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Chapter 19: Descent with Modification ●

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What is Evolution? ○ Darwin noted that current species are descendants of ancestral species ○ Evolution can be defined by Darwin’s phrase descent with modification ○ Change in the genetic composition of a population from generation to generation ○ Evolution can be viewed as both a pattern and a process Concept 19.1: The Darwinian Revolution challenged traditional views of young Earth inhabited by unchanging species ○ Scala Naturae and Classification of Species ■ The Greek philosopher Aristotle (384 ‐322 BCE) viewed species as fixed and arranged them on a scala naturae (ladder of nature) ■ The Old Testament holds that species were individually designed by God and therefore perfect ○ Context: Carolus Linnaeus ■ Carolus Linnaeus interpreted organismal adaptations as evidence that the Creator had designed each species for a particular purpose ■ Linnaeus was the founder of taxonomy, the branch of biology concerned with classifying organisms ■ He developed the binomial format (binomial nomenclature) for naming species (for example, Homo sapiens) ○ Ideas about Change over Time ■ The study of fossils helped to lay the groundwork for Darwin’s ideas ■ Fossils are the remains or traces of organisms from the past, found in sedimentary rock, which appears in layers or strata ○ Paleontology ■ Paleontology, the study of fossils, was largely developed by French scientist Georges Cuvier ■ Cuvier speculated each boundary between strata represents a catastrophe that destroyed many species ○ “The Present is the Key to the Past” ■ Geologists James Hutton and Charles Lyell: Earth’s surface changing in slow, continuous actions (Gradualism) ■ Lyell further proposed that the mechanisms of change are constant over time ■ This view strongly influenced Darwin’s way of thinking ○ Lamarck’s Hypothesis of Evolution ■ Lamarck hypothesized that species evolve through use and disuse of body parts and the inheritance of acquired characteristics ■ The mechanisms he proposed are unsupported by evidence Concept 19.2: Descent with Modification by Natural Selection explains Adaptations of Organisms and the Unity and Diversity of life ○ Darwin’s research ■ Charles Darwin had a consuming interest in nature ■ Darwin first studied medicine (unsuccessfully) and then theology at Cambridge University ■ Naturalist for a five year round the world voyage on the HMS Beagle ○ Voyage on the HMS Beagle ■ Darwin was influenced by Lyell’s Principles of Geology and thought that

Earth was more than 6,000 years old His interest in geographic distribution of species was kindled by a stop at the Galápagos Islands west of South America ■ He hypothesized that species from South America had colonized the Galápagos and speciated on the islands ■ During his travels on the Beagle, Darwin collected specimens of South American plants and animals ■ He observed fossils resemble living species from the same region and living species resemble other species from nearby regions ■ He experienced an earthquake in Chile and observed the uplift of rock* ○ Populations from different islands showed different shells ■ Galapagos Tortoise (Chelonoidis Nigra) ■ 15 subspecies of Galapagos tortoises have been identified, only 11 subspecies survive to this day ■ Population declined from ~ 250,000 to ~3,000 ○ Darwin focused on Adaptation ■ Adaptation= inherited characteristics of organisms that enhance survival and reproduction in specific environments ○ Evolution by Natural Selection ■ In 1844, Darwin wrote an essay on natural selection as the mechanism of descent with modification but did not introduce his theory publicly ■ Natural selection is a process in which individuals with favorable inherited traits are more likely to survive and reproduce ● Survival of the fittest* ○ The Origin of Species and ideas from it ■ In June 1858, Darwin received a manuscript from Alfred Russell Wallace, who had developed a theory of natural selection similar to Darwin’s ■ Darwin quickly finished The Origin of Species and published it the next year ■ Darwin explained three broad observations about life ● The unity of life ● The diversity of life ● The match between organisms and their environment ■ The phrase descent with modification summarized Darwin’s perception of the unity of life ■ The phrase refers to the view that all organisms are related through descent from an ancestor that lived in the remote past ■ In the Darwinian view, the history of life is like a tree with branches representing life’s diversity ■ Fossils of extinct species help to “fill in” the morphological gaps between present-day groups Thomas Malthus ○ Darwin was influenced by Thomas Malthus, who noted the potential for human population to increase faster than food supplies and other resources Artificial Selection, Natural Selection and Adaptation ○ Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a process called artificial selection ○ Darwin argued that a similar process occurs in nature ■

