IB Biology Evolution

percentage contribution of a particular allele to the total of all alleles for that gene within a population

the total sum of all the alleles in a population

a change in allele frequency in a population's gene pool over a number of generations

• The biological species concept defines a species as a group whose members possess similar anatomical characteristics and have the ability to interbreed. This is the most commonly accepted definition of a species. It emphasizes the differences and seperateness of species from one another due to reproductive barriers
• The morphological species concept focuses on the unity of members of a species, and classifies organisms by similarities in body shape, size, and other structural features. The advantages of this concept is that it can be applied to asexual and sexual organisms, and can be useful without information on the extent of the gene flow. The disadvantage is that it is based on subjective criteria, and classification may cause disagreements.
• Other defnitions of species are: Paleontological (focuses on morphologically discrete species known only from the fossil record), ecological (views species in terms of niche), and phylogenetic (set of organisms with a unique genetic history)

• Geographical isolation: natural physical barriers that separate two populations, preventing interbreeding. (pre zygotic)
• Hybrid infertility: two closely related species produce offspring that are infertile (ex mule) (post zygotic)
• Hybrid breakdown: Successive hybrid generations are progressively weaker (post zygotic)
• Hybrid Inviability: Hybrid zygotes or young offspring die (post zygotic)
• Temporal Isolation: populations breed during different times of the day or different seasons preventing interbreeding (pre zygotic)
• Behavioral Isolation: populations that have different courtship rituals (pre zygotic)

• Some species of plants have their origins in accidents during cell division that result in extra sets of chromosomes, a mutational change that results in a condition call polyploidy. (3 or 4 sets)
• virtually never occurs in animals
• Mutation prevents the new plant from interbreeding with diploid plants of the original population, offspring that are produced are sterile
• However, the plants can still produce fertile plants by self-pollinating or mating with others of their kind.
• Polyploid individuals establish a separate population when they are unable to mate with diploid plants

• Speciation is the formation of a new species by splitting of an existing species
• Sympatric ("same country"): two populations in the same area diverge to fill different niches and thus remain separate long enough to become different species.
• -through polyploidy
• -reproductive isolation due to niches being in different areas within the same habitat
• Allopatric ("Other country"): gene flow interrupted when a population is divided into geographically isolated subpopulations.

• Adaptive radiation is the evolution of many diversely adapted species from a common ancestor upon introduction to various new environmental opportunities and challenges. It occurs typically when a few organisms make their way to a new, distant area or when environmental changes cause numerous extinctions. In both these instances, ecological niches become open for the survivors
• Darwin's finches are an example of adaptive radiation:
• A group of particular species of finches became lost and ended up in the Galapagos islands. Different individuals went to different islands. On separate islands, individuals with certain characteristics had an advantage, and their traits were selected over time. Populations were separated by a geographical barrier (water) and slowly specialized into separate niches, leading to speciation

• Convergent evolution is when organisms evolve similar adaptations to a similar niche but do not share a common ancestor
• ex) butterfly, bat, and bird all have wings for flight
• Divergent evolution is when organisms evolve structures of a common ancestor, but are modified to efficiently exploit different niches. The structure appear and function differently, but they retain the same basic internal structure found in a common ancestor
• Ex) Whale flipper and bat wing have a similar bone structure that has been modified as they have adapted to different niches.

Gradualism is the idea that change can take place through the cumulative effect of slow but continuous processes. It is the slow change from one form to another, and the slow and steady evolution of a species. Punctuated Equilibrium combines the ideas of gradualism and catastrophism. It implies long periods without appreciable change and short periods of rapid evolution. Natural disasters such as volcanic eruptions and meteor impacts can interrupt the slow and gradual evolution, causing rapid change in a short period of timeEx) adaptive radiation of mammals. mammals were low in diversity because the dinosaurs were in all available niches. After the asteroid impact, most dinosaur species became extinct. The surviving mammals diversified to fill empty niches.It is likely that both gradualism and punctuated equilibrium contribute to evolution under different circumstances

One example of transient polymorphism is industrial melanism in peppered moths. Transient polymorphism is a change in the frequency of phenotypes over a short period of time due to environmental changes. Peppered moths in England before the industrial revolution were light colored and blended in with the light colored trees in their environment. Dark colored moths were preyed upon more by bird because they did not blend in with the tree. For this reason, they were low in numbers. Over time, industrial soot made the trees darker in color, favoring the survival of darker moths, which became more frequent. When the pollution was cleaned up, the process reversed as light colored moths were once again favored for survival.

