BIOL215

Big Bang Theory

Occurred 10-15 billion years ago

- Expansion and condensation of hydrogen and helium

- Formation of protostars

- Largest protostars explode, producing supernovas

- Our solar system and sun formed after a supernova (4.6 billion years ago)

Earth Formation

Formed 4.6 billion years ago

- Initially molten and composed largely of iron, magnesium, silicon, and oxygen

- Oldest rocks are 4.28 billion years old

- Crust formed 4.2-4.1 billion years ago as Earth cooled 

The Rock Cycle

• fossils get covered in sediments carried by wind or water

• high heating and pressure turns these sedimentary rocks into metamorphic rocks destroying fossil remains

• these are melted in molten lava magma rock

• once cooled they crystalize into igneous rocks

• once again eroded and broken down into sediments

Radioactive Decay

Used to determine the age of rocks and fossils

  - Example: Uranium-238 decays to Lead-206 with a half-life of 4.47 billion years 

• uses the half life of common mineral compounds present in rocks

Zircon Dating

Uses zirconium silicate crystals to determine rock age

  - Incorporates impurities like uranium during formation

  - Stable structure prevents elements from entering or leaving

Sedimentary Rock Dating

• look at volcanic ash along with magma containing minerals

• strata/ sediment layers can be identified by the fossils it contains

Early Earth Atmosphere

First atmosphere: Hydrogen and helium

- Second atmosphere (4.5 - 3.8 billion years ago):

• generated when meteors and comets bombard Earth

  - Generated by volcanic out-gassing and impact bodies

  - Composed of CO2, N2, H2O, and trace amounts of other gases

  - Reducing atmosphere with no free oxygen as presence of O2 would’ve prevented the build-up of organic molecules

Ocean Formation

Formed around 3.8 billion years ago when Earth cooled below 100°C

- Evidence of liquid water by 3.9 billion years ago (banded iron formations)

- High 18O/16O ratio in zircons (isotopes) indicates presence of water by 4.4 billion years ago 

• got salty due to dissolved rocks on land and weathering carried that and other elements used by organisms into it

Evidence for Life

• biomarkers like carbon preserved in zircon in metamorphic rock in west greenland

• stromatolites: laminated structures of microbes and minerals that forms a “rock”

Miller-Urey Experiment

Simulated early Earth conditions using gases like methane ammonia hydrogen to produce organic compounds

  - Produced 17/20 of the amino acids, all the purines, and pyrimidines

• proved life’s building blocks could be synthesized abiotically

Panspermia

Hypothesis that organic molecules or life originated from outer space

  - Supported by evidence from meteorites and interstellar space

Australian meteorite was found to contain a variety of carbon compounds

same with another from mars containing some microorganisms however was disputed

• concludes organic matter can be synthesized abiotically throughought space

RNA world hypothesis

Proposes that early life was based on self-replicating RNA molecules

• one theory says they randomly formed on clay and gained enzymatic properties

• couldve encoded catalytics proteins like reverse transcriptase (copies RNA into DNA)

• DNA is more stable than RNA so it can store more info

- RNA can both store information and act as a catalyst (ribozymes)

- Possible solution to the protein-nucleic acid paradox in early life 

cell formation

Final step in the evolution of early life

- Formation of outer membrane to encase nucleic acids and proteins

- Micelles fuse to form vesicles, creating compartmentalization 

requirements of living organisms

1. Liquid Water: Accounts for 50-90% of an organism's mass; all chemical reactions necessary for life occur in water (universal solvent)

2. Energy Source: Used for metabolism, replication, movement, and resource acquisition (assembles building blocks like C, N)

   • animals used either light or organic/in chemical

3. Essential Elements: Required by organisms to complete their life cycle; includes C, H, O, P, N, S

Phototrophs

Use light energy (400-700 nm electromagnetic radiation), photosynthetically active radiation

Chemotrophs

Use chemical energy, organic C compounds

Chemoorganotrophs: Use organic chemicals

Chemolithotrophs: Use inorganic chemicals (e.g., H2, H2S, NH4+, Fe(II))

