Every individual alive today, the highest as well as the lowest, is derived in an unbroken line from the first and lowest forms - August Frederick Leopold Weismann, German biologist/geneticist (1834-1914)
Evolutionary Biology 
Biological Species Concept 
Scientists have long sought to view the great diversity of organisms as a collection of distinct units. The species, as the atomic unit of diversity, represents a group of interbreeding natural populations that are reproductively isolated from other such groups. When individuals breed offspring, the genes of individuals are shuffled within a common gene pool representing the species' identity. The identity of species is based on the ability to breed, rather than on physical similarity. Limited transfer of genes between species causes different species to take on specific appearances and characteristcis.
Selection and Microevolution 
Individuals will generally show great differences in the number of offspring they mange to contribute to the populations next generation. If differences in individual genotypes affect the bearer's reproductive success, then the frequencies of the genotypes will change over generations; genotypes with higher fitness become more common.
Fitness describes an individual's ability to reproduce successfully. relative to that of other members of its population. It measures changes in the proportion of genes from one generation to the next. Genes associated with higher fitness become more common while reduced fitness will decrease theit proportion. Ftness of a genotype is an averaged quantity which reflects the reproductive outcomes of all individuals with that genotype. When fitness measures the relative quantity of gene copies present in individuals of the next generation, they may have arrived there in one of several different ways. An individual may show greater reproductive success becayse it itself reproduced, or it may have helped relatives with similar genes to reproduce.
Artificial Selection and Breeding 
Consider the work of a professional dog breeder. Lets consider a person trying to obtain a breed that is best suited for hunting of water fowl. The breeder specifically chooses individuals which most closely match the desired traits and selectively breeds them to each other in the hope of obtaining progeny with a combination of useful traits. Such plans can only succeed if:
- phenotypic heritability in morphological and behavioral features is coded by <genes> (e.g. webbed toes, willingness to swim at least partially controlled by genes)
- phenotypic variability is present (some have a particular characteristic, some don't)
- differential survival/reproductive success of phenotypic variants is produced (you pick the ones who do)
Repeated, selective breeding events will alter the proportion of different genes over time. Genes which were present in those individuals that the breeder selected for reproduction will become overrepresented while those that occurred predominantly in discarded individuals will decrease in proportion. Animal breeding is a slow process, however, a combination of strong selection and a high degree of heritability can change the relative abundance of genes in a population up to 10% per generation.
Not all of the selections that we make are done intentionally. Penicillin became widely available during the second world war for the treatment of infected wounds. Just four years after drug companies began mass-producing penicillin in 1943, microbes began appearing that could resist it. With frequent and indiscriminant use of antibiotics we have fostered the emergence of antibiotic resistance in a variety of microorganism. The ability to withstand the effects of an antibiotic occurs when a rare mutation renders a small subset of individuals with lowered sensitivity to the effects of the drug. During the course of antibiotic treatment the wildtype individuals are killed first as intended while the mutants are able to survive a bit longer. If the treatment is stopped before the drug had an opportunity to kill all pathogens regardless of slight differences in sensitivity to it, only resistant individuals will survive and be able to infect new hosts. With each antibiotic treatment that ends prematurely we unintentionally select for those individuals that exhibit a higher ability to tolerate the drug.
Natural Selection 
Natural selection is the process by which favorable traits that are heritable become more common in successive generations of a population of reproducing organisms, while the proportion of less successful traits shrinks. "Favorable" and "successful" are defined in a purely functional sense as environmental conditions allow some individuals to leave more offspring than others. Selection cannot act on the genes per se but rather works on their expression into observable characteristics. Individuals with favorable phenotypes are more likely to survive and reproduce then the genotypes associated with favorable phenotyps will increase in frequency with each generation. Over time, this process can result in the emergence of adaptations that specialize a group of organisms for a particular ecological set of conditions (i.e., microevolution). If different subsets of the population adapt to excel in one of multiple, distinct niches, the emergence of any reproductive barriers between the groups may allow the population's split into separate species (i.e., macroevolution).
