bio120

everything before tt2

Paley’s argument from design

if something has a design, and the design has a purpose, it must’ve been created by someone

• nature must have a creator

Lamarke’s theory

organisms can change its form in its life,

offspring will have some characteristics that their parents gained over their lifetime

August Weismann’s Germplasm theory

inheritance only be gametes, soma/body cells do not function as agents of heredity

genetic info cannot pass from soma to gametes and onto next gen

Darwin and Wallace’s theory of evolution

All organisms have descended with modification from a common ancestor (thus, living things change over time)

process leading to evolution is natural selection operating on variation among individuals

Darwin on Lyell’s theory for uniformitarianism

process that shape the eath’’s surfaces are uniform over time

the world is dynamic (changes) rather than static

change builds up gradually by the same mechanisms as in the past

Darwin on Malthus

favorable variations would tend to be preserved and unfavourable ones would be destroyed

not everything born can survive, struggle for existence

Wallace on Malthus

Only the best fitted live, in every gen, the inferior would be killed off and the superior would remain

Darwin’s mechanism of Natural sleection

Natural selection is heritable variation in fitness

Variation

individual variation in a population

heredity

progeny resemble their parents more than unrelated individuals

differential fitness

some forms are more successful at surviving and reproducing than others in a given environment (more fit than others)

fitness is measured relative to ancestor (ancestor value=0)

Important elements of Darwin’s theory

1. evolution occurs primarily at level of populations (individuals don’t evolve)

2. variation is not directed by environment (individuals dont induce adaptive variation when needed)

3. most fit type depends on the environment

4. “survival of the fitter” evolution works with available variation, will not necessarily achieve perfection

Evidence from geology

earth is very old, immense time for evolution

intermediate forms show transitional fossils linking features of unsimilar relatives (e.g. ungulates and whales)

fossils in younger strata resemble modern species in same region, older strata show more differences

Homology

Similarity of characteristics of two or more species due to inheritance from a common ancestor

Evidence from homology

1. vestigial traits provide evidence of evolution - have no/reduced function, can only be explained by presence of functional traits in ancestors, followed by evolutionary degradation

2. homologous structures are found across all organisms, structural similarity reflects common ancestry, homologous structures have evolved to serve diff. functions.

Evidence from biogeography

1. geographically close organisms resemble each other

2. different groups of organisms adapt to similar environments in diff. parts of the world

   1. geographically isolated regions have unusual organisms (have species adapted to niches unusual for their group)

evidence from domestication

1. lots of heritable variation found within species

2. variation can be selected on, leading to dramatic change over gens.

3. artificial selection is human imposed compared to natural selection in wild

Genotype

genetic constitution of an organism, defined in relation to particular gene/gene combo

e.g. Aa, AaBB

Phenotype

feature of organism when observed, used when describing trait of organism that varies

e.g. size, fur colour, enzyme activity,

Genome

the entirety of an organisms DNA, includes genes and non coding regions

some organelles e.g. mitochondria, chloroplasts, have their own genome

Key conclusions from mendel’s pea experiments

1. inheritance is determined by discrete particles, genes

2. each diploid organism carries 2 copies (alleles) of each gene,

   1. alleles can show dominance/recessivity,

   2. gametes contain only one allele per gene

3. gametes fuse to make offspring

4. offspring inherit one gamete (an allele per gene) from each parent at random

Discrete/discontinuous traits

distinct separable group with no in betweens, mendelian genetics

e.g. red or blue flowers

we can measure dominance and recessiveness, spread of alleles/changes in allele frequency

continuous traits

a trait that varies in amount/degree, qualitative genetics

e.g. height

we can measure selection response as change in average trait value

Mutation

ultimate source of genetic variation, caused by random, undirected errors during replication

increases genetic variation

recombination

crossing over of alleles during meiosis, creates new combos of mutations

increases genetic variation

genetic drift

change in frequency of an existing gene variant (allele) due to random change, stronger effect on smaller populations

decreases genetic variation

Negative (purifying) selection

mutations that reduce fitness are removed by natural selection

decreases genetic variation

positive selection

(aka. adaptation)

mutations that increase fitness will eventually become fixed in a population

decreases genetic variation

gen 1: allele is beneficial, favoured by selection —> gen 2: allele is more present —> as more gens pass, if allele is beneficial, freq. will increase until everyone eventually has this allele

fixation

occurs when polymorphic locus becomes monomorphic due to loss of all but one allele (can occur due to natural selection or genetic drift)

