Biology (Part 8: Evolution)

Founder effect

A more extreme case of genetic drift in which a small population of a species finds itself in reproductive isolation from other populations as a result of natural barriers, catastrophic events, or other bottlenecks that drastically and suddenly reduce the size of the population available for breeding. When the founder of a population has an uncommon allele for a population that is then transferred throughout the population because of the limited size and gene pool.

Bottleneck effect

A type of genetic drift where natural disasters such as fire, earthquake, and flood reduce population size non-selectively, resulting in loss of genetic variation. Certain alleles may end up under or over-represented compared with the original population. If there was a huge earthquake on an island that left just a few kangaroos around and a rare allele increased among the species and their offspring, this is called a bottleneck. Because of there just being a few kangaroos around, it would be more probable for the kangaroos to experience and pass on traits that would not commonly be seen in their original population size.

Genetic drift

Genetic drift describes random changes in allele frequencies in a population. It is particularly powerful in small populations. This occurs when there is drifting towards specific alleles being selected over another by the sole reason of chance/probability. The smaller the population, the more likely it is that there could be genetic drift occurring. Genetic drift can be visualized as a line dividing one gene from another and then a large drift happening towards one side.

Parallel evolution

Species that share a common ancestor, evolve similarly and are under similar circumstances. This is when species have the same lineage and evolve closer together to be similar, using similar mechanisms -for example, the feeding structure in different species of crustaceans -the feeding structure came from mutation of pair of legs, turning them into mouth parts. This is a prime example of parallel evolution: same lineage, similar traits, evolved from similar mechanisms/mutations.

Homologous structures

Structures of species that have a common ancestor, and so are similar in structure. They might not be similar in function. Some homologous structures adapt differently to their environments over a period of time so they have different functions such as flying instead of throwing. The word homologous refers to having the same origin/ancestor. The forelimbs of humans and the forelimbs of bats are one example.

Speciation occurs by

- Adaptive Radiation - Allopatric Speciation - Sympatric Speciation

Causes of species variation

- Mutations - Outbreeding - Random joining of gametes (meaning a male gamete can fertilize any of the female gametes) - Chromosomal crossover during Prophase of Meiosis I Inbreeding limits species variation

Evidence for evolution

- Paleontology Fossils provide evidence of the evolutionary history of organisms. Evolutionists use the development and changes in fossils as reasons to support evolution. Paleontologists infer that whales evolved from land-dwelling animals because fossils of animals closely related to whales have front limbs like paddles, similar to front legs and tiny back limbs. The front limbs of these fossils are in some ways similar to legs, but in other ways they have strong similarities to fins of modern whales. - Species distribution The geographic distribution of organisms follows patterns best explained by evolution, in combination with tectonic plate movement. For example, broad groupings of organisms that evolved before the breakup of Pangaea tend to be distributed worldwide. In contrast, broad groupings that evolved after the breakup tend to appear uniquely in smaller regions of Earth. - Comparative analogous and homologous structures

Heterotroph hypothesis

- This hypothesis states that the first living organism was a heterotrophs, or organisms that obtain their energy by feeding on others (or on organic compounds). Hetero = other, troph = to feed. Before there were other organisms, they would feed on surrounding "left-overs" of their origin. The early atmosphere was reducing and contained simple compounds, like Hydrogen, Water, Ammonia and Methane. - The primary source of energy was UV light. There were other minor energy producers such as lightning and radiation. This energy input formed more complex molecules in primordial soup, such as Purines and Pyramidines (DNA), Amino Acids (Proteins) and Sugars. Energy input broke bonds which allowed for more complex things to form over time. - Eventually, the first organisms were formed, heterotrophs, which created CO₂ as waste product. They digested chemicals in primordial soup, so they were chemoheterotrophs. CO₂ was a precursor for autotrophs to evolve. Photoautotrophs look light and CO₂ to do photosynthesis and formed O₂. This created an oxidizing atmosphere. - The oxidizing atmosphere was a precursor for aerobic metabolism. Aerobes used O₂ to form ATP (animals and humans).

Outbreeding depression

- When progeny resulting from outbreeding exhibit lower fitness in the parental environment than either of their parents or than progeny from crosses between individuals that are more closely related. - This can happen when intermediate genotypes are not adapted to either parental habitat. For example, selection in one population might favor a large body size, whereas in another population small body size might be more advantageous. Individuals with intermediate body sizes are then at a disadvantage. In the Tatra Mountains, the introduction of ibex from the Middle East resulted in hybrids which produced calves at the coldest time of the year. - GOKU This can also happen due to breakdown of biochemical or physiological compatibility. Within isolated breeding populations, alleles are selected in the context of the local genetic background. Because the same alleles may have rather different effects in different genetic backgrounds, there is the potential evolution of different locally adapted gene complexes. Outcrossing between individuals with differently adapted gene complexes can result in disruption of this selective advantage, resulting in a loss of fitness.