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Observation 1. Members of a population often vary in inherited traits (ex. Population of ladybugs, puppies) Observation 2. All species can produce more offspring than the environment can support and many of these offspring fail to survive and reproduce (ex. spore cloud, tadpoles) Inferences 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 2. This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations Ex: the bright pink mutation called erythrism

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Natural Selection ● If some inheritable traits are advantageous, these will accumulate in a population over time and this will increase the frequency of individuals with these traits ● This process explains the match between organisms and their environment

Summary: Individuals with certain heritable traits survive and reproduce at a higher rate than other individuals Over time, natural selection increases the match between organisms and their environment If an environment changes over time, natural selection may result in adaptation to these new conditions and may give rise to new species Note that individuals do not evolve; populations evolve.. So what acts on the individual? -

Natural selection can only increase/decrease heritable traits varying in a population (does not create any) Adaptations vary with different environments

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Natural Selection does not create new traits, but edits or selects for traits already present in the population The local environment determines which traits will be selected for or selected against in any specific population

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Concept 19.3: Evolution is supported by an overwhelming amount of scientific evidence ○ Scientific evidence: new discoveries continue to fill the gaps identified by Darwin in The Origin of Species ○ Four types of data that document the pattern of evolution ■ Direct observations ● Natural selection in response to introduced plant species. Soapberry bugs use their “beak” to feed on seeds within fruits - In southern Florida, bugs feed on balloon vine with

larger fruit, they have longer beaks In central Florida, bugs feed on goldenrain tree with smaller fruit, they have shorter beaks Homology (study of shared ancestry) ● Evolution is a process of descent with modification ● Related species can have characteristics with underlying similarity that function differently ● Homology is similarity resulting from common ancestry ● Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor (ex. Comparative humerus and arm structure) -

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Related species can have characteristics with underlying similarity that function differently ●

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Molecular: The more alike the structures the more closely related the individuals ● Developmental: reveals homologies are not visible in adults ■ The fossil record ● The extinction of species ● The origin of new groups ● Changes within groups over time ● Fossils can document important transitions (ex. Transition from land to sea in the ancestors of cetaceans) ■ Biogeography ● The geographic distribution of species, provides evidence of evolution ● Formerly united in a single large continent called Pangea but have since separated by plate tectonics (Hulton and Lyell) ● Consider when and where different groups evolved A different cause of resemblance: 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 ■ Does not provide information about ancestry ■ Many observations that explain and integrate a great variety of phenomena Why is it called a “Theory”? ■ The predictions of a scientific theory must stand up to continual testing by experimentation and observation ■ Darwin’s theory of evolution by natural selection integrate diverse areas of biological study ■ Ongoing research adds to our understanding of evolution

Chapter 21: The Evolution of Populations ●

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Overview: The Smallest Unit of Evolution ○ Common misconception: organisms evolve during their lifetimes ○ Natural selection acts on individuals, but only populations evolve ○ Consider, for example, a population of medium ground finches on Daphne Major Island — During a drought, large-beaked birds were more likely to crack large seeds and survive, the finch population evolved by natural selection Microevolution is a change in allele frequencies in a population over generations Three mechanisms cause allele frequency change ○ Natural selection ○ Gene flow ○ Genetic drift Only natural selection causes adaptive evolution

