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Adaptive radiation
If a lot of diversification happens in a short amount of time, it is often referred to as an adaptive radiation. Although biologists have different standards for defining an adaptive radiation, it generally means an event in which a lineage rapidly diversifies, with the newly formed lineages evolving different adaptations. The rapid diversification of mammals shown here may constitute an adaptive radiation.

 

Allopatric speciation
In this mode of speciation, something extrinsic to the organisms prevents two or more groups from mating with each other regularly, eventually causing that lineage to speciate. Isolation might occur because of great distance or a physical barrier, such as a desert or river.

 

Analogies (1 of 3) Saberteeth
These skulls belong to extinct animals, and both of them have saberteeth — long, ferocious canines. Would you guess that these saberteeth are homologous — inherited from a common ancestor with extra-long saberteeth?

 

Analogies (2 of 3) Saberteeth
Despite their similarities, the unusual length of these teeth is NOT homologous. One skull belongs to Thylacosmilus, a marsupial mammal. The other belongs to Smilodon, the saber-toothed cat, which is a placental mammal. Marsupial and placental mammals are very different, and diverged from each other a long time ago on the evolutionary tree. Thylacosmilus is more closely related to other marsupials such as kangaroos and koalas than it is to Smilodon. Smilodon is more closely related to other placentals such as housecats and elephants than it is to Thylacosmilus. Saberteeth is not a common trait in the marsupials closely related to Thylacosmilus, or the placentals closely related to Smilodon.

 

Analogies (3 of 3) Saberteeth
As they weren't inherited from a common ancestor, the saberteeth in Smilodon and Thylacosmilus evolved independently from one another. That means that one lineage on one part of the tree of life evolved saberteeth from normal length teeth, and a different lineage somewhere else on the tree also evolved saberteeth from normal length teeth.

 

Analogy (1 of 2) Bird and bat wing diagrams
When we examine bird wings and bat wings closely, we see that there are some major differences. Bat wings consist of flaps of skin stretched between the bones of the fingers and arm. Bird wings consist of feathers extending all along the arm. These structural dissimilarities suggest that bird wings and bat wings were not inherited from a common ancestor with wings.

 

Analogy (2 of 2) Bird and bat wing phylogeny
Bird and bat wings are analogous — that is, they have separate evolutionary origins, but are superficially similar because they evolved to serve the same function. Analogies are the result of convergent evolution.

 

Antibiotic resistance
The evolution of antibiotic resistance occurs through natural selection. Imagine a population of bacteria infecting a patient in a hospital. The patient is treated with an antibiotic. The drug kills most of the bacteria but there are a few individual bacteria that happen to carry a gene that allows them to survive the onslaught of antibiotic. These survivors reproduce, passing on the gene for resistance to their offspring, and soon the patient is populated by an antibiotic resistant infection — one that not only affects the original patient but that can also be passed on to other patients in the hospital.

 

Artificial selection (1 of 5) Fish example
This population of fish exhibits variation in body size. Some have genes for large size and some have genes for small size. This represents genetic variation in the population.

 

Artificial selection (2 of 5) Fish example
When the population is fished, many of the largest fish are removed, so more of the small-bodied fish (and their small-bodied genes) remain.

 

Artificial selection (3 of 5) Fish example
The population reproduces. Each individual passes their genes on to their offspring — however, since there are more small-bodied parents, there are also more small-bodied offspring.

 

Artificial selection (4 of 5) Fish example
In the next generation, the population has evolved: average body size in the population is smaller than it used to be and small-bodied genes are more common than they used to be.

 

Artificial selection (5 of 5) Fish example
This downward trend in body size will continue so long as the largest fish are harvested and there is genetic variation in the population.

 

Artificial selection in the lab (1 of 2)
Guppy spots are largely genetically controlled. Spots that help the guppy blend in with its surroundings protect it from predation — but spots that make it stand out help it attract mates. In this experiment, guppies were raised in ponds that varied in the coarseness of gravel on the bottom. All ponds had predators. After fewer than 15 generations of selection, the markings of guppies in different ponds had substantially diverged as a result of natural selection. In the presence of predators, guppies evolved to blend in with their background.

 

Artificial selection in the lab (2 of 2)
The same experiment was performed in the same pond set-up, but without predators. After fewer than 15 generations of selection, the markings of guppies in different ponds had substantially diverged as a result of natural selection. In the presence of predators, guppies evolved to blend in with their background.

 

Artificial selection of corn
Plants and animals are domesticated through artificial selection, which works like natural selection does, but with humans instead of nature doing the selecting. Here, humans plant only the plump teosinte kernels — the plants that grow from those seeds carry more genes for plumpness, but they still vary in many ways. Over many generations of selection, the frequency of desirable gene variants increases in the population — and so does the quality of the crop.