Autotrophs

Obtain carbon from inorganic sources (CO2), self feeder like plants, phytoplankton etc

Heterotrophs

Obtain carbon from organic molecules, feed on other things like carbs proteins fats from food

earliest life hypotheses either a

Chemolithoautotroph: Obtained energy and carbon from inorganic sources (favored hypothesis)

or

Heterotroph: Used organic matter synthesized abiotically , that matter would absorb to clays so it would have to had used fermentation

• wouldve had to be anaerobic hyperthermophilic and halophilic (thrives at high temp and salt)

• prokaryotic so bacteria or archaea

types of photosynthesis

Anoxygenic Photosynthesis: Early form using sulfur, carried out by sulfur bacteria, not O2 evolving

Oxygenic Photosynthesis: Developed later, carried out by cyanobacteria, producing oxygen appeared around 3.5-2.7 bya, oxygen appeared slowly beacuse it was reacting with Fe in the sea and reduced volcanic gases

consequences of o2 production

• allowed for new type of metabolism, aerobically which has greater energy yield

• changed ocean chemistry

• formed ozone layer

• poisoned anaerobic organisms

Great Oxidation Event

Definition: Transition from anoxic to oxic atmosphere

Timing: Occurred around 2.45 billion years ago

• release of o2 by photosynthesis maybe was most significant effect of life within the geochemistry of earth!!

eukaryotes

organisms with cells containing a nucleus, organelles and 80S ribosomes

• appeared in fossil record 1.7-2.1 bya, capable of endocytosis

• undergo mitosis for cell division

• 100-1000x larger than the other

• contain mix of genetic elements like protein-coding genes, pseudogenes (non-functional), enhancers and binding sites

prokaryotes

have no nucleus, organelles or microtubules and have 70S ribosomes

• outer cell wall composed of peptidoglycan, have a single DNA chromosome

• divide using binary fission

• have circular DNA

• lack large numbers of pseudogenes

• genes producing a common protein can be organized into operons

Endosymbiotic Theory

Theory explaining the origin of eukaryotes

  - Mitochondria and chloroplasts were once free-living bacteria

  - Engulfed by an Archaeon, leading to obligatory symbiosis

  - Mitochondria derived from proteobacterium

  - Chloroplasts derived from cyanobacterium 

strongly supported by data

Lokiarchaeota

- Definition: Newly discovered group of organisms closely related to the ancestral Archaeon that gave rise to Eukaryotes

- Key features:

  - First identified near deep-sea vents off the coast of Norway

  - Includes Prometheoarchaeus syntrophicum, isolated from 2500m deep in Japanese ocean

Organelle evidence for endosymbiotic theory

1. chloroplasts and mitochondria: contain their own DNA, similar to bacterial (no histones, circular)

2. are surrounded by a double membrane (inner resembles a bacterial membrane)

3. ETC of mitochondria is located in inner membrane and is in outer membrane of bacteria

4. show antibiotic sensitivity

5. have ribosomes (70S) like bacteria

secondary endosymbiosis

evidence of a 2nd event seen in two groups of protists

• nucleomorph: remnant of the nucleus of the endosymbiont in the chloroplast

• there are two membranes around the chloroplast

Horizontal Gene Transfer (HGT)

- Definition: Transfer of genetic material between organisms other than by vertical transmission from parent to offspring

- Key points:

  - Occurs through viruses, plasmids, or endosymbiosis

  - Significant impact on prokaryotic genomes (20% of E. coli genome, 1/3 of some prokaryotic genomes)

protists

artificial group (contains groups of less related organisms)
- mostly unicellular eukaryotes including parasitic, photosynthetic and heterotrophic forms

• 12-32 diff phyla

excavates

• diverse group of unicells without a common morphological feature

• originally thought to be ancestral to other eukaryotes

• parasitic, flagellated obligate anaerobes

• ex. trichonympha: symbiotic inhabitant of termite guts containing cellulose-degrading bacteria

