Unit 7 Beta

Natural Selection: the one-page sheet

7.1 Introduction to Natural Selection

Natural selection is a main mechanism of evolution, proposed independently by Charles Darwin and Alfred Russel Wallace. Individuals in a population differ, and some of the differences are heritable. Populations produce more offspring than resources can support, so individuals compete and many die before reproducing. Those whose heritable traits suit the current environment survive and reproduce more, so their alleles become more common in the next generation; repeated over many generations, the population changes. Fitness is measured by reproductive success, the number of offspring that survive to reproduce, and relative fitness compares types with the most successful one. A selective pressure is the feature of the environment that causes these differences. Selection acts on individuals and on variation that already exists; populations, not individuals, evolve.

Natural selection needs three things: heritable variation in a trait, more offspring than can survive, and differences in survival or reproduction linked to that trait.
Charles Darwin and Alfred Russel Wallace proposed it independently (1858); Darwin called evolution descent with modification.
Fitness is reproductive success: the number of offspring that survive to reproduce, not strength or lifespan. Relative fitness = a type's offspring ÷ the best type's offspring.
A selective pressure is a feature of the environment, such as a predator, drought or disease, that makes some heritable traits leave more offspring than others.
Selection acts on individuals, but a population is what evolves, and it can only act on variation that already exists.

The population carries heritable variation: offspring tend to resemble their parents in these traits. Individuals compete for limited resources and face predators, disease and harsh weather, so many die before they reproduce. Individuals with those traits leave more surviving offspring than others: differential reproductive success. The next generation has a higher proportion of individuals with the helpful trait than the last one. The population's makeup changes over time: evolution by natural selection. Individuals do not change their inherited traits; the proportions in the population do.

Charles Darwin: Charles Darwin (1809-1882) and Alfred Russel Wallace (1823-1913) each worked out the idea of evolution by natural selection; their papers were presented together in 1858, and Darwin's book On the Origin of Species followed in 1859. Darwin called evolution descent with modification: living species descend from earlier ones and have changed over many generations.
population: A group of individuals of the same species that live in the same area at the same time and can breed with one another. Populations, not individuals, are what evolve.
heritable variation: Differences among individuals in a trait that are at least partly caused by differences in their alleles, so offspring tend to resemble their parents. Natural selection can change a trait only if the variation is heritable.
overproduction of offspring: Populations produce more offspring than the environment can support, so many individuals die before they reproduce.
competition (ecology): In ecology, the struggle among individuals for the same limited resources, such as food, water, space, light or mates. Because resources are limited, not every individual survives and reproduces.
differential reproductive success: Differences among individuals in how many surviving offspring they leave. Individuals with heritable traits better suited to the current environment tend to leave more, so their alleles become more common.
natural selection: The process in which individuals with certain heritable traits survive and reproduce more than others in a particular environment, so those traits become more common in the population over generations. It is a main mechanism of evolution.
fitness: An individual's contribution of offspring to the next generation: the number of its offspring that survive to reproduce. Relative fitness compares this number with that of the most successful type in the population (set to 1).
selective pressure: Any feature of the environment that makes individuals with some heritable traits survive or reproduce better than others, such as a predator, a drought, a disease or a cold winter.

7.2 Natural Selection

Environments change, and whether a trait is favorable depends on the environment of the moment: peppered moths went from mostly pale to mostly dark as soot darkened trees, and back as the air cleaned. The phenotypic variation that selection acts on is rooted in molecular and cellular variation, such as proteins that differ by an amino acid or are made in different amounts. Selective pressures can be biotic or abiotic. On traits with many values, selection can be directional (shifting the mean), stabilizing (favoring the middle and reducing variation) or disruptive (favoring both extremes). Sexual selection favors traits that increase mating success, and in frequency-dependent selection a phenotype's success depends on how common it is. Over generations, natural selection changes the makeup of a population.

Whether a trait is favorable depends on the environment. An adaptive trait raises fitness in a particular setting; the same trait can be harmful elsewhere.
Phenotypic variation comes from molecular variation: differences in proteins and how cells work, such as hemoglobin that loads oxygen better in thin mountain air.
Selective pressures can be biotic (predators, parasites, competitors, mates) or abiotic (temperature, drought, salinity). Camouflage is favored where predators hunt by sight.
Directional selection shifts the mean; stabilizing selection narrows variation around the middle; disruptive selection favors both extremes.
Sexual selection favors traits that win mates, even at a cost to survival. In frequency-dependent selection, a phenotype's fitness depends on how common it is.