 

Body size over time
Over the history of life, increases in body volume are correlated with sharp increases in the oxygen level of the earth's atmosphere.

 

Bottleneck
In genetics, a population bottleneck is an event in which a population's size is greatly reduced. Gene frequencies in the population are likely to change just by random chance and many genes may be lost from the population, reducing the population's genetic variation. The situation is even more extreme for the genes that are targeted for artificial selection. Humans only allow individuals carrying desirable gene versions to reproduce. This is a bit like going to the gumball machine when you only like cherry-flavored gum: you might reject many pieces of gum based on their color and will wind up with a handful of gumballs with very little variety.

 

Cambrian explosion
The term "explosion" may be a bit of a misnomer. Cambrian life did not evolve in the blink of an eye. The Cambrian was preceded by many millions of years of evolution, and many of the animal phyla actually diverged during the Precambrian.

 

Causes of speciation - Geographic isolation
What was once a continuous population is divided into two or more smaller populations. This can occur when rivers change course, mountains rise, continents drift, or organisms migrate. The geographic barrier isn't necessarily a physical barrier that separates two or more groups of organisms — it might just be unfavorable habitat between the two populations that keeps them from mating with one another.

 

Causes of speciation - Reduced gene flow
Speciation can occur even when there is no specific extrinsic barrier to gene flow. Imagine a situation in which a population extends over a broad geographic range, and mating throughout the population is not random. Individuals in the far west would have zero chance of mating with individuals in the far eastern end of the range. So we have reduced gene flow, but not total isolation. This may or may not be sufficient to cause speciation. Speciation would probably also require different selective pressures at opposite ends of the range, which would alter gene frequencies in groups at different ends of the range so much that they would not be able to mate if they were reunited.

 

Change through time (1 of 4) Leaves
Leaves on trees change color and fall over several weeks.

 

Change through time (2 of 4) Mountains
Mountain ranges erode over millions of years.

 

Change through time (3 of 4) Genealogy
A genealogy illustrates change with inheritance over a small number of years.

 

Change through time (4 of 4) Tree of life
Over a large number of years, evolution produces tremendous diversity in forms of life.

 

Chemical signals and cell fate
Chemical signals influence the fate of cells.

 

Clades (1 of 2) Definition
A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.

 

Clades (2 of 2) Nested clades
Clades are nested within one another — they form a nested hierarchy. A clade may include many thousands of species or just a few. Some examples of clades at different levels are marked on these phylogenies. Notice how clades are nested within larger clades.

 

Codon
1 codon = 1 amino acid

 

Cospeciation (1 of 3)
A species of louse lives on a species of gopher. When the gophers get together to mate, the lice get an opportunity to switch gophers and perhaps mate with lice on another gopher. Gopher-switching allows genes to flow through the louse species.

 

Cospeciation (2 of 3)
When the gopher lineage splits into lineages A and B, lice have few opportunities for gopher-switching, and lice on gopher lineage A don't mate with lice living on gopher lineage B. This "geographic" isolation of the louse lineages may cause them to become reproductively isolated as well, and hence, separate species.

 

Cospeciation (3 of 3)
When lineages have cospeciated, the parasite phylogeny will "mirror" the host phylogeny. This example is somewhat idealized — rarely do scientists find hosts and parasites with exactly matching phylogenies. However, sometimes the phylogenies indicate that cospeciation did happen along with some host-switching.

 

DNA fingerprinting
In DNA fingerprinting, scientists collect samples of DNA from different sources — for example, from a hair left behind at the crime scene and from the blood of victims and suspects. They then narrow in on the stretches of repetitive DNA scattered throughout these samples. The profile of repetitive regions in a particular sample represents its DNA fingerprint, which ends up looking a bit like a barcode. Each bar in the barcode represents one particular stretch of repetitive DNA. Since these repetitive regions are common in the genome and highly variable from individual to individual, no two people (except identical twins) will have exactly the same set of repetitive regions and, hence, the same DNA fingerprint.

 

DNA structure
DNA is made of a long sequence of smaller units strung together. There are four basic types of unit: A, T, G, and C. These letters represents the type of base each unit carries: adenine, thymine, guanine, and cytosine.

 

DNA, RNA, Proteins (1 of 4) DNA
DNA is a long, double-stranded molecule twisted into a helix. It is composed of a chemical code (represented by the letters A, T, G, and C) that describes how to make proteins.

 

DNA, RNA, Proteins (2 of 4) RNA
RNA is similar to DNA, but it is shorter and single-stranded. RNA can carry an "imprint" of DNA information and take it to the place in the cell where proteins are built.

 

DNA, RNA, Proteins (3 of 4) Proteins
Proteins are long chain-like molecules that fold into complicated shapes and perform all sorts of jobs in the cell — from providing raw building materials to running chemical reactions. They are the workhorses of the cell — and, hence, of the organism.

