Scala Naturae and Species Classification

• Species are a unit of the population able to interbreed.
• Evolution is defined as any change in a population over a period.

Scala Naturae and Classification of Species

• Aristotle saw species as fixed and arranged them on a scale of increasing complexity, called scala naturae.
• Each form of life was considered perfect and permanent.
• Carolus Linnaeus founded modern taxonomy, using a nested classification system.
• He developed the binomial format for naming species, like Homo sapiens.
• Linnaeus attributed resemblance among species to the pattern of creation, opposing evolution.

Ideas About Change Over Time

• Fossils helped to lay the foundation for Darwin's ideas.
• Fossils are remains or traces of past organisms, usually in sedimentary rock strata.
• Paleontology, the study of fossils, was developed by Georges Cuvier.
• Cuvier noted that fossils in older strata were more dissimilar to modern forms.
• He believed in extinctions but opposed evolution.
• Cuvier thought each boundary between strata represented a catastrophic event that destroyed many species.
• James Hutton and Charles Lyell suggested geological changes resulted from gradual processes.
• Lyell proposed these processes continue today at the same rate as in the past.
• These ideas influenced Darwin's thinking.

Lamarck’s Hypothesis of Evolution

• Jean-Baptiste de Lamarck was the first to propose an evolutionary mechanism for how life changes over time.
• He hypothesized species evolve through use and disuse of body parts and the inheritance of acquired characteristics.
• Experimental evidence did not support this mechanism.

Darwin’s Research

• Charles Darwin was a naturalist on the HMS Beagle for a five-year voyage around the world.
• Darwin read and was influenced by Lyell’s Principles of Geology during the voyage.
• He observed uplift following an earthquake and inferred similar processes caused fossils of ocean organisms found in the mountains.
• Darwin concluded that the Earth must be much older than traditionally thought.

The Voyage of the Beadle

• Darwin's interest in species distribution was sparked during a stop at the Galapagos Islands.
• He hypothesized that species from the South American mainland colonized the Galapagos and diverged on the islands.

Darwin’s Focus on Adaptation

• Darwin perceived adaptation to the environment and the origin of new species as closely related processes.
• The diverse group of Galapagos finches arose from an ancestral form through gradual adaptations to different environments.
• In 1844, Darwin wrote an essay on natural selection but did not introduce his theory publicly.
• Natural selection is a process where individuals with favorable inherited traits are more likely to survive and reproduce.
• Darwin published "On the Origin of Species by Means of Natural Selection."

Descent with Modification

• Darwin used "descent with modification" to describe his perception of the unity and diversity of life.
• He viewed evolution as descent (shared ancestry, resulting in shared characteristics) and modification (accumulation of differences).
• Darwin envisioned the history of life as a tree with a common trunk representing shared ancestry and branches representing diversity among species.
• Tips of branches represent present-day organisms.
• Unlabeled branches represent extinct groups.
• Each fork represents the most recent common ancestor (MRCA) of the lines that branch from that point.
• Fossils of extinct species help to fill in the morphological gaps between present-day groups.

Artificial Selection, Natural Selection, and Adaptation

• Humans modify other species through selective breeding, called artificial selection.
• Darwin argued that a similar process occurs in nature.
• Observation #1: Members of a population often vary in their inherited traits.
• Observation #2: All species can produce more offspring than the environment can support; many offspring fail to survive and reproduce.
• Inference #1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals.
• Inference #2: This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations.
• Darwin was influenced by Thomas Malthus, who observed that human populations tend to increase faster than food supplies and other resources.
• Darwin applied this concept of overproduction and scarcity of resources to natural populations.
• Populations, not individuals, evolve over time.
• Natural selection can only increase or decrease heritable traits that differ among individuals in a population.
• The specific traits that are adaptive will vary from place to place and over time.
• Evolution is supported by overwhelming scientific evidence.

Evidence for Evolution

• Direct observations
• Homology
• The fossil record
• Biogeography

The Evolution of Drug-Resistant Bacteria

• Staphylococcus aureus is a bacterium commonly found on people’s skin or in nasal passages.
• Methicillin-resistant S. aureus (MRSA) genetic varieties can cause “flesh-eating disease” and potentially fatal infections.
• Treatment of bacterial infections with antibiotics, such as penicillin, has saved millions of lives.
• S. aureus became resistant to penicillin in 1945, two years after it was first widely used.
• S. aureus also evolved resistance to another antibiotic, methicillin, within two years of its widespread use.
• Methicillin works by inhibiting a protein used by most bacteria to synthesize cell walls.
• MRSA bacteria use a different protein for cell wall synthesis; they survive and reproduce at higher rates than others when exposed to methicillin.
• MRSA strains are now resistant to many antibiotics.
• Natural selection does not create new traits but selects for traits already present in the population.
• Evolution by natural selection can occur rapidly in species with short generation times.
• Generation time is the amount of time it takes for a population to double.
• The current local environment determines which traits will be selected for or against in a population.

