bio 221 1-5 pt 1
selection vs evolution
Selection occurs within a population but evolution requires generations.
what do fossils show
show evolution over long time frames
cabbage, broccoli, cauliflower being descendant of wild mustard is an example of
artifical selection
can evolution happen on small time scales
yes
what are darwins 4 postulates
1. variation is pre existing and can be passed on to offspring
2. selection is based on environment
3. not all offspring survive (those who survive is non random)
4. differential reproduction (those with advantageous traits in that space and time are more likely to survive and reproduce)
what was darwins weakness
didn't propose a theory for inheritance, the concept of mutation was not developed until 1900's
what type of evolution did lamarck believe in?
transformational evolution
what type of evolution did darwin believe in?
variational evolution
what is the most powerful direct evidence of evolutionary change
fossils
what does fossilization need
an environment where they can fossilize
who first started study fossils
george cuvier first started studying fossils and first proposed extinctions
what is wrong with the fossil record
it is incomplete, we've only found the easiest to find fossils, hot humid areas rarely have fossils. fossils are also biased because hard and bony parts/ aquatic organisms fossilize better.
why is dating fossils hard
due to changing sediment conditons, if the environment that the fossil was in changes it can obscure the date
how old is the universe? how about the earth?
universe- 13.77 byo and earth- 4.5 byo
how do we know how old the earth is
because of 4.4 byo meteorite in australia and zircon crystals that are also this old, darwin also hypothesized this because of geological formations in england
how does a fully radioactive element decay
at a measurable rate
when were all radioactive isotopes formed
at dawn of solar system
what does the complete absence of shorter lived parent isotopes tell us
that our solar system is ancient
how old is life on earth?
approx 3.8byo, esitmated by principle of superpostion
list these key events from oldest to most recent, fossils of oldest known chordates (incl vertebrates), oldest land vertebrates, dinosaurs, oldest land plant fossils, our common mammalian ancestors, birds, the oldest trackways
520 Mya: fossils of oldest known chordates (incl vertebrates)
480 Mya: the oldest trackways
475 Mya: oldest land plant fossils
360 Mya: oldest land vertebrates
230 Mya: dinosaurs
180 Mya: Our common mammalian ancestor
150 Mya: birds
is there any fossils from the origin of life period
no just zircons and stromatolites
what are the two main hypotheses of the origin of life
deep sea vents and hot springs
what is the deep sea vent hypothesis
that there was tons of energy, carbon and lots of redox worthy chemicals
what is the hot spring hypothesis
that there was tons of energy and nutrients, lots of oxidized minerals
what is the miller-urey experiment
where they tried to recreate the conditons of early earth but failed
what can we hypothesize about the atmosphere and conditions of early earth through rocks?
very little oxygen, lots off ammonia, lots of methane, lots of volcanic activity. These conditions together could cause abiotic synthesis of organic molecules
what is the presumed origion of eukaryotes
1.8bya because of acritarchs
how old were mutlicellular fossils presumed to be
used to think 1.6 byo, interpreted as filamentous algae
635 myo were the oldest fossils intepreted as animals.. what are they?
sponges
what is lifes earliest animals
known as the ediacaran fauna
what did the cambrian, " the innovation era" give rise to
segmentation, 3 axis's, more complexity. (ex. trilobite, mollsucs, and first chordates)
what is the first hypothesis of why the cambiran was the innovation era
Increased O2, allowed more primary productivity, allows emergence of predators, allows inc in body size BUT oxygen levels didn’t necessarily change around Cambrian and larger animals already existed
what is the second hypothesis of why the cambrian was the innovation era?
Evolutionary innovation, evolution of novel traits (ex. Segmentation) allowed increased adaptability (ex. Hox gene cluster evolution may have sparked Cambrian)
what is the third hypothesis of why the cambrian was the innovation era?
Predation and arms race, if predation arose during Cambrian it could explain, inc body size, hard body size, motility/ swimming ability
when did land plants arise? what plants?
the late Ordovician and early Silurian period (450 Mya). Most likely liverwort like organisms, possibly co invaded by fungi, vascular plants evolved after
what is the oldest known land animal fossils ~ 428 mya
millipede
what are amniotes~ 314 mya
amniotes produce shelled eggs
what was the event when the meteor hit earth 66 Mya (end of cretaceous) and caused a massive shift on earth? what happened to organism popualtions
this was the paleogene mass extinction event which caused the loss of big reptiles but the little mammals thrived (prob due to loss of predators)
what did darwin think about assoicating the most recent common ancestor of species.
