BIO5 - Mid unit

Revision babeyy

Evolution by natural selection - List the principles

* All species produce more offspring than the resources can support
* There is natural variation between individuals of a species
* Individuals with advantageous genotypes will be more likely to survive & produce offspring
* Over subsequent generations, the frequency of the advantageous genotype increases, leading eventually to evolution of the species

Requirements for life

* A source of energy
* The sun (top right) for photosynthetic organisms.
* Thermal vents (bottom right) for chemosynthetic organisms.
* A carbon source.
* Liquid water (e.g. geysers).

Processes needed for the origin of life

1\. The non-living synthesis of simple organic molecules (from primordial inorganic compounds)

2\. The assembly of these organic molecules into polymers

3\. The formation of polymers that can self-replicate (enabling inheritance)

4\. Packaging of these molecules into membranes with an internal chemistry different from their surroundings

Primordial sea → List conditions

* High volcanic activity
* High UV radiation (thin atmosphere)
* Lightning
* Water vapour, methane, ammonia, hydrogen

Undersea thermal vents → List conditions

* Life may have arisen at ancient volcanic vents which provided the necessary conditions for life:
* Gases
* Energy (heat)
* A possible source of catalysts (metal sulfides) for life to develop.

Panspermia

* Some bacteria survive similar to space conditions
* Comets contain organic material
* Could have delivered

Proto-cell conditions

* A membrane separating the internal environment from the external environment
* Storage of specific biological molecules
* Ability to replicate

Ribozyme

RNA molecules have the ability to act both as a blueprint and as a catalyst

Relevant properties of RNA

1\. RNA can self-replicate

* RNA is able to store information in a sequence of four nucleotides (similar to DNA)
* Short sequences of RNA have been able to duplicate other molecules of RNA accurately

2\. RNA can act as a catalyst

* Modern cells use RNA catalysts (called ribozymes) to remove introns from mRNA and help synthesise new RNA molecules
* In ribosomes, rRNA is found in the catalytic site and plays a role in peptide bond formation

Earth’s history + Early life

Series of key events that occur

* Evidence for life in microbial mats such as stromatolites are multilayered sheets formed by microorganisms such as archaea and bacteria.

Oxygen enrichment

Oxygen producing bacteria evolved somewhere between 2.5 and 3.0 billion years ago that eventually became photosynthesis.

Transformed planet from an environment of very little free oxygen to one of continuously increasing levels.

* This led to some key events such as the production of oxidized compounds, the evolution of aerobic organisms, changing Earth's atmosphere.
* Formation of an ozone layer restricted UV radiation to allow for the proliferation of a wider range of life forms.

Origins of Eukaryotes

* First appeared \~2 billion years ago.
* evolved from large prokaryotic cells that ingested other prokaryotes.
* symbiotic relationship- endosymbiosis.
* Evidence of multicellular organisms first appeared around 1.1 bya, with abundant multicellular fossils (e.g. the Ediacaran fauna) present by 0.55 bya.

Endosymbiosis

Cell which lives inside another cell with mutual benefit

* Eukaryotic cells are believed to have evolved from early prokaryotes that engulfed other cells by phagocytosis
* Engulfed prokaryotic cell remained undigested as it contributed new functionality to the engulfing cell (e.g. photosynthesis)
* Cell lost some of its independent utility and became a supplemental organelle

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Evidence in organelles:

* Membranes (double membrane bound)
* Antibiotics (susceptibility)
* Division (mode of replication)
* DNA (presence and structural composition)
* Ribosomes (size)

Stromatolite

Microbial mats such as stromatolites are multilayered sheets formed by microorganisms such as archaea and bacteria.

Oxygen Enrichment

* Theorised oxygen producing bacteria 2-3 billion years ago evolved through a process eventually known as photosynthesis
* Transformed the planet
* This led to some key events such as the production of oxidized compounds, the evolution of aerobic organisms, and the changing of the Earth's atmosphere. The subsequent formation of an ozone layer restricted UV radiation to allow for the proliferation of a wider range of life forms.