Individuals differ in phenotype: dark or pale wings, deeper or shallower beaks, hemoglobin that binds oxygen more or less tightly. A favorable trait is favorable only in a particular environment: pale moths on lichen, dark moths on soot. The alleles behind that phenotype become more common in the next generation. The trait's distribution shifts (directional), narrows (stabilizing) or splits (disruptive). A different phenotype becomes favorable and selection reverses: the population tracks its changing environment, generation by generation.

adaptive trait: A heritable trait that increases survival or reproduction in a particular environment, and so has become common through natural selection. A trait is adaptive only relative to an environment.
favorable trait: A favorable trait helps its carriers survive or reproduce better than others in the current environment. Whether a trait is favorable depends on the environment, so it can change when the environment changes.
phenotypic variation: Differences in observable traits among individuals in a population, from body size and color to enzyme activity. Selection acts on phenotypes; it changes a population only when the variation is at least partly heritable.
molecular variation: Differences among individuals in their molecules, such as proteins with slightly different amino acid sequences or different amounts of an enzyme, and in how their cells work. These differences underlie phenotypic variation and so affect fitness.
directional selection: Three patterns of selection on a trait with many values. Directional selection favors one extreme and shifts the mean. Stabilizing selection favors intermediate values and reduces variation. Disruptive (diversifying) selection favors both extremes over the middle and increases variation.
sexual selection: Selection on traits that increase mating success: through mate choice (members of one sex, often females, prefer certain traits) or through competition within one sex for mates. It can produce sexual dimorphism, differences in appearance between males and females.
peppered moth: A European moth whose dark form became common in sooty industrial areas of 19th-century Britain, where pale moths on darkened bark were easier for birds to find, and became rare again after air pollution was cut. The rise of dark moths is called industrial melanism.
frequency-dependent selection: Selection in which a phenotype's fitness depends on how common it is. When rare forms have the advantage, no form can take over, and several forms persist side by side.
biotic factor: Biotic factors are the living parts of an environment (predators, parasites, competitors, food organisms); abiotic factors are the nonliving parts (temperature, water, light, salinity, soil). Either can act as a selective pressure.
camouflage: Coloring or shape that makes an organism hard to see against its usual background, such as a pale moth on lichen-covered bark. Camouflage is favored where predators hunt by sight.

7.3 Artificial Selection

In artificial selection, humans choose which individuals breed according to traits they want, so those traits become more common or more extreme over generations. It needs heritable variation, just as natural selection does, and has produced domesticated animals and crops: dogs from wolves, corn from teosinte, and cabbage, kale, broccoli and other crops from one wild mustard. Selection on one trait can change others controlled by the same genes, and progress slows as heritable variation is used up. Human activity also causes unintended selection. Antibiotics kill susceptible bacteria and leave cells that carry resistance alleles, from random mutation or gene transfer, to multiply, so infections become resistant. Heavy fishing of large fish and poaching for ivory have selected for fish that mature small and elephants without tusks.

In artificial selection (selective breeding), humans decide which individuals reproduce; in natural selection, the environment does. Both act on heritable variation and change populations over generations.
Domestication through artificial selection gave dogs from wolves, corn from teosinte and six crops from one wild mustard. It can only use the variation that exists, and traits can change together when the same genes affect them.
Antibiotic resistance is unintended selection: random mutations or transferred genes make a few cells resistant, the drug kills the rest, and the survivors multiply. MRSA is an example.
Other unintended selection: fishing that removes large fish favors fish that mature small and young; poaching for ivory favors elephants born without tusks.

Breeders can tell individuals apart and pick out those with the most of the trait they want. Only the chosen individuals' alleles reach the next generation, so the trait is more common, or more extreme, in their offspring. Large changes build up, as in dog breeds, corn and the cabbage family, until little heritable variation in the trait remains. Individuals that happen to carry alleles for surviving the change, such as resistant bacteria, leave more offspring: unintended selection. The infection becomes mostly resistant, and the drug stops working against it.

artificial selection: Selective breeding: humans choose which individuals reproduce, based on traits they want, so those traits become more common or more extreme over generations. It works on heritable variation, like natural selection, but people rather than the environment decide who breeds.
domestication: The change of a wild population into one adapted to living with and being used by people, through generations of artificial selection, as dogs came from wolves and corn from a wild grass called teosinte.
antibiotic resistance: The ability of bacteria to survive an antibiotic that kills or stops the growth of most cells of their kind. It comes from random mutations or genes received from other bacteria, and spreads because the antibiotic kills susceptible cells and leaves resistant ones to multiply. MRSA (methicillin-resistant Staphylococcus aureus) is an example.
unintended selection: Selection caused by human activity that nobody intended, such as antibiotic use favoring resistant bacteria, fishing that removes the largest fish favoring fish that mature young and small, or poaching for ivory favoring elephants without tusks.

7.4 Population Genetics

A population's gene pool is all its alleles, and an allele's frequency is its share of all copies of that gene; a change in allele frequencies over generations is microevolution. Mutation supplies new alleles. Genetic drift changes allele frequencies at random, because which individuals breed and which alleles they pass on is partly chance; it is strongest in small populations, where alleles can be lost or fixed quickly whatever their effect on fitness. The bottleneck effect (after a population crashes) and the founder effect (when a few individuals start a new population) are drift in action. Gene flow moves alleles between populations, making them more alike. Nonrandom mating, such as inbreeding, raises the share of homozygotes without changing allele frequencies by itself. Small populations lose genetic variation, which makes them less able to respond to environmental change.