Homology

• Homology is similarity resulting from common ancestry.
• Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor.
• Comparative embryology reveals anatomical homologies not visible in adult organisms.
• At some point in development, all vertebrate embryos have a post-anal tail and pharyngeal arches.
• Vestigial structures are remnants of features that served important functions in an organism’s ancestors but serve no current purpose.

Convergent Evolution

• Convergent evolution is the evolution of similar, or analogous, features in distantly related groups.
• Analogous traits arise when groups independently adapt to similar environments in similar ways.
• An example includes sugar gliders and flying squirrels.
• Convergent evolution does not provide information about ancestry.

The Fossil Record

• The fossil record documents the pattern of evolution.
• It provides evidence that species have changed through time, and many species have gone extinct.
• Fossils shed light on the origins of new groups of organisms.
• Fossils can also document the steps in important transitions.
• For example, the transition from land to sea in the ancestors of cetaceans.

Biogeography

• Biogeography, the scientific study of the geographic distribution of species, also provides evidence of evolution.
• Earth’s continents were formerly united in a single large continent called Pangaea but have since separated by continental drift.
• This allows one to predict when and where different groups evolved.
• Islands generally have many endemic species (found nowhere else in the world).
• Island endemics are often closely related to species on the nearest mainland or neighboring island.
• Darwin suggested that these species arose as a result of colonists adapting to the new environment.

Phylogeny

• Phylogeny is the evolutionary history of a species or group of related species.
• Systematics classifies organisms and determines their evolutionary relationships.
• Organisms share many characteristics because of common ancestry.
• Closely related organisms share many genes, metabolic pathways, and structural proteins.
• Taxonomy is the scientific discipline responsible for the ordered division and naming of organisms.

Binomial Nomenclature

• In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances.
• Two key features of his system remain useful today: two-part names for species and hierarchical classification.
• Binomial refers to the two-part format of the scientific species name.
• The first part of the name is the genus; the second part, the specific epithet, is unique for each species.
• The first letter of the genus is capitalized, and the entire species name is italicized.
• Both parts together name the species (not the specific epithet alone).

Hierarchical Classification

• Linnaeus introduced a system for grouping species in increasingly broad categories.
• The taxonomic groups from least to most inclusive are species, genus, family, order, class, phylum, kingdom, and domain.
• A named taxonomic unit at any level of the hierarchy is called a taxon.

Phylogenetic Trees

• A phylogenetic tree represents a hypothesis about evolutionary relationships.
• Each branch point represents the divergence of two evolutionary lineages from a common ancestor.
• Sister taxa are groups that share an immediate common ancestor not shared by any other group.
• Phylogenetic trees can be drawn horizontally, vertically, or diagonally.
• The order in which the taxa appear at the branch tips does not represent the sequence of evolution.
• The branches of a tree can be rotated around branch points without changing the relationships depicted in the tree.
• Phylogenetic trees show patterns of descent, not phenotypic similarity.
• Phylogenetic trees do not generally show how old lineages are or how much they have changed.
• It should not be assumed that a taxon evolved from the taxon next to it; we can only infer that both taxa evolved from a recent common ancestor.

Morphological and Molecular Data

• Phylogenies are inferred from similarities in morphology, genetics, and biochemistry.
• Only similarities resulting from common ancestry will reflect the evolutionary relationships among organisms.
• Phenotypic and genetic similarities due to shared ancestry are called homologies.
• Organisms with very similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences.
• Systematists must distinguish between similarities resulting from homology and analogy.
• Homology is similarity due to shared ancestry; analogy is similarity due to convergent evolution.
• Convergent evolution occurs when unrelated groups adapt to similar environmental pressures.
• Only homologies can be used to infer phylogeny.
• Homology can be distinguished from analogy by comparing genetic and fossil evidence.
• Molecular homologies are based on the degree of similarity in nucleotide sequence among taxa.
• A single nucleotide insertion or deletion shifts the whole sequence, causing extensive mismatch between sequences that are otherwise quite similar.
• Computer programs can help identify genetic matches by comparing different lengths of DNA.

