TTM AP Bio Evolution

Charles Darwin

• 1809-82; British naturalist, proposed the idea of evolution by natural selection

basic timeline of evolution theory

1. Hutton gradualism

2. Lamarck (pre-Darwin) “giraffe with short neck can stretch his neck out to aquire a long neck, his babies will have long necks” + “if you got a nose job your nose would be passed to babies”

3. Darwin: natural selection selects the fittest giraffes (long necks), short necks can’t reach food, no energy to mate; long necks can reproduce and grow larger in number

You fit the environment and …
or You don’t fit the environment and …

you fit the environment and leave your genes behind
or
you don’t fit your environment and don’t leave your genes behind

adaptive radiation

rapid diversification of a single ancestral lineage into a multitude of new species, each adapted to exploit specific ecological niches

(think Galapagos finches beaks)

darwin 2 observations

1. members of a population often vary in their inherited traits

2. all species can produce more offspring that the environment can support, and many of these offspring fail to survive and reproduce (think seahorses)

artificial selection

humans have modified other species by selecting and breeding individuals with desired traits (most obvious ex is dogs)

darwin 2 inferences

1. individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals (differential reproduction)

2. unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations

Darwin, origin of species, mechanism to explain evolution

natural selection - the process whereby organisms better adapted to their environment tend to survive and produce more offspring

natural selection in depth

• depends on the environment

• acts on existing heritable variation

• whoever fits the environment better, leave more offspring being (differential reproduction again)

  • whoever best FITS their environment

mutations are random and can be:

advantageous, deleterious, or silent

after observing finches + Galapagos tortoise, Darwin proposed that

• species can change over time

• that new species come from pre-existing species

  • all species share a common ancestor

darwin’s theory of evolution is basically

descent with modification: all organisms are related through descent from an ancestor that lived in the remote past and accumulated adaptations to help them survive their environment (pizzly bear?)

parthenogenesis

form of asexual reproduction where embryos develop from unfertilized eggs.. downside being limited genetic variety

evidences of evolution (list)

• direct observation

• homology

• vestigial structures

• embryology

• DNA

• biogeography

• fossils

1. Direct Observation

through observable events, some changes in species have been observed and studied: what stays and remains, observing survivability

observable events - shows evolution is an ongoing process

ex. antibiotic resistance in bacteria, Galapagos finches beak size

2. Homology (2 structure types)

homologous structures: similar structures with different functions

ex. vertebra forelimb similar structure but for different functions (human, dog, horse, bat) ; also leaves

analogous structures: similar structures without shared ancestry — these structures evolved independently to serve the same purpose.
ex. wings in insects and birds

convergent vs divergent evolution

convergent: streamlined shaped bc of similar environment despite being different animal groups (process of developing analogous structures)

divergent: branching into different family groups

3. vestigial structures

vestigial structures: structures that have no apparent function and appear to be residual parts from a past ancestor.
ex. human appendix, pelvic bone of a snake

4. Embryology

Act of comparing embryos to look for common ancestry, provides evidence for evolution since the embryonic form of divergent groups are extremely similar

ex. homologous structures such as gills/tails

5. Fossils

Documents pattern of evolution

a. shows evidence of existence of now-extinct past species

b. showing a chronological progression of life forms over time

index fossil: widespread geographically but existed for specific time period, helps date correlating rock layers its found in

models of evolution

gradualism - evolution generally occurs uniformly and by the steady and gradual transformation of whole lineages. In this view, evolution is seem as generally smooth and continuous.

punctuated equilibrium - most species will show little change throughout most of their geological history, remaining in a state of stasis. Any change generally occurs rapidly and abruptly.

both correct: gradualism over long periods and punctuated in rapid breaks within long periods of stability

6. biochemical evidence: DNA/protein sequences

because all living organisms share a universal genetic code, inherited from a common ancestor, …

• similarities in DNA + AA demonstrate evolutionary relationships, with fewer differences indicating a more recent common ancestor

7. Biogeography

the study of geographical distribution of organisms, where evolution/species distribution aligns with geological and evolutionary events over time

showing that species' geographic distributions reflect their evolutionary histories and movement, rather than just environmental similarity

ex. Continental drift

macroevolution

macro

• large scale changes in gene frequencies

• longer time period

• at/above level of species

• not directly observed, rather fossil evidence

• ex. reptiles —> birds

microevolution

micro'