A gene pool is all the alleles in a population. Allele frequency = copies of that allele ÷ all copies of the gene; for diploids, (2 × AA + Aa) ÷ (2 × N). Microevolution is a change in allele frequencies.
Mutation is the source of new alleles; it is slow but supplies all variation.
Genetic drift is random change in allele frequencies, strongest when population size is small. The bottleneck effect and founder effect are drift after a crash or a new start.
Gene flow (immigration and emigration of alleles) makes populations more alike and can add alleles. Nonrandom mating such as inbreeding raises homozygosity without, by itself, changing allele frequencies.
Drift in small populations causes loss of genetic variation, which leaves a population less able to adapt when its environment changes.

Evolution can be measured as a change in allele frequencies from one generation to the next: microevolution. The gene pool gains variation that other processes can act on. Allele frequencies change by chance from generation to generation: genetic drift. Drift is strongest in small populations, where alleles can be lost or fixed within a few generations, whatever their effect on fitness. Small, isolated populations lose genetic variation and become less able to respond to change; gene flow restores variation and makes populations more alike.

gene pool: All the alleles of every gene in a population at one time. Evolution is a change in the gene pool.
allele frequency: The proportion of all copies of a gene in a population that are one particular allele. In diploids, count two copies per individual: frequency of A = (2 × AA + Aa) ÷ (2 × total individuals). The frequencies of all alleles of a gene add up to 1.
population size: The number of individuals in a population, or, for genetics, the number that breed. The smaller the breeding population, the larger the random changes in allele frequencies from one generation to the next.
microevolution: A change in allele frequencies in a population from one generation to the next. Natural selection, genetic drift, gene flow and mutation all cause it.
genetic drift: Random change in allele frequencies from one generation to the next, because which individuals happen to survive and reproduce, and which alleles go into the gametes that form offspring, is partly a matter of chance. Drift is strongest in small populations and can fix or lose alleles regardless of their effect on fitness.
bottleneck effect: Genetic drift that follows a sharp, sudden drop in population size, from a disaster, disease or hunting. The few survivors carry only some of the original alleles, so the population that grows from them has less genetic variation and different allele frequencies.
founder effect: Genetic drift that occurs when a few individuals start a new population, as on an island. The founders' alleles are a small, chance sample of the source population, so the new population can have very different allele frequencies, including rare alleles made common.
gene flow: Movement of alleles from one population to another when individuals or their gametes (such as pollen) move between them and breed: immigration brings alleles in, emigration takes them out. Gene flow makes populations more alike and can bring in new alleles.
new alleles: Mutation is the source of new alleles in a population. Each gene mutates rarely, but across many genes and individuals new alleles arise every generation, providing the variation that selection and drift act on.
nonrandom mating: Mating in which partners are not chosen at random with respect to genotype: inbreeding (mating with relatives, or self-fertilization) and assortative mating (choosing partners with similar phenotypes). It increases the proportion of homozygotes without, by itself, changing allele frequencies.
loss of genetic variation: A drop in the number of alleles, or in the proportion of heterozygotes, in a population, caused by drift in small populations, bottlenecks, founder events or strong selection. A population with little genetic variation is less able to respond to changes in its environment.

7.5 Hardy-Weinberg Equilibrium

Hardy-Weinberg equilibrium describes a population that is not evolving: its allele and genotype frequencies stay the same from generation to generation. For a gene with alleles at frequencies p and q, p + q = 1, and random union of gametes gives genotype frequencies p² (AA), 2pq (Aa) and q² (aa), which add to 1; the gametes those offspring make carry the alleles at p and q again, whatever the dominance. Equilibrium requires a very large population, no gene flow, no net mutation, random mating and no natural selection. Because real populations rarely meet every condition, the equations serve as a null hypothesis: when observed frequencies differ from the expected ones by more than chance, at least one condition fails, and the pattern of the difference points to the cause.

Hardy-Weinberg equilibrium: allele and genotype frequencies stay constant across generations in a population that is not evolving. It is the null model for evolution.
p + q = 1 for alleles; p² + 2pq + q² = 1 for genotypes (AA, Aa, aa). Only q² can be read straight from phenotypes when a is recessive.
Five Hardy-Weinberg conditions: very large population, no gene flow, no net mutation, random mating, no natural selection.
A deviation from Hardy-Weinberg means a condition fails. Too few heterozygotes suggests inbreeding or self-fertilization; frequencies shifting over generations suggest selection, drift or gene flow.
Dominance does not make an allele more common. Selection against a rare recessive allele is slow, because most of its copies are hidden in heterozygotes.

The chance that a zygote gets two A gametes is p × p, two a gametes q × q, and one of each 2pq (A from the egg and a from the sperm, or the reverse). AA = p², Aa = 2pq, aa = q², and p² + 2pq + q² = (p + q)² = 1. The new gamete pool has A at p² + pq = p and a at q: allele frequencies are unchanged, whatever the dominance. This is Hardy-Weinberg equilibrium. Allele frequencies, genotype frequencies or both move away from the equilibrium values. A difference too large for chance shows that at least one condition is not met, and the kind of difference hints at which one.