Darwin thought, more shared features= more recent common ancestor
what are infromative characters/traits in a phylogeny
vary with the taxa of interest, have different states, can be morphological, behavioural, biochemical, genetic.
why do we need to use taxonomy and phylogenetics?
to reconstruct evolutionary relationships so that trees can reflect shared ancestry
order the 9 domains
life, domain, kingdom, phylum, class, order, family, genus, species
what did mendel determine about hwo traits of offspring were determined
mendel determined that traits of offsprings were determined by parental factors that remained discrete.
what are discrete traits
traits that have no blending
what did mendel use to study traits
hand pollinated pea plants with known traits, he was the first to use math to explain predicted traits in offspring
explain the results of mendels pea experiment
Crossed round and wrinkled peas, all progeny were round (F1)- all showed only one parental phenotype, no blend, these were heterozygote (het) and showed the dominant traits. Then he crossed Rr and Rr and got progeny that were 3 R: 1 W (approximately).
what did mendel find about the nature of how traits come
that traits came in pairs and the genes are halved in germ cells
what are mendels 3 laws
law of dominance, law of segregation, law of independent assortment
what are non mendelian traits
most traits dont follow the phenotypic ratios of mendelian inheritance because of multiple alleles of one gene, influence on other genes and influence of environment
how is variation created in a population of diploid organisms
a diploid (2n) will only carry 2 alleles in an individual but multiple alleles can exist in population which can create variation in a population without necessarily being influenced by other genes or the environment
what are two exmplaes of mutliple alleles
ex. pavilion dardanus butterlfies which have multiple alleles which give rise to multiple wing patterns within the same speices
ex. human ABO blood type has 3 alleles, 9 possible genotype within pop, 4 possible phenotypes
are most traits continous or discrete
most traits are continous
what is a continous trait
where their phenotypic variation exists on spectrum
what causes continous traits
polygenic inheritance, where many genes contribute to the same traits
how much of an impact can the environment have on phenotype
environmental conditions can have a great impact on phenotype, even greater than genotype sometimes.
what are examples of enviornmental condtions that can impact phenotype
These conditions can include, temp, availability of nutrients, presence of toxins/mutagen, some can be the maternal effect
how do you know if a phenotype has a genetic origin or is purely environmental
Easiest way is to force mate individuals with opposite phenotypes if the progeny will follow a Mendelian inheritance pattern in the F2 but most traits aren’t Mendelian.
what is the broad structure of eukaryotic DNA
it is arranged into chromosomes, multiple linear chrosomes. DNA in eurkaryotes is organzied using histone proteins. The DNA wraps around a histone octomer creating a nucleosome.
what is the advantages of how DNA is organized
The organization of DNA protects it from damage, organizes the nucleus and limits access of transcriptional machinery to DNA
where are chromsomes stored, how does it sizes work
chromsomes are stored in the eukaryotic nucleus (membrane bound organelle), chromosome sizes can vary greatly- msot eukaryotes are diploid (2n)
how do soma and germ cells differ.
in the soma of humans cells are diploid but germ cerlls are haploid
what is the general steps of central dogma
DNA to RNA (transcription), RNA to protein (translation). Only one strand of DNA is used as a template.
what carries out translation.
Translation is carried out by ribosome and uses a universal codon table. 3 nucleotides= 1 amino acid
what allows for mutuational tolerance
Redundancy in the genetic code allows mutational tolerance (more than one codon encoding same amino acid. Most of redundancy is @ 3rd codon.)
what gives rise to different cells in eukarytoes
In most euk, each cell contains the exact same entire genome. Only a fraction of genes are expressed giving rise to different cell types.
when does most gene regulation occur
Most gene regulation occurs at the level of transcription initiation. This is regulated by a region of the DNA called the promoter.
what is another common area of gene regulation
alternative splicing
is most of the eukaryotic genome expressed
Most of eukaryotic genome is not expressed and most doesn’t become protein
pseudo genes are
genes that have mutated such that they no longer contain a promoter, hence not being transcribed to mrna
what are genetic markers
markers are specific sequences of DNA, often located throughout the genome, can be used as refrerence points to track the inheritance of genes linked to certain traits. the goal is to find genetic markers significantly associated with the extremes of the trait
what are transposable elements
jumping genes, products of ancient viral infection. Can change positions within the DNA, can cause mutations by disrupting the genes or regulatory regions that they jump to.
