Evolution

Speciation

• The process by which populations genetically diverge (genetic divergence) until they become distinct species

• genetic divergence: the process where separated populations of the same species accumulate different mutations over time.

Isolating mechanisms: Mechanisms which prevent species from interbreeding to produce viable and fertile offspring

Allopatric speciation

• Involves the formation of a new species as a result of a geographical barrier

• Geographical isolation

1. A geographical barrier separates a population preventing gene flow.

2. Different selection pressures act upon each population, favoring different phenotypes and allows genetic differences to accumulate.

3. Over time, sufficient genetic differences accumulate so the different populations can no longer interbreed to produce fertile and viable offspring.

Sympatric speciation

1. Involves the formation of a new species in populations located in the same geographical location

2. Reproductive isolation- due to change in mate choice, change in flowering time, change in behavior.

3. The common ancestor to H.forsteriana and H.belmoreana grew in pH neutral and volcanic (acidic) soils.

4. Some plants managed to grow in higher pH soils, resulting in conditions with less nutrient uptake, causing stress for the plant and earlier flowering times.

5. Earlier flowering time resulted in reproductive isolation between the palms, preventing gene flow from occurring and over time phenotypic differences accumulated, creating different species.

• polyploidy in plants can result in speciation when a plant develops a mutation that causes it to have extra sets of chromosomes, making it no longer able to reproduce with plants with the original plant population.

Evidence of speciation

• Biological (mating)

• Morphological (physical and structural differences)

• DNA differences

Variation

Isolation

Mutations

Selection pressures

Allele frequencies change
New species

Mutations

• mutations are the source of all new alleles and creates genetic variation

• for mutations to be heritable, they must occur in a cell that contributes genetic material to offspring

Point mutations (single base in single nucleotides)

1. Base substitution

• ‘Silent’ mutation

- no change to the amino acid encoded (new triplet codes for same amino acid)

• Nonsense mutation

- a single base substitution which results in the production of a stop codon which prematurely terminates the transcription of the mRNA strand, destroying the proteins function (protein synthesis is ended early).

• Missense mutation

- a different amino acid is encoded, if new amino acid is conservative the protein may still function, if it is non-conservative it can ruin the protein.

2. Base insertion/deletion

• causes a frameshift if the number of nucleotides is not three

Frameshift mutation

• an insertion or deletion of one or more nucleotides where the number of bases added is not a multiple of three. This shifts the ‘reading frame’ from the point of mutation and every codon following is read.

• as every amino acid after the point of mutation changes, it creates a completely non-functional protein.

• frameshift mutations often trigger a premature stop codon which cuts the protein short.

• introduces different amino acids into the encoded protein after the mutation.

Block mutations (changes to segments of a chromosome)

• deletion: a segment of a chromosome breaks off and all the genes in the segment is permanently lost

• insertion: a segment of DNA breaks off from one chromosome and integrates into a new location on the same or different chromosome.

• duplication: a segment of a chromosome is copied, leading to extra duplicate sections which may increase gene expression

• inversion: a segment of a chromosome breaks off, flips 180 degrees and reattaches in a reverse order.

• translocation: segments of two non-homologous chromosomes break off and are swapped between the chromosomes

Effect of mutations

• block mutations may be more severe than a point mutation as it affects a large segment of a chromosome and disrupts multiple genes rather than changing just a single base pair.

• If the number of nucleotides in a duplicated exon is divisible by three, it will not change the reading frame and cause a frameshift. The protein will just be longer.

Aneuploidy: having an abnormal amount of chromosomes (missing one or having have extra).

• an increase in chromosome number would increase the allele frequency of the alleles located on the affect chromosome.

Polyploidy: where a cell/organism has more than two complete sets of chromosomes.

• lethal in humans, mostly seen in plants

The fossil record

Fossil: any evidence of life from the past

Mold fossil: an impression of a past-living organism left in sedimentary rock.

Cast fossil: when a mold is filled with minerals, forming a rock shaped like a specimen.

Trace fossils: preserved physical evidence of an organisms biological activity. E.g. footprints

Body fossils: preserved physical remnants of imprints of all or parts of an organism. E.g. bones, feathers, mold fossils

How fossils form:

• rapid burial in sediments- reduces exposure to scavengers, weather and reduces O2 availability for bacteria. E.g. in lake beds, volcanic ash

• burial in alkaline or O2 depleted environments

• death occurs in very cold environments so remains are frozen

Limitations of fossil record:

• incomplete fossils- fossilisation requires specific conditions so many organisms are not preserved.

• biased- organisms with hard parts, large populations and suitable habitats are more likely to appear in the record.