Hardy-Weinberg equilibrium: The state of a population whose allele and genotype frequencies stay the same from generation to generation, because none of the processes that cause evolution is acting. Worked out independently by G. H. Hardy and Wilhelm Weinberg in 1908, it is the baseline against which evolution is measured.
Hardy-Weinberg equations: For a gene with two alleles at frequencies p and q: p + q = 1 (all alleles) and p² + 2pq + q² = 1 (all genotypes), where p² is the frequency of homozygous dominant individuals, 2pq of heterozygotes and q² of homozygous recessive individuals, in a population at equilibrium.
genotype frequency: The proportion of individuals in a population that have a particular genotype, such as AA, Aa or aa. The genotype frequencies of a gene add up to 1.
Hardy-Weinberg conditions: The five conditions for Hardy-Weinberg equilibrium: a very large population (no genetic drift), no gene flow, no net mutation, random mating, and no natural selection. Each rules out one process that can change allele or genotype frequencies.
deviation from Hardy-Weinberg: A difference between observed allele or genotype frequencies and those Hardy-Weinberg predicts, too large to be due to chance (often judged with a chi-square test). It shows that at least one condition is not met: the population may be evolving, or mating nonrandomly.

7.6 Evidence of Evolution

Several independent kinds of evidence show that living species descend, with modification, from earlier ones. The fossil record, put in order by relative dating (lower layers are older) and given ages by radiometric dating (isotopes decay with fixed half-lives), shows life changing over time, many extinctions, and transitional fossils. Homologous structures, such as the forelimb bones of humans, cats, whales and bats, reveal a shared plan inherited from a common ancestor; vestigial structures are reduced remnants of ancestral ones; and vertebrate embryos share features such as pharyngeal arches. Analogous structures, produced by convergent evolution, look alike without shared ancestry. Biogeography shows species resembling their nearest neighbors in space. Molecular evidence, the similarity of DNA and protein sequences, matches these patterns: the more recently two species shared an ancestor, the more alike their sequences.

The fossil record, ordered by relative dating (lower strata are older) and radiometric dating (decay at a known half-life), shows change over time, extinction and transitional fossils.
Homologous structures share an inherited plan despite different uses. Analogous structures share a function but arose separately, by convergent evolution.
Vestigial structures, such as whale hip bones, are reduced leftovers of structures that were fully developed in ancestors.
Comparative embryology: all vertebrate embryos form pharyngeal arches. Biogeography: island species resemble those of the nearest mainland.
Molecular homology: species with a more recent common ancestor have more similar DNA and amino acid sequences.

Fossils form, and lower layers hold older fossils (relative dating); radioactive isotopes in volcanic layers give ages in years (radiometric dating). The fossil record shows life changing over time: most species that lived are extinct, and transitional fossils link older and later groups. Homologous structures (one bone plan in arms, legs, flippers and wings), vestigial structures and shared embryo features appear across related species. Convergent evolution produces analogous structures that look alike but are built differently, which is why anatomy must be read with care. The more recent their common ancestor, the more similar their DNA and protein sequences: molecular evidence that matches the fossils and anatomy.

extinction: The death of the last member of a species. The fossil record shows that most species that ever lived are extinct; mass extinctions are short periods in which a large share of species disappeared worldwide, as at the end of the Cretaceous period about 66 million years ago.
fossil record: All fossils found so far, placed in order of age. Fossils are remains or traces of past organisms, usually preserved in sedimentary rock. The record is incomplete but shows life changing over time, including transitional fossils with features of both an older and a later group.
relative dating: Ordering rocks and fossils by age without giving years. By the law of superposition, in undisturbed layers (strata) of sedimentary rock, lower layers formed earlier than the layers above them.
radiometric dating: Finding the age of rock or remains from the decay of radioactive isotopes, which change into other elements at a constant rate. The half-life is the time for half of the original isotope to decay; carbon-14 (half-life about 5,730 years) dates recent remains, and isotopes with long half-lives date volcanic layers millions of years old.
homologous structure: A structure shared by different species because they inherited it from a common ancestor, even if it now has different uses, such as the forelimb bones of humans, cats, whales and bats.
convergent evolution: The independent evolution of similar traits in groups that are not closely related, because similar environments or ways of life favored similar solutions, such as the streamlined bodies of sharks and dolphins.
analogous structure: A structure with a similar function, and often a similar form, in different species that did not inherit it from a common ancestor; it is a product of convergent evolution, such as the wings of insects and birds.
vestigial structure: A structure that is reduced and has lost most or all of its ancestral function, such as the small hip bones of whales or the eyes of blind cave fish. Vestigial structures make sense as leftovers from ancestors in which they were fully developed.
comparative embryology: Comparing embryos of different species. Vertebrate embryos all develop pharyngeal arches (and pouches between them) in the neck region, which become gills in fish but parts of the jaw, ear and throat in mammals: evidence of shared ancestry.
biogeography: The study of where species live. Patterns such as island species resembling those on the nearest mainland, and similar environments on different continents holding unrelated species, are explained by species arising from ancestors that lived nearby.
molecular homology: Similarities in DNA and protein sequences among species. Because sequence differences build up over time after two groups separate, species that share a more recent common ancestor have more similar sequences.