Cladistics

• Cladistics classifies organisms by common descent.
• A clade is a group of species that includes an ancestral species and all its descendants.
• Clades can be nested within larger clades, but not all groupings of organisms qualify as clades.
• A taxon is equivalent to a clade only if it is monophyletic, consisting of the ancestor species and all of its descendants.
• A paraphyletic group consists of an ancestral species and some, but not all, of the descendants.
• A polyphyletic group includes distantly related species but does not include their most recent common ancestor.
• In a paraphyletic group, the most recent common ancestor of all members of the group is part of the group.
• In a polyphyletic group, the most recent common ancestor is not part of the group.

Shared Ancestral and Shared Derived Characters

• Organisms have some characters that are shared with their ancestors and some characters that differ.
• A shared ancestral character is a character that originated in an ancestor of the taxon.
• A shared derived character is an evolutionary novelty unique to a particular clade.
• A character can be both ancestral and derived, depending on the context.
• A shared derived "character" can also refer to the loss of a feature.
• The loss of limbs is a shared derived character in all snakes.
• An ingroup is the group of species being studied.
• An outgroup is a species or group of species closely related to but not part of the ingroup.
• Characters found in both the outgroup and the ingroup are assumed to be ancestral.
• Derived characters are assumed to have arisen only once in the ingroup.

Domains

• Early taxonomists classified all species as either plants or animals.
• Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia.
• More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya.
• The three-domain system is supported by data from many sequenced genomes.
• This system highlights the importance of single-celled organisms in the history of life.
• Both domains Bacteria and Archaea are composed entirely of single-celled prokaryotes.
• Only three lineages in the domain Eukarya are dominated by multicellular organisms: kingdoms Plantae, Fungi, and Animalia.
• Kingdom Monera is obsolete because it would have members in two different domains.
• Kingdom Protista is obsolete because it would include members that are more closely related to plants, fungi, or animals than to other protists.
• The tree of life is constantly being revised.

Horizontal Gene Transfer

• The tree of life is based on slowly evolving rRNA genes that code the RNA components of ribosomes.
• Eukaryotes and archaea are more closely related to each other than to bacteria.
• Trees based on other genes indicate a closer relationship between eukaryotes and bacteria.
• Horizontal gene transfer refers to the transfer of genes from the genome of one species to another.
• It is caused by exchange of transposable elements or plasmids, viral infection, or fusion of organisms.
• Horizontal gene transfer was likely common in the early history of life.
• Recent research indicates that on average, 80% of genes in prokaryotic genomes had moved between species at some point.
• Such evidence indicates that the early tree of life may be better represented as a tangled web.

Microevolution

• Microevolution is a change in allele frequencies in a population over generations.
• Allele frequency change is caused by natural selection, genetic drift, and gene flow.

Genetic Variation

• Variation in heritable traits is a prerequisite for evolution by natural selection.
• Mendel’s work on pea plants provided evidence of discrete heritable units (genes).
• Phenotypic variation often reflects genetic variation.
• Genetic variation is the differences in the composition of a gene or other DNA sequences among individuals.
• Some phenotypic differences can be classified on an "either-or" basis.
• Such traits are usually determined by a single gene.
• Other differences are due to the influence of many genes and vary in gradations along a continuum.

Gene pools and allele frequencies

• A population is a group of individuals that live in the same area and interbreed, producing fertile offspring.
• Though populations may not be geographically isolated, individuals tend to breed with other members of their own population.
• A gene pool consists of all the alleles for all loci in a population.
• An allele for a particular locus is fixed if all individuals in a population are homozygous for the same allele.
• The frequency of an allele in a population can be calculated.
• For diploid organisms, the total number of alleles at a locus is the total number of individuals times 2.
• The total number of dominant alleles at a locus is 2 alleles for each homozygous dominant individual plus 1 allele for each heterozygous individual; the same logic applies for recessive alleles.
• By convention, if there are 2 alleles at a locus, p and q are used to represent their frequencies.
• The frequency of all alleles in a population will add up to one (p+q=1).

The Hardy-Weinberg Equation

• The Hardy-Weinberg equation describes the genetic makeup expected for a population that is not evolving at a specific locus.
• If the data observed for the population differ from expected values, then the population may be evolving at that locus.
• Frequency of genotypes:
  • AA (homozygous dominant) = p^2
  • Aa (heterozygous) = 2pq
  • aa (homozygous recessive) = q^2
• Equation: p^2 + 2pq + q^2 = 1
• Frequency of alleles:
  • p = frequency of dominant allele
  • q = frequency of recessive allele
• Equation: p + q = 1