 

DNA, RNA, Proteins (4 of 4) DNA to Proteins
DNA instructions are transmitted via RNA to construct proteins.

 

Evo in the News: Evolutionary history in a tiny package
This news brief, from March 2012, describes the discovery four new species—all miniature chameleons—and explores the concept of island dwarfism.

 

Evolution of HIV virus
Just as fruit flies on separate islands can evolve into separate species, HIV viruses in separate hosts can evolve into separate lineages.

 

Extinction and diversification - Trilobites and ammonites
If extinction happens more frequently than lineage-splitting, that entire clade will go extinct eventually. For example, trilobites and ammonites had high rates of both diversification and extinction.

 

Fitness
Evolution shows that, as much as possible, organisms will evolve to optimize their fitness — the number of descendents they produce for future generations relative to other organisms. So based on evolutionary theory, we would expect organisms to evolve adaptations that would allow them to have more children, grand children, great-grandchildren, and so on.

 

Galapagos finch phylogeny
Genetic sequences show that finches with similar feeding approaches tend to be closely related to one another.

 

Gene expression in different cells
Different cells have different genes expressed.

 

Genes + environment = phenotype
An organism's phenotype is usually the result of both genetic factors, environmental factors, and the interactions between them.

 

Genetic bottleneck
Population bottlenecks occur when a population's size is reduced for at least one generation. Because genetic drift acts more quickly to reduce genetic variation in small populations, undergoing a bottleneck can reduce a population's genetic variation by a lot, even if the bottleneck doesn't last for very many generations. This is illustrated by the bags of marbles shown below, where, in generation 2, an unusually small draw creates a bottleneck.

 

Genetic drift - Large population
Through sampling error, genetic drift can cause populations to lose genetic variation. Imagine that our random draws from the marble bag produced the following pattern: 5:5, 6:4, 7:3, 4:6, 8:2, 10:0, 10:0, 10:0, 10:0, 10:0… Why did we keep drawing 10:0? Because if the green marbles fail to be represented in just one draw, we can't get them back — we are "stuck" with only brown marbles. The cartoon below illustrates this process, beginning with the fourth draw.

 

Genetic drift - Small population
The marble-drawing scenario also illustrates why drift affects small populations more. Imagine that your bag is only big enough for 20 marbles (a tiny bag!) and that you can only draw four marbles to represent gene frequencies in the next generation. Something like this might happen:

 

Genetic drift example (1 of 4)
BB individuals have big beaks, Bb individuals have medium-sized beaks, and bb individuals have small beaks. These birds live in a place where large and small seeds are abundant, but no medium-sized seeds are available. Populations of all big-beaked individuals have a very high average fitness — they can crack open big seeds. Populations of all small-beaked individuals do well (they can manipulate smaller seeds) — but not quite as well as the big-beaked individuals. Medium-beaked individuals have the lowest fitness — they are not particularly good with either big or little seeds (and no medium-sized seeds are available). A graph of these gene frequencies and the population's resulting fitness levels is shown. This sort of graph is called an adaptive landscape.

 

Genetic drift example (2 of 4)
Now imagine a small population of all small-beaked individuals (all bb genotypes). They have a high fitness (they are at a local peak), but not as high as a population of big-beaked individuals. Through gene flow some B alleles are introduced to the population. If selection alone were acting, it would weed these alleles out of the population since they would show up in Bb individuals with lower fitness. Under selection alone, the population could never reach the higher BB fitness peak.

 

Genetic drift example (3 of 4)
However, since the population is small, drift can be a powerful force. Just by chance, the frequencies of the B alleles increase in the population over several generations (and the population moves into a valley in the adaptive landscape). If the B alleles become frequent enough, the population will begin to have BB individuals with high fitness. As this happens, selection begins to increase the frequency of B (the population moves out of the valley and selection pushes it towards the global fitness peak). Eventually, through the action of genetic drift combined with selection, the population moves from one local peak, through a valley of low fitness, to the global fitness peak.

 

Genetic drift example (4 of 4)
In the real world, many, many loci affect the fitness of a population and an adaptive landscape may have multiple peaks and valleys. This graph shows a complex landscape involving just two loci.

 

Greenhouse effect
Just as a glass greenhouse traps heat radiated by the sun, greenhouse gasses in the Earth's atmosphere also trap the sun's heat.

 

Homologous tetrapod limbs (1 of 6)
These four limbs all belong to tetrapods — animals with four legs.

 

Homologous tetrapod limbs (2 of 6)
Notice how these tetrapod limbs are similar to one another: They are all built from many individual bones. They are all spin-offs of the same basic bone layout: one long bone attached to two other long bones.