7.7 Common Ancestry

Every living thing stores its genes in DNA, reads them with a nearly universal genetic code on ribosomes, powers its work with ATP, is bounded by a plasma membrane and runs core pathways such as glycolysis. These shared features were inherited from the last universal common ancestor (LUCA), the most recent population all life descends from. They stay nearly the same because almost any change to them is harmful and is removed by natural selection; genes that change this slowly are called conserved. Eukaryotes also share a nucleus, membrane-bound organelles, linear chromosomes and introns, inherited from a later ancestor of all eukaryotes. Life is grouped into three domains, Bacteria, Archaea and Eukarya, and Archaea share more features with eukaryotes than with Bacteria. Small exceptions, such as a few reassigned codons in mitochondria, are changes made after the shared start, not separate origins.

Universal features of life: DNA, a nearly universal genetic code, ribosomes, ATP, a plasma membrane, and core pathways such as glycolysis. They were present in LUCA, the last universal common ancestor.
Eukaryotes also share a nucleus, membrane-bound organelles, linear chromosomes and genes with introns, inherited from a later shared ancestor.
Life falls into three domains: Bacteria, Archaea and Eukarya. Archaea share histones and a complex RNA polymerase with eukaryotes, so they are closer to us than to Bacteria.
Conserved genes change slowly because selection removes most changes to essential proteins, not because they mutate less.

LUCA already stored information in DNA, read it with the genetic code on ribosomes, used ATP and was wrapped in a membrane, and its descendants inherited all of these. Almost any change to them, such as reassigning a codon, harms many proteins at once and lowers fitness. The systems stay nearly the same in Bacteria, Archaea and Eukarya, and the genes for them are conserved. All of its descendants, the eukaryotes, share these features too, which points to a more recent ancestor of all eukaryotes. The pattern is what common ancestry predicts: groups that share more features share a more recent ancestor.

universal features of life: Features found in every living thing: DNA as the genetic material, a nearly universal genetic code, ribosomes that make proteins, ATP as the energy carrier, a plasma membrane and core pathways such as glycolysis. They point to one shared ancestor of all life.
shared eukaryotic features: Features found together in all eukaryotes and in no prokaryote: a nucleus, membrane-bound organelles such as mitochondria, linear chromosomes, genes interrupted by introns that are spliced out, and a cytoskeleton. They point to one shared ancestor of all eukaryotes.
last universal common ancestor: The last universal common ancestor (LUCA): the most recent population of cells from which every organism alive today descends. It was not the first life; it already had DNA, the genetic code, ribosomes and ATP.
three domains: The three largest groups of life: Bacteria, Archaea and Eukarya. Bacteria and Archaea are prokaryotes; Eukarya are the eukaryotes. Archaea share more features with Eukarya (histones, a complex RNA polymerase) than with Bacteria.
conserved gene: A gene whose sequence has changed very little over long spans of time, so its versions in distantly related organisms are still alike. Its product does a job so central that most changes lower fitness and are removed by natural selection.

7.8 Continuing Evolution

Evolution continues today because environments keep changing, and it can be observed directly as changes in allele frequencies and genomes over generations. Antibiotics, insecticides and herbicides select for resistance alleles that arose by random mutation before the chemical was used, so resistance spreads within years; when a resistance allele carries a cost, it can decline slowly once the chemical is withdrawn. Viruses evolve especially fast because they copy their genomes with many errors, in huge numbers and with short generations: immunity favors new flu variants, so vaccines are updated yearly, and HIV is treated with several drugs at once because a particle resistant to all of them is very unlikely to arise. In coevolution, two species are each other's selective pressures, as in the arms race between a toxic newt and a resistant snake. Long-term experiments and genome sequencing show mutations, duplications and other genomic changes accumulating and spreading as populations adapt.

Continuing evolution: populations keep evolving because environments keep changing. It can be measured now, in allele frequencies and genomes.
Antibiotic and pesticide resistance: resistance alleles exist before the chemical is used; the chemical selects for them. Resistance often carries a cost, so it may fall slowly when the chemical stops.
Viruses evolve fast: error-prone copying, huge numbers and short generations. Immunity and drugs select new variants, so flu vaccines are updated yearly and HIV is treated with several drugs at once.
Coevolution: two species exert selective pressure on each other, as in an evolutionary arms race. Genomic changes, from point mutations to gene duplications, can be tracked by sequencing.