• small scale changes in gene frequencies

• few generations

• within a species/population

• observable, with experimental evidence

• ex. antibiotic resistance

the common misconception

individual organisms evolve

no, rather populations evolve over generations

but natural selection CAN act on individuals
- each individual’s traits affect its survival and reproductive success to other individuals in the population and can leave their genes behind

adaptation

an inherited characteristic of an organism that enhances its survival and reproduction in an environment

gene pool

a way to characterize a population’s genetic makeup

• consists of all copies of every type of alelle at every locus in all members of the population

evolution does not mean perfection

selection can only act on existing variation, and variation is from mutations

• chance, natural selection and the environment interact dynamically

• evolution is not directed

causes of evolution list

Change in allele frequencies in a population over generations

Causes: Mechanisms that can alter allele frequencies in a population

• Variation

• Natural selection

• Non random mating

• Genetic drift

• Gene flow (migration)

1. Genetic Variation (sources of)

a. new genes and alleles can arise by mutation

• only mutations in cells lines that form gametes passed on to offspring

• most mutations happen in somatic cell and are lost when the individual dies

b. sexual reproduction (crossing over, indep assortment) can shuffle existing alleles into new combinations

c. altering gene number or position

1. Genetic Variation

at the gene level: genetic variation is qualified by the % of heterozygous loci in a population: quantified as avg heterozygosity

at the molecular level: genetic variation is quantified by comparing the nucleotide sequence of individuals (rare)

2. natural selection

acts on an organism’s phenotype

only NS consistently increases the frequency of alleles that provide reproductive advantage

selection results in allele being passed to the next generation in proportions that differ from those in the present generation

• ex. DDT resistance fruit flies

can cause adaptive evolution - a process in which traits that enhance survival or reproduction increase in frequency over time

relative fitness

the contribution an individual makes to the gene pool of the next generation relative to the contribution of other individuals

NS alters frequency distribution of heritable traits in 3 ways, depending on which phenotypes are favored

A. directional selection (one extreme)

B. stabilizing selection (mid-range)

C. disruptive selection (both extremes)

heterozygous advantage

heterozygous genotype has a higher relative fitness than either the homozygous dominant or homozygous recessive genotype

3. Non-random mating (sexual, intra, inter selection)

sexual selection - individuals with certain inherited characteristics are more likely than others to obtain mates

intrasexual selection - males compete for mate

intersexual selection: females choose mate

sexual dimorphism

a difference in sexual characteristics between males and females

• one sex (typically male) is more brightly colored

4. Migration/Gene Flow

population integration leads to increase in genetic diversity

5. genetic drift

chance events cause allele frequencies to fluctuate unpredictably from one generation to the next, especially in small populations

two examples of genetic drift:

• founders effect

• bottleneck

founders effect

occurs when a new colony is started by a few members of the original population

population bottlenecks

occur when a population’s size is reduced for at least one generation, always leads to loss of genetic diversity

• rare alleles most likely to be lost in population bottlenecks, sometimes losing them means loss of resistance to rare disease/environment

is a population evolving

genetic variation is required, with one or more factors that cause evolution necessary to be at work

1. population - group of individuals of same species that interbreed

2. gene pool - all copies of every allele at every locus in all member of the population

fixed locus vs two alleles or more

fixed locus - all are homozygous for same allele

2+ alleles - homozygous or heterozygous

hardy-weinberg equilibrium conditions

not evolving and alleles frequencies will stay the same across generations

assumes

• no mutation

• random mating

• no gene flow

• infinite pop size

• no selection

fossil records and macroevolution

fossil record shows macro evolution changes over large time scales including

• emergence of terrestrial vertebrates

• origin of photosynthesis

• long term impacts on mass extinctions

chemical/physical processes + NS produced simple cells in 4 steps

1. abiotic synthesis of small organic molecules, such as amino acids + nucleotides

2. joining of these small molecules into macromolecules, including proteins + nucleic acids

3. molecules packed into probionts/protocells

4. origin of self-replicating molecules eventually makes inheritance possible

Oparin-Haldane hypothesis

Earth’s early atmosphere is reducing enviro (lack of O2), organic compounds could have formed from simple molecules.

• Energy for this organic synthesis could have come from lightning and intense UV radiation

• ocean as primitive soup where life arose

Miller-Urey test

made a lab similar to early Earth conditions, yielded a variety of amino acids + organic compounds.

• showed that abiotic synthesis of organic molecules in a reducing atmosphere is possible

• but instead of forming in atmosphere, first organic compounds prob synthesized near submerged volcanoes/deep sea vents

• AA also found in meteorites

abiotic synthesis of macromolecules (monomers → polymers)

• small organic molecules polymerize when they are concentrated on hot sand, clay, or rock

• replication and metabolism are key properties of life

protobionts/protocells

aggregates of abiotically produced molecules surrounded by a membrane or membrane like structure

• exhibit simple reproduction and metabolism and maintain an internal chemical environment

• could have formed spontaneously from abiotically produced organic compounds (ex. liposomes from lipids added to water)

first genetic material

was RNA not DNA

• RNA molecules called ribozymes have been found to catalyze many different reactions

