bio 1b midterm 1 livia's version

tree of life

- one of most intellectually important, unifying ideas

- idea that there is a common ancestor of life

evidence that life on earth descended from a single common ancestor

- shared molecules (20 amino acids and nucleotides)

- shared macromolecules

- shared mechanisms of dna replicaiton, metabolic pathways, biochemistry

- common genetic code

- similarity of form

- similar dna sequences

3 domains of life

bacteria, archaea, eucarya

archaea

- single celled microbes originally identified as a separate domain by karl woese in 1977 based on rrna genes

- can use a variety of energy sources and can live in extreme environments

bacteria

- single celled microbes, distinct from archaea

- live in most of earth's habitats

- can be beneficial or pathogenic

eukaryotes

- everything else

- includes protists, plants, animals, fungi

prokaryotes

- archaea and bacteria together

- cells do not contain organelles or nucleus

- smaller than eukaryotic cells

archaea and eukaryotes

- more similarly related than other stuff

- same components of dna replication, transcription, translation

- many ribosomal proteins shared but absent in bacteria

- translation factors

- rna polymerases more similar between archaea and eukaryotes

how to interpret phylogenetic trees

- if share a more recent common ancestor, more closely related

- cladogram never accounts for time

- sometimes phylogenetic tree branch length related to time

how many species on earth

- difficult to tell total amount of biodiversity on planet

- between 3 to 100 million

anagenesis

- change in a lineage over time

- one of the two parts of evolution

- species slowly turns into another species without branching

cladogenesis

- splitting of one lineage into 2

- aka speciation

- one of two parts of evolution

example of evolution

- antibiotic resistance

-penicillin

biological evolution

- change over time of the traits of a species

evolution by natural selection requires 4 things

1. variation: individuals within a population variable

2. inheritance: the variations among individuals are passed from parents to offspring

3. exponential growth: all species produce more offspring than environment can support

4. differential success: some traits have an advantage on survival or reproduction (some individuals favored)

carl linnaeus

proposed modern classification system

leclerc and comte de buffon

- entertained idea of evolution

- thought earth might be old

erasmus darwin

- darwin's grandfather

- entertained idea that all live evolved from 1 common ancestor

jean-baptiste lamarck

- offspring acquires the form of their parent

thomas malthus

- argued population multiplies geometrically and food arithmetically

- population will eventually outstrip food supply

charles lyell

- assumption of uniformitarianism

- process we see today also acted in the past

carrying capacity

- number able to be supported by the environment

principle of uniformitarianism

processes we see today also acted in the past

voyage of the beagle

- darwin's 5 year expedition to tahiti and galapagos

- drew a tree of evolution in 1830s

- wrote of preferred traits preserved 1838

how darwin worked to build an argument for evolution via natural selection

- evolution concept existed before him but he proposed natural selection

- selection under domestication

- biogeography: greater similarity of species within same geographic area

- fossil record: new groups don't appear at once but in succession

- homology: similarity of structures in different species often used for different purposes

- vestigial structures

wallace

- came up with natural selection independent of darwin

- travelled through indonesia

mutations

- ultimate source of genetic variation

- mutation in all cells but only ones in germ cells passed to next generation

- somatic mutations not passed down

- mammals have so much genetic material mutations have little impact often

molecular clock

- neutral mutations accumulate

- can figure out when species diverge if know mutation rate

- figure out nodes

- humans is 10^-8 per nucleotide site per generation (60 new mutations per generation)

- can figure out via sequencing genomes of parents and offspring

point mutations

- change in single nucleotide, often during dna replication

- often comes from dad bc more cell division and dna replication when sperm produced

- older fathers means more

other kinds of mutation (not point)

- small insertions or deletions of stretches (duplicated genes)

- chromosomal mutations: chromosomes rearranged, lost, duplicated

- whole genome duplication (occurs in many plants)

mutation rate and allele frequencies

- mutation rates relatively low

- typically have a negligible effect on allele frequencies

directional selection

- favors one direction

disruptive selection

- favors both extremes

stabilizing selection

- favors middle

- most common (bc other options often harmful)

phenotypic selection

- directional, disruptive, stabilizing

genotypic selection

- positive directional, purifying, balancing

positive directional selection

- one allele results in higher rates of survival or reproduction

- advantageous allele will increase in freq every generation and will become fixed

purifying selection

- selection eliminates harmful alleles

- harmful alleles created by mutation and eliminated by selection

- so genetic diseases decrease w/ selection but balanced (increase) via new mutations