a bigger genome is a more complex genome? example?
no gemone size is unrelated to complexity, genome size caries greatly between organisms. ex. sea anemones have more genes than humans.
where do most complex organisms get variation from
from alternative splicing not from gene #
what is alternative splicing
process by which a single gene can produce multiple different versions of protein, occurs during RNA processing. alternative splicing allows for the exons (coding regions) to be arrange in different combinations leading to the production of multiple proteins from the same gene.
what does evolution rely on to drive variation and selection
meiosis
what are the products of meiosis
4 genetically different haploid gametes
through what mechanisms does meiosis generate genetic variation
crossing over, independent assortment, random fertilization
pair of chromosomes have the same blank but potentially different blank
pair of chromsomes have same gene order but potentially different alleles
what is the point of meiosis
it generate genetic variation and haploid gametes.
how does meoisis cause gentic variation
due to the crossing over in prophase I (homo chromo exchange genetic material)
and
independent assortment in metaphase I (homo chromo pairs line up, arrange randomly)
and
random fertilization (random sperm and random egg)
is a mutation always harmful
only the environment determines if a mutation is harmful (most common), neutral, beneficial (rare).
how do asexual organisms get varation
they rely on very rare benefical mutations for variation
what are the 4 types of point mutations
silent muation, missense mutation, nonsense mutation, frameshift mutation
what is a point mutation
change in a single base pair of DNA sometimes due to DNA replication error or exposure to mutagens
what is a silent mutation?
change in DNA seq that doesnt change protein seq
ex. GAA changed to GAG but both of these code for the same amino acid
what is a missense mutation?
a change in a single base pair that results in a codon coding for a different amino acid which can affect protein function
ex. GAG mutated to GTG code for a different amino acid which can affect the protein.
what is a nonsense mutation
point mutation that changes codon to a stop codon, causing protein to be prematurely shortened. Can cause to loos of function or non fuctional proteins.
ex. CAA muated to UAA (stop codon), causes translation to stop early.
frameshift mutation
deletetion/insertion of nucleotide so that the reading frame shifts of the genetic sequence.this leads to a complelety different protein sequence after the point of mutation which can be devastating to protein function
which point mutations effect the protein
missense maybe, nonsense, frameshift
are point mutations rare
no they are common, but the rarer events have greater effects
are aneploid rare
yes, gain/loss of chromosome
what is gene dosage
gain or loss of chromosomes, often have great effects
is the odd of any one base pair mutating low
yes
what is the average number of point mutations that occur in the genome of an indiviudal from one gen to the next.
around 61
what does HW eqbrm allows us to predict
HW allows us to predict the particular phenotypes in offspring for an entire pop
what does HW eqbrm provide
HW eqbrm provides a null hypothesis for testing evidence of evolutionary change.
how could the ratio of genotypes and phenotypes be the same in every generation
if there was no selection/mutation/drift
is H-W eqbrm satisifed in reality
no, to be satisifed a population must be infinitely large, have no net muation, no net migration, mate randomly, and have no selection (no disadvantageous/advantageous traits)
if H-W satisifed how would the pop look
alleles and genotype freq in offspring would be the same as parent gen
what is HW eqbrm equation. p=? q=?
P^2 + 2pq + q^2= 1
p= dominant allele
q= recessive allele
in a pop of chickens there is a locus that determine feather colour. there are two alleles of that gene (A1 and A2). you have a pop where 25% are homozygotes for A1 and 25% are homo for A2. what will be the genotypic frequencies in the offspring if the pop is at HW eqbrm.
a1/a1=0.25, a2/a2=0.25, a1/a2=0.50
of 1000 indiv, 400 are A1/A1, 400 are A1/A2, and 200 are A2/A2... what are the freq of p and q in this generation?
use equation f(p)= (f(A1A1)x2)+f(A1A2)/2x (pop size) - 2 for diploid, and multiple homo by 2 because they have 2 copies. solve for q as well.
p=0.6 and q=0.4. P+Q=1
what are genotypic frequences
refer to the proportions of different genotypes (homozygous domiannt, heterozygous, homo recessive) in a pop.
how do genotypic freq change vs allele freq
genotypic frequency can shift due to non random mating or genetic drift. allele freq shift from mirgation/mutations
does allele frequency change with geneotypic frequency
no
humans have blood type locus called MN that exhibitys a codomonant phenotype (in a hetero they are both M and N phenotype). A population found that 187 indiv were MM, 114 were MN and 19 were NN (of 320 people). what are the frequencies of p and q. what are the expected genotypic freq.
p= 0.7625
q=0.2375
p^2= 0.581 (MM)
2pq= 0.362(MN)
q^2= 0.0564 (NN)
what are the expected counts in a popualtion of 320 people? do they match up with the expected counts?