Before any chemical is used, a few individuals already carry resistance alleles. Susceptible individuals die or reproduce less, while carriers of resistance alleles survive and reproduce. The resistance allele's frequency rises, often within a few years, because pests and microbes have short generations and huge numbers. Each evolves in response to the other (coevolution), so the arms race keeps going. Evolution continues, and scientists can measure it directly as changes in allele frequencies and genomes over time.

continuing evolution: Continuing (ongoing) evolution: populations keep evolving because their environments keep changing. It can be measured directly today, as changes in allele frequencies or genomes over generations, in pathogens, pests, crops and wild populations.
pesticide resistance: The evolution of pests that survive a chemical meant to kill them, such as insects resistant to an insecticide (DDT, pyrethroids) or weeds resistant to a herbicide. Resistance alleles arise by chance before use; the chemical selects for them, so they rise in frequency.
viral evolution: Change in virus populations over time. Fast copying with many errors and huge numbers of particles produce new variants quickly; immunity and drugs select among them, giving new flu strains each year, drug resistance in HIV and emerging viruses that spread to new hosts.
coevolution: Evolution in two species in which each acts as a selective pressure on the other, so a change in one favors a change in the other, as in a toxic newt and the resistant snake that eats it (an evolutionary arms race) or a flower and its pollinator.
genomic change: Change in a population's DNA that can be measured directly over time by sequencing: new point mutations, gene duplications, deletions and rearrangements that accumulate and spread across generations.

7.9 Phylogeny

A phylogenetic tree is a hypothesis about evolutionary relationships. Tips are living or extinct taxa, branches are lines of descent, and each node is the most recent common ancestor of everything beyond it; the root is the ancestor of the whole tree. Two taxa are more closely related the more recent the node where their lines meet, so trees are read at the nodes, not by the order of the tips, which can be rotated freely. A clade is an ancestor and all of its descendants. Cladograms are built from shared derived characters, traits that arose in a group's ancestor, while shared ancestral characters, inherited from older ancestors, cannot sort a group; an outgroup shows which states are ancestral. Of the trees that fit the data, maximum parsimony prefers the one needing the fewest changes. DNA and protein differences give many more characters than body form and, calibrated with fossils, act as a molecular clock to date splits. Trees are revised when new evidence appears, and classification aims to name groups that are clades.

A phylogenetic tree shows hypothesized relationships. Each node is a common ancestor; sister taxa share a node no one else shares. The more recent the shared node, the closer the relationship.
A clade is an ancestor and all its descendants. Shared derived characters mark clades; shared ancestral characters do not. The outgroup shows which states are ancestral.
Read nodes, not tip order: branches can rotate freely, and every living tip has evolved for equally long. No living organism is the ancestor of another.
Maximum parsimony prefers the tree with fewest changes. A molecular clock, calibrated with fossils, dates splits. DNA data are often more reliable than body form, and trees are revised with new evidence.

Each line accumulates its own mutations and adaptations, so the two diverge; on a tree, the split is a node with two branches. Every descendant of that line inherits it (unless it is later lost), so the trait becomes a shared derived character of that group. Taxa that share more derived characters are grouped as having a more recent common ancestor, and the groups nest inside each other as clades. By maximum parsimony, biologists prefer the tree with the fewest changes, and they check it against DNA data, where differences build up roughly in proportion to time. The tree is revised: every tree is a hypothesis about evolutionary history, not a final answer.

divergent evolution: Divergent evolution: the accumulation of differences between groups that descend from a common ancestor, as their lines split and adapt to different conditions. Homologous structures, such as the forelimbs of bats, whales and humans, are its signature.
phylogeny: The evolutionary history of a group of organisms: which lines split from which, and in what order, showing their evolutionary relationships.
phylogenetic tree: A phylogenetic tree: a branching diagram showing hypothesized evolutionary relationships. Tips are taxa, branches are lines of descent, and each node is a common ancestor. Some trees scale branch lengths to time or amount of change.
node: A branch point on a phylogenetic tree, representing the most recent common ancestor of everything that branches from it. The node at the base of the whole tree is the root.
clade: A group made of one ancestor and all of its descendants (a monophyletic group). A group that leaves out some descendants of its common ancestor, such as reptiles without birds, is not a clade.
sister taxa: Two taxa (groups or species) that share a common ancestor, a node, that no other taxon on the tree shares; each is the other's closest relative on the tree.
shared derived character: A shared derived character: a trait that arose in the most recent common ancestor of a group and is shared by its descendants but not by the outgroup. Shared derived characters mark clades.
shared ancestral character: A shared ancestral character: a trait that a group inherited from an ancestor older than the group, so its members and the outgroup share it. It cannot be used to sort members of the group.
cladogram: A tree built from shared derived characters, showing only the order of branching. Branch lengths carry no meaning about time or amount of change.
outgroup: A taxon known to lie outside the group being studied (the ingroup). Character states it shares with the ingroup are taken as ancestral, which shows which states are derived.
maximum parsimony: Maximum parsimony: the principle of preferring the tree that needs the fewest evolutionary changes (gains or losses of characters, or sequence changes) to explain the data.
molecular clock: A method of estimating when lines split from the number of DNA or protein differences between them, assuming differences build up at a roughly constant rate that has been calibrated with dated fossils.
tree as hypothesis: The idea that a phylogenetic tree is a hypothesis about evolutionary relationships, tested and revised as new molecular, fossil or anatomical evidence appears.
taxonomy: The science of naming and classifying organisms. Each species gets a two-part (binomial) name, genus then species, such as <i>Homo sapiens</i>, and is placed in nested ranks: domain, kingdom, phylum, class, order, family, genus, species.

