Section 2: Evolution Flashcards
How can life’s record be divided ?
The hadean, Archean, Proterozoic, and Phanerozoic
How long does the phanerozoic last?
it includes the last half billion years
What does the Phanerozoic period cover ?
going from earliest to latest - the cambrian, ordovician, silurian, devonian, carboniferous, permian
How long ago was earth formed ?
about 4.6 billion years ago
What prevented the oceans being formed before 4 billion years ago
the bombardment of rocks and ice
What was earths early atmosphere like ?
it had little oxygen, and likely contained water vapor and chemicals released by volcanic eruptions (nitrogen, carbon dioxide, methane, amonia, hydrogen)
What stages may have produced simple cells on earth ?
- abiotic synthesis of organic molecules
- the joining of these molecules into macromolecules
- packaging small molecules into protocells
- origin of self-replicating molecules
What was the Miller and Urey experiment ?
They demonstrated that the abiotic synthesis of organic molecules in a reducing atmosphere was possible, essentially the stimulated what the atmosphere would be like at that time and found the production of amino acids
What is another theory for the formation of organic compounds ?
organic compounds may have been produced in deep-sea hydrothermal vents, areas on the seafloor where hot water and minerals gush in from the earths interior
What is another theory for the formation of organic compounds including rocks ?
meteorites may have been another source of organic molecules. Example: fragments of the Murchison meteorite contain more than 80 amino acids and other key organic molecules
What are protocells ?
the compartment where replication of primitive genetic material took place
What could have appeared in protocells ?
replication and metabolism are two things that could have appeared together in protocells
How are protocells formed ?
from fluid-filled vesicles with a membrane-like structure (permeable)
What can protocells do with their permeable membrane ?
they can absorb organic molecules through a selectively permeable bi-layer
What was the first genetic material?
it is thought that RNA was the first genetic material and not DNA, it ha been produced spontaneously from simple molecules
What can ribozymes do ?
they have been found to catalyze many different reactions, they can make complementary copies of short stretches of RNA
What did DNA do to RNA ?
DNA replaced RNA as the replicator, this is because double-stranded DNA is more chemically stable and can be replicated more accurately
What was the oldest single -celled organism ?
The oldest known fossils are stromatolites, rocks formed by the accumulation of sedimentary layers on bacterial mats
How old are stromatolites ?
they date back to 3.5 billion years ago
How are banded rock formations formed ?
they are formed by the photosynthesis of cyanobacteria which then reacted with dissolved iron and precipitated out to produce banded rock formations
When did O2 gradually accumulate ?
between 2.7 and 2.4 billion years ago
What happened during the oxygen revolution ?
oxygen shot up from 1% to 10%, this was the oxygen revolution which caused the extinction of many prokaryotic groups
What is the oldest fossil fate of eukaryotes ?
1.8 to 2.1 billion years
What did the first eukaryotes have ?
they first had a nuclear envelope, mitochondria, endoplasmic reticulum, and cytoskeleton
Where did eukaryotes evolve from ?
from archaea and bacteria
What is endosymbiosis ?
the symbiotic incorporation of one organism by another
How did eukaryotes originate ?
they originated by symbiosis, when a prokaryotic cell engulfed another and it evolve into a mitochondrion
What is serial endosymbiosis ?
it supposes that mitochondria evolved before plastids through a sequence of endosymbiotic events
What is the key evidence that supports the endosymbiotic origin of mitochondria and plastids ?
- inner membranes of both organelles are similar to plasma membrane of living bacteria
- DNA structure & cell division are similar to bacteria
- Both organelles transcribe and translate their own DNA
- Ribosomes are more similar to bacterial then eukaryotic ribosomes
What were the Ediacaran ?
they were an assemblage of larger and more diverse soft -bodied organisms that lived from 635 to 541 mya
What was the Cambrian era ?
it had a lot of diverse species with complex bodies, heads, guts, mouths, legs and hard carapaces, it also provided the first predator prey interactions with many adaptations for defense
Why are there major boundaries between the phanerozoic eras?
they correspond with the major extinction events in the fossil record
What started to colonize the land 500 million years ago?
fungi, plants and animals
What are embryophytes ?
land plants that have a dependent embryo, and are evolved from green algae
What are the most widespread and diverse land animals ? (2)
arthropods and tetrapods
What are tetrapods evolved from ?
lobe-finned fish (around 365 million years ago
When did modern humans originate ?