• Balanced polymorphism is the ability of natural selection to maintain diversity in a population. It maintains stable frequencies of two or more phenotypic forms in a populations.
• Heterozygote advantage: individuals who are heterozygous at a particular gene locus have greater fitness than the homozygotes, causing natural selection to maintain two or more alleles at that locus
• Ex) Sickle-cell Anemia: Heterozygotes have an advantage in malarial regions because they are more fit that either homozygote. The homozygous recessive genotype leads to early death from sickle cell anemia, and homozygous dominant individuals often die early of malaria because they are unprotected from it. The sickle cell allele is common in Africa because heterozygous individuals are protected from malaria and have enough normal hemoglobin to function. This causes the sickle cell allele to be maintained.

• For a gene with two alleles: (except with codominance and incomplete dominance)
• p: the frequency of the dominant allele
• q: the frequency of the recessive allele
• p+q=1
• Assuming random mating in the population
• p²+2pq+ q²=1
• p²= proportion of individuals who are homozygous dominant
• 2pq= proportion of individuals who are heterozygous
• q²= proportion of individuals who are homozygous recessive

• 1) Extremely large population size
• 2) No gene flow
• 3) No mutations
• 4) Random Mating
• 5) No natural selection

A sudden change in the environment, such a a fire or flood, may drastically reduce the size of a population. The survivors have passed through the "restrictive bottle neck" and their gene pool may no longer reflect the original population's gene pool.

Deviations from the expected result which occur because populations are finite in size. It is change due to chance alone. The change is not due to having a quality that is advantageous

natural selection, genetic drift, and gene flow

A few individuals become isolated from a larger populations and establish a new population whose gene pool is not reflective of the source population.

genetic additions and/or subtractions from a population resulting from the movement of fertile individuals or gametes

independent orientation, random fertilization, and crossing over

remnants of structures that served important functions in the organism's ancestors

• To avoid ambiguity from common names when communicating about organisms, biologists refer to each species by a scientific name.
• A system called binomial nomenclature is used.
• The first part of the species name is the genus to which the species belongs to. The first letter is capitalized.
• The second part is the special epithet which is unique for each species within the genus.
• The entire binomial is italicized.
• phylogeny: evolutionary history of species connected by their shared characteristics.
• Organisms are classified by genetic, morphological, ecological, and paleontological evidence
• Classification is used to distinguish between homologous and analogous structures
• Similarities and differences between organisms are used to determine their degree of evolutionary relationship.
• Value: to clear identify the derived characters that define a particular clade, also standardizes communication among scientists

science of classification of organisms into groups

Domain, Kingdom, Phyla, Class, Order, Family, Genus, Species

• All organisms share the same 4 DNA nucleotides and use the same 20 amino acids to make proteins
• The genetic code is universal, meaning all organisms have the same codons
• Transcription, which makes mRNA, and translation, which makes proteins, are the same in all organisms
• This is powerful evidence for common ancestry of ALL life. Difference in DNA sequence show divergence. Enzymes, hemoglobin, and other proteins are compared between organisms to show degree of relationship

• Phylogeny: is the study of evolutionary history of and relationships between organisms
• The sequence of bases in DNA show accumulating mutations separating organisms over time.
• When proteins, ribosomes, and mitochondria are compared, the closer the similarity, the more recent the ancestor.

• Mutations happen at a statistically predictable rate and accumulate over time
• Assume the mutation rate doesn't change
• Evolutionary change in DNA and proteins is influenced by natural selection; some mutations appear/disappear and leave no trace
• Scientists usually use non-coding DNA regions because they are not affected by natural selection
• The number of mutations that separate the organism indicates the age of their common ancestry.

• a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates.
• the assumption is that the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor

• Analogous: similarities not due to shared ancestors but due to ecological niche. They are superficial similarities with large DNA differences
• Convergence (bats and birds developed flight independently using different structures)
• Homologous: Similar internal structures due to shared ancestry, possibly adapted for different functions
• Divergence (whale flipper and bat wing are derived from the forelimbs of a common ancestor mammal)

• Cladograms are constructed by using DNA to determine the relationship between organisms
• Key features, or derived characters, are identified
• Primitive characters (features several clades have in common) link clades to similar clades
• A derived character must be identified to define the clade
• The goal is to find natural connections by using morphological data and genetic data

• Clades get progressively large (from species to domain) and each consecutive clade includes the previous clade
• Clades contain more similarities and unique features as the progress from kingdom to species

• Potassium-Argon Method: Potassium 40 decays into argon 40, which is trapped in igneous rock
• The ratio between potassium and argo is measured to determine the age of the rock
• Because the average decay rate is known, we can determine the probable age of the rock
• Limitations: If rock is subjected to high heat, all argon escapes and the clock resets
• Carbon Method: Carbon 14 decays into Nitrogen 14, age is measured by the ratio of carbon 14 to total carbon
• Used for everything up to 70,000 years, and is generally used to date human artifacts

the number of years it takes for 50% of a radioisotope to decay

• Ardipithecus ramidus
• Australopithecus afarensis
• Australopithecus africanus
• Homo habilis
• Homo erectus
• Homo neaderthalensis
• Homo sapiens

