Carroll Bio 2 - Midterm #3

Origin of the Solar System

The Solar system formed ~4.6 BYA

Originally in the form of a solar nebula, the sun and planets/bodies formed by accretion.

“Goldilocks” Zone

Area of the solar system with the right amount of solar radiation to have liquid water on planets (not gaseous or solid).

Earth is located in this area.

Earth Formation

Earth was formed by accretion from the solar nebula.

It was molten which allowed for densest elements to settle around the core.

Collision of Theia (Mars-sized object) formed the moon and changed Earth’s axial tilt.

Early Earth was hot; any colliding rocks/ice were vaporized on impact, so no water.

Origin of Life Theories

Primordial Soup: Oceans were a collection of organic molecules that reacted together to form complex molecules with energy input.

Primordial Sandwich: Reactions that would create complex molecules react faster with substrate presence (clay/ash).

Miller & Urey Experiment (1953)

Test showing that electricity can create organic molecules from inorganic in simulated early Earth conditions.

Test used silicate glass (not intentional, important because the crust of Earth is mostly silica.

Created amino acids!

Extraterrestrial Life Origin Theory

Life may have started from organic molecules brought by meteoroids we have found.

We know that the molecules aren’t from Earth because they do not match terrestrial stable isotope readings.

Asteroid Bennu

Recent NASA samples of asteroid found 16 amino acids and 5 nucleobases!

Protocells

Enclosed vesicles made of lipid membranes.

Possible origin of life.

RNA World Hypothesis

Suggests ribonucleic acid was the first genetic molecule.

Has the ability to self replicate and act as a basic enzyme.

Peptide-RNA World Hypothesis

Suggests ribonucleic acid was the first genetic molecule, but needed proteins too in order to replicate.

Protein would read RNA and bring corresponding amino acid and code for another protein.

Ex: aminacyl tRNA synthetase.

Characteristics of Living Things

1. Homeostasis

2. Organization

3. Respond to Environment

4. Reproduction

5. Evolution/adaptation

6. Growth/development

Darwinian Transition

The beginning of evolution.

Natural selection starts when self replication begins and membranes get more stable.

Evolution of DNA leads to a genetic explosion.

Variation begins when cells leave the “commune” and become “selfish”, keeping any beneficial chemistry internally.

Geologic Timescale

System used to measure periods of Earth’s history with start/end of each period usually based on significant events relating to life.

Ex: Fermian → Triassic, because of mass extinction.

First Evidence of Life

Period ~3.8 BYA when photosynthetic prokaryotes like cyanobacteria and stromatolites rule.

Around the same time as the darwinian transition, which may have happened multiple times.

Followed by the Oxygen Revolution.

Stromatolite

Form of early prokaryote which layered itself between layers of sediment in early Earth.

Oxygen Revolution

Period ~2.8 BYA when dominant cyanobacteria had let out huge amounts of oxygen into the oceans which then outgassed into the atmosphere.

Evidence of this event appears in the presence of rust in sediment layers from early Earth (rust requires oxygen).

Cyanobacteria can’t live well in oxygen rich environments so it was sort of like accidental suicide.

Followed by the First Eukaryotes.

First Eukaryotes

Period ~1.8 BYA when cells evolved increasingly complex structures like organelles and could take advantage of the high oxygen content.

Some of these new organisms took in cyanobacteria which evolved to function as organelles in a process called endosymbiosis.

Ex: mitochondria, chloroplasts, nitroplasts.

Followed by the First Metazoans.

First Metazoans (Animals)

Period ~1.2 BYA when the still relatively new eukaryotes evolved to have multicellular structures. It took until ~600 MYA for truly complex organisms to evolve.

Multicellularity required adaptations for cell adherence, recognition, and organization.

First ever documented complex multicellular life were algae called Ediacaran Biota.

Followed by the Cambrian Explosion.

Cambrian Explosion

Period ~580 MYA when the first evidence of predator-prey interactions were found among animals, causing a biological arms race which drove fast evolution.

Many ancestors of modern day animals evolved during this period.

Trilobites were the most common of these new animals, with them being the most common fossil anywhere.

Followed by the Terrestrial Invasion.

Terrestrial Invasion

Period ~500 MYA when some newly diversified organisms (especially plants) from the cambrian explosion made the move onto land for the first time.

Land provided unfiltered sunlight and increased [CO₂] for plants, but also required support against gravity, new nutrient acquisition, and fungal symbiosis.

Fungi were *maybe* the first on land, ~1 BYA!!!

Followed by the first eukaryotes.

Tiktaalik

A species of partly terrestrial fish which evolved ~365 MYA and is the ancestor of ALL tetrapods.

They were a transitional species and had gills and fins BUT also had lungs and a mobile neck (non-fish traits)

They may have moved towards land to avoid predators.

