Lecture #1 Chapter 22~ Descent with Modification: A Darwinian View of Life

Evolution Evolution: the change over time of the genetic composition of populations Natural selection: populations of organisms can change over the generations if individuals having certain heritable traits leave more offspring than others (differential reproductive success) Evolutionary adaptations: a prevalence of inherited characteristics that enhance organisms’ survival and reproduction November 24, 1859

Evolutionary history Georges Cuvier (1769-1832) Paleontology: The study of fossils Charles Lyell (1797-1875) Uniformitarianism: Geological processes have not changed throughout history Charles Darwin (1809-1882) Evolution: Organisms adapt to their environment and these changes are inherited by offspring Gregor Mendel (1822-1884) Inheritance: Genetic inheritance through pea plants Alfred Wallace (1823-1913) Evolution: Natural Selection is how evolution occurs. Carolus Linnaeus (1707-1778) Taxonomy: the naming and classification of organisms James Hutton (1726-1797) Gradualism: Geological changes occur slowly over a long period of time Jean Baptist Lamarck (1744-1829) Evolution: Organisms have specific adaptations Thomas Malthus (1766-1834) Populations: Economic paper on the population growth in England

Evolution Time Line

Descent with Modification 5 observations: 1- Exponential fertility 2- Stable population size 3- Limited resources 4- Individuals vary 5- Heritable variation

Observations Exponential fertility: Organisms have the ability to produce such a large number of offspring they would increase exponentially if all organisms in the population reproduced. Stable Population Size: The population of a organism is stable. It is neither increasing or decreasing with the exception of seasonal changes. Limited Resources: There are not enough environmental resources for all, the organisms must compete for available resources. Individual Variation: Individuals have different traits and phenotypes. Heritable Variation: The phenotypic traits and variation is inherited by offspring.

Descent with Modification 3 Inferences: 1- Struggle for existence 2- Non-random survival 3- Natural selection (differential success in reproduction)

Inferences Struggle for existence: Non-random mating: Organisms fight to survive through competition for resources (ex: food, shelter, predators, etc.) Non-random mating: Those that are the most fit are the most likely to mate Natural selection: Predators, nature, etc. select those that are better suited to the environment leading to a gradual change toward favorable characteristics .

Achieving Descent with Modification Artificial Selection: an external force selects which mating events occur Occurs in domesticated plants and animals How Mendel discovered genetics How animals produce greater amounts of milk, etc. Natural Selection: random mating events The effects of predator/prey relationships Mates chosen upon organisms will

Artificial Selection Animals: Plants: Humans have used artificial selection to create specific types of animal food products Plants: Humans have used artificial selection to produce more resilient plants Plants produced through artificial selection include hybrid plants

Natural Selection Predator/Prey relationships: Environmental factors: Predators determine which organisms are the most fit Organisms that are the most able to avoid predators, find food, shelter, etc. survive to reproduce Environmental factors: Availability of food and shelter, as well as weather determines which organisms survive to preproduce

Evolution evidence: Biogeography Geographical distribution of species Physical barriers such as lakes, rivers, mountains, oceans, etc. Examples: Islands vs. Mainland Australia Continents

Evolution evidence: The Fossil Record Succession of forms over time Transitional links Vertebrate descent

Evolution evidence: Comparative Anatomy Homologous structures (homology) Descent from a common ancestor Vestigial organs Ex: whale/snake hindlimbs; wings on flightless birds

Evolution evidence: Comparative Embryology Pharyngeal pouches, ‘tails’ as embryos

Comparative Embryology Evolutionary evidence: Embryology : the study of embryonic development; comparison of the development of fetal development Scientists compare the development of various organisms to determine how similar the organisms are Similarity in embryonic development suggests evolutionary links

Evolution evidence: Molecular Biology Similarities in DNA, proteins, genes, and gene products Common genetic code

Final words…... “Absence of evidence is not evidence of absence.”

