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Flashcards in Topic 5- Evol Theory Deck (81):
1

The origins of life

• Earth is around 4.5 billion years old.
• The earliest fossil record of bacteria is dated to about 3.6 billion years ago.
• The first eukaryote (cell with nucleus) evolved between 2.7 & 1.5 billion years ago.
• The first multicellular organism appeared 640 million years ago.

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Emergence of vertebrates

• The first vertebrates evolved some 525 million years ago.
• Reptiles first emerged 320 million years ago.
• Dinosaurs emerged around 230 million years ago.
• Mammals emerged about 200 million years ago.
• Primates emerged around 65 million years ago (PNAS, 2010 107 (11): 4797–4804)

3

Lineage

• A series of ancestral and descendant populations through time.
• Usually refers to a single evolving species, but may include several species descending from a common ancestor.

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Gene

unit of heredity, DNA

5

Gene frequency

what percentage of the individuals in the population have this gene

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Biological evolution:

occurs when there is a change in gene frequency in a population over time

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Genome

• The entire complement of DNA sequences in a cell or organism.
• A distinction may be made between the nuclear genome and the organelle genomes (e.g., those of mitochondria and plastids).

8

Genotype

• The set of genes possessed by an individual organism.
• May refer to an organism’s genetic composition at a specific locus or set of loci under consideration.

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Allele

• One of multiple forms of the same gene, presumably differing by a mutation of the DNA sequence.
• Alleles are usually recognized by their phenotypic effects.

10

Trait

A trait is a distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined, or be a combination of the two.
• No trait is perfect.
• Every trait must be analyzed in terms of the benefits and costs of the trade-offs inherent in a particular trait.
• Natural selection favors traits that improve the fitness (reproductive success) of individuals and their kin.

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Fitness

• The success of an entity in reproducing.
• The average contribution of an allele or genotype to the next generation or to succeeding generations.
• Genes that generate traits that increase an individual’s fitness are more likely to be passed to the next generation

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Evolution steps
IMPORTANT

• Step 1: The origin of genetic variation
by random mutation or recombination followed by
• Step 2: changes in frequencies of alleles and/or genotypes, caused by natural selection and/or random genetic drift

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Origins of variation

• Mutation
• Recombination

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Mutations

• Random
• Result in change in DNA sequence
• May have no effect on fitness of organism
• May be harmful (reduce fitness) to
organism
• May be beneficial (increase fitness) to organism
• May be beneficial in one way and harmful in another way to the organism

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Recombination

• Individuals inherit their genes and not their genotype from their parents.
• The meiotic cell division that forms the male and female gametes in sexually reproducing organisms involves two processes (recombination and assortment/segregation) which shuffle parental alleles into a unique combination in each egg or sperm.
• Every egg produced by a female and every sperm produced by a male are unique.

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Two processes in meiosis which shuffle genes

• 1st is recombination during which homologous chromosomes exchange segments of DNA sequence, thereby creating new allele combinations on each chromosome.
• 2nd is independent assortment/segregation
of chromosomes into haploid gametes.

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Variation

Individual members of a species vary in traits that effect their ability to compete for resources and reproduce.

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Inheritance

Some subset of this variation is heritable.

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Selection

Differential survival and reproduction among these variant forms leads to increased representation of successful traits in the next generation

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Genetic Drift

Random changes in frequencies of alleles and/or genotypes within a population.

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Evolution

Natural selection or/and random genetic drift over generations produces change in composition of frequencies of alleles and/or genotypes in a lineage
• Change in gene frequency may be due to selection that increases reproductive success
• Change in gene frequency may also be generated by random processes which dominate when the genetic of phenotypic variants do not differ in their effect on reproductive success, that is, when their variation is neutral compared to fitness

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Allele frequency

• The proportion of gene copies in a population that are a given allele.
• The probability of finding a given allele when a gene is taken randomly from the population.

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Genotype frequency

• The proportion of the population with a specific allele pair at a particular locus

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Evolution

• Changes in frequencies of alleles and/or genotypes, caused by natural selection or/and random genetic drift.
• Such changes transpire by the origin and subsequent alteration of the frequencies of genotypes from generation to generation within populations, by alteration of the proportions of genetically differentiated populations within a species, or by changes in the numbers of species with different characteristics, thereby altering the frequency of one or more traits within a higher taxon.

