BIOL 359 Test 1

Ancient greek views of evolution

Anaximander: species formed from water- descendence from fish
Empedocles: Heads, limbs, other organs joined at random → some combos fit for survival
Plato: idealism- all natural phenomena are imperfect representations of a true essence

Aristotle’s view of evolution

Static world- fixed essences; templates for all species. Movement from inanimate matter to ‘higher forms of nature’ from least to most perfect. Permanent, unchanging. Christianity → ladder of nature and the great chain of being.

Carolus Linnaeus

Father of Taxonomy. Systema Naturae classification of species; framework for taxonomy.

Jeane Baptiste Lamarck

Philosophie Zoologique. Species Change over time into new species by inheritance of acquired characteristics (use and disuse).

Erasmus Darwin

Species are modified versions of previous forms. Grandfather of Darwin.

Georges Cuvier

Father of comparative anatomy, paleontology, part of Catastrophism → Earth modeled by great catastrophes that resulted from forces that no longer operate today.

Catastrophism

Influenced by Georges Cuvier. Earth is modeled by great catastrophes that resulted from forces that no longer operate today. Christian reconciliation of geological history with the age of the Earth (according to bible).1654: Archbishop James Ussher said Earth was 5650 years old in 4004 BC. Lightfoot: Elaborated on exact timings.

James Hutton

Father of Geology and the principle of Uniformitarianism → Geological processes today are the same as in the past.

Charles Lyell

‘Principles of Geology’ published, influencing geology as a cornerstone. Ended catastrophism with evidence for uniformitarianism.

Charles Darwin

Father of Evolutionary Biology. Medicine at Edinburgh before becoming a clergyman. Examination of finches → species change. Struggled with other ideas- didn’t explain adaptation.

Alfred Russel Wallace

Contacted Darwin- similar ideas to Darwin’s natural selection. Published together.

Darwin’s evolutionary theory

1859. All species, living or extinct, descended without interruption from one or few original forms of life, and are subject to the theory of Natural Selection.

Johann Gregor Mendel

Mendelian genetics and the gene. Seemed incompatible with natural selection but later was found to be.

Morgan, Sturtevant, Bridges

Genes are on chromosomes

Dobzhansky, Mayr, Simpson, Stebbins & Rensch

Natural Selection: heritable variation consistent with evolution at all levels.

JBS Haldane, RA Fisher, Sewall Wright

Mathematical description of genes in populations. Founders of Population genetics.

Rise of Molecular Biology

Watson and Crick: structure of DNA → Practical DNA sequencing → Developmental genetics reveals deep homologies in developmental genes → Genomics and the sequencing of entire genomes

Intelligent Design theory

Alternative ‘scientific theory’ to explain biological complexity and origins. Idea that Darwinian evolution can’t achieve such complex processes. Significant controversies with school systems. Not a scientific theory- not falsifiable or internally consistent, or even testable.. Evolution- scientific fact and theory. Began with William Paley, popularized with Michael Behe, Discovery Institute and Center for Cultural Renewal.
Idea of irreducibly complex mechanisms that cant function without all parts present- no precursors for evolution. However: various ‘older’ species in same lineages can have simpler versions that show evolution of the same mechanisms/traits.
Counterarguments: If a biological structure is so complex, why introduce something more complex?
Why are the designs so lousy? Unoptimized anatomy.

Evidence for evolution- selective breeding

Researchers bred mice over 24 generations to run more on an exercise wheel. Selected group ran 2.78x as far as the control group

Evidence for evolution- Direct observation

After a drought, a wild population of field mustard evolved an earlier average flowering time. 1997: more days. 2004: less. Between: flowering time was between both purebred populations for hybrids.

Fruit fly larvae foraging behavior was observed- at higher densities, larvae that travelled further (rovers) were favored over those that didn’t (sitters).

Apple Maggot flies- original host is hawthorn. 300 years ago, apples were introduced and now some flies have evolved to use apples as a host. Evolutionary changes related to earlier apple ripening times. Beginning of a new species.

Evidence for evolution- vestigial structures and organs

Royal Python- vestigial limbs. Brown Kiwi: vestigial wings. Humans: tailbones, muscles involved for ‘goosebumps’ that are used in other primates. Stickleback fish: armor disappears when transitioning into freshwater populations.