Chromalveolates

- Definition: A supergroup of eukaryotes containing various algae and non-photosynthetic groups

- Key members:

  - Dinoflagellates, apicomplexa, ciliates, brown algae, diatoms

  - Important primary producers and consumers in aquatic ecosystems

- Notable features:

  - Many acquired chloroplasts through secondary endosymbiosis 

avelolates: dinoflagellates

• hetero/photo trophic species

• some are symbionts of coral invertebrates ( living in tissues transferring sugars into the corals )

thing causes paralytic and hemolytic shellfish poisoning

Rhizaria

Definition: A group of heterotrophic eukaryotes united by molecular data

- Key features:

  - Consume prokaryotes and eukaryotes

  - Many produce pseudopodia for feeding

  - Significant contributors to zooplankton communities in oceans 

plantae

• include red and green algae and have plasmids that arose through primary endosymbiosis

• unicellular, colonial and multicellular forms

Unikonts

- Definition: A group containing various protists, animals, and fungi

- Key members:

  - Parasitic protists, slime molds, amoebae, animals, fungi

  - Includes choanoflagellates, resembling cells of sponges

- Significance:

  - Multicellular organisms appeared within this group ~600 million years ago

Evolution

- Definition: Any change in inherited traits of a population from one generation to the next

  - Explains diversity of life

  - Can be spontaneous through physical processes

  - Involves gradual form modification over generations

• change in allele frequencies from one generation to the next

lineage

chain of ancestor-descendent connections over time

Natural Selection

- Definition: The process that results from the differential survival or reproductive success of a lineage

• causes heritable phenotypes with genetic basis that change in response to the environment

• more effective in bringing about change in large populations

• rate of this happening is an estimate of selection

• consequence of this process is an adapatation

• variable over time and can result in rapid evolutionary change

Fitness W_i

- Definition: A measure of reproductive success

- Types:

  - Relative fitness: Absolute fitness scaled by a standard (compared to others)

  - Absolute fitness: Rate of replication

adaptation

the fit between an organism and its environment

• formally the heritable phenotype that increases fitness and has arisen due to natural selection in the current environment

• a consequence of natural selection

• can occur because there is heritable variation

• xxx to one environment comes at the cost of xxx to another environment

evidence for evolution - design versus descent

• all life uses the same basic inefficient materials and processes

• this is only explained by the fact that we all descend from a common ancestor

• common descent: children resemble their parents, we are similar and we share ancestral genes

• designing an organism would make use of a wider array of processes

homologous trait

similar because of inheritance from a common ancestor. ex: human arm, seal flipper, bat wing

evidence for evolution - extinction

• majority of species are extinct, species living now only represent ~1% of total biodiversity

• fossils are abundant and diverse, more living species have gone extinct than are currently living

• species lifespan is about 5my

• ex. fossil horses first originated in asia but there were species everywhere that evolved over 55my, each species lived ~3my

evidence for evolution - adaptation

• function and ancestry contribute to the evolution of the form

  ex. large marine animals like whales, fish and sharks share a fusiform body shape that minimizes drag in the ocean

• sharks share a CA w fish but whales are mammals descended from a hippo-like terrestrial ancestor

• thus these animals share body plan through adapting to aquatic life NOT shared ancestry

Vestigial Organ

An organ or structure that has lost its original function through evolution

Adaptive Radiation

- Example: Galapagos finches from a common mainland ancestry within the last 3 my another example of their adaptations is beak length increasing after a long drought

• environment acts as a potent source of selection

- Definition: The process by which organisms/a lineage diversify rapidly into several new ecological niche specialists

• resource driven selection

Theory of Evolution

  - Composed of many hypotheses, modification with descent resulting in a change in the genetic composition of a population, contingent and only makes use of materials available to it

  - Not progressive (no species is inherently better than others)

  - Involves not just selection, but also drift, migration, and mutation

  - Undirected, with no intelligent designer

DOES NOT occur for good of the species

Topology

Definition: Alternative evolutionary histories represented in phylogenetic trees

Phylogeny

- Definition: A tree-like diagram showing evolutionary relationships, history of a lineage(s) (populations, genes or species)