• fossils can be destroyed or remain undiscovered- through erosion, geological processes or burial.

Transitional fossils:

• fossils that show traits that are common to both its ancestral group and descendant group

• E.g. archaeopteryx exhibits the traits of both theropod dinosaurs and modern birds.

Dating fossils

• radioactive decay: The process in which unstable an atomic nucleus loses energy by emitting radiation and becomes stable   

•     causes of changing allele frequencies in a population’s gene pool, including environmental selection pressures, genetic drift and gene flow; and mutations as the source of new alleles

Absolute dating: an actual date

• uses radiometric dating techniques based on the rate of radioactive decay to measure age

• Carbon 14 has a half life of 5730 years an is the most commonly used radioisotope for dating organic material. Decays into nitrogen 14.

• carbon 14 can only be used when the fossil is present and is less than 60,000 years old.

• Potassium has a half life of 1.3 billion years and a dating period of 100,000+ years.

• Radioisotopes are unstable atoms that decay into more stable products

• ‘Half life’ is the time taken for half the radioisotope atoms to decay

Relative dating: gives a date relative to another date of another fossil

Law of faunal succession: states that fossil organisms appear in a predictable, specific vertical order through sedimentary rock layers. Because sedimentary rock is formed by the accumulation of sedimentary layers on top of each other, the fossils closer to the surface must be younger than the ones below them.

Index fossils:

• a group of wide spread fossils which only existed for a short time and have a known age

• can be used as reference to easily determine the relative age of unknown fossils

determining relatedness

• it is not possible to identify relatedness if a fossil in too small and both species are extinct so it cannot be determined whether if fertile offspring could be produced.

Phylogenetic trees- phylograms and cladograms

Phylogenetics: the study of evolutionary relationships between species

How a phylogenetic tree is constructed:

1. obtain homologous DNA/amino acid sequences from different species

2. align sequences and identify differences between them

3. compare the number/pattern of differences

4. infer which species share the most recent common ancestors

5. start with the two most closely related species

Limitations when constructing a phylogenetic tree:

• Table of amino acid sequences- silent mutations are not detected

• only comparing relationships of each species with one species rather than with each other.

• only one protein is analysed

• only a short segment of amino acids is compared

Branches on a phylogram

• show evolutionary change and genetic divergence

• shows how a specific group of organisms has evolved over time.

• branch length indicates the amount of mutations/genetic change.

• branch length can indicate elapsed time since the genetic divergence of two species

• nodes represent a common ancestor

Cladograms

• shows evolutionary relationships

• branch lengths carry no meaning

• branching order is based on shared derived traits

Evidence of relatedness between species- Comparative anatomy

Structural morphology

• Homologous structures: physical features in different species that have the same basic structures inherited from a common ancestor, but may serve different functions. *Homologous structures indicate the species arose from a common ancestor.

• Vestigial structures: functionless biological features from past ancestors that are no longer used. E.g. remnants of hind limb and pelvis bones in whales. *Vestigial structures tell us that organisms change over time and share a common ancestor.

• Analogous structures: features with a similar function but arise from different basic structures between species. E.g. wings of bats and moths. *Indicates no recent common ancestors.

Disadvantages of structural morphology:

• analogous evolutionary pressures can produce similar

Molecular homology: the study of similarities in DNA/RNA, or protein sequences between different species to understand their evolutionary relationships.

DNA sequences:

Nuclear DNA:

• evidence of both maternal and paternal lineage

• large amount of data (larger genomic capacity than mtDNA)

• undergoes recombination

• contains majority of the genome (over 99%)

mtDNA:

• inherited through the maternal lineage

• has a higher mutation rate than nuclear DNA

• has a high copy number which makes it easier to extract from ancient/degraded fossils.

• no recombination (pure maternal genetic lineage making it more reliable)

• can be used with a molecular clock.

Molecular clock:

• uses the accumulation of genetic differences to estimate the time since two species diverged from a common ancestor

more genetic differences—→ more time since divergence

fewer genetic differences—→ generally more recent common ancestor

Amino acid sequences: mutations in DNA can change the amino acid sequences. A smaller amount of differences in amino acids indicate a more recent common ancestor.

Disadvantages of molecular homology:

• some DNA sequences are highly conserved (remained unchanged over time)

• mutations occur at different rates

• analogous evolutionary pressures can produce similar sequences

Genetic hybridisation

1. Dna samples from two species are extracted

2. the samples are heated to approx 95 degrees celsius

3. the high temperature breaks down the hydrogen bonds between the complementary nitrogenous bases, separating the double stranded DNA into two separate strands.