MM 0.58 of 320= 185
MN 0.36 of 320= 115
NN 0.05 of 320= 16
roughly match
genetic dynamic within a pop depends on
the connection between the pop
anything that violates H-W eqbrm can lead to
evolution- mutation, natural selection, migration,drift
is evolution always selective/directional
no, sometimes random events like drift and mutation happen
drift is often considered a sampling error why?
because it is random and no selected for.
how can we measure drift
computer simulation or with a drosphila lab experiment
what is the impact of drift dependent on?
impact of drift is dependent on pop size. The larger the population the more genetic stability. The smallest populations have the biggest fluctuations and fixation is least likely
what happened during drosphila lab experiment
researcher mates 8 females to 8 males each gen, 107 lab pop of D.melanogaster each found with 16 bw/bw^75 heterozygotes. Found: over 19 gens, bw^75 allele is lost, bw allele is fixed after 30 gen.
what does it mean for an allele to be fixed
when every indiv in the pop has the same allele at a particular gene location, no genetic variation for that particular gene in the pop- only one allele exists and it is the only form of that gene being passed on
does genotype freq change with allel freq change
yes, any small shifts in allele freq plugged into HW would turn into big shifts in genotype freq.
what is the problem with drift, esp in small popualtions
big problem for conservation because don't necessarily want the 2 extremes and drift makes the wild extreme more common. At a point of a species being endangered the odds of an allele being fixed increases
what are two special types of drift
bottleneck and founder effect.
what is the likelihood of an allele being lsot during a bottle neck related to
related to how common it is in the original population. Rarer alleles simply less likely to make through bottleneck, more likely to be lost. Ex: northern elephant seal. Was nearly hunted to extinction (20 indiv left), population expansion after a constriction lead to the bottleneck effect now observable in the genetic diversity of the extant population
what is founder effect
small group of indiv from a larger pop start a new pop, the founders are the only subset of genetic diveristy present. As a result, new pop may have different allele freq than original pop and certain alleles may be over or underrepresented
ex. the mutiny of the bounty
what is the interbreeding coeffcient? (F)
the calculated egree to which an indiv is inbred. F= proportion of individuals in a population who are autozygous.
what does autozygous mean
allele that is inherited identically by descent from both parent, allele comes from common ancestor. both copies of allele are identical
what does allozygoous mean? how is it calcualted
two copies of a gene in an indivual are not identical by descent, no common ancestor. 1-F= fraction that are allozygous
what is the proportion of heterozygotes in a population expected to be when there is no inbreeding. 2pq(1-F). what if there is inbreeding
if no in breeding, F=0, het= 2pq= HW
If there is inbreeding, F>0, F<1, the proportion of 2pq= less than H-W predictions.
you observed in one pop, gold that the heterozygote freq is 0.48. are they inbred? p=0.4, q=0.6. purpel heterozygot freq=0.24.
if 2pq= H0= null hypothesis for expected # of hets
H0= He (expected het)
H= H0-H0F (observed het freq)
F= H0-H/ H0 or F= 2pq- observed freq of het/ 2pq
'
what about population purple
F=0 not in bred for gold F=0.5 inbred for purple
what is the problem with inbreeding
inbreeding does not change allele freq but increases homozygosity
why is increased homozygosity bad
allows recessive, deleterious alleles to persists and reduce viability. Their effect only obvious when homozygous.
what is an example of disadvantageous inbreeding
the hapsburgs family where 50% hapsburgs children died before during 1 where as the rest of spanish pop ~ 80% survived
how do landscape genetic affect gene flow
when populations are separated by geographical barriers, because members of pop tend to be sedentary then gene flow is low, then pop will genetically differentiate over time due to drift.
how do lynx and bighorn sheeps exemplify connectedness
lynx have greater home ranges so over the same distances show greater connectdetness than big horn sheep
why is it that the farther the geographical distance between pops the greater the genetic difference?
usually, this is bc that means there is been a greater amount of time that has passed since the two pops have interacted. These distances can also be used as pop fingerprints. To determine where an indiv came from
more gene flow means what for variation and drift
Landscape features (including man made) can influence home ranges and gene flow.
