appeared and disappeared often

• each character state is unique to single branch

Phylogenies are hypotheses

• based on the best available evidence

• analysis of synapomorphies

Monophyletic groups form clades

• are more morphologically similar than polyphyletic

A node represents the point at which a lineage splits

• bifurcate, never more than 2

By analyzing whether a state is present or absent we can interpret relatedness among species

Polytomy (biologically not true)

• more than 2 lineages coming out of one spot

• it means we have to go back, revise, and gather more data

It is unlikely that changes are happening so often

• morphological changes are not changes in one nucleotide, they’re large changes

Homoplasy: character state similarity not due to common descent

Convergent evolution: independent evolution of a similar trait

• body of fish and dolphin

• flight in birds and bats

  • bats have bones throughout the wings, birds have feathers mostly

  • bones represent homology → bone shape is similar

  • flight surfaces are homoplasy as they evolved independently

Evolutionary reversal: reversion back to an ancestral character state (might be by a mutation)

The dark body from the top of the dolphin and shark is so it blends with the ocean. From the bottom, it’s light to blend with the sky.

Coelacanth

• closest living relatives to tetrapods

• existed for 400 million years

• movement of fins different from what you would see in other fish

Eusthenopteron

• evolved on Earth after Coelacanth

• hypothesis that fins became hind limbs

Lobe fine to developing arm of a lizard

Coelacanth lobe-fins have extension-forming lobes

• prediction of intermediate species between eustenopteron and lizards

• use rock layers to find fossils from that time frame

Tiktaalik

• fishapod

• not fish nor tetrapod

• flat head, unusual fins like reptile

• scales and gills like fish

• moved on land

Qikiqtania

• newly discovered

• returned to sea

• progression was not linear

Homology can be obvious or not

• teeth of humans and teeth of beaver -obvious

• teeth of human and elephant trunks -not obvious

Mammalian ear bones are homologous to early synapsid jaw bones

• bones separated themselves from the jaw bone and grow slowly compared to jaw as an organisms grows more complex

• hypothesis: early mammalian species detected vibration through the lower jaw

Archaeopteryx

• ancient wing

• evidence suggesting birds came from dinosaurs

• feathers like birds

• tail, teeth, claws like reptiles

• feathers used for other things:

  • maybe gliding while jumping

  • thermoregulation

  • mate attraction

  • keeping eggs warm in nest

Feathers evolved before flight

• flight is an exaptation

  • natural selection co-opts a trait for a new function

Archaornithura

• dinosaur looks like bird more than reptile

By studying the shared ancestors of birds and deriving behaviours when feathers first evolved scientists confirm that feathers are an exaptation

Lecture 7

Tiktaalik is a transitional fossil that shares some character states with tetrapods and some with lungfishes and coelacanths

Only lobe-fins have a chain of sturdy bones anchoring the fin

Darwin believed:

• must be variation in a population

• some of that variation must be heritable

• survival and fitness is based on that variation (not random)

Variation can also occur within species

• heritable variation in populations was a necessary ingredient in natural selection

Zigzag snails have many different patterns but are the same species

Strawberry poison dark frogs are all individuals of the same species but have different patterns

Mutations are the ultimate source of genetic variation

• any change in out genomic DNA

• must reside in our DNA

Approximately 800+ genes that affect height

Human body has 30 trillion cells

• 3 important molecules for life: DNA → RNA → Protein

• central dogma is a forward pattern

DNA

• deoxyribonucleic acid (missing an oxygen)

• sugar + phosphate group + base

• A, T, C, G

Pyrimidines: C and T (long name, small molecule)

Purines: A and G (short name, large molecule)

Pair up based on A-T and C-G

• things are unhappy when A tried to pair with C/G

• creates a bump in the DNA

• repair mechanisms go to fix the repair

• but which one needs to be repaired is unknown

• if the wrong one is repaired, then a mutation arises

DNA replication

• essential for growth and replication

• mutations are introduced during replication

  • usually corrected but sometimes left

Eukaryotic DNA

• organized into chromosomes

• supercoiled around itself and around histone molecules

• X view of chromosomes is during metaphase

Karyotype is the arrangement of all chromosomes

Ploidy is the number of copies of unique chromosomes

• adder’s tongue (fern) has 96 copies of 15 chromosomes (1440 chromosomes total)

Gene

• basic unit of heredity

• segment of DNA whose nucleotide sequences code for proteins or RNA or regulate the expression of other genes

• changes in when it is expressed, where it is expressed, and how much of it is expressed

RNA

• ribonucleic acid

• single-stranded

• uracil replaces thymine

mRNA

• messenger RNA

• transcript copy of gene

• encodes specific polypeptide

• takes message from nucleus to cytosol

rRNA

• ribosomal RNA

• primary component of ribosome

• catalytic activity

tRNA

• transfer RNA

• clover-shaped

• carries amino acid to ribosome

snRNA

• small nuclear RNA

• splicing and other function

miRNA

• micro RNA

• gene regulation

• joins with a protein, the protein cleaves off a little bit and the complex goes to mRNA to find complimentary base pair and stops translation

siRNA

• small interfering RNA

• for genetic manipulation

dsRNA

• double-stranded RNA

• two complimentary siRNA strands

Protein

• polypeptide

• combinations of 20 amino acids

• primary structure: sequence of amino acids

• secondary structure: local folding into helices or sheets

• tertiary structure: three-dimensional folding

• quaternary structure: happens with some proteins where they interact with other proteins

Somatic mutations → passed to daughter cells

Germline mutations → heritable

Craig Ventor

• pioneered genome sequencing within his genome

• found that between paired chromosomes, there were millions of changes

Point mutations:

• synonymous → change in base but no change to amino acid

• nonsynonymous → change in base altering the amino acid

• nonsense mutation → premature stop codon

Insertion or deletion

• can be in-frame (combinations of 3)

• or frameshift (not in combinations of 3)

Chromosomal mutations

• involve multiple genes

Chromosome fusion

• two chromosomes fused

• we think our chromosome 2 is two chimpanzee chromosomes fused together

Genome duplication

• polyploidy

• the entire genome (ex. human all 23 pairs of chromosomes) copied

Proline amino acid changes

• only amino acid with slightly different configuration

• leads to kinks in protein

• one side of protein blocks the other side, interruption gene expression

Cis-regulatory elements

• near/within focal gene

• promoter, enhancer, or silencer

Trans-regulatory elements

• often far away from focal gene

• bind to cis-regulatory elements

• transcription factors, activator, repressor

Alternative splicing → allows different combinations of exons

Bacteria and Archaea

• variation occurs via mutation

Eukaryotes

• mutations in germline are inherited

• sex introduces genetic variation via recombination

Crossing-over (genetic recombination)

• meiosis

• after duplication

Independent assortment

• independently, but while genetic recombination occurs

• random distribution of homologous chromosome pairs into gametes

Two children from the same parent can be genetically identical but the chances are very slim, considered negligible.

Genotype: genetic makeup

Phenotype: manifestation of the genotype of an organism

• morphological

• developmental

• physiological

• behavioural

Polymorphism: any genetic difference among multiple individuals in a population

Allele: different forms of a gene

Mendel with the peas

• he selected traits that are one gene and two alleles (dominant/recessive)

• simple discrete traits

• he would have had a more difficult time if more factors affect phenotypes (genetic polymorphisms)

Polyphenism

• single genotype produces multiple phenotypes depending on the environment

• phenotypic plasticity → multiple phenotypes

Quantitative traits

• numerical value

• more complex traits

• ex. height

• have continuous phenotypic variation

• could be because of the environmental component

  • may had poor diets so lower heights compared to ladinos