 

Homologous tetrapod limbs (3 of 6)
Whales, lizards, humans, and birds all have the same basic limb layout. But how did such different animals wind up with the same sort of limb? The answer is that they inherited it from a common ancestor, just as cousins might inherit the same trait from their grandfather.

 

Homologous tetrapod limbs (4 of 6)
This evolutionary tree shows the relationships between different tetrapod lineages, all of which evolved from a single common ancestor. This 350 million year old animal, the first tetrapod, had limbs with one long bone (the humerus) attached to two other long bones (the radius and ulna). Its descendants, including whales, lizards, humans, and birds, as well as many others, inherited the tetrapod limb from this ancestor.

 

Homologous tetrapod limbs (5 of 6)
Not all similarity is homology. Since the octopus, sea star and grasshopper limbs don't have bones, they are not homologous to tetrapod limbs.

 

Homologous tetrapod limbs (6 of 6)
This tree shows how the octopus is related to tetrapods, and the points in their evolutionary histories when their limbs evolved. Tetrapod and octopus limbs evolved independently after their point of common ancestry, so they were not inherited from a common ancestor. Therefore, they are not homologous. The same is true of the grasshopper leg and the sea star arm.

 

Horizontal gene transfer
Bacteria can get new gene variants through horizontal gene transfer - they can pass genes back and forth to one another directly.

 

Humans on the tree of life
This tree is based on morphological and genetic data. Chimpanzees and humans form a clade with genes sequences that differ by only 1%. This genetic similarity made it hard to figure out exactly how these two primates are related, but recent genetic studies have strongly suggested that chimpanzees and humans are each other's closest living relative.

 

Inbreeding depression
The offspring resulting from inbreeding tend to have health problems and lower reproductive success. This is known as inbreeding depression. Inbreeding depression occurs because of a quirk of natural selection and genetics. As natural selection acts on a population, it weeds out genes that have disadvantageous effects, but it can only weed out these genes if they are actually expressed in an individual. For dominant gene versions, that's no problem. Individuals carrying dominant genes with a detrimental effect will be selected against, and eventually, these genes will be purged from the population. For recessive gene versions, however, the story is a bit different. Recessive genes are only expressed when an individual carries two copies of them. Once natural selection has removed most of the detrimental recessive genes from a population, these seldom wind up paired with an identical copy and are effectively hidden from the effects of natural selection. This means that most populations carry many deleterious recessive gene versions that are very rarely expressed — except in cases of inbreeding. Closely related individuals are likely to carry the same deleterious recessive gene versions and pass two copies of that gene on to their offspring.

 

Macroevolution
Macroevolution refers to evolution of groups larger than an individual species.

 

Mass extinction
For any one species, extinction may seem catastrophic. But over the grand sweep of life on Earth, extinction is business as usual. Extinctions occur continually, generating a "turnover" of the species living on Earth. This normal process is called background extinction. Sometimes, however, extinction rates rise suddenly for a relatively short time — an event known as a mass extinction. Mass extinctions kill off many species, but the empty niches left behind may allow other lineages to radiate into new roles, shaping the diversification of life on Earth.

 

Mass extinctions - Five major
Mass extinctions are, by definition, harsh, but they each seem to be disastrous in their own unique way.

 

Mechanisms of evolution (1 of 4) Mutation
A mutation could cause parents with genes for bright green coloration to have offspring with a gene for brown coloration. That would make the genes for brown beetles more frequent in the population.

 

Mechanisms of evolution (2 of 4) Migration
Some individuals from a population of brown beetles might have joined a population of green beetles. That would make the genes for brown beetles more frequent in the green beetle population.

 

Mechanisms of evolution (3 of 4) Genetic drift
Imagine that in one generation, two brown beetles happened to have four offspring survive to reproduce. Several green beetles were killed when someone stepped on them and had no offspring. The next generation would have a few more brown beetles than the previous generation — but just by chance. These chance changes from generation to generation are known as genetic drift.

 

Mechanisms of evolution (4 of 4) Natural selection
Imagine that green beetles are easier for birds to spot (and hence, eat). Brown beetles are a little more likely to survive to produce offspring. They pass their genes for brown coloration on to their offspring. So in the next generation, brown beetles are more common than in the previous generation.

 

Mechanisms of microevolution (1 of 4) Mutation
Some green genes randomly mutated to brown genes, causing brown coloration. However, since any particular mutation is rare, this process alone cannot account for a big change in allele frequency over one generation.

 

Mechanisms of microevolution (2 of 4) Migration
Some beetles with brown genes immigrated from another population, or some beetles carrying green genes emigrated.

 

Mechanisms of microevolution (3 of 4) Genetic drift
When the beetles reproduced, just by random luck more brown genes than green genes ended up in the offspring. In the diagram at right, brown genes occur slightly more frequently in the offspring (29%) than in the parent generation (25%).