Lecture #2 Chapter 23~ The Evolution of Populations

Population genetics Population: a localized group of individuals belonging to the same species Species: a group of populations whose individuals have the potential to interbreed and produce fertile offspring Gene pool: the total aggregate of genes in a population at any one time Population genetics: the study of genetic changes in populations

Modern synthesis/neo-Darwinism: formed in the 1940’s it states that the population is the unit of evolution and natural selection has significant role as the most important mechanism “Individuals are selected, but populations evolve.” The selection of individuals in a population allows certain traits to be passed from one generation to the next and the overall population changes

Hardy-Weinberg Theorem Serves as a model for the genetic structure of a nonevolving population (equilibrium) 5 conditions: 1- Very large population size 2- No migration 3- No net mutations 4- Random mating 5- No natural selection

Hardy-Weinberg Theorem Very large population size In small populations, genetic drift can can alter allele frequencies No migration There must be no transfer of alleles between two populations No net mutations A mutation alters the gene pool Random mating The selection of mates for particular characteristics does not allow for the necessary random mating No natural selection Differential survival and selection favor the transmission of some alleles but not others

Hardy-Weinberg Equation p=frequency of one allele (A) q=frequency of the other allele (a); p+q=1.0 (p=1-q & q=1-p) P2=frequency of AA genotype 2pq=frequency of Aa plus aA genotype q2=frequency of aa genotype; p 2 + 2pq + q 2 = 1.0

Microevolution, I A change in the gene pool of a population over a succession of generations Genetic drift: changes in the gene pool of a small population due to chance (usually reduces genetic variability)

Microevolution, II The Bottleneck Effect: type of genetic drift resulting from a reduction in population such that the surviving population is no longer genetically representative of the original population Usually a result of natural disaster

Microevolution, III Founder Effect: a cause of genetic drift attributable to colonization by a limited number of individuals from a parent population Seen on the various Galapagos Islands

Microevolution, IV Gene Flow: genetic exchange due to the migration of fertile individuals or gametes between populations reduces differences between populations

Microevolution, V Mutations: a change in an organism’s DNA (gametes; many generations); original source of genetic variation raw material for natural selection

Microevolution, VI Nonrandom mating: inbreeding and assortive mating both shift frequencies of different genotypes Selection for specific characteristics

Microevolution, VII Natural Selection: differential success in reproduction; only form of microevolution that adapts a population to its environment

Population variation Polymorphism: coexistence of 2 or more distinct forms of individuals (morphs) within the same population Geographical variation: differences in genetic structure between populations (cline)

Variation preservation Prevention of natural selection’s reduction of variation Diploidy 2nd set of chromosomes hides variation in the heterozygote Balanced polymorphism 1- heterozygote advantage: hybrid vigor i.e., malaria/sickle-cell anemia 2- frequency dependent selection: survival & reproduction of any 1 morph declines if it becomes too common i.e., parasite/host

Natural selection Fitness: contribution an individual makes to the gene pool of the next generation 3 types: A. Directional B. Diversifying C. Stabilizing

Natural selection Directional Selection Diversifying Selection Shifts the overall makeup of the population to favor one extreme or the other Ex: Dark snails are selected over light or medium snails Diversifying Selection Selection favors both extreme over the intermediate individuals. Ex: Light and Dark snails are selected over the medium Stabilizing Selection The intermediate phenotype is selected over either of the extremes Ex: The medium snail is selected over the light or the dark snail

Sexual selection Sexual dimorphism: secondary sex characteristic distinction Ex: Physical size or plumage Sexual selection: selection towards secondary sex characteristics that leads to sexual reproduction Ex: The use of feathers to attract a mate

“Perfect” Organisms Organisms are locked into historical constraints. Adaptations are often compromises. Not all evolution is adaptive. Selection can only edit variation that exists. - Evolution cannot create perfect organisms

Lecture #3 Chapter 24 ~ The Origin of Species

Macroevolution: the origin of new taxonomic groups Speciation: the origin of new species 1- Anagenesis (phyletic evolution): accumulation of heritable changes 2- Cladogenesis (branching evolution): budding of new species from a parent species that continues to exist (basis of biological diversity)

What is a species? Biological species concept (Mayr): a population or group of populations whose members have the potential to interbreed and produce viable, fertile offspring (genetic exchange is possible and that is genetically isolated from other populations)

Reproductive Isolation (isolation of gene pools), I Prezygotic barriers: impede mating between species or hinder the fertilization of the ova Habitat (snakes; water/terrestrial) Behavioral (fireflies; mate signaling) Temporal (salmon; seasonal mating) Mechanical (flowers; pollination anatomy) Gametic (frogs; egg coat receptors)

Reproductive Isolation, II Postzygotic barriers: fertilization occurs, but the hybrid zygote does not develop into a viable, fertile adult Reduced hybrid viability (frogs; zygotes fail to develop or reach sexual maturity) Reduced hybrid fertility (mule; horse x donkey; cannot backbreed) Hybrid breakdown (cotton; 2nd generation hybrids are sterile)