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Microevolution

usually refers to slight relatively short term changes within a species.

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Macroevolution

usually meaning the evolution of substantial phenotype changes, typically great enough to place the changed lineage into a distinct new species or higher taxon.

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Convergent evolution

• Evolution of similar features independently in different evolutionary lineages, usually from different antecedent features or by different developmental pathways.

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Human examples of convergent evolution

• Lighter skin color has appeared to have arisen through different biochemical pathways in Europeans and East Asians.
• Lactase persistence in adulthood has arisen through different genetic pathways in Europe, East Africa, and the Middle East.
• Sickle cell hemoglobin has emerged independently in Africa and India

29

Artificial selection
(= selective breeding)

• Selection by humans of a deliberately chosen trait or combination of traits in a (usually captive or domesticated) population.
• The human breeder of animals or plants is the active agent that directs selection for a characteristic to change in the population for a specific purpose.
• Dog breeds ranging from chihuahuas to great danes and St. Bernards have been artificially selected for from wolves by humans.
• Hundreds of cultivars of apples have been developed through artificial selection by humans.
• Gene-editing through the CRISPR-Cas9 could be considered within the realm of artificial selection

30

Natural selection

• Operates when variation in reproductive success correlates with heritable trait variation
• Results in the increase in frequency of the reproductively successful
• The differential survival and/or reproduction of entities that differ in one or more characteristics.
• The entities may be alleles, genotypes or subsets of genotypes, populations, or, in the broadest sense, species.
• To constitute natural selection, the difference in survival and/or reproduction can not be due to chance, and it must have the potential consequence of altering the proportions of the different entities.
• Usually the differences are inherited.
• Natural selection is not synonymous with evolution.
• Evolution can occur by processes other than natural selection, especially genetic drift.
• Natural selection can occur without any significant evolutionary change, as when natural selection maintains the status quo by eliminating deviants from the‘optimal’
phenotype.

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Four necessary conditions for natural selection

• Variation in reproductive success
• Variation in the trait of interest
• Nonzero correlation between the trait
and reproductive success
• Trait is heritable

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Natural selection is not random

• While mutational and recombination events are random, natural selection is not.
• Natural selection can result in change of gene allele frequency that generates traits that increase fitness.

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Inability of natural selection to
achieve absolute perfection

• Selection may fix only those genetic variants with a higher fitness than other variants in that population at that time.
• It can not fix the best of all conceivable variants if they do not arise, or have not yet arisen.
• Even the best possible variants fall short of perfection due to various constraints.
• Darwin noted that, “natural selection will not produce absolute perfection”.

34

Fitness vs optimality

• Optimality implies a perfect fitness match of a phenotype with its environment.
• While natural selection aspires toward a perfect fitness match, this optimal perfection is not achieved because environments are not static and are ever changing.
• Optimization models also help us to test our insight into the biological constraints that influence the outcome of evolution.
• They serve to improve our understanding about adaptations, rather than to demonstrate that natural selection produces optimal solutions

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Adaptation

• A process of genetic change in a population whereby, as a result of natural selection, the average state of a character becomes improved with reference to a specific function, or whereby a population is thought to have become better suited to some feature of its environment.
• An adaptive trait is one that enhances fitness compared with at least some alternative traits.
• A feature that has become prevalent in a population because of a selective advantage conveyed by that feature in the improvement of some function.

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Positive selection

Selection for an allele that increases fitness.

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Negative selection

A disadvantageous allele is lowered in frequency and perhaps entirely eliminated.

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Example of evolution of larger body size

• Mutation causes an allele which increases body size.
• Smaller body size selected against (negative selection).
• Larger body size selected for (positive selection).
• Results in population evolving to a larger body size.

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Balancing selection

• Number of selective processes by which multiple alleles (different versions of a gene) are actively maintained in the gene pool of a population at frequencies above that of gene mutation.
• An example of balancing selection is heterozygote advantage where an individual who is heterozygous at a particular gene locus has a greater fitness than a homozygous individual e.g., people who are carriers of the sickle cell allele.

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Individual selection

• The individual is the most important unit on which selection acts.
• A form of natural selection consisting of nonrandom differences among different genotypes (or phenotypes) within a population in their contribution to subsequent generations.