Symbiosis

1) Parasitism - when a species requires another species as a host to live, harming the host in the process 2) Commensalism - an organism requires another species as a host to live, but doesn't harm or benefit the host in the process 3) Mutualism - symbiotic relationship between two organisms that confers fitness on both

Stabilizing selection

A type of natural selection that favors the average individuals in a population. This process selects against the extreme phenotypes and instead favors the majority of the population that is well adapted to the environment. It is often shown on a graph as a modified bell curve that is narrower and taller than the norm. Human birth weight deviation is an example of stabilizing selection. Babies that are too small lose weight quickly and are more prone to diseases, whereas larger babies are difficult to deliver. Therefore, average weight babies are selected for by stabilizing selection.

Hardy-Weinberg assumptions

Allele frequencies must remain constant throughout each generation. In order for this to occur, there cannot be any natural selection, no genetic drift (the isolation of a group of species, when genes from one place move to another via migration which result in the huge loss of that species or genes from that place), no mutations, and mating cannot be isolated and must be random.

Disruptive selection

Also known as diversifying selection. When species that are exhibiting extreme characteristics survive and species that show intermediate characteristics have a small chance of survival. Extreme phenotypes are selected for rather than the common ones like stabilizing selection. The most well known example of disruptive selection is Darwin's study of finches. The finches with average beaks were unable to survive while finches with beaks that adapted well to nature were able to produce more offspring and attain more food.

Outbreeding

Also known as outcrossing, it is the mating of nonrelatives and is the opposite of inbreeding. This most commonly occurs withing the same species but can also occur with similar species, which produces hybrids. Outbreeding produces heterozygotes which gives rise to more variation.

Gene flow

Change of allele frequency from a gene pool, caused by accumulation or reduction of population by migration. If wolves were to immigrate into a population of coyotes and begin mating, this bringing in of new alleles is called gene flow. It is genes flowing in or out of a population. If wolves leave a coyote population, genes are flowing out.

Lamarck vs Darwin

Darwin believed that evolution occurred through natural selection. He published his theories after Lamarck did. Most of Lamarck's major theories were incorrect, such as someone with acquired traits like muscle build will pass these traits on to their offspring. Charles Darwin and Jean-Baptiste de Lamarck both thought that life had changed gradually over time and was still changing, that living things change to be better suited and adapted to their environments, and that all organisms are related. They both agreed that life evolved from fewer, simpler organisms into many, more complex organisms. Darwin stated that changes in species was due to procreation or breeding. Those species that spawned changes which helped to adapt to the new conditions, survived, while those that didn't eventually died. ​ Lamarck's theory held that species underwent changes in response to changes in their environment. One example is giraffe necks. Lamarck contended that as trees began to grow taller, giraffes responded to the change by growing longer necks so that they could continue to feed. His second contention was that this change was permanent for as long as the new environmental conditions continued to apply. In other words, nature chose the best possible solution and, organisms (species), responded accordingly. Darwin's natural selection said that through survival of the fittest, a mutation happened that caused a giraffe's ancestors to grow longer necks, and because those ancestors had better access to food than ones with shorter necks, they reproduced more, outnumbering and eventually replacing the short-neck ones.

Natural selection

Darwin's theory is based on survival of the fittest (the best suited mutations become dominant), individual competition (certain phenotypes of a species are selected for), population stability, and reproductive potential. It is based on the limited amount of resources available to a certain species. Natural selection is not necessarily about the strongest species surviving, but rather the one that its environment selects to be the most adaptive in respect to it.

Neutral variation

Differences in DNA sequence that do not confer a selective advantage or disadvantage. For example: eye color or fingerprints. There is nothing selective about the variation in human fingerprints, yet there is variation. Nothing in the world will select for one type of fingerprint variation over another.

Endosymbiotic theory

Eukaryotic cells may have evolved when multiple cells joined together into one and formed symbiotic relationships. An endosymbiont is an organism that lives inside another. Mitochondrion and chloroplasts were once free-living cells. They were prokaryotes that ended up inside of other cells (host cells). They may have joined through phagocytosis or may have been parasites. Over time the organelle and the host cell evolved together. This theory is supported because mitochondria and chloroplasts have double membranes just like prokaryotes do. They also have their own circular DNA which replicates independent of the genomic DNA. They have their own ribosomes, which have 30S and 50S subunits like those of prokaryotic ribosomes. They divide by binary fission just like bacteria do. Mitochondrial DNA also lacks the common proteins found in other DNA.