Diversified selection

selection can act to maintain diversity over the long term (e.g. heterozygote advantage)

increase (or retains) genetic variation

gene flow

movement of genetic material from one population to another

decreases differences between population

increases genetic diversity (introduces new alleles to your population)

mutation-selection balance

less fit types reintroduced by mutation, selection acts to remove them

classical school model

selection maintaining variation

heterozygote advantage, frequency dependent selection, fitness varies in space or time, (genetic based)

balance school model

classical school model

morgan, muller

low heterozygosity, low polymorphism, wild type is “normal” genotype,

selection is typically negative

Balance school model

Dobzhansky, ford

heterozygote advantage, high heterozygosity, high polymorphism,

selection favours diversity

advantages of studies in enzyme polymorphism

many loci can be examined, can be used in nearly any organism, heterozygotes can be identified

variation is examined closed to DNA level, provides genetic marker loci for other studies

selectively neutral variation

negative selection eliminates detrimental mutations, positive selection fixes beneficial mutations, so the only mutations that create genetic variation are selectively neutral

synonymous substitution

AKA a silent substitution (not always silent tho)

change of a nucleotide base that does not result in the change in the amino acid

nonsynonymous substitution

mutational change of a nucleotide base that causes a change in the amino acid

10x more likely to become fixed than synonymous ones

parthenogenesis

asexual reproduction with an egg without fertilization

clonal propagation

asexual reproduction without an egg

sexual reproduction

2 parents contribute genetic material to offspring

meiotic, reductive division to form gametes, fusion of gametes

asexual reproduction

1 parent contributes to genetic material

no meiotic reductive division, offspring are genetic replicas (clones) of parents

two fold cost of meiosis

sexual females contributes only 50% of gene copies to next gen 

transmission bias favours asexuals in competition with sexual females

costs of sex

sexual reproduction breaks up favourable combos of alleles

time and energy to find/attract mates, increased energetic costs of mating, risk of predation/infection, cost of producing males

benefits of sex

favourable combos of mutations brought together more rapidly

harmful mutations can be eliminated

benefits of genetic variation in variable/unpredictable environments (lottery models)

tangled bank hypothesis

may encounter diff. (heterogenous) environments, variation helps to acclimatize

spatial hypothesis

red queen hypothesis

conditions (e.g. temp) can change over time, variation can help an organism survive

temporal hypothesis

Case study: rotifers in diff environments (lec6)

Tested for rates of sex in homogenous and heterogenous environments- was found that there was more sex in heterogenous environments

Supports tangled bank hypothesis

Case study - evening primrose Oenothera

Asexual species are found to be on tips phylogenetic trees, greater accumulation of deleterious mutations w no way to purge bad mutations

outbreeding

mates are less closely related 

inbreeding

mates are more closely related

ONLY DECREASES heterozygosity

outcrossing

mating with someone else (either by in/out breeding)

fusion of gametes from 2 parents - derived from meiotic reductive division

selfing (self-fertilization)

mating with yourself, common in plants

fusion of gametes from 1 parent

most extreme form of inbreeding, NOT asexual reproduction

loses 50% of heterozygosity everytime you breed

factors leading to inbreeding

structure of local population enhances mating among relatives

hermaphroditic organisms have potential for self-fertilization

in small populations, even random mating can lead to mating among relatives

genetic effects of inbreeding on population

changes genotype frequencies - increases homozygosity, decreases heterozygosity

does not change allele frequencies

does not change polymorphism

inbreeding depression

reduction of fitness of inbred offspring compared to outcrossed offspring

leads to lower viability/survival and/or lower fertility 

inbreeding depression disfavours inbred offspring → favours outcrossed mating systems

genetic consequences of inbreeding

heterozygosity reduced by 50% per generation with selfing

competition between homozygous genotypes and genetic drift of small populations can reduce polymorphism

homozygosity for deleterious recessive alleles results in inbreeding depression

inbreeding depression CAN change allele frequencies (selection acts against deleterious alleles → allele freq. changes)

short term effects of selfing

can spread via natural selection if:

• rare pollinators/mates make selfing a better option

• transmission advantage 

  • low inbreeding depression

long term effects of selfing

low diversity and inefficient selection

higher extinction rates

outcrossing is more prevalent in macroevolution

selective advantage

amount by which some individuals of a given genotype are better adapted to a given environment, reflects relative differences in fitness

adaptation

trait that contributes to fitness by making organism better to survive/reproduce in a given environment compared to prior ancestral trait

evolutionary process that leads to origin and maintenance of traitsf

fitness

genetic contribution of individuals to next gen, relative to other individuals, as a result of differences in viability and fertility - relative quantity (not absolute survival/offspring number)

natural selection

selection by abiotic and biotic environment, no goal, affects all organisms

artificial selection

selection by humans towards a goal

stabilizing selection

average traits are favoured

directional selection

one extreme is favoured

disruptive selection

both extremes are favoured

Case study: peppered moths

light and dark forms exist, dark moths were rare but increased as industrial pollution increased

mechanism of selection due to predation by birds (difference in moth camouflage depended on trunks)

dark moths in polluted areas, light moths in unpolluted areas

after the clean air act, dark moths became rare again

Case study: heavy tolerance of metals in plants

tolerant genotypes will be closer to mines

gene flow between pastures and mines were restricted because difference of flowering time