Concept 21.1: Genetic variation makes evolution possible ● Variation in heritable traits is a prerequisite for evolution ● Mendel’s work on pea plants provided evidence of discrete heritable units (genes) ● Phenotypic variation often reflects genetic variation ○ Genetic variation among individuals is caused by differences in genes or other DNA sequences ○ Some phenotypic differences are due to differences in a single gene and can be classified on an “either-or” basis ○ Other phenotypic differences are due to the influence of many genes and vary in gradations along a continuum ● Genetic variation can be measured at the whole gene level as gene variability ● Gene variability can be quantified as the average percent of loci that are heterozygous (have two different alleles for a locus) ● Genetic variation can be measured at the molecular level of DNA as nucleotide variability ● Nucleotide variability rarely results in phenotypic variation ● Most differences occur in noncoding regions (introns) ● Variations that occur in coding regions (exons) rarely change the amino acid sequence of the encoded protein ● Phenotype is the product of inherited genotype and environmental influences ● Natural selection can only act on phenotypic variation that has a genetic component ● Some members of the same species have different environmentally controlled phenotypes ● Sources of Genetic Variation ○ New genes and alleles can arise by… mutations ○ A mutation is a change in the nucleotide sequence of DNA ○ Only mutations in cells that produce gametes can be passed to offspring ○ A “point mutation” is a change in one base in a gene ○ The effects of point mutations can vary: ● Mutations in noncoding regions are often harmless ● Mutations to genes can be neutral because of redundancy in genetic code ● Mutations that alter the phenotype are often harmful ● Mutations that result in a change in protein production can sometimes be beneficial ● Altering Gene Number or Position ○ Chromosomal mutations that delete, disrupt or rearrange many loci are typically harmful ○ Duplication of small pieces of DNA increases genome size and is usually less harmful ○ Duplicated genes can take on new functions by further mutation ○ An ancestral odor-detecting gene has been duplicated many times: humans have 350 copies of the gene whereas mice has 1000 ● Rapid Reproduction ○ Mutation rates are low in animals and plants ○ The average is about one mutation in every 1000 genes per generation ○ Mutation rates are often lower in prokaryotes and higher in viruses ○ Short generation times allow mutations to accumulate rapidly in prokaryotes and viruses ● Sexual Reproduction

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In organisms that reproduce sexually, most genetic variation results from recombination of alleles Sexual reproduction can shuffle existing alleles into new combinations through three mechanisms: crossing over, independent assortment, fertilization

Concept 21.2: Hardy Weinberg equation can be used to test whether a population is evolving (Gene pools and allele frequencies) ● A population is a localized group of individuals capable of interbreeding and produce fertile offspring (same place, same time) ● 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 are homozygous for the same allele Concept 21.3: Natural Selection, Genetic Drift, Gene Flow can alter allele frequencies in a population ● Natural Selection: differential success in reproduction results in certain alleles being passed to the next generation in greater proportions (for ex: an allele that confers resistance to DDT increased in frequency after DDT was used widely in agriculture) ● Genetic Drift: the smaller the sample, the more likely it is that chance alone will cause deviation from a predicted result— describes how allele frequencies fluctuate unpredictable from one generation to the next— tends to reduce genetic variation through losses of alleles, esp. in small populations ● The Founder Effect: occurs when a few individuals become isolated from a larger population— allele frequencies in the small founder population can be different from those in larger parent population due to chance ● The Bottleneck Effect- results from drastic reduction in population size due to a sudden environmental change- by chance, the resulting gene pool may no longer be reflective of the original population’s gene pool- if the population remains small, it may be furthered by founder effect Concept 21.3: Natural Selection is the only mechanism that consistently causes adaptive evolution ● Evolution by natural selection involved both chance and “sorting” ● New genetic variations arise by chance, beneficial alleles are “sorted” and favored by natural selection ● Only natural selection consistently results in adaptive evolution, an increase in frequency of alleles that improve fitness ● Relative fitness is the contribution an individual makes to the gene pool of the next generation, relative to the contributions of other individuals ● Selection indirectly favors certain genotypes by acting directly on phenotypes ● Three modes of natural selection: directional, stabilizing, disruptive a. Directional selection: favors individuals at one end of the phenotypic range b. Stabilizing selection: favors individuals at intermediate variants, against extremes c. Disruptive selection: favors individuals only at the extremes ● The key role of natural selection in adaptive evolution ○ Striking adaptations have arisen by natural selection- such as certain octopuses can change color rapidly for camouflage- the process increases frequencies of alleles that