Adaptive radiation

Evolution of an animal or plant group into a wide variety of types adapted to specialized modes of life. Adaptive radiations are best exemplified in closely related groups that have evolved in a relatively short time. The numerous Darwin's Finches that were said to have evolved from one ancestor are an example of this. Because there were many different environments on the island for the finches to colonize, they were said to have done so at a very quick rate.

Microevolution vs Macroevolution

Explains evolution for groups of species, rather than evolution in individual species. Just like individual evolution, macroevolution has more than one proposed theory as to how species evolve. - Macroevolution looks at changes over a long amount of time and among a group of species. Microevolution looks at changes over a short period of time among a single species and/or new ones that develop as a result. - Microevolution happens on a small scale (within a single population), while macroevolution happens on a scale that transcends the boundaries of a single species. Despite their differences, evolution at both of these levels relies on the same, established mechanisms of evolutionary change: mutation, migration, genetic drift and natural selection.

Polyploidy

Having more than 2 sets of chromosome (>2n). Common in plants but rare in animals. If an individual has two copies of each chromosome (diploidy), their offspring may have four copies (tetraploidy). A tetraploid individual cannot mate with a diploid individual, thus creating reproductive isolation. It is much easier for plants to self-fertilize than it is for animals. A tetraploidy plant can fertilize itself and create offspring. For a tetraploidy animal to reproduce, it must find another animal of the same species but of opposite sex that has also randomly undergone polyploidy.

Hybrid sterility

Hybrid zygotes sometimes develop into adults, but the adults fail to develop functional gametes and are sterile. When a male donkey and a female horse mate and produce a mule, this mule is sterile. Because this mule has the postzygotic isolating mechanism (ensuring that species stay separate) of hybrid sterility, it is able to function normally, however they are unable to produce offspring.

Balanced polymorphism

Polymorphism - the condition of occurring in several different forms. When two different versions of a gene are maintained in a population of organisms because individuals carrying both versions are better able to survive than those who have two copies of either version alone. The evolutionary process that maintains the two versions over time is called balancing selection. An example is seen in the set of liver enzymes that act like an assembly line to detoxify poisons and other chemicals. Different alleles for these enzymes can affect how well an organism can protect itself from exposure to harmful chemicals. An especially active form of a detoxifying enzyme, which is encoded by a specific allele, can cause accumulation of potentially harmful intermediates. If the other allele encodes an enzyme with low activity, the potential for this enzyme to cause harm is lessened, and the benefits of its activity will be felt by the organism. If an individual has two copies of the very active allele or two copies of the low-activity allele, it may not survive well. In the first case, too much enzyme activity will result in high levels of the harmful intermediate, and in the second case, too little enzyme activity will be present for detoxification. Therefore, the best situation for the organism is to have one copy of each allele. Because of this, both copies are maintained in the population.

Molecular phylogenetics

The branch of phylogeny that analyzes genetic and hereditary molecular differences in DNA sequences of different species to gain information on an organism's evolutionary relationships. This results in a phylogenetic tree. For example, humans are said to have over 95% of the same DNA sequencing compared to chimpanzees, and are very similar in structure and in ways appearance. The more similar a human's nucleotide DNA sequence is to another species, the more similar they are to each other.

Sympatric speciation

The formation of a new species without a geographic barrier. Occurs in populations that live in the same geographic area (ranges of populations overlap). The barrier is a mechanical barrier. Populations of a species that share the same habitat become reproductively isolated from each other. There are 3 types of this: 1. Balanced polymorphism 2. Polyploidy 3. Hybridization

Chemical evolution

The formation of complex organic molecules from simpler inorganic molecules through chemical reactions in the oceans during the early history of the Earth; the first step in the development of life on this planet. The period of chemical evolution lasted less than a billion years. It was said to have finalized when the ozone layer formed. It stopped because the newly synthesized oxygen with its ozone layer prevented the UV light from synthesizing new substances.

Allopatric speciation

The formation of new species in populations when a population is divided by a geographic barrier preventing interbreeding. Gene frequencies diverge due to natural selection, mutation and genetic drift. If the gene pool diverges enough, interbreeding cannot occur once the barrier is removed. New species could form after a forest fire separates a population into two different ones because of their potentially different environments, mutations, etc.