• ex. ribozymes can make complementary copies of short stretches of their own sequence or other short pieces of RNA

sedimentary rock and fossils

sedimentary strata reveal the relative ages of fossils

• absolute ages of fossils can be determined by radiometric dating

  • parent isotope decays to daughter isotope at a constant rate

geologic record divided into (A, P, P)

Archean, Proterozoic, and Phanerozoic eons

Phanerozoic: encompasses multicellular eukaryotic life

• divided into three eras: the paleozoic, mesozoic, and cenozoic

oldest known fossils

stromalites, rock like structures composed of many layers of bacteria and sediment (3.5 bya)

• prokaryotes were earth’s sole inhabitants from 3.5-2.1 bya

oxygen revolution

2.7 bya

• posed a challenge for life

• provided opportunity to gain energy from light

  • allowed organisms to exploit new ecosystems

first eukaryotes

2.1 bya

• hypothesis of endosymbiosis: mitochondria/chloroplast consumery

• serial endosymbiosis: supposes that mitochondria evolved before plastids through a sequence of endosymbiotic events

  • evidence: similarities in inner membrane structures and functions, these organelles transcribe and translated their own DNA, ribosomes more similar to prokaryotic than euk ribosomes

origins of multicellularity

1.5 bya

• second wave of diversification gave rise to algae, plants, fungi, animals: oldest known fossil is small algae 1.2 bya

• snowball Earth hypothesis confined life to equatorial region

Cambrian explosion

sudden appearance of fossils resembling modern phyla 535 mya

• first evidence of predator-prey interactions

colonization of land

500 mya

• fungi, plants, and animals began to colonize land

  • arthropods/tetrapods are the most widespread and diverse land animals

pangea

formed 250 mya, effects:

• reduction in shallow water habitat

• colder and drier climate inland

• changes in climate as continents moved towards/away from the poles

• changes in ocean circulation patterns leading to global cooling

breakup leads to allopatric speciation

the five extinction events

Time Period Name	Millions of years ago	% of species  on Earth killed	Main type of species killed	Cause
Ordovician Extinction	450 mya	50%	Marine invertebrates (brachiopods, trilobites	glaciation, leading to dramatic falls in sea level
Devonian Extinction	360 mya	70%	Marine life and early land dwellers	global cooling, ocean anoxia, asteroid impact
Permian Extinction	251 mya	marine: 96% land: 70%	marine, mammal-like reptiles and insects	Siberian trap volcanoes during Pangea formation
Triassic	200 mya	50%	large amphibians, therapsids, archosaurs	volcanic eruptions during the breakup of pangea, global warming
Cretaceous Tertiary Extinction	65.5 mya	75%	non-avian dinosaurs	asteroid impact and massive volcano eruptions

mass extinction

when more than 50% species extinct

• can alter ecological communities and the niches available to organisms

• paves way for adaptive radiations

adaptive radiation

the evolution of diversely adapted species from a common ancestor upon intro to new environmental opportunities

• mammals went under adaptive radiation after extinction of terrestrial dinosaurs

• disappearance of dinosaurs (except birds) allowed for the expansion of mammals in diversity and size

• Hawaii as regional adaptive radiation: organisms colonize new environments with little comp

heterochrony

evolutionary change in the rate or timing of developmental events

• can have significant impact on body shape

• can alter timing of reproductive development relative to the development of non reproductive organs

• paedomorphosis

paedomorphosis

rate of reproductive development accelerates compared with somatic development

• sexually mature species may retain body features that were juvenile structures in an ancestral species

homeotic genes + hox genes

determine such basic features as where wings and legs will develop on a bird or how a flower’s parts are arranged

hox: class of homeotic genes that provide positional info during development

• if hox expressed in the wrong location, body parts can be produced in the wrong location

• evolution of vertebrates from invertebrates associated with alterations in Hox genes

• dupilcating Hox important in evolution of new vertebrate characteristics

evolution is not goal oriented

most novel biological structures evolve in many stages from previously existing structures

• the appearance of an evolutionary trend does not imply there is some intrinsic drive toward a particular phenotype

phylogeny tree vs cladogram

phylogram shows evolutionary/genetic distance, the branch lengths infer time

cladograms only show related characteristics

clade

clade is a group of species that includes an ancestral species and all its descendants

clades can be nested in larger clades

phylogeny three things to keep in mind

1. evolution produces tree-like, not ladder-like relationships

   1. left to right reading has no correlation with levels of advancement

2. choice of formatting left or right doesn’t matter

3. you can rotate branches around nodes without changing evolutionary relationships

validity of phylogenetic tree

valid

monophyletic - signifying that it consists of the ancestor species and all its descendants

invalid

paraphyletic - grouping consists of an ancestral species and some, but not all, of the descendants

polyphyletic - grouping consists of various species with different ancestors