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Inclusive, direct & indirect fitness

• In 1964, William D. Hamilton introduced the concept of inclusive fitness of an allele, its effect on both the fitness on the individual bearing it (DIRECT FITNESS) and the fitness of genetic relatives that carry copies of the same allele (INDIRECT FITNESS).
• An individual organism has inclusive fitness, with both direct and indirect components.
• Selection based on inclusive fitness is called kin selection because these other individuals are the bearer’s genetic relatives (kin).

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Inclusive fitness

• Sum of direct and indirect fitness
• The fitness of a gene or genotype as measured by its effect on the survival or reproduction of both the organism bearing it and the genes, identical by descent, borne by the organism’s relatives (kin).

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Altruistic behavior

• Behavior in which one individual helps another, seemingly at its own risk or expense.

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Kin Selection

• The fundamental principle of kin selection is that an allele for such an altruistic trait can increase in frequency only if the number of extra copies of the allele passed on by the altruist’s beneficiary (or beneficiaries) to the next generation as a result of the altruistic interaction is greater, on average, than the number of allele copies lost by the altruist.
• Hamilton’s Rule formalizes this principle.

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Hamilton’s Rule

• An altruistic trait can increase in frequency if the benefit (b) received by the the donor’s relatives, weighted by their relationship (r) to the donor, exceeds the cost (c) of the trait to the donor’s fitness.
• Altruism spreads if br > c.

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Altruistic behavior of a sentry

• The meerkats of South Africa’s Kalahari Desert live in colonies of 20-30 animals, most of whom are siblings.
• Colony members work together to forage, care for their young, guard their underground network of burrows, and defend their territory from incursions by other meerkat families.
• Altruistic behavior includes “sentry”animals that put themselves at risk and warn the group of approaching predators.
• This increases the indirect and inclusive fitness of the sentry, since most members in his community are close genetic relatives.
-Meerkat is an example of altruistic behavior of a sentry

47

Sexual selection

• Differential reproduction as a result of variation in the ability to obtain mates.
• Variation in the number of offspring produced as a consequence of a competition for mates.

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Intrasexual competition

• Intrasexual competition between members of the same sex (usually male-male).
• Intrasexual selection drives the selection of attributes that allow alpha males to dominate other males to gain breeding rights to females in the group.
• Some deer species fight with their antlers to gain mating rights over females in the herd.

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Intrasexual selection involving sexual dimorphism of body size

• Differences in male and female body size.
• Association between greater sexual dimorphism in body size in species (e.g., gorillas) with social systems where dominant males compete with other males for mating rights over females in group.
• Dominant males tend to have higher testosterone levels than other males.

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Intersexual competition

• Intersexual selection favors traits that improve mating success even if they decrease individual health or survival.
• For example a male peacock’s long colorful feathers improves his reproductive success by being more attractive to females but reduces his chances for survival because he moves more slowly and can not fly.

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Mate choice (Intersexual selection)

• Members of one sex (often female) select their mate according to a set of specific characteristics that are perceived as attractive.
• For example, the bright plumage of a male peacock does not help it physically overcome rival males, however, female peacocks tend to prefer male peacocks with bright plumage.
• A brightly colored male peacock has a sexual selective advantage.

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Intersexual selection
MHC detection

• Women are attracted to scents of men who are most unlike themselves in major histocompatibility complex genes (MHCs)
• Human mate pairs with similar MHCs tend to be less fertile with higher miscarriage rates
• The more dissimilar the MHCs of a human male/female pair, the better their offspring immune systems will be at detecting foreign proteins, e.g., viruses or toxins

53

Sweaty T-shirts & human mate choice: MHC genes, body odors, & odor preferences

• Sweaty T-shirt experiment by Swiss scientists demonstrated that odors influence human mate choice
• Females not on oral contraceptives sniffing the T-shirts recently worn by males favored the scent of those whose immune response genes were different from their own
• Odor preferences of women on oral contraceptives were reversed as they favored the scent of men whose immune response genes were similar to their own
• Wedekind, C. et al. (1995). "MHC-dependent preferences in humans". Proceedings of the Royal Society of London 260: 245–49.
• Female use of oral contraceptives appears to interfere with a females ability to select male mates based on MHC

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Neutral selection

• Change in gene frequency generated by random processes that produces phenotypic variants that do not differ in their effect on reproductive success, that is, when their variation is neutral compared to fitness.