4. the single stranded DNA from both species are mixed together and allowed to cool

5. as it cools, complementary bases form hydrogen bonds with one another, resulting with a hybrid DNA.

• The closer the species are related, the higher the temperature it will take to separate the hybrid DNA strand.

Ways of using fossil and DNA evidence (mtDNA and whole genomes)

DNA evidence

• bioinformatics allows scientists to quickly compare the sequences between species. and enables researchers to process large amounts of DNA.

• mtDNA can be used to determine evolutionary relatedness, to identify common ancestry and for constructing phylogenetic trees.

• Molecular clocks calculate an estimate of divergence times

Whole genomes

• can compare DNA sequences, shared mutations and similarities and differences across genomes.

Fossil evidence

• Fossil evidence can be used to determine relative age

• comparing fossils show evolutionary change over time

• the fossil record determines when organisms existed

Human evolution

Mammals

• a variety of teeth including incisors, canines, pre-molars and molars.

• three bones in middle ear to aid hearing

• various amounts of body hair or fur throughout life time

• mammary glands to produce milk for offspring

• a diaphragm separating chest from abdomen

Primates

• large cranium relative to body weight

• prehensile hands and feet of five digits each and a opposable thumb to grasp objects

• longer gestational periods that allow growth of foetal brain

• foward facing binocular eyes

Hominoids

• increased cranium size and larger brain

• Y-5 pattern on molars

• lack of tail to sit upright

• shorter spine ‘C’ shaped spine

• generally longer arms than legs

• long narrow pelvis

Hominins

• most central foramen magnum to allow bipedalism

• largest cranium capacity and brain size ( except neanderthals)

• ‘S’ shaped spines to support weight vertically

• longer feet and arched heels

• shorter arm to leg ratio

• larger femur angle

• bowl shaped pelvis

Bipedalism

• keeps the body cool due to less surface area being exposed to sunlight

• able to visually scan environment for food or potential predators

• frees hand to carry offspring or objects

Cognitive and behavioral evolution

• evolution of homo genus is linked to increased brain size

• development of complex cognitive skills

Behavioral changes

• making/using fire

• cooperating in group activities

• the development of art, language, music and math

• use of symbols

Hominin advantages

• increased brain size in hominins indicates increased intelligence, which would be a selective advantage to survival.

Natural selection

Evolution: the change in allele frequency of a gene in a population over time.

• evolution is measured by the changes in allele frequencies in a populations gene pool over generations.

• If the allele frequencies have changed over successive generations, it indicates the population has evolved.

Allele: alternate forms of a gene

Genetic variation: the differences in DNA sequences and alleles between individuals’ within a population of species.

Increased genetic variation

• having high genetic variation increases the likelihood that at least some individuals would have a favourable phenotypic variation if there is a selective agent.

Decreased genetic variation

• reduces the ability of the population to adapt to future environmental changes- lowers genetic fitness.

• less variation between individuals leads to fewer alleles for natural selection to act upon.

Environmental selection pressures

• random mating

• selective breeding (artificial selection)

• advantageous alleles are not created by the environment because they a needed, but the variation already exist due to mutation.

• selection pressures favors individuals with beneficial alleles, increasing its frequency as it is passed on to offspring.

• fitness: refers to an individuals’ ability to survive, mate , reproduce successfully in its environment and pass on it’s alleles on to the next generation. If an allele increases fitness under particular environmental conditions, individuals’ carrying it may leave more offspring.

• however, an allele that is advantageous in a environment may not be beneficial in another environment with different selection pressures.

Chance events

Gene pool: the complete set of alleles present in a particular population.

Genetic drift: random changes in allele frequencies caused be chance events.

• unlike natural selection, genetic drift can occur to alleles favoured or not.

• genetic drift has a larger impact on small populations as random events are unlikely to dramatically alter allele frequencies in large populations

Bottle neck effect

• when the size of a population is drastically reduced for at least one generation, as the result of natural disasters or emergence of disease.

• the few survivors that reproduce may be unrepresentative of the original population due to altered allele frequencies.

• the resulting population will be genetically very similar to the original population.

Founder effect

• when a small group is isolated from a population and forms a new population in a different location where no other population already exists.

• as founders only carry a small sample of the original gene pool, the new population may have very different allele frequencies.

• the small population size means the gene pool of the new population is highly likely to have reduced genetic variation.

Gene flow: the movement of alleles between populations

• gene flow changes allele frequencies by introducing or removing alleles from a population’s gene pool

• can make populations more genetically similar as populations regularly exchange alleles, over time allele frequencies may become more similar.

• therefore gene flow can reduce genetic differences between populations.

• In contrast genetic drift can increase the genetic differences between isolated populations.