Endosymbiosis

* An endosymbiont is a cell which lives inside another cell with mutual benefit
* Eukaryotic cells are believed to have evolved from early prokaryotes that engulfed other cells by phagocytosis
* The engulfed prokaryotic cell remained undigested as it contributed new functionality to the engulfing cell (e.g. photosynthesis)
* Over generations, the engulfed cell lost some of its independent utility and became a supplemental organelle

Evidence for endosymbiosis

* Membranes (double membrane bound)
* Antibiotics (susceptibility)
* Division (mode of replication)
* DNA (presence and structural composition)
* Ribosomes (size)

Direct fossil

Body fossils:

* Bones, teeth, shells, leaves

Indirect fossils

Trace fossils: Footprints, tooth marks, tracks, burrows, etc.

Fossil record

The totality of fossils, both discovered and undiscovered, is referred to as the fossil record

* Changes occurred in the features of living organisms (evolution) ◻
* new species emerging (divergence and speciation) and extinctions
* Demonstrates a change in an organism's characteristics from an ancestral form

Law of fossil succession

* the age of the rock layer (strata) in which the fossil is found Sedimentary rock layers develop in chronological order, such that lower layers are older and newer strata form on top Each strata represents a variable length of time that is classified according to a geological time scale (eons, eras, periods)
* This chronological sequence of complexity by which characteristics appear to develop is known as the **law of fossil succession**
* Newer species likely evolved as a result of changes to ancestral species
* Transitional fossils demonstrate the intermediary forms that occurred over the evolutionary pathway taken within a single genus

Conditions for fossilisation

* Rapid burial (high pressure)
* Lack of oxygen / no decomposition by bacteria
* Preservation of remains (i.e. not consumed or removed by scavengers)

Biogeography

* Biogeography describes the distribution of lifeforms over geographical areas, both in past and present times
* Biogeography provides evidence for evolution because it suggests that closely distributed species share a common lineage
* If speciation was random, the distribution of structurally similar species would be expected to be scattered

The centre of origin

* Each plant and animal species originated only once. The place where this occurred is the centre of origin.
* Related species are usually found in close physical proximity (supporting the concept of speciation via gradual divergence)
* Fossils found in a particular region tend to closely resemble the modern organisms of the region

Homologous structure

Anatomical features that are similar in basic structure despite being used in different ways are called homologous structures

Ex

* Tetrapods (organisms with 4 limbs) all have very similar bone structures in their limbs (pentadactyl), despite different functions for the limbs.
* This indicates a common ancestor, followed by evolutionary changes and natural selection.

Analogous structure

* Analogous structures arise from different origins, usually via convergent evolution due to similar niches/selection pressures

Vestigial structure

Vestigial structures are small remnants of organs which previously in a species’ evolutionary history were useful.

* Vestigial wings in the kiwi
* Vestigial pelvic bones in snakes and whales
* Vestigial appendix in humans

The structures generally do not completely disappear as; the selection pressure for that to happen is not there, the genes for their presence are still active, or they still have a minor function.

Comparative embryology

During embryonic development, very different organisms show similar structures from earlier stages in their evolutionary development. This is evidence for common ancestry.

DNA hybridisation

* Amino acid sequences are determined by inherited genes and differences are due to the accumulation of mutations.
* The degree of similarity of these proteins is determined by the number of mutations that have occurred.
* Distantly related species have had more time for differences to accumulate.
* In DNA hybridisation DNA strands can be separated with sufficient heat and will reform (re-anneal) as the temperature falls
* Single-stranded DNA from different species can be mixed together to identify the degree of similarity (as measured by complementary base pairs). Closely related sequences will join together (hybridise) more strongly as they share more complementary base pairs
* The strength of the hybrid molecule (and degree of similarity) can be measured by how much heat is required to separate the strands

Homeobox (Hox) Genes

* The basic structure of many animals is similar - for example, a human, a mouse and a fly all have a head end, a tail end, eyes and limbs.
* The same group of genes provide the instructions for these body parts in all three organisms - the homeobox genes.
* The actual genes that determine the shape and structure of the eye are different, but the gene to grow an eye is the same.