Molecular Clock

A technique which can estimate the divergence of a species from its ancestor by comparing divergence to mutation rate.

divergence time = divergence / mutation rate (if mutation rate constant)

Back-calculating by looking at common genes and finding the time difference between mutations.

Ex: finding the original case of HIV

Extinctions in Biology

99% of species that ever existed no longer exist due to these events.

There were 5 specific instances in history where these events which killed off ~75% of known species. Sharks & jellyfish have survived all 5!

A background rate of species dissapearence is always present.

End-Permian Extinction

A notable period of ~500,000 years where extreme volcanism caused 96% of species to go extinct.

K/Pg Boundary

Either a giant asteroid collision or extreme volcanism caused the many species including the dinosaurs to go extinct.

Atmospheric covering by debris blocked sunlight cooled the earth greatly, allowing fungi to thrive.

Mammals being warmblooded aided with their takeover and resistance to fungi.

Keller Theory

Idea that even without the asteroid there would have been vulcanism around 66 MYA which would have caused a mass extinction.

Statistically, vulcanism is the most sigificant factor in mass extinctions.

Hardy-Weinberg Equilibrium (HWE)

A mathematical method used to detect evolution in relation to genotype and allele frequencies.

States that in the absence of evolution, the allelic frequency for a gene in a population will not change between generations.

Based on simple probability laws.

Requirements for HWE

A population must meet these criteria to lack evolution:

1. No mutation

2. Large population (low genetic drift)

3. No selection

4. No gene flow

5. Random mating

HWE Equations for 2 Allele System

p + q = 1

p² + pq + q² = 1

p = probability of dominant allele, q = probability of recessive allele.

p² = probability of homozygous dominant, pq = probability of heterozygous, q² = probability of homozygous recessive.

Allele-phenotype conversion

# of alleles = 2x the # of phenotypes.

Microevolution

The change in frequency of certain alleles in a specific population between generations.

5 different types of change.

If HWE is disproven for a population then one of the types of change above is likely responsible.

Null Hypothesis

Idea stating that HWE hardly ever happens in nature and is used for comparing observed vs. expected traits in a chi-squared test (statistics).

Microevolutionary Processes

1. Mutation

2. Genetic drift

3. Selection

4. Gene flow

5. Non-random mating

Mutations

Microevolutionary process where new alleles are created, increasing heterozygosity.

Ultimate source of all variation and mostly random as well as selectively neutral.

It is rare for mutations to benefit organism.

Ex: lead resistance adaptation in humans > neanderthals

Genetic Drift

Microevolutionary process where allelic richness decreases randomly so eventually heterozygosity decreases too.

Selection

Microevolutionary process where impact varies depending on genotype.

Gene Flow

Microevolutionary process where immigration tends to increase heterozygosity.

Non-random Mating

Microevolutionary process where a specific trait is selected for by members of the population.

Decreases rate of heterozygosity and other homozygote genotype.

Inbreeding is similar to genetic drift.

Assortative vs. Dissasortative.

Ex: female birds picking males with brighter feathers, increases bright feather freq.

Assortative Mating

Type of mating that increasese homozygosity.

Disassortative Mating

Type of mating that increasese heterozygosity.

Preferential mating between individuals with different traits.

Darwin and Wallace

Early 19th century scientists who made broad observations of the patterns of life.

Noted the adaptation to environment, shared characteristics, and the richness of diversity in life.

James Hutton

Early geologist whose work focused on the processes of erosion and their effects.

Came up with the idea that sediments are deposited predictably based on certain natural rules.

Sediments from erosion/weathering/gravity go to the lowest point and layer together.

Inspired Darwin into his study of species.

Charles Lyell

Early geologist who believed in unformitarianism: the idea that the mechanisms of change are slow and constant.

Proposed that changes in Earth’s surface resulted from continuous processes, eg the present is the key to the past.

Weathering and erosion can be measured to calculate the age of mountains, etc…

Fossilization

The process by which the remains, marks, or traces of an organism are preserved in the Earth's crust.

Organism dies → gets covered in sediment → bones lithificate → erosion exposes preserved remains

Age of a preserved animal can be determined by relative/radiometric dating.

Conditions for Fossilization

Preservation of organisms is less likely in a soil rich area

Good preservation is much more likely in a coastal sandy area due to the sand moving and burying the remains quickly.

Hard animals are also more likely to preserve better than soft-bodied animals.

Relative Dating

A technique used to estimate the age of fossil based on the position of the fossil in stratigraphic layers of sediment.

The more layers have piled up on top of a fossil the older it is.

Can compare the age of 2 different fossils but cannot get an accurate age.