195,000 years ago
Who published origin of species ?
it was published by charles Drawin in 1859, focused on the great diversity of organisms and their origins
What are the three ideas from origin of species (Darwin 1859) ?
- The unity of life (life has common/shared characteristics, decent w/ modification
-The diversity of life (natural selection, speciation)
-Adaptation
What is the unity of life ?
all organisms are related through descent from an ancestor that lived in the remote past
How is the unity of life modeled ?
Through the tree of life
How did Darwin explain the necessity for adaptation ?
natural selection is the only mechanism that consistently causes evolution
What was Lamarck’s (1809) hypothesis of evolution ?
hypothesized that species evolve through use and disuse of body parts and inheritance of acquired characteristics
What was the voyage of beagle ?
Darwin collected specimens from south america, observed that fossils resembled living species from the same region, it was from 1831 - 1836
What is artificial selection ?
modifying species by selecting and breeding individuals with desired traits
What are darwins 2 observations about natural selection?
- members of a population often vary in inherited traits (genes)
- all species can produce more offspring than the environment can support
What where darwins 2 inferences about natural selection ?
- some individuals in a given environment leave more offspring than others, because their inherited traits give them a higher probability of survival
- The unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits (genes) in the population
What is an example of favorable characteristics?
peppered moths during the industrial revolution - turning from being peppered to completely black
What is an important thing to remember about evolution?
individuals do not evolve only populations
What is the modern synthesis theory by Mendel ?
Modern synthesis incorporated genetic knowledge into the theory of evolution, evolution acts on variants of genes
What is the definition of natural selection (Mendels modern synthesis)?
alters allele frequencies over generations by differenced over generations by differences in fitness (reproductive success)
What is genetic drift?
altering of allele frequencies via stochastic (random) processes
What is gene flow ?
altering of allele frequencies via the movement of allele among populations
What is the founder affect ?
This happens when a few individuals become isolated from a larger population, the allele frequencies can be different from the bigger population so the smaller population changes
What is the bottleneck effect ?
occurs when there is a drastic reduction in population size due to sudden change in environment, the gene pool might not reflect the original population
What is gene flow and how does it occur ?
it is the movement of alleles among populations, transferred through the movement of fertile individuals or gametes (pollen/sperm). It affects variation among populations over time
What can gene flow do to a population ?
It can increase the fitness of a population, a good example of this is the resistance to pesticides
What are the different modes of natural selection ?
Directional selection - shifts the overall makeup of the population, favors variants of one extreme
Disruptive selection - favors variants at both ends of distribution (example: mice being either white or black)
Stabilizing - removes extreme variants from the population, preserves intermediate types
What is allopatric speciation ?
occurs with geographic separation of populations, gene flow is interrupted or reduced when a population is divided into geographically isolated subpopulations (this could be from rivers, canyons, etc.
How do tectonics lead to allopatric speciation?
it divides the population by the creation of natural barriers, example - snapping shrimp diverged 3 to 9 million years ago by the formation of the Isthmus of Panama
How is allopatric speciation facilitated ?
It is facilitated by genetic drift and the founder affect
Where is another place that is where allopatric speciation would occur ?
Islands are a good example of this, one would be the finches that Darwin found that all come from the same species but diverged eventually
What is sympatric speciation ?
Speciation without separation of populations, requires pre or post zygotic barriers to develop between species
How does sympatric isolation occur ?
some ways would be:
- Hybridization
-Polyploidy
-sexual selection
-habitat differentiation
What is hybridization ?
When two different species reproduce
What is polyploidy ?
the presence of extra sets of chromosomes due to accidents during cell division, more common in plants than animals (can produce a new biological species in a generation)
What is an autopolyploid?
an individual with more than two chromosome sets derived from a single species (reduced fertility)
What is an allopolyploid?
a species with multiple sets of chromosomes derived from different species - can successfully mate with each other, but cannot interbreed with either parent species (look at slide 32 and 33 -speciation 2 for diagram)
What are the levels of polyploidy?
-Triploid 3x
-Tetraploid 4x
-Pentaploid 5x
-Hexaploid 6x etc.