Artificial selection

Artificial selection is the identification by humans of desirable traits in plants and animals, and the steps taken to enhance and perpetuate those traits in future generations.

Selective breeding

Selective breeding is a form of artificial selection, whereby humans intervene in the breeding of species to produce desired traits in offspring

Fossil dating techniques

* By examining layers of sedimentary rock, geologists developed a time scale for dividing up earth history.
* Radiometric-dating techniques allowed scientists to put absolute dates on divisions in the geologic time scale.
* Relative dating -- determine whether the rock is older or younger than other rocks (index fossils moment)
* Absolute dating -- use radiometric dating techniques to determine how long ago the rock formed in the exact number of years
* Not all rocks can be dated absolutely, so combinations of techniques are used.

Index fossils conditions

Used to define/ identify geological periods

• Distinctive features (E.g., physical characteristics such as shells)

• Widespread over large geographic areas (It’s not just found on one small island for example)

• Abundant/large numbers (increases the chance of some being fossilised when they die)

• Limited in geologic time (provides a narrow time window for comparison)

5 main fossil types

Petrified:

* The word “petrified” means “turning into stone.”
* Petrified fossils form when minerals replace all or part of an organism.
* Water is full of dissolved minerals. It seeps through the layers of sediment to reach the dead organism. When the water evaporates, only the hardened minerals are left behind.

Mold/ cast

* A mold forms when hard parts of an organism are buried in sediment, such as sand, silt, or clay.
* The hard parts completely dissolve over time, leaving behind a hollow area with the organism’s shape.
* A cast forms as the result of a mold.

Carbon film

* When an organism dies and is buried in sediment, the materials that make up the organism break down.
* Eventually, only carbon remains.
* The thin layer of carbon left behind can show an organism’s delicate parts, like leaves on a plant.

Trace - Trace fossils show the activities of organisms.

Preserved remains:

* Amber
* Tar
* Ice

Mechanisms of evolutions

* Gene pools and selection
* Speciation
* Microevolution and macroevolution

Gene Pools

the sum of all alleles within the genes of a population of a single species.

* Populations with large and diverse gene pools tend to have increased biological


* diverse population often contains enough genetic variation so that there will be an availability of suitable genes that are necessary for survival.


* Populations with narrow gene pools containing low diversity are more likely to suffer from reduced fitness and are more likely to become extinct.

Natural Selection

increases the frequency of characteristics that make individuals better adapted and decreases the frequency of other characteristics leading to changes within the species

* Natural selection may produce phenotypic change over time.
* The direction of change will depend on the selection pressure. (ex Galapagos finches)

Sexual selection

a type of selection where the presence of a particular trait provides greater success in obtaining mates and reproducing.

* These traits may relate to fitness (for example bigger, stronger males), but in some cases they could actually be counterproductive to survivability (for example bright plumage in birds that makes them more visible to predators).
* It can lead to a situation referred to as non-random mating, where not all individuals have the same opportunity to pass on their alleles/genes.

Artificial selection

Artificial selection is the identification by humans of desirable traits in plants and animals, and the steps taken to enhance and perpetuate those traits in future generations.

Effects of selection

Phenotypic distribution:

* Stabilising selection
* Directional selection
* Disruptive selection

Stabilising Selection

* Ex human birth weight
* Lower and higher birth weights aren’t rlly favourable

Directional selection

Certain phenotypes are more favourable so phenotypic expression gradually shifts to one side (ex peppered moths)

Disruptive Selection

Individuals at both extremes of a phenotypic range are favoured over intermediate variants (two peaks).

* Disruptive selection may occur when environmental conditions are varied or when the environmental range of an organism is large.
* This can lead to speciation.

Mutations as allele source

* Mutations can therefore change the frequency of existing alleles by competing with them.
* Recurrent spontaneous mutations may become common in a population if they are not harmful and are not eliminated.