7.10 Speciation

By the biological species concept, a species is a group of populations whose members can interbreed and produce fertile offspring; for fossils and asexual organisms, body form (the morphological species concept) is used instead. Speciation happens when populations become reproductively isolated. Prezygotic barriers prevent mating or fertilization: habitat, temporal, behavioral, mechanical and gametic isolation. Postzygotic barriers act after a hybrid zygote forms: hybrid inviability, hybrid sterility and hybrid breakdown. In allopatric speciation a geographic barrier stops gene flow, and mutation, drift and different selective pressures drive the separated gene pools apart until barriers evolve. In sympatric speciation isolation arises in one place, as when polyploidy makes a plant's offspring unable to breed with the parent population. Where related populations meet in a hybrid zone, selection against unfit hybrids can strengthen barriers (reinforcement). Speciation may be gradual or happen in bursts separated by long stasis (punctuated equilibrium), and an adaptive radiation produces many species that fill open niches.

Biological species concept: a species is a group that can interbreed and produce fertile offspring. Speciation happens when populations become reproductively isolated.
Prezygotic barriers stop mating or fertilization: habitat, temporal, behavioral, mechanical, gametic. Postzygotic barriers act on hybrids: inviability, sterility, breakdown.
Allopatric speciation starts with a geographic barrier; sympatric speciation happens in one place, often by polyploidy in plants.
Speciation can be gradual or come in bursts (punctuated equilibrium). Adaptive radiation: many species from one ancestor fill open niches. These patterns are macroevolution.

Gene flow between the two parts stops. Allele frequencies in the two gene pools change in different directions. Reproductive barriers arise, prezygotic ones that block mating or fertilization and postzygotic ones that make hybrids die or be sterile. They are now separate species, reproductively isolated by the biological species concept: allopatric speciation. A new species forms in the same place (sympatric speciation), sometimes in one generation.

niche: A species' niche is its role and way of life: the conditions it tolerates, the resources it uses and how it gets them. Open niches, such as unused foods on new islands, give room for new species to form.
species: By the biological species concept, a group of populations whose members can interbreed in nature and produce viable, fertile offspring, and that cannot do so with other groups. The morphological species concept, based on body form, is used for fossils and asexual organisms.
reproductive isolation: The condition in which barriers prevent two populations from interbreeding and producing fertile offspring, so no gene flow passes between them and their gene pools stay separate.
speciation: The formation of new species: one population splits into two (or more) that become reproductively isolated from each other.
prezygotic barrier: A reproductive barrier that acts before a zygote forms, by preventing mating or fertilization: habitat, temporal, behavioral, mechanical or gametic isolation.
postzygotic barrier: A reproductive barrier that acts after a hybrid zygote forms: hybrid inviability (the hybrid dies young), hybrid sterility (the hybrid adult is sterile, like a mule) or hybrid breakdown (later hybrid generations are weak or sterile).
allopatric speciation: Allopatric speciation: speciation that begins when a geographic barrier, such as a river, mountain range or stretch of sea, divides a population, stopping gene flow so the parts evolve separately.
sympatric speciation: Sympatric speciation: speciation without geographic separation, within one area. In plants it often happens by polyploidy; in animals it can follow a shift to a new food source or habitat in the same place.
punctuated equilibrium: Punctuated equilibrium: the pattern in which species change little for long periods (stasis) and change rapidly over short periods, often around speciation. The contrasting pattern of slow, steady change is called gradualism.
adaptive radiation: The rapid evolution of many species from one ancestor as its descendants adapt to many different niches, often after reaching new habitats with few competitors or after a mass extinction.
hybrid zone: A region where two closely related populations or species meet and interbreed, producing hybrids. If hybrids are less fit, selection can strengthen prezygotic barriers there (reinforcement); otherwise the two may merge or the zone may stay stable.
macroevolution: Evolution at or above the level of species, such as the origin of new species and larger groups, adaptive radiations and extinctions, seen over long spans of time.

7.11 Variations in Populations

Genetic variation lets populations survive change. When a new disease or environmental stress arrives, individuals whose alleles happen to give disease resistance or tolerance survive and reproduce, and natural selection acts through them. Populations with little variation, because they are small, inbred or reproduce as clones, are vulnerable: few or none of their members may carry useful alleles. Monocultures of genetically uniform crops show this most clearly, from the Irish potato famine to the loss of the Gros Michel banana; mixed plantings slow outbreaks because resistant neighbors block spread. Small wild populations can be restored by gene flow that brings in new alleles. Variation also exists in molecules, such as enzyme forms suited to different temperatures. Heterozygote advantage keeps variation in a population: where malaria is common, carriers of one sickle-cell allele survive best, so both alleles remain common, a form of balancing selection.