More gene flow means increased variation means less drift.
F1
first filial generation
gene flow
movement of alleles between different pops through migration or interbreeding of indiv. increase genetic diversity within a pop by introducing new alles from another pop, it can reduce genetic differences between populations, and it can prevent speciation (formation of new species) by maintain connectivity.
landscape genetics
knowledge of geography allows researchers to explore how genotypes vary across landscapes.
bottle neck
(type of drift) when a population undergoes a rapid constriction in population size, then expands = the allele freq in surviving population may not reflect the freq in original population
founder effect
(type of drift), occurs when an offshoot of a bigger population establishes a new population, therefore the new population will be dependent on alleles the founders carry. Typically the alleles that are most common will be most represented (but there is randomness)
inbreeding depression
inbreeding increases homozygosity and brings recessive (and sometimes deleterious) alleles to surface. Declines in survival and fecundity are due to inbreeding humans.
inbreeding
mating with close relatives, violates HW assumption of random mating. Selfing is the most extreme form, and shows how inbreeding reduces the proportion of heterozygotes in a population.
sib-mating
suppose we could magically label individual alleles and follow them through subsequent generations. Ex. Label one copy of A1 in a male with an asterisk (*). Potential for diversity is reduced. after 1 gen A1* may have been passed to both son and daughter, if siblings mate= 25% chance that offspring will have both alleles from grandfather
no subdivision
individuals can interact with one another very easily (pigeons)
intermediate subdivison
there are little pockets of individuals that can move between subdivision but its not contiguous (snowshoe hares in edm)
genetic drift
happens when the H-W assumption of an infinite population is violated. Random changes in the frequency of two or more alleles/haplotypes/genotypes therefore we have to consider drift as a force that can cause allelic change (evolution) that are not due to selection.
extreme subdivsion
populations that are completely isolated from one another
population
group of interacting (potential) and potentially interbreeding individuals of a particular species
population genetics
the study of allele distributions within and among populations and how they change over time
Evolution
different forms arise from changes in allele frequency. it is specifically defined as a change in inherited traits in a population over time, Darwin described it as descent with modification. Evolution is not synonymous with natural selection, natural selection is a mechanism of evolution but not the only mechanism and it may result in evolution if selection causes a change in allele frequencies (genetic structure of pop) over time.
4 mechanisms of evolution
muation, drift, natural select, gene flow.
new: aritifcal selection
mutation as a mechanism of evolution
mechanism that drives heritable variation (not all mutations do this)
drift as a mechanism of evolution
random changes to the genetic makeup of a population (mutation is a mechanism of drift, there are several others too)
natural selection as a mechanism of evolution
caused by the interaction of genotype with the environment.
gene flow as a mechanism of evolution
migration between populations
artifical selection as a mechanism of evoltuion (new)
now an important driver of evolution (goes hand in hand with natural selection, new)
rate of evolution depends on 3 things
Rate of reproduction
Selective forces
Environmental change
who is georges cuvier
anatomist, found life forms that went extinct. Thought extinction was only caused by catastrophe
who is jean baptise lamarck
zoologist, curated fossils and extant mollusks. Saw gradual change in individuals. Suggested species change over time based on the use and disuse theories. Also that change comes from interactions with the environment that can be passed onto offspring.
what did lamarck get wrong
He got a few things wrong ( that microbes arise from spontaneous generation, that humans were the most complex species therefore they have been around the longest and the inheritance of acquired traits which is partially wrong because it has some applications.)
who is charles lyell
geologist, found that landforms are not fixed but slowly changing because of geological processes, estimated earth was older than biblical 6000 years. Also proposed extinction.
who is thomas malthus
talked about survival of the fittest in a human population. Human pop increases faster than food supply (demand outpaces supply). Completion leads to survival of the fittest because resources are always limited .
who is alfred russel wallace
Naturalist, came up with natural selection independent of Darwin. Encouraged Darwin to publish.
who is charles darwin
Collected specimens and fossils found patterns of distribution of traits (particularly distribution of beak lengths in finches between Galápagos Islands). Wrote “ the origin of the species by natural selection). Descent with modification but he did not understand how modification or inheritance occurred.
what is galapagos
far from mainland South America, relatively young islands, little gene flow isolated pop were a result of bottle neck.
what is the 3 principles of descent with modification. explain them
Variation- exists in all species
Artificial selection- enhancement of desired traits
Distribution of species in time and space- if there is descent with modifications, then similar species with modifications should be found in similar areas.