More offspring are produced than finite resources can support. Individuals thus can be viewed as in a constant struggle for existence. Individuals within a population are rarely clones, they commonly show variation in phenotypes as well as genotypes. Some of this variation in behavioral phenotypes is heritable. As successful variants are more likely to survive and reproduce, their genotypes will be become overrepresented in the next generation
Density-independent and density-dependent growth models: Exponential Model: a species can potentially increase in numbers according to a geometric series -- Thomas Robert Malthus (1766-1834) Logistic Model: the rate of population increase may be limited, i.e. it may depend on population density -- Pierre Verhulst (1838). Carrying Capacity (K): an environment's maximum persistently supportable load (Catton 1986).
Natural selection is the process by which environmental effects lead to varying degrees of reproductive success among individuals of a population of organisms with different hereditary characters, or traits. The characters that inhibit reproductive success decrease in frequency from generation to generation. It is the process whereby certain genes (alleles) gain greater representation in the following generations compared to other alleles. Adaptations are the complement of traits that increases the fitness of the owner. An individual's Fitness or Reproductive Success is the relative probability that an animal of a particular genotype and phenotype will manage to contribute its genes to the next generation
Example: Mimicry 
A major concern of animals and other critters is to protect themselves from predators in order to survive and reproduce and pass their genes off to a new generation. Many animals have evolved adaptations known as antipredator devices such as camouflage and chemical toxins. Animals use camouflage to blend in with their environments in an attempt to be unrecognizable by predators. Other organisms such as the monarch butterfly contain chemical toxins that are secreted into the predator’s mouth when it attempts to eat the butterfly. The monarch butterfly also has warning coloration that gives a warning sign to predators to remind them that the butterfly is toxic and should not be eaten.
These antipredator devices are so successful that other organisms have been known to mimic them. The organism that is mimicked is known as the model and the third party that is deceived by the model and its mimic is known as the receiver. The mimics have learned to take advantage of the color patterns and markings that predators have learned by experience to avoid. The model is usually a species that has an abundant population and has successfully warded off predators with an antipredator device.
Organisms have learned to mimic their surroundings or environment in an attempt to “hide” from predators. For example, lizards have learned to mimic tree trunk color which proves to be very successful as predators will simply move past them as they believe that they are simply looking at a tree. Another example of this type of mimicry can be seen with the Katydid who will mimic a leaf in both color and shape in an attempt to be hidden.
Some prey animals have evolved certain patterns on their bodies that mimic other animals in an attempt to startle their predators. The most common example of this type of mimicry can be found in some moths and butterflies who flash eye spots on their wings to predators. These eye spots startle the predator who believes that the eyes belong to a much larger animal that may be a threat to them.
In one form of mimicry known as aggressive mimicry, an organism will mimic a signal that is either deceptive or attractive to its prey. One example of this involves the praying mantis who will mimic flowers to attract insects that they can then capture and eat. Organisms can also imitate the behaviors of other organisms. Moth caterpillars, for example, will imitate the motion and body movements of a snake in order to scare off predators that are usually a prey item for snakes.
One of the most popular types of mimicry involves the warning coloration found on inedible or toxic organisms such as the monarch butterfly. Once these toxic organisms have adapted this warning coloration which warns predators to stay away, other organisms may start to mimic this warning coloration in an attempt to stay alive. Batesian mimics are those mimics that imitate unpalatable species even though they are palatable. Therefore, one species is harmful while the other is harmless. The wasp is a great example of Batesian mimicry. The wasp is the model species in this example as it possesses a sting which enables it to escape from predators. The bright warning coloration of the wasp has been mimicked by many other insects. Even though the mimics are harmless, the predator will avoid them due to bad experiences with wasps with the same coloration. With Müllerian mimicry, many unpalatable species share a similar color pattern. Müllerian mimicry proves to be successful as the predator only has to be exposed to one of the species in order to learn to stay away from all the other species with the same warning color patterns. The black and yellow striped bodies of social wasps, solitary digger wasps, and caterpillars of the cinnabar moths warn predators that the organism is inedible. This is a great example of Müllerian mimicry as all of these unpalatable, unrelated species have a shared color pattern that keeps predators away.
Mimicry is a very successful antipredator device that species have evolved over many generations. As one can see, organisms have come to mimic many different characteristics such as color patterns and behaviors. However, selection only favors the mimics when they are less common than the model. Therefore, the fitness of mimics is “negatively frequency-dependent.”