Genetic drift

* Due to random chance, not all individuals in a gene pool pass on their genes to the next generation.
* causes random changes in the gene frequencies.
* Alleles may become: Lost Fixed (present in all individuals)
* Greater in small populations.
* Although genetic drift is a mechanism of evolution, it doesn't work to produce adaptations.

Founder effect

* When a small number of individuals migrate away or become isolated from their original population they will have a small and probably non-representative sample of alleles from the parent population’s gene pool.
* The colonizing population may evolve in a different direction than the parent population.

Population bottleneck

* This occurs when the breeding population is reduced by 50% or more.
* Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size. They also decrease genetic diversity.

Co-evolution

When 2+ species affect each others evolution

Speciation

A species is a group of organisms able to interbreed and produce fertile offspring.

A population of one species can only evolve into more than one species if groups within the population become isolated from each other by barriers that prevent exchange of genes (gene flow).

Types of genetic isolation

* Prezygotic isolation – occurs before fertilisation can occur (no offspring are produced)
* Postzygotic isolation – occurs after fertilisation (offspring are either not viable or infertile)

Pre-zygotic isolating mechanisms

Post-zygotic isolating mechanisms

Allopatric speciation

Occurs when a physical barrier divides a population.

Sympatric speciation

Occurs when species within the same area become reproductively isolated, usually due to some sort of behavioural change.

Splitting vs budding

* Splitting: A species could split into two populations that evolve differently until they eventually become separate species.
* Budding: A small part of the species population could “bud off” from the main part and evolve rapidly to form a new species.

Divergent evolution

Divergent evolution occurs when a common ancestral species evolves into a number of new species. These species have adaptations allowing them to occupy different niches.

(adaptive radiation is a good example)

Convergent evolution

Where similar niches and selection pressures exist, species without a recent common ancestry may evolve to have similar physical characteristics, to suit the similar environment.

Phyletic Gradualism vs punctuated equilibrium

**Phyletic gradualism:** If the environment remains stable, organisms may undergo very little change over time and evolution is slow and gradual.

* The process is considered a smooth and continuous process and any big changes are the result of the accumulation of many small changes over a long period of time.
* An example might be the slow evolution of the modern horse from ancestral species.

**Punctuated equilibrium:** After long periods with little or no change, an isolation event separates a small population of individuals. With a different gene pool or a burst of mutations, this isolated group rapidly evolves into a separate species.

Microevolution - Include mechanisms

* describes evolutionary changes that occur over a relatively short period of geologic time (such as between generations) and results in diversification within a species
* Microevolution is evolution in a single population.
* It works within a group of organisms that interbreed with each other and share a gene pool.
* It can be detected through changes in gene frequency over time.
* The mechanisms for microevolution can directly affect gene frequencies in a population. These include:
* Mutations
* Gene flow
* Genetic drift
* Selection

Macroevolution - include patterns

* Macroevolution is evolution on a large scale over longer periods of time, generally above the species level.
* Macroevolution encompasses larger trends and transformations in evolution, such as the origin of mammals and the radiation of flowering plants.
* The basic mechanisms of microevolution - mutation, gene flow, genetic drift, and natural selection - can produce macroevolutionary change if given enough time.
* Some macroevolution patterns include:
* Stasis - some lineages remain unchanged for long periods of time
* Characteristic changes - for example gaining or losing body parts
* Speciation - the rate and frequency at which branching occurs
* Extinctions - this can be rare, frequent, or across many lineages (mass extinction events)

Population genetics

the study of genetic variation within populations, and involves the examination and modelling of changes in the frequencies of genes and alleles in populations over space and time.

Hardy-Weinberg equilibrium

A principle stating that the genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors.

When mating is random in a large population with no disruptive circumstances, the law predicts that both genotype and allele frequencies will remain constant because they are in equilibrium.