Larger brain leading to increased intelligence, decrease sexual dimorphism, reduction in jaw length and teeth size, omnivory, fully erect posture, total bipedalism, flatter face, reduced brow ridge; longer legs and shorter arms; broadening of pelvis, feet adapted for walking, straightening of the fingers

Fossi are not often found in good quality and there aren't a lot of them. Many times layers containing fossils aren't exposed or easily accesible. COnditions for fossil formation are rare. Human ancestors originated in Africa and places with dry climates where it is hard for fossils to form. Erosion limits fossils because it destroys them. Short time span does not allow for many fossils to form. Weathering and Natural Disasters destroy fossils. Because fossil record is incomplete, dates are highly questionable. Many fossils are partial, so we have to guess to fill in the gaps. Many transitional forms are missing and clades are difficult to define because we can't find a definite common ancestor. Early hominids were preyed upon and their bones could have been scattered or destroyed

Larger brain allows more diversity of food sources. Hunting and gathering is more efficient in coordinate groups with many tools. Communication allows trading of food. They could hunt an animal that they otherwise would not be able to handle because of new hunting techniques and teamwork. Larger brain allowed them to make better tools. The brain is 5% of our body mass, and take up 20% of energy. A larger brain, although needing more energy, allows better nutrition through more efficient hunting and gathering. With better nutrition, the bigger the brain becomes with more energy available.

Genetic evolution is the change of allele frequencies in a reproducing population over time. Cultural evolution is the accumulation and passing on of ideas and techniques through teaching and learning. Both are passed from one generation to the next. The unit of genetic inheritance is the gene, the unit of cultural evolution is a meme (word/gesture/technique/symbol)

• Cultural evolution allows us to change and control our environment, allowing humans to overcome some selection pressure. Cultural evolution is more important to the development of society. Humans have evolved very little genetically in the past 200,000 years, so the changes in lifestyle over that time can be attributed almost entirely to cultural evolution. Cultural evolution allows us toe consciously improve our survival ability
• ex) diabetics

• Non-living synthesis of simple organic molecules
• - The miller-urey experiment illustrates that under certain conditions complex organic molecules needed for life can form spontaneously. This could have occurred in deep sea vents or tidal pools using energy from volcanic heat, electrical discharge from storms, or intense UV radiation
• Assembly into polymers
• -Catalysts from clay minerals or metal sulfides from deep sea vents or hotsprings
• -Ribozymes are RNA polymers that carry out catalytic processes (copying). As a solution of monomers dries out on clay the monomers polymerize (forming chains)
• Self Replicating molecules
• Ribozymes form 3 dimensional shapes which can catalyze many reactions such as self replication. A more efficient self-copying molecule would become more common (natural selection)
• Packaging in membranes
• -coacervates (probionts) form lipid bi-layer which allows the concentration of organic molecules inside. If Ribozymes exists inside lipid bi-layer it might be a precursor to a living cell

• Design: Water heated in a flask to simulate primordial sea with geothermal heat. Simulated early atmosphere with ammonia, methane, hydrogen gas, and water vapor. Electrodes, representing lightning, provide continuous electric discharge. Cold water condenser used to cool vapors much like the early atmosphere would have.
• Results: Amino acids and other organic molecules were produced. Nucleotides, sugars, lipids, adenine, ATP were also produced with later experiments
• Assumptions: Proportions of gases, missing some gases (simplified atmosphere), atmosphere was a reducing atmosphere, highly concentrated energy

• Deep sea hydrothermal vents: metal sulfides act as catalysts.
• Volcanic Gases provide raw materials for chemosynthesis
• Volcanic Ash enriches surrounding area with minerals
• Tidal Pools: Pools dry out and concentrate molecules which increase chances of polymerization. Clay minerals present for catalyzing first polymerizations
• Extraterrestrial Locations: Mars has clear evidence of past water, possibly had a reducing atmosphere (currently oxidizing), Titan highly reducing atmosphere similar to early earth, but its possibly to cold for polymerization, Europe (moon of jupiter) heated by tidal pull, surface with thick ice crust, probably liquid water under ice, rock layer in center

• Self replication and catalyzing other reactions
• Reaction rate increased in the presence of short polypeptides

Anaerobic photosynthetic bacteria, cyanbacteria split water to release oxygen as result of photosynthesis. Much of early oxygen would have been taken up by metals in rock. Eventually leads to free oxygen --> oxidizing atmosphere

• Mitochondria and chloroplasts may have both once been free living prokaryotes
• Evidence: Double membrane, inner membranes resemble bacterial membranes, have own genetic code which is identical to prokaryotes' genetic code single circular strand. Replicate similar to binary fission, they have their own ribosomes which are similar to bacterial 70s ribosomes. Same shape and size as bacteria.
• Uncertainties: Timing and sequence hard to determine because micro fossils are hard to find