Lamarckism
Transformational evolution, forms change in their lifetime and that is passed on . Everything changes and change is heritable
Darwinism
Variational evolution, only a few survive and persist
fossils
trace of past life that has fossilized through a slow process of mineralization, rare but numerous, many organisms don’t fossilize because it required perfect conditions of desiccation (dehydration) and mineralization. Soft tissues rarely fossilize.
fossilized structures that readily fossilzie
bones/ teeth- readily fossilize
trace fossils
indirect evidence of life, not of the organism but from the organism (ex. Subfossil: fossilized footprints, a coprolite (poop). Important for determining the physiological method of the organism.
chemical fossils
organisms engage in chemical reactions that leave a mark in geological time (ex. Fossils fuels represent carbonaceous deposits of fossilized marine algae)
zircon
crystals the preserve specks of carbon used for dating
radiometric dating
based on the principle of radioactive decay, these radioactive isotopes decay at a steady state (denoted by their half life)
Half life
amount of time for half of the atoms in a unit of element to decay to daughter products
eon
largest unit of time (can be thousands or millions of years long), delineated by major changes to earth's system
Hadeon Eon (hellish eon- 4.55 to 3.8 bya ):
no evidence of life, very volatile, inhospitable, no liquid water
Archaeon Eon (3.8-2.5 bya
earliest forms of unicellular life, life was limited to the oceans ( which contained oxygen, nutrients and energy) as with only trace oxygen in the atmosphere. Bacteria first then Archaea. stromatolites.
principle of superposition:
dating the rock layering to date fossilized chemical life forms in that layer (estimate). Uses radiometric dating (ex. Uranium for old things and carbon for young things (<50k years).
C14
allows us to date tissue itself, can be naturally replenished in atmosphere (< 50k years)
stromatolites
layered structures formed by chemical reactions of ancient bacteria (oldest fossils). Ex. In Ontario there are iron banded formations - chemical signatures of ancient life, only from biotic processes.
Proterozoic Eon (2.5 bya- 500 mya)
beginnings of eukaryotic and multicellular life. Great oxygenation Event (2.5 bya- 2.2 bya), oxygen content in the atmosphere increased significantly due to the rise of photosynthetic bacteria. Oxygen is a strong selective pressure because it is so reactive, this along with other pressures probably led to the evolution of eukaryotes.
Phanerozoic Eon (500 Mya- present)
the Cambrian explosion marked the evolution of the modern day animal body plan, this eon and forwards is depicted in greater detail, more visible life.
3 eras
Paleozoic (old life), Mesozoic (middle life), Cenozoic (new life)
4 chemical biomarkers of ancient prokaryotic life:
LUCA: last universal common ancestor
Prokaryotes: no membrane bound nucleus (bacteria and archaea)
Eukaryotes: archaea evolved internal membranes
Archaea: “extremophile”, prokaryotic, ancient archaeon that evolved in eukaryote.
acritarchs
single celled organisms of ambiguous origin. Large, structurally complex biological specimens. How we presumed origin of eukaryotes .
animals biomarker
has this biomarker (chemical signature)- cholesterol like molecules
ediacaran fauna
mostly fossilized sponges, jellyfish and comb jellies, front like organisms. Small animals with simple morphology. Almost completely wiped out by a mass extinction.
The cambrian
most extensive period of adaptive radiation and formation of new life forms, around 541 Mya the entire ocean ecosystem was reorganized and new animal body plans emerged, Cambrian animals had modern body plans (invention of segmentation and 3 axis (r/l, d/v, a/p), notochord, more complex). Most major extant animal phyla make their first appearance in deposits (550 Mya) . Appearance of hard body parts, and huge variety of form, feeding methods and locomotion. Best known deposit is the Burgess Shale.
end of Devonian
vascular plants evolved. Earth was covered in ferns, horsetails and first seed plants . Land plants got more sun but they need to stand up and were susceptible to dehydration
amniotes
produced shelled eggs. 3 forms - diapsids (2 holes behind eye sockets like reptiles), synapsids (1 hole behind eye sockets like horses), and dinosaurs (230 Mya- Mesozoic).
