Bio 2 exam 3

Ch 19-22

Evolution

population gene pool becomes different over time

• causes extinction and origin of species

Evolutionary processes (6)

1. natural selection

2. mutation

3. gene flow

4. genetic drift

5. non-random mating

6. constraints, trade-offs

What did Charles Darwin and Alfred Wallace do?

Evolution by natural selection

• species change over time

• share a common ancestor and diverge

• changes explained by natural selection

Natural selection

increased relative individual fitness of certain individual phenotypes within a population (aka some individuals survive better)

• variation in traits

• heritable

• related to fitness

• acts directly on phenotype and indirectly on genotype

Consequence of natural selection

favored phenotypes become dominant in the population and are passed down —> evolution

Allele frequency

proportion of each allele in the population (A vs a)

• change in this = evolution

Genotype frequency

proportion of each genotype in the population (AA vs Aa vs aa)

Adaptation

favored traits spread in the population through natural selection

Artificial selection

selective breeding by humans

• needs genetic variation for the desired trait

Mutation

genetic variations that provide material for evolution by (natural) selection

• is the mutated or WT trait better?

Gene flow

movement of genes in/out of a population

• emigration and immigration

Genetic drift

random changes in allele frequencies over generations

• mostly impacts small populations

• bottleneck and founder effects

• harmful allele typically remains

Bottleneck effect

random event where only some survive —> lower genetic diversity

• impacts large populations as well

Founder effect

dispersal event causes population to split up into different locations —> lower genetic diversity

Neutral allele/trait

neither beneficial (helpful) nor deleterious (harmful)

Nonrandom mating

individuals prefer to choose some mates over others

• if changes genotype frequencies —> no evolution

• if changes allele frequencies —> evolution

Homozygous increase

individuals prefer to mate with their own genotypes

Heterozygous increase

individuals prefer to mate with a different genotype

Sexual selection (nonrandom mating)

individuals of one sex prefer to mate with particular individuals in other sexes

• only in species with sexual reproduction and 2+ sexes

• changes allele frequencies

Intersexual selection

individuals of one sex prefer to mate with individuals of another sex with certain phenotypes

Intrasexual selection

individuals of one sex compete to access mates

• only the winner gets to mate

Asexual reproduction

no fertilization

• vegetative and parthenogenesis

Vegetative reproduction

clones from non-sexual tissues

Parthenogenesis

genetically variable clones from germ cells

• meiosis (typically incomplete) but no fertilization

Sexual reproduction

meiosis in germ cells and fertilization

• isogamy, anisogamy, hermaphroditism

Isogamy

similar gametes in both parents

Anisogamy

different gametes: gametic sex

• possible sexual dimorphisms by sex determination systems —> sexual selection

Hermaphroditism

sequential and simultaneous (sometimes self-fertilization)

• one dominant sex, if dies, other sex changes to dominant

Sexual dimorphism

observable differences in male and female traits of the same species

• gametic sex does not always result in clear dimorphism

• sex roles are diverse

Constraints

Preexisting physical and chemical limits on evolution (constraint)

• lack of genetic variation prevents evolution

Trade-offs

Balance costs and benefits in adaptations

• balance must be positive to evolve

Discrete variation

traits affected by one locus are qualitative

Continuous variation

traits affected by more than one locus are quantitative

• types of selection apply to quantitative traits

Stabilizing selection

mean/average phenotype is favored by natural selection

• after evolution: some variation is lost, mean stays the same

Directional selection

phenotype different from the mean is favored by natural selection

• after evolution: mean changes, variation is not lost

Disruptive selection

phenotypes vary in both directions from the mean are favored by natural selection

• after evolution: mean stays the same, variation increases

Frequency-dependent selection

maintains genetic variation within populations

• 2+ phenotypic variations

• frequency of each phenotype determines fitness

Advantage of heterozygotes

maintains polymorphic loci

• heterozygotes outperform homozygotes under variable environmental conditions

Geographic variation

maintains genetic variation in geographically distinct populations

• different local selection pressures for each population

Phylogeny

the evolutationary history of relationships among organisms

Phylogenetic tree

represents historical relationships among lineages

Binomial nomenclature

Used to name organisms, 2 part names in Latin (genus + species)

• proposed by Carolus Linnaeus

Naming rules

capitalized genus + lowercased species + who made the name

Taxon

any group of organisms at the same taxonomical level

Clade

a taxon including all evolutionary descendants (node to tips)

Monophyletic group

common ancestor + all descendants

• AKA a clade

Polyphyletic group

does not include direct common ancestor

• come from different clades

Paraphyletic group

common ancestor + some descendants

Synapomorphies

shared derived traits

• ex. gizzard in both crocodiles and pigeons

Homologous traits

share similar evolutionary origins

• ex. similar bone shapes/structures in bat vs. bird wings

Analogous traits

evolve through convergent evolution

Convergent evolution

evolving independently for the same function

Evolutionary reversal

trait goes back to its original function

• ex. fins in dolphins > hands in humans

Homoplasies

similar traits that come from convergent evolution or evolutionary reversals

Molecular clocks

use mutation rates to label dates for evolutionary events

• rate of change/slope of the graph line

Phylogenetic trees can be built based on ?

synapomorphies

Principle of parsimony

the best phylogenetic tree requires the fewest evolutionary changes (lowest # homoplasies)