Disruptive factors to Hardy Weinberg equilibrium

The Hardy-Weinberg equilibrium can be disturbed by a number of forces including:

* Mutations - adds new alleles and is a source of variation
* Natural selection - can increase or decrease certain phenotypes
* Non-random mating (sexual selection) - not all individuals will get to pass their alleles on to the next generation
* Genetic drift - can randomly alter allele frequencies
* Gene flow - can add or remove alleles in a population

Cladistics

method of classifying organisms into groups of species called clades (from Greek ‘klados' = branch)

Clades

Each clade consists of an ancestral organism and all of its evolutionary descendants Members of a clade will possess common characteristics as a result of their shared evolutionary lineage

* Clades can be organised according to branching diagrams (cladograms) in order to show evolutionary relationships

Cladograms

* Constructed cladograms all typically share certain key features:
* Root – The initial ancestor common to all organisms within the cladogram (incoming line shows it originates from a larger clade)
* Nodes – Each node corresponds to a hypothetical common ancestor that speciated to give rise to two (or more) daughter taxa \\
* Outgroup – The most distantly related species in the cladogram which functions as a point of comparison and reference group
* Clades – A common ancestor and all of its descendants (i.e. a node and all of its connected branches)

Phylogeny

Evolutionary history

Molecular evidence

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* When comparing molecular sequences, scientists may use:
* Non-coding DNA
* Gene sequences
* Amino acid sequences
* Non-coding DNA gives the best means of comparison (mutations occur more regularly) → base change in other sequences affect proteins
* Amino acid sequences used to compare distantly related species
* RNA/DNA used to compare closely related organisms

Molecular clocks

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* Genes/ protein sequences may mutate at *relatively* constant rates
* If ROC is reliable, scientists calculate divergence time according to differences

Limitations:

* Different genes change at different rates
* ROC may differe between different organism groups
* ROC is non-linear → changes may be reversed

Evolution of organisms - Plants

* Evolved from green algae (likely from charophytes)
* Why? Bc similarities in chlorophyll, chloroplasts, cell walls and DNA
* Steps required for evolution
* Transition from water to land
* Vascular tissue
* Seed evolution
* Diversification of the angiosperms
* Pros:
* Harsh environment
* Heat
* Desiccation (drying out)
* UV radiation
* Gravity
* Rewards:
* CO2
* Sun
* No competition/ herbivores

Evolution of organisms - Animals (p1)

Features:

* Multicellular organisms
* Heterotrophic
* No cell walls
* Often mobile

Evolution

* Approximately 900-1000mya single celled organisms, like choanoflagellates, formed colonies consisting of individuals
* Diversified between 500-1000mya
* Exoskeleton development → structural support/ protection
* Vertebrates (notochords from jawless fish) → increased agility/ movement speed
* Jaw → food availability / predation
* Skeleton → Further increased speed/ agility

Evolution of animals - terrestrial

Adaptations required

* Temperature changes
* Air breathing
* Structural support
* Dehydration
* Reproduction
* UV radiation

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* Amphibians
* likely evolved from lobe finned fish ancestor in shallow environments
* Moist skin for O2 diffusion, lungs and amniotic eggs
* Ectothermic (cant regulate body temp)
* Reptiles
* Kertain forming scales (waterproof), amniotic membrane + soft shelled eggs
* ectothermic
* Dinosaur extinction
* Birds
* Modified scales → feathers
* Hollow bones
* Elongated metaCARPALS
* Wishbone
* Sternal Keel
* Air sacs + lungs
* Limited organs (save weight)
* Hard shelled eggs
* Keratin beaks
* Mammals
* Early likely from nocturnal monotremes
* fur (keratin)
* Warm blooded
* Live young (except monotremes)
* Suckle young w milk
* Dentition - adaptive teeth

Primate evolution + features

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A primate ancestor would have had the following features:

* Arboreal (tree dwelling) habit
* Grasping hands and feet
* Long, mobile limbs
* Quadrupedal locomotion
* Binocular vision
* Upright sitting position
* Nails instead of claws on most digits

Primates have a combination of features that are unique to their group. Their anatomy is well adapted to an arboreal (tree- dwelling) lifestyle. They possess:

* Superior intelligence
* Often complex social behaviour
* A highly developed problem solving ability

Hominids vs hominins

**hominids**

The group consisting of all modern and extinct Great Apes. Anatomical features common to all hominids:

