CHAPTER OUTLINE
27.1 Theory of Evolution
Charles Darwin proposed the theory of evolution after his observations of geological formations and species variation during his five-year voyage on the HMS Beagle. Evolution proposes that species arise, change, and become extinct due to natural forces. Darwin’s predecessor, Lamarck, developed the theory of inheritance of acquired characteristics, which that states that the environment can bring about inherited change. Changes to an organism’s visible characteristics, or phenotype, acquired during an organism’s lifetime do not result in genetic changes that are heritable.  Darwin’s theory of natural selection states that: individual organisms within a species exhibit variation that can be passed from one generation to the next, organisms compete for available resources, individual organisms within a population differ in terms of their reproductive success, organisms become adapted to conditions as the environment changes. 
27.2 Evidence of Evolution
Evolution is all the changes that have occurred, due to differential reproductive success, in living organisms over geological time.
Fossil Evidence
     Fossils are the remains and traces of past life or any other direct evidence of past life.
Geological Timescale
   As a result of studying strata, scientists have divided Earth’s history into eras,     

and then periods and epochs. The absolute dating method relies on radioactive   

dating techniques to assign an actual date to a fossil.   
Biogeographical Evidence
     Biogeography is the study of the distribution of the range and distribution of plants and    

animals in different places throughout the world. 
Mass Extinctions
   Extinction is the death of every member of a species. During mass extinctions, a       

large percentage of species become extinct within a relatively short period of      

time. So far, there have been five major mass extinctions. 
Anatomical Evidence
     Structures that are anatomically similar because they are inherited from a common ancestor are called homologous structures.  In contrast, analogous structures serve the    same function, but are not constructed similarly, nor do they share a common ancestry.     Vestigial structures are anatomical features that are fully developed in one group of organisms but that are reduced and may have no function in similar groups.
Biochemical Evidence
     When the degree of similarity in DNA nucleotide sequences or the degree of similarity in   amino acid sequences of proteins is examined, the more similar the DNA sequences are,     generally the more closely related the organisms are. 
We Can Observe Selection at Work
Researchers have recorded the evolution of traits in natural populations over decades.
Humans as Agents of Evolution
Humans can artificially modify desired traits in plants and animals by selecting to      