Modern Synthesis of Evolution

The fusion (merger) of Mendelian genetics with Darwinian evolution that resulted in a unified theory of evolution. It is sometimes referred to as the Neo-Darwinian theory. Introduced several changes in how evolution and evolutionary processes were conceived. It proposed a new definition of evolution as "changes in allele frequencies within populations," thus emphasizing the genetic basis of evolution. (Alleles are alternate forms of the same gene, characterized by differences in DNA sequence that result in the construction of proteins that differ in amino acid composition.) Four forces of evolution were identified as contributing to changes in allele frequencies: genetic drift, gene flow, mutation pressure, and natural selection. Of these, natural selection is the only evolutionary force that makes organisms better adapted to their environments. Genetic drift describes random changes in allele frequencies in a population. It is particularly powerful in small populations. Gene flow describes allele frequency changes due to the immigration and emigration of individuals from a population. Mutation is a weak evolutionary force but is crucial because all genetic variation arises originally from mutation, alterations in the DNA sequences resulting from errors during replication or other factors. It is currently believed that the majority of mutations are neutral, since they do not cause any detectable change in the organism. Mutations that are advantageous usually have a small phenotypic effect. Advantageous mutations may be incorporated into the population through the process of natural selection. Changes in species therefore occur gradually through the accumulation of small changes. The large differences observed between species involve gradual change over extensive time periods. Speciation results from the evolution of reproductive isolation, often during a period of allopatry, in which two populations are isolated from one another.

Phyletic gradualism

The hypothesis that says evolution occurs by the accumulation of many small changes over a long time period, or that evolution has a fairly constant rate. New species arise by the gradual transformation of ancestral species. But this is said to be unlikely because intermediate stages of evolution are missing from the fossil record. Fossils only reveal major changes in groups of organisms. Gradualists say that the fact that fossil evidence shows species suddenly appearing with little signs of any transitional forms is due to the incompleteness of the fossil record.

Punctuated equilibrium

The hypothesis that says species exhibit small evolutionary net change, yet remain almost constant (in stasis) until significant change occurs due to the change in environment. Then there are major changes over short intervals, with equilibrium most of the time between these major changes. Fossils show major changes in groups of organisms. It is said that species originate too rapidly to enable their origins to be traced by paleontologists (punctuation), and then persist unchanged through geological time in stasis (equilibrium).

Hardy-Weinberg equilibrium

Used to calculate the genetic variation of a population at equilibrium. The equation states that the amount of genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors. Equation: p² + 2pq + q² = 1 - p is the frequency of the "A" allele and q is the frequency of the "a" allele in the population. - p² is the frequency of the homozygous genotype AA - q² is the frequency of the homozygous genotype aa - 2pq is the frequency of the heterozygous genotype Aa - In other words, all of the homozygous and heterozygous individuals must add up to 1 (100%) All of the allele frequencies for all the alleles at a given locus must add up to be 1 (100%), so: p + q = 1 If the p and q allele frequencies are known, then the frequencies of the three genotypes may be calculated using the Hardy-Weinberg equation. The equation can also be used to measure whether the observed genotype frequencies in a population differ from the frequencies predicted by the equation. Again, in order for genetic equilibrium to hold true p + q = 1, and p² + 2pq + q² = 1.

Isolating mechanisms

The reproductive characteristics which prevent species from fusing. These are particularly important in the biological species concept, in which species of sexual organisms are defined by reproductive isolation, i.e. a lack of gene mixture. Two broad kinds of isolating mechanisms between species are typically distinguished, together with a number of sub-types: - Pre-mating isolating mechanisms. Factors which cause species to mate with their own kind (assortative mating). a) Temporal isolation. Individuals of different species do not mate because they are active at different times of day or in different seasons. b) Ecological isolation. Individuals mate in their preferred habitat, and therefore do not meet individuals of other species with different ecological preferences. c) Behavioral isolation. Potential mates meet, but choose members of their own species. d) Mechanical isolation. Copulation is attempted, but transfer of sperm does not take place. For example, some flowers are incompatible due to their specific pollinators. - Post-mating isolating mechanisms. Genomic incompatibility, hybrid inviability or sterility. a) Gametic incompatibility. Sperm transfer takes place, but egg is not fertilized. b) Zygotic mortality. Egg is fertilized, but zygote does not develop. c) Hybrid inviability. Hybrid embryo forms, but of reduced viability. d) Hybrid sterility. Hybrid is viable, but resulting adult is sterile. e) Hybrid breakdown. First generation (F1) hybrids are viable and fertile, but further hybrid generations (F2 and backcrosses) may be inviable or sterile.