enhance survival and reproduction Adaptive evolution occurs as match between an organism and its environment Continuous, dynamic process only natural selection does this, genetic drift and gene flow are not consistent to do this Sexual Selection ○ Natural selection for mating success ○ Can result in sexual dimorphism, marked differences between the sexes in secondary sexual characteristics ○ Male showiness due to mate choice can increase a male’s chances of attracting a female, while decreasing survival chances ○ Intrasexual (within sex) often males compete ○ Intersexual (between sexes- more choosy) often females ○ Female preferences evolve in the “good genes” hypothesis ■ If male genetic quality or trait is health, preference increases ○ Diploidy maintains genetic variation in the form of hidden recessive alleles ○ Heterozygotes can carry recessive alleles that are hidden from effects of selection Balancing selection occurs when natural selection to on maintains stable frequencies of two or more phenotypic forms in a population ○ Balancing selection includes heterozygote advantage and frequency dependent selection ○ Occurs when heterozygotes have a higher fitness than do both homozygotes ○ Natural selection will maintain both alleles at that locus ■ Ex: sickle cell allele causes mutations but helps against malaria too ○ Frequency dependent selection occurs when the fitness of phenotype declines if it becomes too common in population ○ Selection can favor whichever less common ■ Ex: such as right mouthed and left mouthed fish to eat fish in a pond ○ ○

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Why Natural selection does not produce perfect offspring ○ Selection can only act on existing variations ○ Evolution is limited by historical constraints ○ Adaptations are often compromises ○ Chance, natural selection and environment interact

Chapter 22: The Origin of Species ●

Speciation: the process by which one species splits into two or more species - Speciation explains the features shared between organisms due to inheritance from their recent common ancestor - Speciation forms a conceptual bridge between micro and macro evolution

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Microevolution: consists of changes in allele frequency in a population over time Macroevolution: broad patterns of evolutionary change above species level Species Concepts ○ Endless source of debate ○ Numerous concepts exist ○ Can be defined in a way that: ■ Enables classification (taxonomy) ■ Corresponds to discrete groups of organisms ■ Helps us understand how discrete groups arise (process) ■ Represent products of evolutionary history (historical) ■ Applies to the widest array or organisms

Concept 22.1: Biological Species Concept emphasizes isolation ● Species in latin means “kind” or “appearance” ● Biologists compare morphology, physiology, biochemistry and DNA sequences when grouping organisms ● This concept states that a species is a group of populations whose members have the potential to interbreed in nature and produce viable and fertile offspring (do not breed successfully w others) ● Gene flow (transfer of alleles in a population) allows for gene pool of a species to be held together to resemble each other more ● Reproductive Isolation: existence of barriers that impede two species from producing viable and fertile offspring, can occur before or after fertilization ● Prezygotic barriers clock fertilization from occurring by impeding different species from attempting to mate, preventing successful completion of mating, hindering fertilization if mating is successful ○ Habitat Isolation: Two species encounter each other rarely, or not at all because they occupy different habitats even though not physical barriers ○ Temporal barriers: species that breed at different times of the day, seasons, years ○ Behavioral Isolation: courtship rituals and other behaviors unique to a species ○ Mechanical Isolation: morphological differences preventing successful mating ○ Gametic Isolation: sperm of one species may not be able to fertilize eggs of another species ● Sometimes fertilization occurs.. allowing for hybrids to appear ○ Postzygotic barriers prevent the hybrid zygote from developing into a viable, fertile adult — Reduced hybrid viability or fertility ○ Reduced hybrid viability: genes of different parent species may impair survival ○ Reduced hybrid fertility: even if hybrids are vigorous, they may be st...