- Key features:

  • Parents/species/populations are at nodes: represent common ancestors for all descendent species

  • Tips represent species

  • Branches connect species, converging at nodes, trees do not depict a hierarchy or continuum

pedigree

individuals

• in a sexual species, a node represents a recombined genome from two parents

• any number of offspring can result

clade

a common ancestor and all its descendents

Taxon

- Definition: A named group of species, genus, order, or class

- Note: Different traits define the categories

monophyletic groups

clade, represents all species descended from a common ancestor

paraphyletic group

a group that leaves out some taxa, sharing a common ancestor

polyphyletic group

a group that includes taxa descended from multiple common ancestors

Linnean classifications

• he organized species in names based on shared characters

• modern taxonomy aims to construct more accurate phylogenies in terms of evolutionary history

• his was NOT an evolutionary taxonomy

characters (character states)

identifiable, heritable traits

• states would refer to present or absent

• ancestral or derived (ex. vestigial organs appendix) NOT primitive and advanced

outgroup

species that is outside of the clade whose relationships we wish to resolve

• shares a common ancestor with the monophyletic clade of interest

• character states resemble those of the common ancestor

• allows for a direction to be set from ancestral (shared w the xxx) to derived (not shared) on an evolutionary change

synapomorphy

shared derived character state

• homologous characters because they’re inherited from a common ancestor

• including gene sequences

• has evolved independently in multiple taxa from a shared ancestor

• is only character type that can be used to resolve phylogenetic relationships because it 1) differs from the outgroup and 2) is shared by some but not ALL taxa in the clade being studied

homoplasy

character state similarity NOT due to common descent rather caused by

• convergent evolution or evolutionary reversals, or parallel evolution

• so its the same character but NOT bc of evolutionary histories

Convergent Evolution

Distantly related species evolve similar traits due to similar selective pressures.

they resemble eachother more than their ancestors did

- Examples: Bats and birds, porcupines and hedgehogs (wings and spikes)

evolutionary reversals

reversion back to an ancestral character state eg. swimming in whales

• especially common in DNA sequences because each site takes ¼ character states and mutation can access all of them

Parsimony

- Definition: The principle of choosing the simplest explanation or hypothesis, fewest evolutionary steps is preferred

- Application: In phylogenetics, favoring trees with fewer character state transitions 

Polytomy

- Definition: An unresolved branching in a phylogenetic tree

- Usage: When we can't determine exact relationships between species

Homology

- Definition: Similarity due to shared evolutionary history

- Example: coelacanth Fish fins are xxx to tetrapod limbs as theyre more lobed and stronger

another example: mammalian ear bones are xxx to bones of reptile jaws, they evolved over time to work in the inner ear of the opossum

exaptation

natural selection co-opting a trait for a new function: ex panda’s thumb

exons

protein coding genes

• under strong purifying selection because function will be preserved and tends to evolve slowly

introns

neutral in the eyes of selection and evolve faster

Parallel evolution

Similar traits evolve independently in related lineages

Bootstrapping

- Definition: A resampling technique used in phylogenetic analysis

- Process:

  - Resamples the dataset multiple times

  - Constructs trees from each resampled dataset

  - Provides support for phylogenetic inferences 

distance matrix methods

lineages that are more genetically similar are more likely to be closer related

Maximum Likelihood Method

- Definition: A statistical approach for phylogenetic tree construction

- Key features:

  - Uses a molecular evolution model

  - Calculates probability of observing the data given a tree

  - Selects the tree with the highest probability (best xxx)

bayesian methods

start w a model and a tree, change the tree slightly many times

• generates probability distribution of possible trees, those with the highest probability are preferred

is HIV monophyletic?