 

Mechanisms of microevolution (4 of 4) Natural selection
Beetles with brown genes escaped predation and survived to reproduce more frequently than beetles with green genes, so that more brown genes got into the next generation.

 

Microevolution
Microevolution is evolution on a small scale — within a single population. That means narrowing our focus to one branch of the tree of life.

 

Microevolution - Change in gene frequency
Microevolution is a change in gene frequency in a population. Suppose you sample a beetle population this year, and determine that 80% of the genes in the population are for green coloration and 20% of them are for brown coloration. You go back the next year, repeat the procedure, and find a new ratio: 60% green genes to 40% brown genes. You have detected a microevolutionary pattern: a change in gene frequency. A change in gene frequency over time means that the population has evolved.

 

Microevolution - The size of the sparrow
Sparrow populations in the north are larger-bodied than sparrow populations in the south. This divergence in populations is probably at least partly a result of natural selection: larger-bodied birds can often survive lower temperatures than smaller-bodied birds can. Colder weather in the north may select for larger-bodied birds. As this map shows, sparrows in colder places are now generally larger than sparrows in warmer locales. Since these differences are probably genetically based, they almost certainly represent microevolutionary change: populations descended from the same ancestral population have different gene frequencies.

 

Microevolutionary change can accumulate into macroevolution
Over many generations, evolutionary processes that act at the population level can lead to macroevolutionary change.

 

Mitochondrial genes (1 of 2)
Mitochondria are passed from mother to child — your mitochondrial genes are a genetic gift from your mother alone. The genes in the nuclei of your cells (your nuclear genes) come from both parents.

 

Mitochondrial genes (2 of 2)
Nuclear DNA is inherited from all ancestors. Mitochondrial DNA is inherited from a single lineage.

 

Modes of speciation (1 of 4) Allopatric
New species formed from geographically isolated populations.

 

Modes of speciation (2 of 4) Peripatric
New species formed from a small population isolated at the edge of a larger population.

 

Modes of speciation (3 of 4) Parapatric
New species formed from a continuously distributed population.

 

Modes of speciation (4 of 4) Sympatric
New species formed from within the range of the ancestral population.

 

Mutation (1 of 4) Substitution
A substitution is a mutation that exchanges one base for another (i.e., a change in a single "chemical letter" such as switching an A to a G).

 

Mutation (2 of 4) Insertion
Insertions are mutations in which extra base pairs are inserted into a new place in the genes.

 

Mutation (3 of 4) Deletion
Deletions are mutations in which a section of genes is lost, or deleted.

 

Mutation (4 of 4) Frameshift
Since protein-coding genes is divided into codons three bases long, insertions and deletions can alter a gene so that its message is no longer correctly parsed. These changes are called frameshifts.

 

Mutation - DNA
When a cell divides, it makes a copy of its DNA — and sometimes the copy is not quite perfect. That small difference from the original DNA sequence is a mutation.

 

Natural selection (1 of 4) Variation
There is variation in traits. For example, some beetles are green and some are brown.

 

Natural selection (2 of 4) Differential reproduction
There is differential reproduction. Since the environment can't support unlimited population growth, not all individuals get to reproduce to their full potential. In this example, green beetles tend to get eaten by birds and survive to reproduce less often than brown beetles do.

 

Natural selection (3 of 4) Heredity
There is heredity. The surviving brown beetles have brown baby beetles because this trait has a genetic basis.

 

Natural selection (4 of 4) End result
End result: The more advantageous trait, brown coloration, which allows the beetle to have more offspring, becomes more common in the population. If this process continues, eventually, all individuals in the population will be brown.

 

Natural selection - Beetle example
Over the course of many generations, green beetles have been selected against, and brown beetles have flourished.

 

Natural selection in a test tube
How do biologists "evolve" RNA in a test tube? The same way that a population of organisms evolves in the real world: natural selection.

 

Neutral theory - Selection and drift on scale
The neutral theory of molecular evolution suggests that most of the genetic variation in populations is the result of mutation and genetic drift, not selection. The theory suggests that if a population carries several different versions of a gene, odds are that each of those versions is equally good at performing its job — in other words, that variation is neutral: whether you carry gene version A or gene version B does not affect your fitness.

 

Pace of evolution (1 of 3) Slow and steady
The preservation of many transitional forms, through layers representing a length of time, gives a complete record of slow and steady evolution.

 

Pace of evolution (2 of 3) Quick jumps
If evolution happens in "quick" jumps, we'd expect to see big changes happen quickly in the fossil record, with little transition between ancestor and descendent. Here, the descendent preserved in a layer directly after the ancestor, showing a big change in a short time, with no transitional forms.