* No tail
* Semi-erect or fully erect posture
* Broad chest, pelvis, and shoulders
* Relatively long arms and mobile shoulder joints
* Large brain
* Examples:
* Human
* Chimpanzee
* Gorilla

**Hominins**

The group consisting of modern humans, extinct human species and all our immediate ancestors. Anatomical features and habits:

* Bipedal with modified feet, thigh bone, pelvis, and spine
* Large cerebral cortex (forebrain)
* Reduced canines (and teeth in general)
* Prominent nose and chin, reduced eye ridges
* Body hair short or very reduced
* Highly sensitive skin
* Complex social behaviour
* Examples:
* Australopithecus
* Paranthropus
* Homo

Human characteristics

* Bipedalism
* Larger brains
* Increased intelligence
* Teeth changes
* Loss of body hair

Adaptations for Bipedalism

* Forward pointing big toe
* Transverse arch to absorb impact
* Foramen magnum at base of skull
* Carrying angle of femur
* Strong knee joint
* Lower & broader pelvis
* Strong gluteal muscles

Selection pressures for bipedalism

Australopithecines

As many as four species of genus Australopithecus existed, ranging from southern Africa, through East Africa, to Chad in the north.

Australopithecus afarensis

* ‘Lucy’
* 4.0-2.7 mya
* Bipedal, walked erect, but also arboreal
* Human-like hands and teeth
* Brain capacity of about 375-550 cc
* Apelike face with a sloping forehead, a distinct ridge over the eyes, flat nose and a chinless lower jaw
* Between 1.0m and 1.5m tall (sexual dimorphism)

Genus Paranthropus

Paranthropus were a group of species that exploited low-grade vegetable food sources (nuts, root tubers and seeds) resulting in (megadont) species with very large teeth.

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* Went extinct though

Homo Erectus

H. habilis → H. ergaster → H. erectus

2 mya - 400 000 ya

* Early examples had a 850cc brain size, which increased to 1100cc
* The species definitely had speech (enlarged Broca’s area, region of brain for speech, and structure of jaw & throat)
* H. erectus developed tools, weapons and fire and learned to cook food
* Face had massive jaws with huge molars, no chin, thick brow ridges, and a long low skull
* Sturdier in build and much stronger than the modern human

Adaptations for running

* Loss of hair, sweat for cooling, high SA:V
* Elongated legs
* Nuchal ligament (back of neck) stabilises head
* Thickened joint surfaces in knees and other high impact joints
* Plantar arch in foot acts as a spring
* Achilles tendon
* Well developed gluteus maximus
* More muscles attached to the lower spine for support

Selection For Reduced Body Hair

Evolution of the Human Brain

* Intelligence is not just a function of brain size: relative brain size appears to be more important (brain size compared to body size).
* Modern humans have a brain volume three times larger than that predicted for an average monkey or ape with our body size.
* Another important factor is the organization of the brain, evident in the development of the areas concerned with spoken language.
* Two areas of the brain have become highly developed in modern humans:
* Broca’s area concerned with speech
* Wernicke’s area concerned with comprehension of language.

Homo neanderthalensis

* 350 000 - 30 000 ya
* Shorter, more robust frame
* Skull has low forehead, strong brow ridges and occipital bone
* Broad nasal cavity (to warm air)
* Barrel shaped chest and compact body conserve heat
* Evidence of tools, fires, care for injured people, burial customs, music

Homo sapiens (also called Cro-Magnon)

* Homo sapiens evolved in Africa - better suited for a hot climate
* Moved into Europe approximately 90,000 ya
* Brain is around 1400cc with a high frontal lobe/forehead
* Complex tools, agriculture, music, art, abstract concepts
* The first anatomically modern humans appear possibly as early as 300,000 years ago in Africa and the Middle East.
* Underwent a sudden cultural revolution about 40 000 years ago, with the appearance of Cro-Magnon culture.
* Using a wider range of materials, their tools kits became markedly more sophisticated.
* They were skilled hunters, tool-makers and artists (cave art and music).