Example: Industrial Melanism of Peppered Moths 
Within one hundred years (1850 to 1950); the dotted whitish form of the peppered moth (Biston betularia) was almost entirely replaced by the melanic (black) form. The melanic form appeared to be best suited for survival against the soot that had collected on forest tree trunks from pollution because the moths could camouflage with their resting area on the tree. The dotted whitish form of the peppered moth was no longer predominant in this environment because they were easily detected and predated on. How does this happen? Many animals have anti-predator adaptations. Adaptations are defined as “a heritable trait that either spread because of natural selection and has been maintained by selection to the present or is currently spreading relative to alternative traits because of natural selection.” Anti-predator adaptations suggest that a heritable trait, which enables the organism to hide from predators by seeking cover against a background, has spread by natural selection because of reproductive success. H.B. D. Kettlewell’s experiments on the peppered moths, as well as, those conducted by R.J. Howlett and M.E.N. Majerus have proven that the peppered moth’s preference for their resting places on trees are anti-predator adaptations.
In 1955, H.B. D. Kettlewell published his study on pepper moths: Selection Experiments on Industrial Melanism in the Lepidoptera. Kettlewell hypothesized that the dotted whitish form of the peppered moth were more likely to be eaten than the melanic form because they could be easily detected against the soot covered trees. His studies showed that the moths that were easily identified by humans were at a higher risk of predation from birds. The dotted whitish form was at higher risk of predation than the melanic form in the polluted environment.
Howlett and Majerus further examined this hypothesis in their study: The Understanding of Industrial Melanism in the Peppered Moth, published in 1987. They tested it by pinning 50 of both forms of the peppered moths on pale and dark tree trunks.
Calculations: Moths in Polluted (dark) Woodland
Dotted Whitish Form: (30/50) x 100 = 60% Melanic Form: (20/50) x 100 = 40%
60% - 40% = 20% The Dotted Whitish form is predated on 20% more than the melanic form in the polluted woodland.
Moths in Non-polluted (pale) Woodland
Dotted Whitish Form: (15/50) x 100 = 30% Melanic Form: approx. (30/50) x 100 = 60%
60% - 30% = 30% The Melanic form is predated on 30% more than the dotted whitish form in the nonpolluted woodland.
Their studies showed that the dotted whittish form was preyed on 20% more than the melanic form in the polluted woodland. The melanic form is predated on 30% more than the dotted whitish form in the nonpolluted woodland.
In addition to the difference in predation, their studies also showed that in both the polluted and nonpolluted environments the moths that were located on the limb joints instead of the trunks were less likely to be preyed on.
Howlett and Majerus showed that the dotted whitish form was at a higher risk of predation when resting against the polluted (dark) trees. The melanic form had a greater chance of survival and reproduction because they were less likely to be detected against the soot-covered trees, the same findings of Kettlewell years before. Their experiment proved that the melanic form was an anti-predator adaptation, which is why the dotted whitish form had become so rare. The melanic form had become the dominant trait for survival and reproduction in the polluted woodland.
Example: Antipredator Adaptations used by the Monarch Butterfly 
The relationship between prey and predators continually changes. Prey need to find ways to outsmart predators in order to survive and reproduce. One way monarch butterflies increase their fitness is by forming huge groups of up to ten million. Increasing group size lowers the probability that any one monarch butterfly will be captured. This is known as the “dilution effect.” Moreover, butterflies located in the center of a large group are more likely to survive than those on the outside . Monarch butterflies that choose to migrate to closed-area overwintering sites are less likely to be attacked by a predator. Also, by reacting as a group to the movement of a predator, monarch butterflies are better able to scare away predators. This “mass startle effect” is thought to stun the predators and provide time for the butterfly to escape (true shock and awe indeed). The aforementioned are collective ways in which the butterfly behaves in order to elude a predator. There are, however, certain individual inherent features that the monarch butterflies possess that increase their probability of avoiding a predator.
Monarch butterflies contain chemicals that are toxic to many predators. Evidently, this makes other similar but harmless species envious. In Batesian mimicry, a palatable species attempts to mimic an unpalatable species in an attempt to increase its own fitness. The monarch butterfly species is one that some Batesian mimics model themselves after perhaps because the monarch butterflies are so successful at avoiding predators . The Batesian mimics, although they are not harmful to predators, experience increased fitness because they model a potentially harmful species such as the monarch butterfly. Although monarch butterflies do not gain an increase in fitness as models of Batesian mimics, they do benefit from Müllerian mimicry. In Müllerian mimicry, two unrelated toxic species converge on a similar morphology. If more than one unpalatable species has a similar morphological trait, then the predators may more easily recognize a Müllerian mimic as potentially harmful. This saves both the mimics and the predators time and energy.