 

Pace of evolution (3 of 3) Irregular fossil preservation
We expect to see a jump in the fossil record if evolution has occurred as a "quick" jump, but a jump in the fossil record can also be explained by irregular fossil preservation. This possibility can make it difficult to conclude that evolution has happened rapidly.

 

Pace of evolution hypotheses (1 of 4)
In many cases, we seem to observe "bursts" of evolution in the fossil record. In this example, in a lower rock layer, you see ancestor 1. In the next rock layer, you see species 2 and 3. Species 2 looks the same as ancestor 1. Species 3 is morphologically distinct, but is clearly also descended from ancestor 1. What happened?

 

Pace of evolution hypotheses (2 of 4)
Hypothesis 1: Phyletic gradualism - slow and steady divergence of lineages. The "burst" of evolution is a geological illusion. It only looks like a burst because a lot of time — say, 5 million years — passed between the times when the two rock layers were laid down. In this period of time, species 3 gradually diverged from ancestor 1 through a series of transitional forms, but these transitional forms were not preserved.

 

Pace of evolution hypotheses (3 of 4)
Hypothesis 2: Punctuated equilibrium — a large amount of change in a short time, tied to a speciation event. Species 2 and 3 are only 100,000 years younger than ancestor 1, and all the evolutionary change connecting them took place in this short time. The "burst" of evolution is really a burst. Transitional forms between ancestor 1 and species 3 did exist, but for such a short amount of time that they were not preserved in the fossil record.

 

Pace of evolution hypotheses (4 of 4)
Hypothesis 3: Macromutation — a big mutation produces sudden evolutionary change skipping over transitional forms. The "burst" of evolution is really a burst — there was a lot of evolutionary change in a very short amount of time. Species 3 was produced by a mutation that radically changed the offspring of ancestor 1 in many ways. Such extreme mutants are sometimes called "hopeful monsters." This hypothesis is consistent with the fossils; however, based on other observations, we do not have clear evidence that such extreme yet adaptive mutations generally occur. Nevertheless, it is possible that mutations affecting development have far-reaching phenotypic effects and have played an important role in the evolution of life.

 

Parsimony (1 of 5) Vertebrate character matrix
Character data for some major vertebrate lineages. Characters were limited to characters that are likely homologous (note that many vertebrate lineages and many characters were excluded from this example for the sake of simplicity).

 

Parsimony (2 of 5) Vertebrate ancestor characters
From studying fossils and lineages closely related to the vertebrate clade, we hypothesize that the ancestor of vertebrates had none of these features.

 

Parsimony (3 of 5) Amniotic egg clade and phylogeny
We focus in on the group of lineages that share the derived form of the egg character, an amniotic egg (A), and hypothesize that they form a clade (B.)

 

Parsimony (4 of 5) All clades and phylogeny
If we go through the whole table like this, grouping clades according to shared derived characters (C) we get the following hypothesis (D).

 

Parsimony (5 of 5) Comparison of two hypotheses
The parsimony principle tells us to choose the simplest scientific explanation that fits the evidence. Hypothesis 1 requires six evolutionary changes and Hypothesis 2 requires seven evolutionary changes, with a bony skeleton evolving independently, twice. Although both fit the available data, the parsimony principle says that Hypothesis 1 is better — since it does not hypothesize unnecessarily complicated changes.

 

Patterns in macroevolution (1 of 5) Stasis
Many lineages on the tree of life exhibit stasis, which just means that they don't change much for a long time.

 

Patterns in macroevolution (2 of 5) Character change
Lineages can change quickly or slowly. Character change can happen in a single direction, such as evolving additional segments, or it can reverse itself by gaining and then losing segments. Changes can occur within a single lineage or across several lineages. Lineage A changes rapidly but in no particular direction. Lineage B shows slower, directional change.

 

Patterns in macroevolution (3 of 5) Trilobite example
Trilobites, animals in the same clade as modern insects and crustaceans, lived over 300 million years ago. Their fossil record clearly suggests that several lineages underwent similar increases in segment number over the course of millions of years.

 

Patterns in macroevolution (4 of 5) Lineage splitting
Patterns of lineage-splitting (or speciation) can be identified by constructing and examining a phylogeny. The phylogeny might reveal that a particular lineage has undergone unusually frequent lineage-splitting, generating a "bushy" tuft of branches on the tree (Clade A, below). It might reveal that a lineage has an unusually low rate of lineage-splitting, represented by a long branch with very few twigs coming off (Clade B, below). Or it might reveal that several lineages experienced a burst of lineage-splitting at the same time (Clade C, below).

 

Patterns in macroevolution (5 of 5) Character change
Extinction can be a frequent or rare event within a lineage, or it can occur simultaneously across many lineages (mass extinction). Here, a mass extinction cuts short the lifetimes of many species, and only three survive.

 

Peripatric speciation (1 of 5)
Only a few fruit fly larvae survived the journey from the mainland to colonize the island.