- persistence at low frequencies in human populations

- hemophilia and muscular dystrophy

- most common

balancing selection

- heterozygotes have higher fitness than either homozygote

- both alleles maintained

- sickle cell malaria

genetic drift

- random change in allele frequencies that occurs bc pop not infinitely large

- is evolution without differential reproductive success (changes don't occur bc particular allele preferred)

- can occur in

1. drift is greater in small populations

2. allele frequencies change at random

3. drift leads to loss of genetic variation over time

4. drift can cause harmful alleles to become fixed in a pop

bottleneck

- reduction in size of existing population

- reduces genetic diversity

founder event

- establishment of a new population of smaller size

- reduces genetic variation

- leads to many genetic diseases having higher frequencies in particular ethnic groups or populations

- e.g. high type 2 diabetes in native americans

gene flow

- reduces genetic diversity

- homogenizes populations, reduces genetic differences between populations

- responsible for spreading of alleles from genetically engineered plants and animals into wild species

- salmon that die early interbreed w wild salmon

microevolution

- change within species or population

- changes in allele frequency over one or more generations

- four forces apply to microevolution

1. mutation

2. natural selection

3. gene flow

4. genetic drift

macroevolution

- evolutionary processes and changes that occur at or above species level

- selection on species-level traits

- mass extinctions

- origins of new higher taxa, morphologies

- longer timescale

- does not include speciation

- evidence mostly from fossil record

population

- group of individuals of same species living in same area at same time

- have potential to interbreed

alleles

- different forms of genes

gene

- sequence of nucleotides that encodes a specific product

- e.g. protein

phenotype

- appearance of trait

genotype

- term used to describe alleles

- Aa and AA etc.

mutation

- ultimate source of variation in population

- necessary for evolution

- random changes in organism's genome

- can be expressed or nonexpressed region

- mutations are random but the advantages from the phenotypic alterations is nonrandom

natural selection

- process in which individuals have certain inherited traits tend to survive and reproduce at higher rates than individuals without those traits

adaptation

- a heritable trait that increase the ability of an organism to survive and reproduce in a particular environment

- natural selection is only force of evolution that results in adaptation

- cannot occur without mutation, but can only be an adaptation if favored via natural selection

positive selection

- trait favored

negative selection

- against the trait

dispersal

- movement of individual from its birth site to its breeding site

- good bc lowers competition

- may lead to gene flow

isolating mechanisms

- may cease gene flow between two populations

- can lead to speciation

hardy-weinberg equilibrium

- requires no evolutionary forces

- and random mating (can be considered form of selection)

bacteria as testing

- have small genomes so easier to sequence and track changes

- even in large populations mutations can be lost via genetic drift

- but less easy for bacteria bc have horizontal gene transfer (but not too diff from yeast)

- can study repeatability of evolution

selection over time

- strong initial selection then ideal trait's value gets lower

- selection in a new environment gets comparatively weaker as population gets closer to new optimum

sexual selection

- individuals with particular inherited characteristics more likely than others to acquire mates

- not about fertility

- leads to sexual dimorphism

sexual dimorphism

- differences between exes

- driven by how unequal investment in gamete production

- unequal investment in reproduction (pregnancy, lactation)

bateman's principle

- variance in reproductive success greater among males than among females

- male reproductive success limited by number of matings with females

- female reprod. success limited by number of offspring she can produce and raise

- females invest much more so are limiting resource for reproduction

intrasexual selection

- competition between individuals of one sex

intersexual selection

- mate selection by opposite sex

fisher's runaway model

- explanation sexual selection

- females prefer males w extreme traits

- leads to sons w extreme traits and daughters w preference for extreme traits

good genes model

- explanation for sexual selection

- males w certain traits preferred bc traits associated w higher fitness

hybridization

- can lead a gorup to have non tree-like structure

- may have multiple ancestors?