Evidence for evolution- Lab experiments

Bacteriophage mutant of a virus that only infects P. Syringae can infect both P. Syringae and P. pseudoalcaligenes is grown in P. pseudoalcaligenes culture for 150 generations- virus now only infects P. pseudoalcaligenes. New species.

Evidence for evolution- Natural populations

Three spine sticklebacks: Same species that live in the same area can slowly evolve to live in different parts of the same environment. Many of these still interbreed as subpopulations even when looking completely different, but eventually they can become distinct species.

Siberian Green Warbler: Ring species- live in a ring around the Tibetan plateau and display several differences as variants. Area where variants meet again but can’t interbreed- one variant dispersed far to the west.

evidence for evolution- fossil record

Georges Cuvier- paleontology. Alt hypothesis: evolution has occurred→ Changes in the organisms found in the fossil record should be observed, and strong geographic patterns are observed with respect to organism in the fossil record and those that exist today.

Law of succession: Fossils in a geographic region are more related to extant fauna in the region than in organisms in different regions.

Evidence for evolution- transitional forms

Blennies: Fish in the transition of moving to land. Prefer to stay on land, can leap great distances on land.
Archaeopteryx: between dinosaurs and birds. Have flight feathers for gliding.
Odontochelys: Transitional turtle- shoulder blades are in the process of developing under the ribs (that become the shell), instead of regular amniotes that have shoulder blades above ribs.

Evidence for Evolution- Homology

Structural homologies: mammals and bone structures- differ in shape and form but basic structures are the same (two forearm bones, one arm bone, etc.). Plants can have very similar structures as well.

Developmental homologies: Similar embryos across different species; differentiation later in development. Testes: start near the heart, move down to where they ultimately are positioned. Sharks also have testes near the heart.

Genetic code: All organisms share codons, molecular machinery. Pseudogenes- genes no longer in use that are shared among different organisms.

Evidence for evolution- Age of the Earth.

Uniformitarianism- huge amounts of time required to create mountains and other geological strata in nature. Thus, a 6000 year old Earth is not possible. Radiometric dating: Measuring based on atom isotopes and half-lives elapsed in particular samples. Less isotopes mean less half-lives elapsed and vice versa. Earth is 4.6 billion years old, and life has been present for at least 3.2 million years.

Fundamental Geological principles

Principle of Superposition: Younger geological layers sit on top of older ones.
Principle of Original Horizontality: lava and sedimentary rocks were originally laid down horizontally.
Principle of Cross Cutting Relationships: Rocks that intrude into others are always younger.
Principle of Inclusions: Boulders or other fragments found in a body of rock are older than hosts.
Principle of Faunal Succession: More recent life forms are closer to recent fossils than older ones.

Correspondence among scientific datasets

Plate tectonics, continental drift, and fossil record provide evidence that Earth and organisms have changed over time.

Natural Selection

Differences in the survival and reproduction of phenotypes, leading to differences in their contribution to the next generation, resulting in a change in the frequency of heritable
phenotypic variations in populations over time.
- Acts on individuals but consequences occur in populations.
- Results in adaptive evolution.
- Dynamic- differs by generation.
- produces new traits with mutation
- Nonrandom, but not progressive, doesn’t look ahead, doesn’t lead to perfection.

Components of Natural Selection

• Living things produce more offspring than can be supported

• There is constant struggle for existence

• Individuals vary by phenotypes

• heritable variation

• Individuals best adapted to current conditions are most likely to survive and reproduce

• Heritable adaptations are passed down

• Acts on phenotypes, but evolution only occurs with allele frequency changes

Evolutionary Fitness

Contribution of an individual to the next generation. Three elements:
Viability/Mortality: Ability to survive and reach reproducible age
Sexual Selection: Ability to procure a mate
Fecundity selection: Family size- amount of gametes produced.

Darwin’s postulates

• Individuals within a species are variable

• Some variations are heritable (proportion of trait variation attributable to genotypes)

• More offspring are produced than survive, and some are more successful than others in survival and reproduction

• Non-random survival and reproduction of individuals

• Those that survive and reproduce the most are the most fit

Darwin’s Finches and his postulates

Variable populations: Finches were marked for wing/tail length, beak width/depth/length. All were found to be variable.

Heritable Variation: Beak size similarity was measured between parents and offspring. Strong statistically significant positive relationship found in beak size similarity. Regression line is between 0 and 1.