What are examples of polyploids?
oats, cotton, potatoes, tobacco and wheat
How does sympatric speciation occur?
sexual selection can drive sympatric speciation, selection of color can drive this (fish from lake Victoria)
What else can sympatric speciation do ?
it can result in the appearance of new ecological niches/habitats
Where does common ancestry show up in mammals?
It shows up in our bones, example humans, cats, whales, bats all have similar bone structures in there upper appendages (humerus, radius, ulna, carpals, metacarpals, phalanges
What is castle’s experiment on rat coat color ?
starting hypothesis was: selection cannot change a trait beyond the original variation, BUT they found that there were completely new fur patterns and lots of intermediates (original hypothesis = wrong)
How do we trace evolutionary events ?
by comparing DNA sequences of individuals or species
What are fossils usually found in?
Fossils are remains or traces of organisms from the past,
usually found in sedimentary rock, which appears in
layers called strata
Fossils are biased towards what?
The fossil record is biased in favor of species that
-existed for a long time
-were abundant and widespread
-had hard parts, such as shells or skeletons
How are rocks and fossils are dated?
Fossil age can be determined using radiometric dating.
Each isotope has a known half-life, the time required
for half the parent isotope to decay
Fossils contain carbon isotopes that accumulated in the
organisms when they were alive
* The age of fossils can be estimated by measuring the
ratio of the radioactive isotope carbon-14 to the stable
isotope carbon-12
* Radiocarbon dating can only be used to date fossils up
to 75,000 years old
What is used to date older fossils?
Radioactive isotopes with longer half-lives are used to
date older fossils
* Uranium 238 half life equals 4.5 billion years
* Organisms do not take up isotopes with long half-lives
* The age of older fossils can be estimated by dating volcanic rock layers above and below the fossil
What is macroevolution? (and examples)
Macroevolution is the broad pattern of evolution above
the species level (fossils help document)
* origin of groups of organisms
* the Cambrian ‘explosion’
* the emergence of terrestrial vertebrates and plants
* the impact of mass extinctions
* the origin of key adaptations (innovations), such as
flight, eyes, flowers
* adaptive radiations
When was the Origination of major animal phyla?
Origination of major animal phyla: Ediacaran/Cambrian
seen at burgess shales
What does the cambrian explosion refer to?
The ‘Cambrian explosion’ refers to the apparent sudden
appearance of fossils resembling modern animal phyla
in the Cambrian period (535 to 525 million years ago)
The oldest fossil assigned to an extant animal phyla
lived 560 million years ago
Remember: A few animal phyla appear even earlier: sponges, cnidarians, and molluscs
What animal phyla came before the cambrian?
DNA analyses suggest that sponges evolved 700
million years ago and the common ancestor to
several other animal phyla lived 670 million years
ago
What does the fossil record show about mammals?
§ Mammals belong to the group of animals called
tetrapods
§ The evolution of unique mammalian features can be
traced in the fossil record
§ For example, mammalian jaws and teeth evolved
gradually over time, in a series of steps
§ Darwin called this ‘descent with modification’
What are exaptations?
Exaptations are structures that evolve in one context but become co-opted for a different function
* Structures do not evolve in anticipation of future use; natural selection can only improve a structure in the context of its current utility
Examples of evolutionary trends?
GO TO LECTURE 14 - “Fossils, global change and extinction”
What are examples of Fossils showing appearance of evolutionary novelties?
- Key innovations (jaw hinges and ear bones of early
mammals) - Wings
- Flowers (angiosperms)
- Eyes
What were the Consequences of continental drift?
- Organisms must adapt, move, or risk
extinction as the climate changes in response
to continents moving toward or away from the
equator - Separation of landmasses can lead to
speciation due to isolation (allopatric
speciation) - Historically this generates realms
What are realms?
Tectonics generate ‘Realms’
Large regions where life has been evolving in relative isolation for a long period of time separated by geographical features e.g. oceans, broad deserts, high mountain ranges
What are the Floristic realms?
Holarctic - USA + Europe and north
Paleotropics - Africa + south Asia + islands
Neotropics - South America
Capensis - South Africa and southern
Australis - Australia
What changed the course of evolution on earth?
Atmosphere: Oxygen, cyanobacteria and plants
Cyanobacteria evolved photosynthesis, i.e. splitting water to make oxygen. Stromatolites and thrombolites (W.