Embryology

The study of the development of embryo in different organisms. Used for comparison of the relationship among several different species of organisms. Humans, pigs, fish, and chickens all have similar embryonic development which is often cited as evidence that they have evolved from a common ancestor. Similarities in stages of development can be used to determine evolutionary relationships between organisms. Ontogeny (also ontogenesis or morphogenesis) is the origination and development of an organism, usually from the time of fertilization of the egg to the organism's mature form—although the term can be used to refer to the study of the entirety of an organism's lifespan. Ontogeny, embryology and developmental biology are closely related studies and the terms are sometimes used interchangeably.

Artificial selection

When a person selects specific traits that are desirable and decides to artificially select them. This can often times create a new species. Kale, broccoli, cauliflower, cabbage, brussels sprouts, and kohlrabi all originated from one wild mustard species.

Origin of Life

There is no "standard model" on how life started. Most accepted models are built on molecular biology and cell biology: - When there were the right conditions, some basic small molecules were created. These are called monomers of life. Amino acids are one type of these molecules. These basic building blocks are common throughout space. Early Earth would have had them all. Early Earth favored production of organic molecules (Amino Acids) with high amounts of C, H, and N and less O (primordial soup). The theory is that with massive amounts of energy from many sources, bonds formed between atoms. An experiment with electrical discharge made simple Amino Acids, further experimentation produced 20 Amino Acids, lipids (phospholipids formed bilayers for cell membranes), and all 5 Nitrogenous bases. - Nucleotides might have joined up into random RNA molecules. This might have resulted in self-replicating ribozymes (RNA world hypothesis). - Competition for substrates would select mini-proteins into enzymes. The ribosome is critical to protein synthesis in present-day cells, but we have no idea as to how it evolved. - Early on, ribonucleic acids would have been catalysts, but later, nucleic acids were specialized for genomic use. - The basic chemicals from which life is thought to have formed are: Methane (CH₄) Ammonia (NH₃) Water (H₂O) Hydrogen sulfide (H₂S) Carbon dioxide (CO₂) or carbon monoxide (CO) Phosphate (PO₄³⁻) Molecular oxygen (O₂) and ozone (O₃) were either rare or absent. - Three stages Stage 1: The origin of biological monomers Stage 2: The origin of biological polymers Stage 3: The evolution from molecules to cells - Evolution may have commenced early, some time between Stage 1 and 2 - The earliest evidence of life is stromatolites, which are photosynthetic bacteria (primitive prokaryotes)

Sexual selection

When certain physical traits, such as pronounced coloration, increased size, or striking adornments in animals grants the possessors of these traits greater success in obtaining mates. From the perspective of natural selection, such increases in mating opportunities outweigh the risks associated with the animal's increased visibility in its environment. An example is when a female elk selects a male deer with large antlers who wins a battle against another male elk. This type of sexual selection is referred to specifically as male competitiveness. This favors males with high levels of strength and larger antlers, which leads to elk with larger antlers and strength being more favored in reproduction. Sexual selection results in reproduction that is a type of nonrandom mating rather than random mating.

Directional selection

When one trait is favored extremely over another. Dark moths were favored over the lighter peppered moths when soot from the Industrial Revolution made the trees darker in color and easier to spot the lighter colored moths. Darker moths were camouflaged by the tree bark and were directionally selected.

Heterozygote advantage

When the heterozygous genotype has a higher relative fitness than the homozygous dominant and recessive genotypes. For example in sickle cell anemia, the heterozygous phenotype is resistant to malaria, giving it an advantage in areas with high malaria when compared to the homozygous phenotypes. This also results in balanced polymorphism.

Coevolution

When two or more species reciprocally affect each other's evolution. For example, an evolutionary change in the morphology of a plant might affect the morphology of an herbivore that eats the plant, which in turn might affect the evolution of the plant, which might affect the evolution of the herbivore, etc. Coevolution is likely to happen when different species have close ecological interactions with one another. These ecological relationships include predator/prey and parasite/host, competitive species and mutualistic species. In coevolution between a predator and prey, both evolve together because only specific prey survive while only certain predators are able to find food and survive.

Convergent evolution

When two species have different ancestors, yet have analogous traits which they have developed over a period of time due to independent adaptations. Analogous structures are structures of species that are similar in function but are not derived from the same evolutionary origin (don't have a common ancestor). They are different in structure but similar in function because they adapted similarly to their environment. Wings of insects, bird wings and bat wings are one example.

Divergent evolution

When two species share a common ancestor. Chances are that these two species have similar traits, but they don't have the same traits under every circumstance. In other words, it is independent development of dissimiliar characteristics in 2 or more lineages sharing a common ancestry. For example, seals and cats are both mammals belonging to the order Carnivora, but differ in appearance, live in different environments and adapt to different selection pressures.