• allowed tolerant alleles to be maintained

tolerance alleles decreased as you moved further away from mine (didn’t need to evolve for tolerance)

Case study: vision in stickleback fish

directional selection (depending on which part of the water)

• clear water: against red-shifted vision

• black water: for red-shifted vision

on one position along the chromosome, there was no genetic variation - strong directional selection that picked one gene over all others

selective sweep

selection causes a new mutation to increase in frequency so quickly that nearby alleles hitchhike and also increase in frequency

population

group of individuals of a single species occupying a given area at the same time

migration

movement of individuals from one population to another

gene flow

movement of alleles from one population to another, doesn’t require migration/movement of individuals

genetic drift

stochastic (random) changes in allele frequency due to random variation in producing offspring and death

• most important when populations are small

population bottleneck

single sharp reduction in abundance, usually followed by rebound

causes loss of diversity

founder events

colonization by a few individuals that start a new population

colonizing group contains limited diversity compared to source population

extreme loss of diversity

phenotypic plasticity

ability of a genotype to modify phenotype in response to particular environment

occurs through modifications to development, growth and/or behaviour, often an adaptation to unpredictable environments

• not all phenotypic plasticity is due to adaptation

reciprocal transplant study

growth of equivalent genotypes in contrasting environment and comparing their relative performance

• can separate phenotypic variation into genetic and environmental components

• enables measurement of selection against non-local genotypes

• can provide evidence for/against local adaptation

darwin’s origin of species

group of organisms that are sufficiently similar in phenotype

biological species concept

group of interbreeding natural populations that are reproductively isolated from other groups

• if they cant reproduce they’re not from the same species

reproductive isolation is key to distinguishing species

allopatric speciation

geographic speciation

biological populations of the same species become geographically isolated from each other, preventing gene flow and leading to reproductive isolation over time

sympatric speciation

process where new species evolves while ancestral species continues to inhabit same geographic region

• must happen rapidly, much rarer than allopatric speciation

prezygotic barriers

prevent mating or fertilization, no zygote forms

• geographical, ecological

• temporal

• behavioural

• mechanical

• cellular (sperm-egg compatibility)

Case study: apple maggot flies

Habitat and temporal isolation

arrival of domesticated apples caused host shift, different timing of host plant fruiting caused different timing of fly mating on host plant

gene flow reduced by 94% in sympatry (same region)

postzygotic barriers

prevents proper functioning of zygotes once they are formed

• caused by combo of genes with low fitness in the hybrid

• arises as an indirect byproduct of evolution acting separately in diff. populations (cannot be directly favoured by natural selection)

intrinsic barriers: inviability, sterility, abnormal development of hybrids

extrinsic barriers: ecological mismatch of hybrid phenotype to environment

Case study: mule

sterile cost of male donkey and female horse

can’t further breed to get another mule due to chromosomal mismatch (62 from m donkey, 64 from f horse)

Case study: genetic distance and fruit flies

the farther the genetic distance, the more reproductively isolated they are

ecological speciation

local adaptation can lead to RI and speciation

• distinct evolutionary responses to different selective pressures

• local adaptation NOT NECESSARY, but accelerates population divergence

Case study: Benthic vs Limnetic sticklebacks

sticklebacks colonized freshwater lakes

2 morphs evolved, differ ecologically and morphologically 

hybrids have lower fitness in each habitat, females prefer males of own morph

adaptive radiation

rapid diversification (ecologic and phenotypic diversity) from an ancestral species into multiple new forms

differ in traits allows for exploitation of a range of habitats and resources

causes of adaptive radiations

colonization of competition free zones

extinction of competitors

key innovation (evolution of a new trait that provides access to new resources

ability for speciation (RI evolves easier in some clades)hy

hybridization

exchange of genes between species as a result of interspecies mating 

• can sometimes reverse speciation process and merge 2 species into one

polyploidy

describes an organism, tissue, cell with more than 2 complete sets of homologous chromosomes

are reproductively isolated from parental species - sympatric speciation

exhibits new phenotypes, allows exploitation of new habitats

show hybrid vigour due to heterozygosity (allopolyploids)

allopolyploidy

when a polyploid offspring comes from hybridization between 2 parental species

autopolyploidy

when a polyploid offspring is derived from a single parental species

monophyly

a clade, describes a group made up of ancestor and all its descendants

paraphyly

group made up of an ancestor and some (but not all) of its descendants

polyphyly

group that does not contains MRCA of all members