Australia). Fossils from 2700mya.
Oxygen is toxic to most other bacteria, so they poisoned almost everything else. It also made an ozone atmosphere. Vascular plants helped raise the oxygen levels further, allowing larger animals onto land (O2 20% today).
Extinction?
- The fossil record shows that most species that have
ever lived are now extinct - Extinction can be caused by changes to a speciesʼ
biotic or abiotic environment - At times, the rate of extinction has increased
dramatically and caused a mass extinction
How many mass extinctions to date?
The “Big Five” Mass Extinction Events
* In each of the five mass extinction events, 50% or more of marine species became extinct
MORE INFO - GO TO LECTURE 14 - “Fossils, global change and extinction”
What is adaptive radiation?
Adaptive radiation is the rapid evolution of diversely
adapted species from a common ancestor
* Adaptive radiations may follow
* mass extinctions
* the evolution of novel characteristics
* the colonization of new regions
Examples of worldwide adaptive radiations?
§ Mammals radiated after the extinction of terrestrial dinosaurs
§ Disappearance of dinosaurs (except birds) opened ecological niches, allowing for the expansion of mammals in diversity and size
§ Other notable radiations include photosynthetic prokaryotes, large predators in the Cambrian, land plants, insects, and tetrapods
What is another source of variation ?
recombination is a source of genetic variation
What will result in different phenotypes ?
different allele combinations
What are examples of duplicate genes (paralogs) ?
-globins
-Opsins(rhodopsin, 3 colour opsins)
-Olfactory receptor genes
What causes mutations ?
- errors during DNA replication
-errors in recombination
-UV lighting
-chemical mutagens
What can happen if mutations change the protein ?
it may change the chances of survival of the individual and reproduction (fitness)
What happens if the mutations don’t change the protein ?
they usually don’t affect the fitness of the individual, mutations also occur pretty regularly
What is something that DNA sequence analysis can do ?
it can distinguish between homology and convergent evolution,
- homology = shared evolution
- Convergent evolution = independent origins of a similar trait
What other species do humans share a very similar genome to ?
chimpanzees and humans share almost an identical genome
What are some human specific traits ?
bipedalism (using two legs/walking on two legs), as well as increased brain size
What is important to remember about fossils that look like humans ?
not all fossils are ancestors of ours, some are extinct side-lineages
What are the two models for modern human origins ?
the multiregional mode and the out-of-africa model
Where is human diversity greatest ?
it is greatest in Africa, which is predicted by the out-of-africa model
What is a simple conclusion about genetic phylogenies ?
most of out ancestors lived in Africa ~ 60kya
Up until when did Neanderthals exist in Europe ?
Up until 35,000 years ago
What is speciation?
Speciation, the process by which one species splits
into two or more species
Two forms are anagenesis and cladogenesis
Why does cladogenesis make sense as a common form of speciation?
Cladogenesis can increase species number and explains why there are so many species in the world and how they are related in the tree of life
How many species are there?
Published estimations of world species number
1.7 million (described)
4 million to 100 million (estimated)
Synonymy could be as high as 40% (e.g. same
species given two different names)
One reasonable estimate for the total number alive
is 12.5 million
We know about fewer than 1 in 8 of the species in
the world (microscopic ones undiscovered)
What are the species richness of insects and angiosperms?
GO TO LECTURE 16 - “Species and speciation”
What is a group that is very poorly known but contains many undiscovered species?
Fungi 100,000 species have been described
1.5 million species may exist
What are the 4 discussed species concepts?
Morphological species
Biological Species
Ecological species concept
Phylogenetic species concept
What is binomial nomenclature?
Binomial Nomenclature
Carolus Linnaeus, 1753
Genus, specific epithet
What is reproductive isolation?
Reproductive isolation can be classified by whether factors act before or after fertilisation
Prezygotic barriers -
Habitat isolation
Temporal isolation
Behavioural isolation
Mechanical isolation
Gametic Isolation
Postzygotic -
Reduced hybrid viability
Reduced hybrid fertility
Hybrid breakdown
What is introgression?
Introgression: genes from one species moved into other species
Exp. grolar bears
What are 3 ways of seed disperal?