For many years the viceroy butterfly (Limenitis archippus) was thought to be a Batesian mimic of the Monarch. As it turns out, the viceroy can, depending on its diet, be more unpalatable than the monarch, thus both species benefit from resembling the other because a predator eating either one may become ill and avoid both in the future. Thus both species are examples of Müllerian mimicry.
Monarch butterflies display aposematism or warning coloration. This warning coloration is meant to be very conspicuous. Monarch butterflies make themselves conspicuous by having bright orange areas on its wings. Predators quickly learn that prey containing these bright colors are potentially harmful. For example, when a blue jay consumes a monarch butterfly, it vomits shortly after. From that point on, the blue jay associates features of the monarch butterfly, such as its bright colors, as unpalatable. Because of their morphological features, Batesian mimics, Müllerian mimics, and many other aposematic species all gain from the monarch’s unpalatability.
Sexual Selection 
Sexual selection, a subcategory of natural selection, was first recognized by Charles Darwin and occurs when individuals differ in their ability to compete with others for mates or to attract members of the opposite sex. By heavy courtship, fighting, or large territorial possession, males heavily compete for females. Even though a male may win a fierce competition for the mate of his choice, it is ultimately the female who decides on a partner that she wants. The female is often successful in her attempts to control reproduction by being choosy and having particular preferences for a male mate.
Females typically have a relatively larger investment in producing offspring. While a single male can often fertilize all of a female's eggs, she will not produce more offspring by mating with more than one male. By and large, a male's reproductive success increases with the number of mating opportunities he obtains, whereas a female's reproductive success is largely limited by how many offspring she can physically bear . This results in sexual selection, in which eager males compete with each other, and females become choosy in which males to mate with. Bateman's studies on mating behavior in fruit flies suggested that the origins of the unequal investment reside in the fact that male gametes (sperm) are cheaper to produce than eggs. Animals are therefore fundamentally polygynous, as a result of being anisogamous.
- A female can have only a limited number of offspring, whereas a male can have a virtually unlimited number, provided that he can find females willing to mate with him. Thus females generally need to be much choosier about who they mate with.
- A male can easily produce sperm in excess of what it would take to fertilize all the females that could conceivably be available [...] Hence the development of the masculine emphasis on courtship and territoriality or other forms of conflict with competing males.
- In most animals the fertility of the female is limited by egg production which causes a severe strain on their nutrition. In mammals the corresponding limiting factors are uterine nutrition and milk production, which together may be termed the capacity for rearing young. In the male, however, fertility is seldom likely to be limited by sperm production but rather by the number of inseminations or the number of females available to him... In general, then, the fertility of an individual female will be much more limited than the fertility of a male... This would explain why in unisexual organisms there is nearly always a combination of an undiscriminating eagerness in the males and a discriminating passivity in the females.
- Among polygynous species, the variance in male reproductive success is likely to be greater than the variance in female reproductive success.
- The female, with the rarest exceptions, is less eager than the male... she is coy, and may often be seen endeavouring for a long time to escape.
Intersexual Choice: Why does she consider the trait "attractive"? 
Females choose mates based on many factors. One important factor is male adornments, or ornaments. For example, Marion Petrie and Tim Halliday concluded that the removal of eyespots from a peacock's tail significantly reduces his attractiveness to females. Thus, females are extremely conscious of the visual stimuli provided by males. Other factors involved in female preference in mate selection include body coloration or "gifts" the male may present to the female before copulation. A mother is expected to always want the best for her child, even if it is a future child. Females select mates with certain traits, because they want their children to be healthy, viable, and reproductively successful. A direct and heritable benefit of mate choice by females is the assurance of bearing offspring that will survive well and display high general fitness. Non-genetic benefits of mate choice include fecundity advantages, food, parental care, or a good territory. All of the benefits, both heritable and nonheritable, ultimately lead to the greater survival of a female's offspring.