Modes of speciation (based on how gene flow is interrupted) Allopatric: populations segregated by a geographical barrier; can result in adaptive radiation (island species) Sympatric: reproductively isolated subpopulation in the midst of its parent population (change in genome); polyploidy in plants; cichlid fishes

Adaptive Radiation Adaptation from a common ancestor when placed into varied ecological systems. Caused by migration New ecological niches

Examples of Adaptive Radiation Hawaii – Hawaiian archipelago illustrates diversity and adaptation Kauai: oldest and most humid island Maui: some vegetation grows even on dry side Hawaii: active volcano, very dry, very wet side of island Most organisms are found only on the archipelago

Punctuated equilibria Tempo of speciation: gradual vs. divergence in rapid bursts; Niles Eldredge and Stephen Jay Gould (1972); helped explain the non-gradual appearance of species in the fossil record

Punctuated equilibria Species change most as they arise from ancestral species Relatively little change occurs after Eldredge & Gould’s model contrasts with the model of gradualism

Growth & Development Heterochrony: change in the rate or timing of developmental events Can change physical features as well as timing of reproductive development Allometric Growth: Proportioning that helps give a body its specific form Small changes in these rates changes the adult form substantially

Evolution Continued Evolution is not goal oriented Bushes do not grow toward only one point, organisms do not evolve along a single lineage. Speciation creates several branches, many which become extinct The species that survives the longest and produces the most offspring determines the direction of major evolutionary trends “Species Selection”

Lecture #4 Chapter 25 ~ Phylogeny & Systematics

Phylogeny: the evolutionary history of a species Systematics: the study of biological diversity in an evolutionary context The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock Paleontologists

The fossil record Sedimentary rock: rock formed from sand and mud that once settled on the bottom of seas, lakes, and marshes Dating: 1- Relative ~ geologic time scale; sequence of species 2- Absolute ~ radiometric dating; age using half-lives of radioactive isotopes

Homology vs. Analogy Homology – similar characteristics due to common ancestry Hawaiian silversword plants Analogy – similar characteristics due to environmental pressures and natural selection Australian and North American burrowing moles

Biogeography: the study of the past and present distribution of species Pangaea-250 mya √ Permian extinction Geographic isolation-180 mya √ African/South American reptile fossil similarities √ Australian marsupials

Mass extinction Permian (250 million years ago): 90% of marine animals; Pangea merge Cretaceous (65 million years ago): death of dinosaurs, 50% of marine species; low angle comet

Phylogenetics The tracing of evolutionary relationships (phylogenetic tree) Linnaeus Binomial Genus, specific epithet Homo sapiens Taxon (taxa)

Phylogenetic Trees Cladistic Analysis: taxonomic approach that classifies organisms according to the order in time at which branches arise along a phylogenetic tree (cladogram) Clade: each evolutionary branch in a cladogram Types: 1- Monophyletic single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram

Phylogenetic Trees 2- Polyphyletic members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion 3- Paraphyletic lacks the common ancestor that would unite the species; does not meet cladistic criterion

Constructing a Cladogram Sorting homology vs. analogy... Homology: likenesses attributed to common ancestry Analogy: likenesses attributed to similar ecological roles and natural selection Convergent evolution: species from different evolutionary branches that resemble one another due to similar ecological roles

A Cladogram

Phylogram Branch length – represents the number of changes that have taken place (DNA Sequence) The greater the length the greater the change in the DNA

Ultrametric Trees All organisms from a common ancestor have survived for the same number of years Equal chronological amounts of time are represented by equal lengths on the tree

Phylogeny as Hypothesis Phylogenic Trees give rise to evolutionary hypotheses Using maximum parsimony and maximum likelihood, scientists develop evolutionary hypotheses Occam’s razor Assumptions Molecular comparison

Genomes Orthologous genes – homologous genes in different gene pools due to speciation Paralogous genes – gene duplication creating multiple copies in the same genome

Genome Evolution Orthologous genes are widespread 50% of genes are traceably orthologous between humans and yeast Paralogous genes do not appear at the same rate as phenotypic complexity Humans have 5x as many genes as yeast despite complexity differences

Universal Tree of life 1960’s – DNA is universal in all organisms, therefore, all organisms must have a common ancestor DNA identifies branching patterns Region must be sequenced Must have evolved slowly