 

Peripatric speciation (2 of 5)
These few survivors just by chance carry some genes that are rare in the mainland population. One of these rare genes happens to cause a slight variation in the mating dance. Another causes a slight difference in the shape of male genitalia. This is an example of the founder effect.

 

Peripatric speciation (3 of 5)
These small differences, which are rare on the mainland, drift to fixation in the small population on the island over the course of a few generations (i.e., the entire island population ends up having these genes).

 

Peripatric speciation (4 of 5)
As the island population grows, the unique reproductive features on the island result in a cascade of changes caused by sexual selection. These changes optimize, or at least improve, the fit of male and female genitalia to one another and female sensitivity to nuances of the mating ritual. Flies also experience natural selection that favors individuals better suited to the climate and food of the island.

 

Peripatric speciation (5 of 5)
After some generations, the island flies become reproductively isolated from the mainland flies. Peripatric speciation has occurred.

 

Phylogenies (1 of 3) Tree-like not ladder-like
Evolution produces a pattern of relationships A B C D among lineages that is tree-like, not ladder-like.

 

Phylogenies (2 of 3) Left to right
Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."

 

Phylogenies (3 of 3) Order doesn't matter
For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary. These phylogenies are equivalent.

 

Polytomy (1 of 3)
Often, one sees phylogenies that include polytomies, nodes with more than two descendent lineages, creating a "pitchfork."

 

Polytomy (2 of 3) Lack of knowledge
A polytomy may mean that we don't have enough data to figure out how the lineages are related. There are six possible solutions to this polytomy. Often, gathering more data can resolve a polytomy.

 

Polytomy (3 of 3) Rapid speciation
A polytomy may mean that multiple speciation events happened at the same time.

 

Punctuated equilibrium (1 of 8) Stasis
Stasis: A population of mollusks is experiencing stasis, living, dying, and getting fossilized every few hundred thousand years. Little observable evolution seems to be occurring judging from these fossils.

 

Punctuated equilibrium (2 of 8) Isolation
Isolation: A drop in sea level forms a lake and isolates a small number of mollusks from the rest of the population.

 

Punctuated equilibrium (3 of 8) Strong selection and rapid change
Strong selection and rapid change: The small, isolated population experiences strong selection and rapid change because of the novel environment and small population size: The environment in the newly formed lake exerts new selection pressures on the isolated mollusks. Also, their small population size means that genetic drift influences their evolution. The isolated population undergoes rapid evolutionary change. This is based on the model of peripatric speciation.

 

Punctuated equilibrium (4 of 8) No preservation
No preservation: No fossils representing transitional forms are preserved because of their relatively small population size, the rapid pace of change, and their isolated location.

 

Punctuated equilibrium (5 of 8) Reintroduction
Reintroduction: Sea levels rise, reuniting the isolated mollusks with their sister lineage.

 

Punctuated equilibrium (6 of 8) Expansion and stasis
Expansion and stasis: The isolated population expands into its past range. Larger population size and a stable environment make evolutionary change less likely. The formerly isolated branch of the mollusk lineage may out-compete their ancestral population, causing it to go extinct.

 

Punctuated equilibrium (7 of 8) Preservation
Preservation: Larger population size and a larger range move us back to step 1: stasis with occasional fossil preservation.

 

Punctuated equilibrium (8 of 8) This process would produce the following pattern in the fossil record
This process would produce the following pattern in the fossil record: Evolution appears to happen in sharp jumps associated with speciation events.

 

Recognizing homologies - Crocodile/mouse limb bones
The same bones (though differently shaped) support the limbs of mice and crocodiles. Homologous bones are colored alike.

 

Regulatory genes
Certain genes control where and when other genes are expressed.

 

Reproduction (1 of 6) Egg, sperm, and zygote
Eggs and sperm carry only half the usual number of chromosomes — just 23 unpaired chromosomes, carrying one version of each gene. When the egg and sperm get together, the baby receives the normal 23 matched pairs.

 

Reproduction (2 of 6) Chromosome duplication
When eggs and sperm are produced, the parent cell first copies each chromosome, leaving the duplicate pairs attached to one another.

 

Reproduction (3 of 6) Recombination
Producing eggs and sperm is our first opportunity for mixing and matching genes. When the mother makes an egg, her chromosomes first find their matched partners and exchange some genes with each other. That's called recombination. Because of this shuffling, genes from the mother's mom and genes from the mother's father can wind up next to one another on the same stretch of genes. (The same thing happens in the father's sperm.)

 

Reproduction (4 of 6) Meiosis, step one
Meiosis, step one

 

Reproduction (5 of 6) Meiosis, step two
Meiosis, step two

 

Reproduction (6 of 6) Zygote with recombinant genes
When egg and sperm meet, the baby inherits a combination of genes that is totally unique: it carries versions of genes from all 4 grandparents plus any mutations that occurred when the mother and father were making the egg and sperm.