- Passive Attraction Theory: Sensory Bias, conspicuous signals make an individual more likely to attract the attention of a mating partner. Elaborate sensory cues alert the female that the male is reproductively superior to others. Male adornments may more readily elicit the mating responses of some females who will thus mate preferentially in favour of the adorned males .
- Nuptial gifts: spermatophore; territory, protection, resources; courtship indicative of parental investment. e.g., Dung beetle
- The Good Genes Hypotheses regards assessment of the mate's state of health as a general indicator of viability and quality. Females exhibit mate choice in order to provide their offspring with a partner's genes that will advance their offspring's chances of survival or reproductive success. The healthy mate theory occurs when females prefer males healthy enough to produce and maintain elaborate ornaments. A good example of this is in female house finches, who choose male mates based on their bright coloration. Bright coloration tells the female that the male is more resistant to pathogens and parasites. In Hamilton and Zuk's "Revealing Signal Theory" bright ornaments reveal a genuinely healthy individual in good condition. In conditions where parasites ralter male showiness and parasite resistance is largely inherited, females ought to choose those with bright coloration.
- Zahavi's Strategic Choice Handicap Theory: the presence of a costly trait is indicative of otherwise good underlying genes that allow an individual to prosper despite this handicap
- Fisher's Run-away Selection: Females that mate with attractive males are compensated for reduced fecundity by bearing attractive offspring with higher than average mating success . This "Sexy Sons Hypothesis" works by alligning the presence of a particular morphological characteristic in males with a preference for it in females. Choosy females create a positive feedback loop favoring both males with these attributes and females that prefer them.
- Genetic Compatibility: MHC locus genes in human mate choice
- The Good Parent Theory suggests that choosy individuals ought to select partners on the basis of how well they will care for their offspring, e.g. as the female searches for a paternal male.
Inbreeding refers to an elevated amount of breeding between close relatives. The resulting increase in homozygosity of the population exposes recessive, deleterious traits in homozygous form and may lead to inbreeding depression where inbred individuals exhibit reduced health and fitness and lower levels of fertility.
The introduction of genetic material from unrelated individuals into a breeding line increases genetic diversity, thus reducing the incidence of disease or genetic abnormalities. It is used in breeding to restore vigor, size and fertility to a breeding line.
Sexual Selection and Ornamentation in Males 
Sexual selection refers to the process by which changes in gene frequencies result from individuals that are better than others at either competing for or at attracting mates -- it is the evolution of traits based on differences in mating success among individuals if (1) some traits increase the ability to compete with individuals of the same sex for access to mates, or (2) some traits increase the ability to attract individuals of the opposite sex. Ornamentation in males, which are commonly the competing sex, may result from different evolutionary forces. Sexual selection is always harsher on the competing sex.
- Species recognition Ornamentation in breeding individuals may serve in a quick recognition of others as members within a pool of genetically compatible breeding partners.
Intrasexual Competition and interference 
Dominant individuals often gain preferred access to mates, desirable territory, or other advantages that will enhance the individual's chances for transmitting its genes into future generations.
- Precopulatory: A common form is based on an individual's ability to physically dominate a rival. In situations where groups of mates can be readily monopolized this will likely lead to increasing size in the competing sex. Fur seal females, which rely on a small stratch of beach for giving birth, can be monopolized easily in harems.
Winning in ritualized contests, producing a louder signal, or masking an opponent's call; dominance in social groups; territorial exclusion; alternative mating strategies; sexual interference
- mate guarding;
- mating plugs; partners remain attached e.g. wolves;
- Bruce effect is a form of pregnancy disruption when a female mammal is exposed to an unknown male. Examples may also include post-implantation failure in many species of rodents .
- sperm competition: e.g. primate or bat mating systems
Basic Models of Molecular Evolution 
Adaptational Models 
Adaptational Models are rooted in the view that natural selection plays the dominant role in structuring an organism's morphology, physiology, and behavior. The extant phenotype thus is the product with adaptations that have its possessor allowed to reproduce more successfully than individuals with alternative traits.