Radiometric Dating

A technique used to find the precise age of a fossil based on the presence/abundance of certain radioactive isotopes with known half lives.

Ex: Carbon¹⁴ dating works up to ~60,000 years.

George Cuvier

Credited as the first paleontologist for his work focusing on fossils.

He was interested specifically in documenting how older fossils resemble modern animals much less.

Jean Baptiste Lamarck

Early biologist credited with patenting the first theory of evolution.

His theory was based on the idea that traits were acquired throughout life and then passed down to their offspring. His work was partly proved by methylation!

Inspired by Cuvier’s work in the new field of paleontology, he noticed a trend in nautilus fossils. Throughout the layers of sediment, fossils that were found at similar depth had more similar shell sutures.

Lamarck’s Theory of Evolution (2)

1. Law of use/disuse: if an organism uses a body part more than another than it will grow and vice versa.

2. Inheritance of Acquired Traits: traits that have been developed over the life of an organism will be passed down to their offspring.

3. Inner Want: Organisms had an inherent feeling of necessity to adapt to their environment.

Charles Darwin

Early Biologist credited with discovering the first mechanisms of natural selection and the evolution.

Journeyed around the word before writing his book: On the Origin of Species.

Made the first phylogenic tree and discovered variation before genes were discovered!

Natural Selection

Always increases fitness (only microevolution force to do so).

More offspring are born than will actually survive.

Organisms with better adapted traits are more likely to live longer and repoduce more, thus spreading them through the population

Fitness is not determined by individual but instead by the environment.

Acts on phenotype, but allele frequencies also change.

Behavioral traits are included in traits.

Evolution

Heritable traits get passed down to offspring, with variation popping up along the way.

Common ancestry where life is connected together chronologically by a tree.

Has no goal/end point, monkeys weren’t destined to evolve into humans (cladogenesis).

Nebraska Sandhill Mice Study

Experiment where mice were put in specific sandy or muddy parts of an environment in closed off fences.

Mice from andy areas had lighter coats, while muddy area mice had darker coats.

Each pen had local mice (from that specific area) and non-local mice inside.

Left the mice in pen over time and found that the local mice survived better.

The reason for this selection based on coat color was due to the effect it had on camoflage/predation.

Cladogenesis

Speciation process where a single ancestral species splits into 2+ distinct, genetically independent descendant species.

Population

The smallest unit of evolution.

Generation

The smallest unit of evolutionary time (individuals do not evolve!)

Offspring

The currency of evolution.

Macroevolution

The accumulation of small genetic changes that add up to larger morphological changes.

Evolution Speed

Evolution is generally a very slow process but it can also happen over a few days (Harvard E. coli study)

Rate of evolution is determined by selective pressure (environment), generation times, standing variation, and mutation rates.

Selective Pressure

An external environmental factor that reduces/increases reproductive success of certain phenotypes within a population, driving natural selection and evolution rate.

Includes events called selective sweeps.

Generation Time

Time required for a population of organisms to double.

Low times allow for a high rate of potential evolution.

Standing Variation

The presence of more than one allele at a particular locus in a population.

The more different alleles present the higher the rate of potential evolution.

Selective Sweep

Event where a trait spreads through a population very fast due to its evolutionary advantages.

2 kinds: hard vs. soft

Hard Selective Sweep

A kind of selective sweep where the trait spreading is caused by a new mutation in the population

Ex: human skin color

Soft Selective Sweep

A kind of selective sweep where the variation already exists in the genome of the population but is only selected for and spreads in a new environment.

Phenotypic plasticity

The ability of a specific trait in an individual to change expression depending on the environment without any genetic changes.

Can impede evolution by breaking the phenotype → genotype connection and lowering allele frequency despite selection.

Can also encourage evolution by colonizing new habitats, which will lead to new/novel traits.

It is a form of acclimation, not adaptation.

Human Lead Tolerance

Lead was very common in the environment with 73% of tooth samples showing high levels.

Our resistance for lead may have given humans an edge against neanderthals.

NOVA1 allele which codes for early brain development and speech (SNP) became fixed in a hard selective sweep for humans.

NOVA1 may have had some lead resistant properties.

Stabilizing Selection

Mode of natural selection where an intermediate variant (often heterozygote) is favored.

Reduces phenotypic variation by moving towards one specific.

Directional Selection

Mode of natural selection where one extreme variant (often homozygote) is favored.

Shifts phenotypic variation and results in evolutionary trends over long time.

Ex: horses tend towards bigger bodies and smaller toes.

Exaptation

A trait that performs a function useful to an organism, but which was not originally shaped by natural selection for that specific use.

Ex: whale pelvic bones being used for mating

Disruptive Selection

Mode of natural selection where both extreme variants (homozygotes) are favored.

Increases phenotypic variation.