Genetic variation makes it more likely that some individuals survive a new disease or environmental change; selection then acts on them.
Population vulnerability: small, inbred or clonal populations have few alleles, so one stress can wipe them out. A monoculture of identical plants is the extreme case.
Disease resistance alleles usually exist before the disease arrives. Variation in molecules, such as enzyme forms suited to different temperatures, helps populations fit their surroundings.
Heterozygote advantage keeps alleles common: sickle-cell carriers resist malaria, so both alleles persist where malaria is common.

Individuals differ in how they respond to stresses, including diseases and environmental changes the population has never met. Individuals whose alleles happen to give disease resistance or tolerance survive and reproduce, while others die. The population persists and adapts, because natural selection had variation to act on. It is unlikely to include any individuals that can survive the new stress, so it is vulnerable to being wiped out. selection keeps both alleles in the population, preserving variation even though one homozygote is harmed.

population vulnerability: Population vulnerability: how likely a population is to be wiped out by a new disease or environmental change. Populations with little genetic variation (small, inbred or clonal) are the most vulnerable, because few or none of their members carry alleles that let them survive.
monoculture: A crop of a single variety, often genetically uniform or even clonal, grown over a large area. Because every plant shares the same alleles, one pathogen strain can destroy the whole crop, as in the Irish potato famine and the losses of the Gros Michel and Cavendish bananas.
heterozygote advantage: A situation in which heterozygotes have higher fitness than either homozygote, so selection keeps both alleles in the population (a form of balancing selection), as with the sickle-cell allele where malaria is common.
disease resistance: The ability of some individuals, because of the alleles they carry, to avoid infection or survive a disease that kills others. Resistance alleles often exist in a population before the disease arrives.

7.12 Origin of Life on Earth

Earth formed about 4.6 billion years ago, and the oldest widely accepted fossils, stromatolites and microfossils, are about 3.5 billion years old, so life appeared within roughly the first billion years. Early Earth had almost no free oxygen and abundant energy from lightning, ultraviolet light and volcanic heat. Experiments such as Miller and Urey's show that organic monomers like amino acids form from simple molecules given energy (abiotic synthesis); hydrothermal vents, with chemical energy and catalytic minerals, are another proposed setting. Monomers can join into polymers on clay or other mineral surfaces, which concentrate them and favor dehydration reactions, and fatty acids assemble into vesicles that can enclose RNA, forming protocells. The RNA world hypothesis proposes that RNA came first because it can both store information and catalyze reactions as ribozymes, as rRNA still does in the ribosome; later, more stable DNA took over storage and proteins took over most catalysis. Each step is supported by experiments, but how and where they happened is still debated.

Early Earth: formed about 4.6 billion years ago, with almost no free oxygen. The oldest widely accepted fossils, stromatolites, are about 3.5 billion years old.
Abiotic synthesis: the Miller-Urey experiment showed that amino acids form from simple gases and energy. Hydrothermal vents are another proposed setting.
Monomers can join into polymers on clay or mineral surfaces. Fatty acid vesicles can enclose RNA to make protocells.
RNA world: RNA can store information and catalyze reactions (ribozymes), so it may have come before DNA and proteins.

Simple molecules reacted to form organic monomers such as amino acids and nucleotide parts, as spark experiments show (abiotic synthesis). Dehydration reactions joined them into polymers, including short RNA chains, without enzymes. Protocells formed: membrane-bound packages that keep their contents together and can grow and divide. RNA that copied itself better became more common: natural selection began acting on molecules (the RNA world). DNA took over information storage and proteins took over most catalysis, leaving RNA as the go-between, as in cells today.

early Earth: Earth in its first billion years. It formed about 4.6 billion years ago; it probably had oceans by about 4.4 billion years ago, frequent volcanoes and impacts, and an early atmosphere with almost no free oxygen, so ultraviolet light reached the surface.
earliest life: The oldest evidence of life. Widely accepted fossils, stromatolites (layered mounds built by microbial mats) and microfossils, date to about 3.5 billion years ago; older chemical traces are debated.
abiotic synthesis: The formation of organic molecules, such as amino acids and nucleotides, from simple inorganic molecules without living things, using energy such as lightning, ultraviolet light or heat (prebiotic chemistry).
Miller-Urey experiment: The 1953 experiment by Stanley Miller and Harold Urey that passed electric sparks through water vapor, methane, ammonia and hydrogen in a closed apparatus and produced amino acids, showing that organic molecules can form without life.
hydrothermal vent: A hydrothermal vent is an opening in the sea floor where hot, mineral-rich water pours out. Vents offer chemical energy and catalytic mineral surfaces, so they are one proposed setting for the origin of life.
abiotic polymerization: Abiotic polymerization: the joining of monomers into polymers without enzymes, favored on mineral surfaces such as clay, which concentrate monomers, and in pools that dry out, which remove water from dehydration reactions.
protocell: A membrane-bounded droplet or vesicle, for example of fatty acids, that encloses molecules such as RNA and can grow and divide: a model of a stage between nonliving chemistry and the first cells.
RNA world hypothesis: The hypothesis that early life used RNA both to store genetic information and to catalyze reactions (as ribozymes), before DNA took over information storage and proteins took over most catalysis.