 

Sampling error
Imagine a game in which you have a bag holding 100 marbles, 50 of which are brown and 50 green. You are allowed to draw 10 marbles out of the bag. Now imagine that the bag is restocked with 100 marbles, with the same proportion of brown and green marbles as you have just drawn out. The ratio of brown to green marbles "drifts" around (5:5, 6:4, 7:3, 4:6 …).

 

Sickle Cell (1 of 3) Genes
Sickle cell anemia is caused by a mutation at the genes level.

 

Sickle Cell (2 of 3) Protein
Normal hemoglobin (left) and hemoglobin in sickled red blood cells (right) look different; the mutation in the genes changes the shape of the hemoglobin molecule, allowing it to clump together.

 

Sickle Cell (3 of 3) Cell
Normal red blood cells (top) and sickle cells (bottom)

 

Speciation example (1 of 5)
The branching points on this partial Drosophila phylogeny represent speciation events that happened in the past.

 

Speciation example (2 of 5)
The scene: a population of wild fruit flies is minding its own business on several bunches of rotting bananas, cheerfully laying their eggs in the mushy fruit.

 

Speciation example (3 of 5)
Disaster strikes: A hurricane washes the bananas and the immature fruit flies they contain out to sea. The banana bunch washes up on an island off the coast of the mainland. The fruit flies mature and emerge onto the lonely island. The two portions of the population, mainland and island, are now too far apart for gene flow to unite them. At this point, speciation has not occurred — mainland and island fruit flies can mate and produce healthy offspring.

 

Speciation example (4 of 5)
The populations diverge: Ecological conditions are slightly different on the island, and the island population evolves under different selective pressures and experiences different random events than the mainland population does. Morphology, food preferences, and courtship displays change over the course of many generations of natural selection.

 

Speciation example (5 of 5)
So we meet again: When another storm reintroduces the island flies to the mainland, they will not readily mate with the mainland flies since they've evolved different courtship behaviors. The few that do mate with the mainland flies, produce inviable eggs because of other genetic differences between the two populations. The lineage has split now that genes cannot flow between the populations.

 

Stomata (1 of 3) Function
Carbon dioxide enters, while water and oxygen exit, through a leaf's stomata. Stomata control a tradeoff for the plant: they allow carbon dioxide in, but they also let precious water escape.

 

Stomata (2 of 3) Tradeoff
Levels of carbon dioxide in Earth's atmosphere change over time — so at times when the atmosphere is carbon-dioxide-rich, plants can get away with having fewer stomata since each individual stoma will be able to bring in more carbon dioxide. During those high-carbon-dioxide times, plants with fewer stomata will have an advantage and will be common. On the other hand, when carbon dioxide levels are low, plants need many stomata in order to scrape together enough carbon dioxide to survive. During low-carbon-dioxide times, plants with more stomata will have an advantage and will be common.

 

Stomata (3 of 3) Indicators of CO2 and temperature
Stomata of fossil plants can be used to directly estimate past carbon dioxide levels, and those carbon dioxide levels can then be used to make an indirect estimate of temperature. Typically (although there are exceptions to the rule), fossils with many stomata (low carbon dioxide) came from times of low global temperature, and fossils with few stomata (high carbon dioxide) came from times of high global temperatures.

 

Three domains
The three domains: Archaea, Bacteria, and Eukaryota.

 

Timeline of human evolution
Important events in human history, with approximate dates, which reflect the evidence currently available

 

Transitional forms - whale evolution
Transitional forms in whale evolution, highlighting the transition of the walking forelimb to the flipper.

 

Understanding phylogenies (1 of 4)
Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendents of that ancestor. As you move from the root to the tips, you are moving forward in time.

 

Understanding phylogenies (2 of 4)
When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.

 

Understanding phylogenies (3 of 4)
Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.

 

Understanding phylogenies (4 of 4)
Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

 

Vertebrate phylogeny - Amphibia, synapsida, sauropsida
Vertebrate phylogeny

 

Vertebrate phylogeny with characters
Evolutionary relationships of major vertebrate groups.

 

Vertebrate phylogeny with time
This phylogeny represents vertebrate evolution. The lengths of the branches have been adjusted to show when lineages split and went extinct.

 

Virus evolution and virulence
There is an evolutionary trade off between virus virulence and virus transmission. A virulent virus does a lot of damage to its host, and produces a lot of offspring. However, if the host's illness prevents the host from coming into contact that new hosts that the virus could jump to, the virus actually has relatively low evolutionary fitness. In contrast, a virus that is less virulent could infect far more hosts because the hosts are well enough to come in contact with many other potential hosts.