The Cenozoic:
age of mammals (66 Mya-present), earliest fossils of ape ancestry. 55 Mya- primates, 20 Mya- apes, 7 Mya- hominins, 0.2 Mya- Homo sapiens
phylogenies
evolutionary history of a lineage
Phylogenetic trees
Visual representation of phylogeny
Ernst Haekel:
developed the first real trees, included time scales, trees can demonstrate evolutionary relationship and time.
will henning
worked on fly taxonomy and came up with an approach to phylogenetics that was more systematic; cladistics.
cladistics
relationships among taxa follow a dichotomous branching pattern= branch in pairs
Shared, derived traits (synapomorphies) that provide for relative recentness in common ancestry
Principle of parsimony
Cladogram should be consistent with the inferred pattern of historical relatedness
outgroup
A species known to have or suspected to have split off prior to main diversification event, are necessary to root the tree (a distinct starting point). The outgroup is not a primitive species but it does have ancestral traits and other derived traits
informative character states: can be coded as binary
0: in outgroup considered ancestral
1: a state that is different than outgroup
synapomorphy
shared, derived trait. Trait that is present in more than one group. found in 2 or more speices from common ancestor. trait that is new to the clade and distinguishes that clade from other organisms.
symplesiomorphy
shared, ancestral trait. Present in both Ingroup and outgroup
ex. vertebral colum for vertebrates.
autapomorphy
derived trait found in only one taxon. only in one species. defines a single lineage
ex. long neck for giraffes even within mammals unique for giraffe
homoplasy
represents convergent evolution, character states that are present in more than one taxon but arose independently due to similar environmental pressures or functional needs
winga of bats, birds, insects
homology
character states that are present in more than one taxon but arose from a common ancestor
limbs of humans, cats, whales, bats
polytomy
comb, represents an unresolved tree
systematics
scientific study of all kinds and diversity of organisms and all relationships among them
taxonomy
science of describing, naming, and classifying species of living and fossilized organisms. (Is subject to change)
phylogenetics
the study of evolutionary relationships among organisms
who is carl linnaues
created the first systematic binomial naming system for organisms. Each organisms was given a genus, specific epithet (species name). Created the 3 kingdoms, plants (regnum vegtabile), animals (regnum animals), minerals (regnum Lapideum). Then the smaller categories, class, order,genus, species. His mistakes was that minerals aren’t alive and that humans as different subspecies, also didn’t believe species could evolve
nomenclature general rules
No two species within the same kingdom can have the same name
You can’t name stuff after yourself but you can name it after other people.
Has to grammatically make sense in Latin, but sometimes using indigenous names from the region the specimens are found (ex.tiktaalik roseae- first animals to leave ocean)
Classify organism by domain, kingdom, phylum, subphylum, class, order, family, genus and species
Only genus and species are italicized/ underlined.
Everything except species should be capitalized
Each successive level is nested within another
types
designated example specimen(s) representing a species. Used to determine if an unknown organism belongs to that species. Usually considered the best representation of a species, housed in museums and collections, they must be available to the public and to researchers
alleles
variants of a gene
holotype
single designated specimen used a ‘type’, the ‘name bearer’.
paratype
collection of specimens used a type for a species
genotype
the genetic makeup of an organism, genotypes are heritable. Individuals inherit alleles. One genotype can lead to several different phenotypes depending on how the gene is expressed (genotype + environment = phenotype).
phenotype
the physical manifestation of that sequence is the phenotype, the phenotypes are not inherited. The phenotype (manifestation of the gene) is what selection acts on, can include physiological processes, developmental processes, behaviours
the law of dominance
the dominant allele is expressed in a het (heterozygote).
law of segregation:
all alleles are equally represented in gametes. 50;50 chance of giving one allele to offspring.
law of independent assortment:
genes on different chromosomes assort independently (ex. Colour and shape are independently assorted/inherited).