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Neutral selection: At the genetic level, many genotypes may produce the same phenotype because

• Genetic code is redundant with mutations that are synonymous substitutions which do not result in a change in the amino acid produced
• Some DNA is not expressed
• Some amino acid substitutions produce no change in the function of the protein
• Development is canalized which buffer the phenotype against genetic and environmental perturbations

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Mechanisms causing random change that drive genetic drift

• Neutral variation in reproductive success
• Mendel’s Law of Segregation states that there are two alleles present at a locus in a heterozygote diploid organism, and the probability that one of them will get into a given gamete is 50% (flip of a coin)

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Bottleneck

A severe, temporary reduction in population size.

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Founder effect

The principle that the founders of a new small population carry only a fraction of the total genetic variation in the source population.

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Genetic drift

Random changes in the frequencies of alleles or genotypes within a population.

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Causes of Bottlenecks

• Migration
• Infectious Disease
• Predation
• Famine
• Environmental catastrophe • War or genocide
• Cultural isolation

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Potential causes of dramatic reduction in population size resulting in reduction of genetic diversity

• Migration of small population breaking off from main source population
• Infectious disease epidemic causes dramatic mortality of most of population
• Predation causes dramatic mortality of most of population
• Famine causes dramatic mortality of most of population
• Environmental disaster causes dramatic mortality of most
of population
• War or genocide causes dramatic mortality of most of population
• Cultural isolation (e.g., Amish) prevents a small population from reproducing with larger surrounding population

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Genetic bottlenecks & founder effects

• Whether a new small population is the result of disease, famine, predation, environmental catastrophe, war, genocide, or the migration of a small number of individuals from a larger parent population, the resulting new population is dramatically smaller then the original parent population which creates a genetic bottleneck.
• Genetic bottle necks may generate conditions for a founder effect i.e., a new small population whose members carry only a fraction of the total genetic variation in the original source population and may have a high frequency of certain alleles that were rare in the original parent population (Fig 3.7)

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Founder effect

• The establishment of a new population by a few original founders which carry only a small fraction of the total genetic variation of the parental population [Ernst Mayr, 1963].

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Genetic drift

• In small populations, in the absence of selection, random variation in allele frequencies from genetic drift can cause the allele either to disappear (0% frequency in the population) or become fixed (100% frequency in the population).

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Genetic drift

• In large populations, in the absence of selection, allele frequencies tend to change very slowly over generations.
• In small populations, in the absence of selection, the stochastic nature of reproductive processes means that alleles may be lost (0% frequency in the population) or fixed (100% frequency in the population) within a few generations.
• The changes due to genetic drift are not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success.
• Fairness in meiosis and neutral variation in reproductive success drive genetic drift

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Bottlenecks, founder effects, and subsequent population growth

• Bottleneck generates a small population compared to original source population size.
• This small population tends to be influenced by genetic drift but may also be influenced by natural selection.
• Subsequent expansion of this population is derived from only a small sampling of genetic diversity present in the original source population.
• An allele that was rare in the original source population may be in high frequency in the bottleneck produced small population and its subsequent expanded population.

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Finnish founder population

• The Finnish population is a highly isolated population formed approximately 2,000 years ago by a founder population characterized by low population count, relative homogeneity, and isolation.
• Through a bottleneck migration, the Eastern Finnish population is estimated to have been founded by only 20-30 families.
• Although a rapid population increase occurred, the Finns in this area remained a highly homogenous population.
• More than 33 rare genetic diseases were found to be more prevalent in the Finnish population than in other populations.
• Aspartylglucosaminuria is autosomal recessive and occurs when aspartylglucosaminidase activity is deficient and results in the gradual development of mental retardation.
• Several mutations can cause this disorder, however, 98% of the cases in Finland have the identical mutation which suggests that almost all Finnish cases arise from a single founder event.

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Founder effect & drift

• New small population has decreased genetic variation, an increase in inbreeding, and an increased sensitivity to genetic drift.
• This can be observed in the limited gene pool of Iceland, Faroe Islands, Easter Islanders and those native to Pitcairn Island.