• consists of 4 groups MNOP, first two evolved direclty from SIV in chimps and last two evolved from same than in gorillas

• attacks white blood cells causing immune deficiencies

• MNOP all evolved independently from an SIV ancestor but they share a common mutation NOT found in SIV

• thus this was not a single spill over event rather its convergent evolution

Phylogenetic Independent Contrasts

- Definition: A method for comparing traits across species while accounting for phylogenetic relationships

• looks at correlation among traits based on evolutionary independent transitions

- Application:

  - Used to test correlations between traits

  - Helps avoid false conclusions due to shared ancestry 

• take the mean of two traits branching off the same node

Synonymous Substitutions (dS)

- Definition: Mutations in DNA that don't change the amino acid sequence

- Characteristics:

  - Governed by chance alone

  - Used as a molecular clock for estimating divergence times 

• often but not always selectively neutral

non-synonymous mutations

change the AA sequence of a protein and more likely to be subject to selection

neutral theory of molecular evolution

Kimura (1968) formalized it

• most evolution at molecular level is NOT selective and is governed by processes associated with genetic drift

• neutral mutations become fixed in lineages at regular rates

• support for the theory arose from substitutions in cytochrome c gene which showed more distantly related species had more substitutions and a linear relationship

selectionists

• argued the abundant genetic variation in natural populations resulted from selection

• so if theres a bunch of diff niches in environment, selection will preserve the fittest type in each niche and maintain diversity

• preserves specialist in each niche

• sometimes called balancing selection

neutralists

believe that most genetic variation was selectively neutral, did not impact fitness

Selective Sweep

Definition: The process by which a beneficial mutation rapidly increases in frequency in a population, a beneficial allele fixes mare quickly than a neutral allele

- Example:

  - D614G mutation in SARS-CoV-2 spike protein

genetic hitchhiking

mutations that are linked physically to the selected allele ‘hitchhike’ to high frequency

Purifying Selection

- Definition: A type of natural selection that removes harmful mutations

- Indicator:

  - dN/dS ratio less than 1 

non-synonymous substitutions (dN)

change protein, faster evolution

Tajima’s D

uses two estimates of genetic diversity to ask whether a population is evolving neutrally or not

• S = number of variable sites

• pi = mean number of differenences between a pair of sequences

these both estimate theta = the quantity of genetic diversity in a population under neutrality

D = theta_pi - theta_S

• tells us whether a population is evolving neutrally or not

D = 0 is neutral

D < 0 = directional selection( more rare alleles than expected, suggests selective sweep eliminated variation happened recently)

D > 0 = balancing selection (fewer rare alleles than expected, suggests selection favours distinct alleles in the same population)

Macroevolution:

• Starts with speciation

• Involves large-scale evolutionary changes over time

• considers broader changes in diversity at higher taxonomic levels and how this is distributed

microevolution

changes in allele and gene frequencies within populations

speciation

how genetic changes within populations lead to new evolutionary clumps

• defined in terms of reproductive isolation = will thus create a new species

biogeography

study of the distribution of species across space and time

dispersal

movement of populations from one region to another with limited or no return exchange ex. marsupial evolution : most living are found in Australia but oldest fossils were found in china and north america evolved w a mix of this and the other because the modern day marsupial has CA from N america and S america too

vicariance

formation of geographic barriers to dispersal that divide a once-continuous population. ex. if continent divides and population splits there could be more species so for marsupial their phylogenetic patterns mirror the order in which the continents broke up

anagenesis

wholesale transformation of a lineage from one form to another

• not our understood definition of evolution, things did not evolve gradually, there were species that took over eachother

punctuated equilibria

periods of stasis followed by brief periods of rapid morphological change linked to speciation

• sees speciation and morphological change happening simultaneously

ex. bryozoans diversification pattern works well with this model

gradualism

slow, gradual morphological changes over time resulting in speciation

• involves anagenesis and speciation

turnover

number of species eliminated and replaced per unit time

standing diversity

number of species present in an area at a given time

ecological opportunity

presence of vacant niche space

• absence of competitors opens this up for a lineage

• leads to adaptive radiation

key innovation

trait(s) that allows a lineage access to new resources

evolutionary novelty

new genetically based trait

• used to improve in totally new conditions, take whatever enzymes you have and grow faster