Neutralist Models 
Alternative accounts for the evolution of traits focuses on genetic drift as a primary determinant for characteristics ranging from genes to complex traits. This acknowledges a significant role for historical contingencies, where present phenotypes of population members are largely determined by the genetic makeup of a small number of founding individuals. Although this view does not deny the role of natural selection in determining the course of adaptive evolution, the theory attributes a large role to genetic drift. When one compares the genomes of existing species, the vast majority of molecular differences do not influence the fitness of the individual organism. As a result, the theory regards differentiation in such features as neither subject to, nor explicable by, natural selection. Theoretical considerations suggest that such a process is most effective in small populations and when selecting among traits that are largely adaptively neutral.
Speciation and Macroevolution 
Speciation is the evolutionary process by which new biological species may arise. Natural speciation has taken place over the course of evolution, although the relative importance of different mechanism in driving biodiversity remains a subject of debate. Debate also relates to the rates at which speciation events may occur over geologic time. Although some evolutionary biologists claim that speciation events have remained relatively constant over time (i.e., Phyletic Gradualism), palaeontologists such as Niles Eldredge and Stephen Jay Gould have argued that species may remain unchanged over long periods of time with speciation occurring in relatively brief intervals (i.e., Punctuated Equilibrium).
Allopatric Speciation 
In allopatric speciation, two subgroups of a population become geographically isolated from each other (i.e., allopatric populations) through geographical or geological events. As these isolated populations undergo genotypic and phenotypic divergence, they are subjected to different selective pressures and may undergo genetic drift. New species form when the populations evolve independently such that they are no longer able of exchange genes when they come back into contact.
Peripatric and Parapatric Speciation 
New species are formed when isolated, small peripheral populations split from the main population and occupy a novel ecological niche. Since small populations often undergo bottlenecks, genetic drift may drive the latter into significant genetic divergence (i.e., peripatric specieation). If geography only accounts for a partial separation, individuals of each species may come in contact across the barrier from time to time, but reduced fitness of heterozygotes leads to selection for reproductive barriers that prevent breeding between the two species.
Sympatric Speciation 
In symptric speciation species diverge while inhabiting the same place. This may happen when a diploid cell undergoes failed meiosis, producing diploid gametes, and self-fertilizes to produce a tetraploid zygote. Alternatively, subgroups of a species may become dependent on different host organisms within the same area. With reduced fitness of heterozygotes, the emergence of reproductive barriers will drive the groups towards two distinct species.
- Alcock, J. 2001. Animal Behavior: An Evolutionary Approach (7 ed.) Sinauer Associates Inc., Massachusetts. pp. 341
- Pike K. 1999. Antipredator Adaptations by Monarch Butterflies. Entomology at Colorado State University, Posted in 1999. Colorado State University. Accessed December 6, 2004.
- Mappes J. & RV Alatalo. 1997. Batesian mimicry and signal accuracy. Evolution 51: 2051-2053
- Ritland, D.; L. P. Brower (1991). "The viceroy butterfly is not a Batesian mimic". Nature 350: 497–498. doi:10.1038/350497a0. http://www.nature.com/nature/journal/v350/n6318/abs/350497a0.html. Retrieved 2008-02-23. "Viceroys are as unpalatable as monarchs, and significantly more unpalatable than queens from representative Florida populations.".
- Clutton-Brock TH. 1990. Reproductive Success: Studies of Individual Variation in Contrasting Breeding Systems. University Of Chicago Press.
- Bateman AJ. 1948. Intra-sexual selection in Drosophila. Heredity 2: 349-368
- Williams GC. 1966, Adaptation and natural selection: a critique of some current evolutionary thought. Princeton, N.J: Princeton University Press
- Huxley JS. 1938. 'The present standing of the theory of sexual selection', in de Beer, G.R., Evolution: Essays on aspects of evolutionary biology, Oxford: Clarendon Press, pp. 11-42
- Darwin CR. 1871. The Descent of Man and Selection in Relation to Sex, Hurst and Co.
- Bateson P. 1983. Sexual Selection by Female Choice by Peter O'Donald. in Mate Choice. (pp.53). Cambridge: Cambridge University Press.
- Andersson M. 1994. Costs of Mate Choice; Direct Benefits of Mate Choice. In Sexual Selection. Princeton, New Jersey: Princeton University Press.
- Bruce HM. 1959. An exteroceptive block to pregnancy in the mouse. Nature 184: 105.
- Storey AE & DT Snow. 1990. Postimplantation pregnancy disruptions in meadow voles: Relationship to variation in male sexual and aggressive behavior. Physiology and Behaviour 47: 19–25