breed individuals with preferred traits, thereby increasing the frequency of desired traits.  This type of human-controlled breeding is called artificial      selection.
Evolution in Natural Populations
Recent research on the Galápagos finches demonstrates that evolutionary change      can sometimes be observed within the timeframe of a human life span.
27.3 Microevolution
Many traits can change temporarily in response to a varying environment, these are not evolutionary changes. Microevolution pertains to evolutionary change within populations.
Microevolution in the Peppered Moth
     Population genetics is the field of biology that studies the diversity of populations at the    level of the gene. A population is all the members of a single species that occupy a particular area at the same time and that interbreed and exchange genes.
Allele Frequencies
   The gene pool refers to the alleles of all genes in all individuals in a      population.  The sum of allele frequencies in a population for any gene of any      diploid organism is equal to 1.
Hardy-Weinberg Equilibrium
   A population in which allele frequencies do not change over time is said to be in      genetic or Hardy-Weinberg equilibrium-a stable, nonevolving state. The   principles of the Hardy-Weinberg equation indicate that allele frequencies in   a gene pool will remain at equilibrium after one generation of random mating in a     large, sexually reproducing population as long as five conditions are met: 1) no      mutations, 2) no genetic drift, 3) no gene flow, 4) random mating, and 5) no       selection. 
27.4 Processes of Evolution   
     Five Agents of Evolutionary Change
The opposite of the five Hardy-Weinberg conditions can cause evolutionary change.
   Mutations
   Mutations, which are genetic changes, are the only source of new variation in a        population.
Genetic Drift
   Genetic drift refers to changes in the allele frequencies of a gene pool due to       the random meeting of gametes during fertilization. Genetic drift has greater      effects in smaller populations because there are fewer gametes to sort. The      bottleneck effect and the founder effect are both examples of genetic drift. 
Gene Flow
   Gene flow is the movement of alleles among populations when individuals or      their gametes migrate from one population to another and breed in that new     population.
Nonrandom Mating
   Nonrandom mating occurs when individuals are selective about choosing a mate with a preferred trait.
Natural Selection
   Natural selection is the process that allows some individuals, with an advantage      over others, to produce more offspring. Evolution by natural selection requires     individual variation, inheritance, overproduction, and differential reproductive          success. The fitness of an individual is measured by the number of fertile    offspring produced throughout its lifetime.
Stabilizing Selection
With stabilizing selection, extreme phenotypes are selected against, and
individuals near the average are favored.
Directional Selection
Directional selection occurs when an extreme phenotype is favored and            the distribution curve shifts in that direction. 
Disruptive Selection
In disruptive selection, two or more extreme phenotypes are favored            over any intermediate phenotype. 
Maintenance of Variation
     The maintenance of variation is beneficial because populations with limited variation    may not be able to adapt to new conditions should the environment change and may    become extinct.
Diploidy and the Heterozygote
Only alleles that are expressed (cause a phenotypic difference) are subject to natural selection. In diploid organisms, this fact makes the heterozygote a potential protector of recessive alleles that might otherwise be weeded out of the gene pool by natural selection. 
27.5 Macroevolution and Speciation
Macroevolution is evolution on a large scale. Species is defined as a group of organisms that are capable of interbreeding and are isolated reproductively from other organisms. Reproductive isolation of similar species is accomplished by either prezygotic isolating mechanisms, which are in place before fertilization, or postzygotic isolating mechanisms, which are in place after fertilization. 
The Process of Speciation
     Speciation has occurred when one species gives rise to two species. Allopatric speciation occurs when populations become separated by a geographic barrier and gene flow is no longer possible. Sympatric speciation occurs when a single population    divides into two reproductively isolated groups without being geographically isolated.
Adaptive Radiation
     Darwin’s finches provide an example of adaptive radiation, the proliferation of a species by adaptation to different ways of life.  
The Pace of Speciation
     Currently there are two hypotheses about the pace of speciation: phyletic gradualism, which states that change is very slow, but steady, and punctuated equilibrium, which    says that long periods of no visible change are followed by rapid periods of speciation.
27.6 Systematics
Systematics is the study of the evolutionary history of biodiversity, it is a quantitative science that uses characteristics of living and fossil organisms, or traits, to infer the evolutionary relationship among organisms.
Classification
Taxonomy is the branch of systematic biology concerned with identifying, naming, and classifying organisms. A taxon is the general name for a group containing an organism or group of organisms that exhibit a set of shared traits. Classification is the process of naming and assigning organisms or groups of organisms to a taxon. Taxonomists use several categories of classification: species, genus, family, order, class, phylum, kingdom, and domain. 
Phylogeny
     Phylogenetics is the branch of systematic biology that studies the evolutionary relatedness among groups of organisms, which can be arranged in a phylogeny. Caldistics is one method phylogeneticists use to construct a phylogeny called a       cladogram. Branches in a cladogram are called clades, which contain a most recent      common ancestor and all its descendants. Only shared derived traits, which are shared     among all individuals, define a clade.
Linnaean Classification Versus Phylogenetics
In many instances Linnaean classification is not consistent with new understandings about phylogenetic relationships. Therefore some phylogeneticists have proposed the International Code of Phylogenetic Nomenclature (PhyloCode), which sets forth rules to follow in naming of clades.
Three Domain Classification System
A domain is a classification category higher than the kingdom. The two prokaryote groups were classified into the domain Bacteria and the domain Archaea.  The domain Eukarya contains kingdoms for all eukaryotes, including protists, animals, fungi, and plant.