Polyphenism
more than 1 discrete trait can arise from a single genotype at a single locus (genetic location= gene), due to the influence of environment. Ex. Aphids can be wingless or winged as adults with the same genotype because they have different phenotypes from nutrition profiles during development. This is an irreversible phenotype.
basis of QTL analysis (quantitative trait locus analysis)
study of genetics of extremes- look for variants/loci that are more likely associated with the extreme traits. Sometimes the loci found are not the genes themselves but are genetically linked to the determinant locus.
the LOD scores
the log of odds, ex. lod score of 2 means 100x likelihood of being associated with height.
phenotypic plasticity
the same genotype can manifest as different phenotypes depending on the environment and can change in a lifetime. Ex. Hydrangea flower color can change based on soil pH. If soil has neutral ph- flower is white, if soil is acidic- flower is blue, if solid is basic-flowers are pink. You can take white flower cuttings and grow in soil of different ph and the colour changes, same genotype but different phenotype.
common garden exp
Take two individuals with distinct phenotypes and environments and grow them in the same environment to see if those phenotypes stay. Ex. Blue flower plants tend to grow on east slopes, white flower plants tend to grow on west slopes and then we swap them, after moving to a new environment the plants display a parental phenotype therefore it is most likely genetic.
proteins
the machines of the cell and where variation allows selection. chains of amino acids folded into unique 3D structures, structures can be simple or complex. Structures can be made from one amino acid chain= monomer. Structures can be made from multiple amino acids= oligo or polymer.
dna
a polymer of nucleotides arranged into a double helix, it is double stranded, antiparallel (strands of DNA run in opposite directions of each other), complementary ( A=T, G=C).
hemoglobin is a heterotetramer meaning
2 genes that make one functional protein.
Genes
a sequence of DNA that encodes a trait that can be selected for.
chromsomes
molecules of DNA where there are thousands of genes.
promoter
a sequence of DNA that regulates transcription initiation. Bound by proteins called transcription factors.
mitosis
generates genetically identical daughter cells (diploid to diploid)
meiosis
generates genetic variation and haploid gametes (diploid to haploid)
meiosis- crossing over
physical exchange of DNA between pairs of chromosomes.
Meiosis- independent assortment
2 pairs of chromosomes assort independently (equally likely segregation patterns)
meiosis- random fertilization
sperm that fertilizes isn;t necessarily the strongest, all sperm are different (and eggs).
mutations
change to the genetic sequence or content of an organism, they are common and occur during DNA replication (whenever DNA is being copied there is a chance of error). Many mutagens (things that cause mutations) in the environment like UV light.
are mutations random
Every mutation is equally likely therefore every nucleotide can change. Mutations are random/non directional, and comes before selection, environment determines if the mutation is beneficial, neutral or harmful (not adaptively directed).
how can mutations be inherited
Most mutations are not inherited and they must occur in germline to be heritable, most mutations happen in soma.
point mutations
substitution of a single base with a different base, can be transitions of transversions. Has to happen at the same position on the same strand. In DNA a change in sequence is reflected in mRNA. If a point mutation happens in a coding region it can result in a simple protein mutation, can be synonymous or no synonymous.
transitons
purine with purine (A-G) or pyrimidine (C-T) with pyrimidine
transversions
pyrimidine with purine or vice versa
synonymous
silent, no effect on amino acid sequence= mutational tolerance due to redundancy in the genetic code.
non-synonymous:
change amino acid sequence, can be missense (encodes the wrong aa and may affect the structure/function of a protein), can be non sense (creates a premature stop codon and a truncated protein, this will affect the structure and may affect the function)
indels
these are insertions and deletion of 1+ nucleotides. If indels occur in a protein encoding sequence it causes a frame shift that affects all amino acids/codons after index.
inversions
flipping of a DNA segment within a chromosome, often causes no major changes.
duplication
repeating the same sequence often in tandem with the original ex. ABCD—> ABCBCD (can have dosage effects, often a result of transposable elements- jumping genes)
translocations
originally separate chromosomes to break and fuse with another chromosome
karyotype
the #, size, shape, arrangements of an organism's chromosomes. Change in karyotype can affect fertility of an individual and viability of the offspring.
Aneuploid
unbalanced # of chromosomes, 2n +1 or 2n-1
Polyploid
duplication of entire genome, often results in sterility (esp if off # of chromsomes
Tetraploids
4n, are more fertile than triploids (3n)
Autopolyploids
genome duplication within same species
Allopolyploids
genome amplification due to hybridization between 2 species