SEED DISPERSAL: Zoochory (animals), anemochory (wind), hydrochory (water)
What is vicariance?
Vicariance : divides populations that were once continuous by the creation of natural barriers
Differences between allopatric and sympatric speciation?
Speciation types
Allopatric: occurs with geographic separation of populations
genetic drift
the founder effect
Prezygotic or postzygotic reproductive barriers
Sympatric: occurs in populations that live in the same geographic area
Hybridisation
Polyploidy
Sexual selection
Habitat differentiation
What are two ways of identifying species?
Dichotomous Keys
DNA barcoding
Explain morphological species concept:
a species is something that has an accepted species name usually based on resemblance (morphology)
§ The morphological species concept defines a species by
structural/morphological features (resemblance)
§ It applies to sexual and asexual species but relies on
subjective criteria
Explain biological species concept:
The biological species concept emphasizes reproductive isolation
A species is a group of individuals whose members have the potential to interbreed in nature and produce viable, fertile offspring
Explain ecological species concept:
The ecological species concept defines a species
in terms of its ecological niche
§ It applies to sexual and asexual species and
emphasizes the role of disruptive selection
Explain Phylogenetic species concept:
Members of a species should belong to the same
clade (phylogenetic group)
What is a hybrid zone?
§ A hybrid zone is a region in which members of
different species mate and produce hybrids
§ Hybrids are the result of mating between species
with incomplete reproductive barriers
What are outcome of hybrids?
We have seen earlier how hybrids often have reduced fitness compared with parent species
§ Reinforcement
§ Fusion
§ Stability
What is phylogeny?
Phylogeny is the evolutionary history of species
How many domains are on the modern tree of life?
Modern day tree of life there are three domains of
life
What do the trees of life show?
Trees show branching (cladogenesis) & time
What are three Properties of phylogenetic trees?
branch point, sister taxa, basal node
What is a branch point?
Each branch point represents the divergence of
two evolutionary lineages from a common
ancestor
What is a sister taxa?
Sister taxa are groups that share an immediate
common ancestor that is not shared by any other
group
What is a basal node?
A basal node shows where a taxon diverges early in
the history of a group and originates near the
common ancestor of the group
What are homologies?
Phenotypic and genetic similarities due to shared
ancestry are called homologies
Define clades/cladistics:
§ Cladistics groups organisms by common ancestry
§ A clade is a group of species that includes an
ancestral species and all its descendants (also
called monophyletic)
§ Clades can be nested in larger clades, but not all
groupings of organisms qualify as clades
What are three branching patterns?
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group
What are Phylogenetic reconstruction - methods?
§ When constructing a phylogeny, systematists need
to distinguish whether a similarity is the result of
homology or analogy
§ Homology is similarity due to shared ancestry
§ Analogy is similarity due to convergent evolution
What are the differences between Shared ancestral and shared derived characters?
§ A shared ancestral character is a character that
originated in an ancestor of the taxon (e.g. four limbs
in mammals which is also found in other tetrapods)
§ A shared derived character is an evolutionary
novelty unique to a particular clade (e.g. hair in
mammals)
Define ingroup and outgroups?
§ The outgroup is a group that has diverged before
the ingroup (the group under study)
§ Characters shared by the outgroup and ingroup are
ancestral characters that predate the divergence of
both groups from a common ancestor
What are Maximum parsimony & Maximum likelihood ?
§ Maximum parsimony assumes that the tree that
requires the fewest evolutionary events
(appearances of shared derived characters) is the
most likely
§ Maximum likelihood is based on probability rules
about how DNA changes over time and assumes a
tree can be found that reflects the most likely
sequence of evolutionary events
What are the uses of phylogenetic trees?
§ Dating trees and timing of evolution when
fossils not available (molecular clocks)
§ Classification and taxonomy
§ Comparative biology (evolution of
characters)
§ Prediction of traits
What are molecular clocks?
A molecular clock uses constant rates of evolution
in some genes to estimate the absolute time of
evolutionary change
§ Nucleotide substitutions are assumed to be
proportional to the time since they last shared a
common ancestor
§ Molecular clocks are calibrated against branches
whose dates are known from the fossil record
§ Individual genes vary in how clocklike they are
What is the order of identifications?