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Interaction between drift & selection

• In a finite population size, allele frequencies may be simultaneously affected both by selection and chance (drift).
• The effect of random genetic drift is negligible if selection on a locus is strong relative to the population size.
• Genetic drift is predominate if selection is weak on a locus.
• Genetic drift is usually predominate when populations are small.
• Deleterious mutations can become fixed (100% frequency in the population) by genetic drift, especially if selection is weak and the effective population size is small.
• A slightly advantageous mutation is less likely to be fixed by selection if the population is small than if it is large, because it is more likely to be lost simply by chance.

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Acclimatization

• Acclimatization occurs in a short period of time (days, weeks, or months) and within the organism's lifetime.
• Acclimatization to high altitude continues for months or even years after initial ascent, and ultimately enables humans to live more comfortably in this environment.
• Humans who migrate permanently to a higher altitude naturally acclimatize to their new environment by developing an increase in the number of red blood cells to increase the oxygen carrying capacity of the blood, in order to compensate for lower levels of oxygen in the air.

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Spandrel

• Gould and Lewontin (1979) introduced the term spandrel, which refers to traits that have arisen as by-products of other evolved adaptations.
• Spandrel is a phenotypic characteristic that is a byproduct of the evolution of some other character, rather than a direct product of adaptive selection.
• An example is the human nose evolved for breathing and regulating air temperature, but a by-product of this evolved structure is its ability to hold up eye glasses.
• There was NOT selection for a nose structure that could hold up eyeglasses, but rather selection for a structure that could breath in and regulate air temperature; a by-product of this evolved structure is its ability to hold up eye glasses.

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Exaptation

• Gould introduced the term exaptation referring to a trait that currently performs a particular function but originally arose as an adaptation for another function.
• A trait that resulted from selection for something other than the trait’s current function.
• The function of a gene, tissue, or structure other than the function it was originally adapted for.
• Can also refer to the adaptive use of a previously non-adaptive trait.
• An example is feathers on birds probably evolved as insulation in reptilian ancestors but were later exapted for flight.

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Speciation

• Evolution of reproductive isolation within an ancestral species, resulting in two or more descendent populations.

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Species

• The biological members of a group of populations that interbreed or potentially interbreed with one another under natural conditions.

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Types of speciation

• Allopatric
• Sympatric
• Peripatric

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Allopatric speciation

• Allopatric implies that two different populations have geographical ranges that do not overlap.
• Reproductive barrier forms between two populations from having geographically different ranges.
• Geographical barriers emerge because of topographical or climate change.
• Small scale geographical barriers because of local variation in the habitat of a slowly dispersing species.
• Single population separates from main population. • Over time the two populations diverge. • Divergence may be due to natural selection
causing different adaptations to different environments.
• Or if one of the populations initially consisted of a few founder individuals, divergence may be due to genetic drift.
• Eventually the two populations reach a point where they can not interbreed even if a physical barrier separating them is removed, and new species will have formed.
• Responsible for much of the present biodiversity.
• The ancestral species is divided by geographical isolation leading to reproductive isolation and speciation.
• If mixing subsequently occurs by removal of the geographical barrier, interbreeding does not occur

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Sympatric speciation

• A population diverges into two reproductively isolated populations without the existence of a geographical barrier preventing mating between the two groups.
• A mechanism for sympatric speciation may be, for example, a sub-population that becomes particularly well adapted to procuring a particular food resource, thus creating ‘specialists’in relationship to a particular food resource which may outcompete generalists for the resource.
• Since this sub-population clusters around its preferred food source, it may then develop reproductive isolation from the general population.

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Peripatric speciation

• Peripatric: Population peripheral to most of the other populations of a species.
• Peripatric speciation: Speciation by evolution of reproductive isolation in peripatric populations as a consequence of a combination of genetic drift and natural selection.

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Gradualism

• The proposition that large differences in phenotypic characters have evolved through many slightly different intermediate states.

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Phyletic gradualism vs punctuated equilibrium graph

• Each horizontal branch is not supposed to be perfectly horizontal, and typically represents 10,000 – 100,000 years of divergence time.

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Punctuated equilibrium

• A pattern of rapid evolutionary change in the phenotype of a lineage separated by long periods of little change.
• A hypothesis intended to explain the above pattern, whereby phenotypic change transpires rapidly in small populations, in concert with the evolution of reproductive isolation.
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