phylogeny and classification

- taxonomy reflects degrees of relatedness

- tree shows descent not phenotypic similarity

- can be used to understand origin of species, evolution of traits, diseases, forensic analysis

- don't describe how advanced a species is

- can use to understand when traits analogous not homologus

branch point

- where lineages diverge

- more recent common ancestor means more related

ancestral lineage

- common ancestor of all taxa

basal taxa

- one step up from outgroup (within the ingroup)

polytomy

- branch point has unresolved pattern of divergence

- has >2 taxa from one point

- means can't figure out who most closely related to who

monophyletic

- contains ancestral species and all of descendants

- e.g. mammals

- monophyletic groups also called clades

- if all groups monophyletic then is phylogentic classification system

paraphyletic

- group contains ancestral species and some but not all of descendants

- reptiles

polyphyletic

- contains distantly related species but not most recent common ancestor

- e.g. marine mammals

homology

- similarities due to shared ancestry

- forelimb of bat and monkey

- can determine with alignment of molecular data

analogy

- similar due to convergent evolution

- wing of bat and bird

- evolved independently

synapomorphies

- shared derived characteristics

- traits that evolved in the most recent common ancestor of a group and are shared by all its descendants

- traits that define new clade

parsimony

- simplest is best

outgroup

- species more distantly related than all other ones

- but more distant is less useful

- used to identify ancestral character state

rate of evolution

- if no selection, then rate of evolution of dna dequences equal to mutation rate

- equales # of new mutations multiplied by probability that new mutation fixed

- K = (2Nu) x (1/2N) = u

- n*2 bc is sperm + egg (number of genes in diploid population)

- k = u = the substitution and fixation rate of a mutation

- can infer how much time elapsed

endosymbiont theory for origin of eukaryotes

- eukaryotic organelles originated from small prokaryotes

- mitochondria + chloroplasts bacteria like

- circular chromosomes w prokaryotic ribosomes

- have means to transcribe and translate dna

- + align w bacteria on phylogenetic tree

hiv transmission in criminal case

- phylogenetic alaysis of hiv-1 sequence of victim compared and most closely related to patient's

flu vaccine

- can draw phylogeny of influenza

- evolve very quickly

- phylogenetic pattern can help predict most effective vaccine for next year

biological species concept

- group of actually or potentially interbreeding organisms reproductively isolated from other such groups

- members of diff species don't interbreed under natural conditions

- if do, don't produce viable or completely fertile offspring

- focuses on reproductive isolation

- connection to gene flow

- idea that species rather than individuals evolve

biological species concept limitations

- cannot apply to fossils

- cannot apply to asexual organisms

- unclear if can interbreed when separated

- not practical to test

- some species hybridize but remain distinct over time

morphological species concept

- individuals of same species similar to one another in morphology

- most traditional approach

- can apply to fossils, asexual organisms, separated

- but difficult to know what differences in morphology important for distinguishing species

- polymorphic but not used to distinguish species sometimes

- usually same species identified as bsc bc gene flow so similar populations

phylogenetic species concept

- species smallest group of individuals that share a common ancestor and have same synapomorpheis

- defines species as small clades

- but problem w determining degree of difference needed to call something separate species

species definitions

- important for practical purposes

- legal protection for species

reproductive isolation

- arises due to barriers in gene flow

- a single gene can have major effect

pre-mating, prezygotic barriers

- no mating no fertilization

- geographic

- habitat

- behavioral

- temporal

- pollinator

post-mating prezygotic barriers

- after mating occurs but before fertilization

- gametic

- mechanical

postzygotic barriers

- after fertilization

- hybrid inviability

- hybrid sterility

- hybrid breakdown

geographic barrier

- species different geographic areas

- do not encounter each other

habitat isolation

- species may occupy different habitats within same area

- two species of cricket, one likes loamy soil one likes sandy

- flies mate on hawthorn or apple trees

pollinator isolation

- closely related species isolated bc rely on different pollinators

temporal isolation

- breed at different times of day, years, diff years

behavioral (mating) isolation

- differ in mating behaviors

- diff songs, etc.

mechanical isolation

- inhibition of fertilization between two species bc of mechanical differences in reproductive structures

- genitalia of many species evolve rapidly