Kingdom
Phylum
Class
Order
Family
Genus
Species
Keep Plucking Chickens Or Face Getting Sacked
What were the five kingdoms that got replaced by the three domains?
§ Five kingdoms were previously recognized: Monera
(prokaryotes), Protista, Plantae, Fungi, and Animalia
§ More recently, the three-domain system has been
adopted: Bacteria, Archaea, and Eukarya
When does convergence evolution occur?
§ Convergent evolution occurs when similar
environmental pressures and natural selection
produce similar (analogous) adaptations in
organisms from different evolutionary lineages
What is key to selection?
Competition for limited resources is key to
selection
* Because resources are limited (generally more offspring produced than can survive) there is competition.
* Thus all advantages or disadvantages (i.e. fitness) are
relative – you only need to beat the competitors who are there, not a hypothetical ideal.
Explain selection strengths:
- Trait with a slight selective advantage might mean that those individuals produce 101 offspring compared to only 100 for those without the trait
- This is a 1% selection coefficient. s=0.01
- Seems very little, but given time this results in change in the population
- Light moths had a disadvantage in industrialised
regions in 19th century Britain - s = -0.2 = 20% disadvantage [this is BIG in evolutionary terms]
- 1848-1896 (50 years) the dark form rose to 98% frequency
Where does variation come from?
- Traits are only heritable when they are determined or
influenced by variation in our genes. - New variants arise from DNA mutation
- Mutations are random
- Whether the mutation persists or not is non-random and depends on whether it helps (positive selection), hinders (negative selection) or neither (neutral) the organism survive and reproduce
How quickly will the new mutation
spread?
- How long will it take for the new mutation to become fixed? (= present at 100% frequency)
- The answer depends on both the size of the population and the strength of selection
How long does it take for a new variant
to become the new normal?
- How long does it take for a black-causing mutation to
arise in a population of light-coloured mice? - CHANCE + TIME
- How quickly will that mutation spread?
- SELECTION + TIME
(mice example lecture 20 labeled as 21)
Summary of the evolution section:
GO TO LECTURE 24 - “Evolution summary lecture”
Define Allele:
alternative DNA sequence of a gene or locus
Define Locus:
position in the genome
Define Homozygote:
individual where both alleles are the same
Define Heterozygote:
individual with two different alleles
Define Population:
group of individuals of the same species who live in
the same area and interbreed
What is the definition of evolution in genetics?
Evolution is a change in the genetic composition of a
population = changes in allele frequencies over time.
What are the Conditions for Hardy Weinberg
Equilibrium to occur?
- No new mutations
- Random mating
- No selection
- Extremely large (infinite) population size
- No gene flow (migration)
- This is an idealised (Wright-Fisher) population. It is a
convenient simplification. - HWE describes a situation where no evolution is happening. If we test HWE and find it does not hold, then we know there is something interesting to look for
(flower example in lecture 23)
What are things that might be happening
to break Hardy Weinberg Equilibrium?
- Assortative mating (non-random)
* Results in fewer heterozygotes than expected –
Wahlund’s Principle - Natural selection
- Gene flow (migration)
- Genetic drift
What is genetic drift?
- Without selection, migration, mutation, etc. there is
nothing driving the allele frequency up or down. - It “drifts” randomly – GENETIC DRIFT
- Genetic drift describes chance events in evolution
Define bottle neck and founders event:
GO TO LECTURE 23 - for diagrams
What are the characteristics of genetic drift?
- Small populations
- Random (unpredictable) change in allele frequencies.
- Some genetic variation can be totally lost
- Some deleterious (harmful) alleles can become fixed
What are three types of natural selection?
directional, disruptive, stabilizing
GO TO LECTURE 23 - for diagrams
Give examples of balancing selection:
- Selection acts to keep the variation in the population
* We don’t see one allele replacing the other - Frequency-dependent selection
* Whether something is advantageous or not
depends on how common it is. - Heterozygote advantage
* e.g., immune system genes – heterozygotes have
more capacity to recognise pathogens
What happens in a part of the world
where malaria infections are common?
- Individuals homozygous for the normal beta-globin are susceptible to malaria infection.
* Hb/Hb - Individuals homozygous for the sickle-cell beta globin
allele have severe sickle-cell disease
* HbS/HbS
GO TO LECTURE 23 - for full info