Consensus (phylogenetic) tree

computed because results are different depending on the traits used

Mathematical models

required to build phylogenetic trees from extensive molecular data (nucleotide sequences)

• more flexible than parsimony

• maximum likelihood

Comparing gene and protein sequences to identify evolutionary changes

compare aligned homologous sequences

• mutations in DNA accumulate at different rates over time

  • (rate = molecular clock)

  • regulatory sequences accumulate less mutations than protein-coding regions

  • exons accumulate more mutations than introns

Observed vs. actual number of changes between aligned sequences

Observed # underestimates actual # from common ancestral sequence

• multiple substitutions would be undetectable

• calculate evolutionary divergence

Evolutionary divergence

calculate by considering possible rates of change in mathematical model

Different types of substitution

None, single, parallel (2+ same change), coincident (2+ different change), multiple (2+ different change in same sequence), back (evolutionary reversal)

Synonymous substitutions (silent)

neutral to natural selection, accumulate over time

• *mutation rate is same as non-synonymous

Non-synonymous substitutions

under natural selection

• mostly deleterious/removed

• some almost neutral

• some beneficial/favored

Selection in genes among different populations/species

detect by comparing rate of synonymous and non-synonymous substitutions

Rate of synonymous/non-synonymous substitutions

• ~1 = neutral

• syn < non-syn = positive selection

• syn > non-syn = purifying selection

Genome sizes

differ by orders of magnitude

• prokaryotes < eukaryotes

• larger =/= greater complexity

• large genomes have more non-coding DNA

• selection against non-coding is stronger in large populations

Sexual reproduction

results in recombination of genomes by crossing over during meiosis and combination of gametes

Sexual reproduction disadvantages

• recombination breaks up adaptive gene combinations

• sex reduces # genes each individual passes

Sexual reproduction advantages

• repair damaged DNA

• purging deleterious mutations

• new combinations of alleles

Lateral gene transfer

horizontal movement of genes between lineages that results in gain of new functions

• increased genetic diversity, new functions in new DNA

• bacterial transformation, transposons, hybridization of species

Reticulations

events of horizontal gene transfer, includes inheritance proportion #

Eukaryote gene families

result of gene duplication

• evolutionary tinkering

• concerted evolution

Evolutionary tinkering

copies diversify in form and function; 1 original copy and other mutated copies

• mutations can be beneficial/favored or not/pseudogenes

Concerted evolution

copies do not diversify in form and function

• unequal crossing over

• biased gene conversion

Unequal crossing over

misalignment of repeats > crossing over > increase in copies

• can quickly spread or eliminate copies with new substitutions

Biased gene conversion

one gene copy damaged > repair with template from favored sequence > extra favored copy is added to original chromosome

Cascade of TFs

establishes body segmentation in animals

• maternal effects genes

• segmentation genes

• hox genes

Maternal effects genes

mRNA and proteins, sets up anterior-posterior axes of the body

Segmentation genes

determine boundaries and polarity of each segment

• gap genes: organize broad areas on anterior-posterior axis

• pair rule genes: divide embryo into units of 2 segments

• segment polarity genes: determine boundaries and anterior-posterior organization

Hox genes

determine role of each segment; what organ develops at each location

• encode TFs to determine role

• homeobox

Homeobox

conserved sequence in hox genes that codes for a homeodomain (in TF)

• binds to DNA to regulate gene expression

Homeotic mutations

in hox genes, can replace organs

Genetic toolkit of hox genes

we all share a conserved developmental toolkit

• similar chromosomal arrangement

• ordered as they are expressed

Developmental modules (ex. body parts)

can evolve independently within a species; changes in forms and functions

• genetic switches

Genetic switches

control how the genetic toolkit is used (on/off genes)

Modularity

allows independent evolution of developmental processes

• heterometry

• heterochrony

• heterotopy

• mutations of developmental genes

Heterometry

amount of gene expression

Heterochrony

timing of gene expression

Heterotopy

location of gene expression

Sexually reproducing species

group of actually/potentially interbreeding natural populations that is reproductively isolated from other groups

Speciation

divergence of lineages and emergence of reproductive isolation between lineages

Dobzhansky-Muller model

explains evolution of reproductive isolation

• ancestral lineage can separate into 2 if there is a barrier to gene flow (ex. geographic isolation)

• descendant lineages now evolve independently

• can experience allele fixation over time

• barrier can disappear and allow lineages to interbreed, but they are now incompatible and can cause low fitness/death

Allele fixation

loss of polymorphism result in just 1 allele in a locus (ex. A is fixed and a disappears, so only AA)

Reproductive isolation

increases with genetic divergence, is not all or nothing

Reproductive compatibility

decreases with geographic isolation and genetic divergence

• greater difference with greater mutation rate

Speciation by centric fusion

normal chromosome pairing is not possible in hybrids after centric fusion

• D-M model is applied to chromosomes instead of loci

• takes only a few generations in comparison to reproductive isolation, which takes millions of years

Centric fusion

chromosomal rearrangement

Allopatric speciation

mutation, genetic drift, local adaptation due to physical barriers that separate a population OR founder effects when a group crosses an existing barrier

• most common mode of speciation (but slow)

• lineages split, reproductive isolation (D-M)

• pairs of extant closely-related sister species