Negative Frequency Dependent Selection

Mode of natural selection which favors the less frequent phenotype.

As phenotype frequency decreases, fitness increases.

Ex: lizards with stripes most common, predators look for stripes and eat them, lizards wthout stripes more fit.

Positive Frequency Dependent Selection

Mode of natural selection which favors the more frequent phenotype.

As phenotype frequency increases, fitness increases.

Ex: frogs with bright colors most common, predators know animals with those colors poisonous, predator eats non-colorful frog.

Genetic Drift

Microevolutionary process where a change in allele frequency happens between generations by random chance.

Decreases variation and heterozygosity as rare alleles are lost.

Has more potent effects on smaller populations.

Can cause harmful deleterious alleles to become fixed.

The Bottleneck Effect

A sharp, random reduction in a population's size and gene pool caused by an environmental disaster or human activity, which decreases variation.

A type of Genetic Drift.

The Founder Effect

A type of genetic drift that occurs when a small group of individuals separates from a larger main population and establishes a new, isolated colony.

Decreases variation and promotes deleterious alleles.

Gene Flow

Microevolutionary process where alleles move between populations.

Decreases variation between populations (inter not intra).

Tends to increase variation and heterozygosity.

Can have positive/neutral/negative effects on fitness depending on selection — if variation means better fitness then positive, and vice versa.

Non-random Mating

Microevolutionary process where sexual selection plays a key role in determining effects on variation.

5 types: sexual, assortative, disassortative, and inbreeding

Sexual Selection

A type of natural selection where traits evolve because they help an organism get mates and reproduce, even if those traits reduce the individual's chance of survival.

Tends to decrease average fitness.

Ex: antlers on bucks help them get mates but take energy, get stuck, and can be deadly.

Intrasexual Selection

A type of sexual selection where members of the same sex compete for access to mating.

Typically seen in males.

This type of selection typically promotes larger size or other beneficial traits for competition depending on the scenario.

Intersexual Selection

A type of sexual selection where members of one sex chooses which of the other sex they will mate with.

Typically in females due to higher nutrient investment for reproduction.

Good genes hypothesis, states that females are choosy for specific male traits because these traits are honest indicators of genetic health.

Ex: male bird of paradise so colorful, easy prey, if they survive then they are more fit than others.

Inbreeding

Mating between genetically related individuals.

Assortative Mating

Preferential mating between individuals with similar traits.

Disassortative Mating

Preferential mating between individuals with different traits.

Why No Perfect Organisms?

Selection is limited and can only work with preexisting traits.

Ex: whale hip bones can’t just disappear

Adaptations are usually tradeoffs

Ex: Northwestern garter snake can eat poisonous newts but becomes lethargic, easy prey.

Speciation

Evolutionary process in which 1 species splits into 2+ species.

It is not the same as hybridization.

Reproductive Isolation

Geographic barriers that prevent populations from successfully reproducing with one another.

Hybridization

Reproduction between genetically distinct populations or species, producing a hybrid offspring.

Does not necessarily produce a new species.

Scala Naturae

Aristotle's concept that organisms could be arranged in a hierarchy from simpler to more complex forms.

Linnaean Taxonomy

A hierarchical classification system developed by Carl Linnaeus, still used today.

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

Morphological Species Concept

Defines species based on shared anatomical structures and physical characteristics.

How we traditionally distinguish species.

Can be arbitrary because individuals within a species may look different (dimorphism).

Phylogenic Species Concept

Defines species as the smallest discernable cluster of individuals descending from 1 common ancestor.

Emphasizes the evolutionary process and genetics.

All species go extinct or speciate.

Ecological Species Concept

Defines a species as a group of organisms who share common lineage and fill similar niche.

Might classify interbreeding groups as 2 seperate species.

Emphasizes disruptive selection.

Biological Niche

All of the interactions between an organism and its environment.

Biological Species Concept

Defines a species as a group of individuals who have the potential to interbreed in nature and produce viable and fertile offspring.

Emphasizes gene flow between populations which helps maintain genetic similarity within the species.

Parthenogenesis

A form of asexual reproduction in which an embryo develops from an unfertilized egg.

Advantages: Faster reproduction and colonization

Disadvantages: Genetic homogeneity, Low genetic diversity among individuals

Ex: Komodo dragons, California condors

Facultative Parthenogenesis

The ability to reproduce asexually under certain conditions while retaining the ability to reproduce sexually.

Fish & Speciation

97% of water is salt water on Earth, so you would expect more species of salt water fish to exist in the world.

Of the ray-finned fish there are 15,149 freshwater species: 14,736 saltwater species

This is caused by the high degree of geographic isolation between fresh water bodies which lower gene flow and boost variation.

Species Richness

The number of different species present in a particular environment.