Excess of offspring: Drought occurred, and strong correlation between population size and seed availability. Only a fraction of the population survived. Variable survival means selection occurs.

Nonrandom survival and reproduction: Drought survivors had a different average beak size and other morphological characteristics- larger beak sizes to more easily eat seeds.

Cane toads and natural selection

Cane toads were introduced to australia and have toxic skin glands. Snakes that ate them would die, marking an increase in snakes with smaller jaws and slender builds (can’t eat cane toads). Marked decrease in jaw size in Green tree snakes, red bellied black snakes.

Unnatural Selection

'Natural Selection’ induced by humans-
e.g. Big Horn Sheep progressively getting smaller horns after trophy hunting before breeding seasons
e.g. Average size of atlantic cod has gone down through generations of fishing
e.g. Bacterial resistance to antibiotics

Types of Variation

Genetic Variation: Parents → offspring. Different phenotypes due to different genotypes.

Environmental variation: Different phenotypes depending on exposure to different environments, even with the same genotype(e.g. Water fleas develop armor when in a habitat with predators)

Environment Interactions: Different phenotypes depending on interaction of genotypes within an environment. (e.g. Leopard Geckos and other reptiles- male/female development based on temperature of eggs)

Phenotypic Plasticity

genetically identical individuals can have different phenotypes in different environmental conditions. Environmental Variation.

Reaction Norm

range of phenotypes that a genotype can have as a result of different environments. Different genotypes have different reaction norms. Genotype by environment interaction.

Mutation

Any heritable change in genetic material. Raw material for other evolutionary sources.
-Single gene mutation: affect one gene
- Chromosomal mutation: Affect many genes.
- Limited effect on allele frequencies and starts at a low frequency. Strong effect with selection.

Point Mutations

Single base pair changes. Introduce new alleles.
Transitions: More common- purine → another type of purine or pyrimidine → other type pyrimidine
Transversion: Purine → Pyrimidine
Synonymous: amino acid not changed. Source of silent mutations due to redundancy in genetic code
non-synonymous: amino acid is changed

Nonsense mutation

mutation that causes a stop codon to appear prematurely.

Indels (insertions/deletions)

Insertion or deletion of 1+ nucleotides in DNA sequence- result in reading frameshifts (highly deleterious).

Pleiotropy

Single mutation affects multiple phenotypic traits. Most mutations that cause phenotypic changes are pleiotropies.
Ex: Phenylketonuria (PKU) caused by absence of enzyme converting phenylaline to tyrosine. Build-up of phenylaline. Causes a variety of mental conditions and changes to appearance, along with conditions like eczema and microcephaly.

Fitness Effects

Neutral mutations: no effect on fitness. Synonymous mutations are not always neutral due to codon bias → only one or two codons usually used in an organism for one amino acid.

Deleterious: reduce fitness. In general outnumber beneficial mutations by a large margin (ex: bacteriophage f1, C. elegans reduction in fitness with accumulated mutations).

Beneficial: Increase fitness.

Lethal: Results in death before reproduction.

Non-synonymous mutations: Not always non-neutral.

Disadvantageous mutations that have benefits: Sickle Cell Anemia

Homozygous for sickle cell anemia: deficiency in oxygen transport, but is more resistant to malaria. Heterozygous for sickle cell anemia: favored in areas where malaria is endemic → mutation is always present.

Mutation rates

Individuals: Diff DNA Pol can make errors at different rates → correction efficiency can correlate with point mutation rates.

Species: Generation time and longevity can influence mutation rates. Ex: Elephants and mice can have the same mutation rate.

Genomic regions: Arguments that mutation rate is lower in regions of genome that are more likely to be deleterious. In debate.

Gene duplication

Duplication with:
Unequal crossing over: chromosomes align incorrectly → non-allelic loci cross over → deletion and a new gene

Retroposition: Introns spliced out by transcription → Reverse transcription → integration of new gene

Loci retain function, gain new function, become pseudogenes, or evolve to build gene families.

Paralogous

Genes duplicated within a genome and diverge in function. Like analogy

Orthologous

Genes that share a common ancestral sequence, separated with speciation events. Like Homology

Chromosomal Mutations- Inversions

ionizing radiation- usually large regions of chromosomes. Affect linkage, gene order.
- Breaks and reanneals in opposite orientation.

Genetic Cline

Increase or decrease in the frequency of an allele or genetic variant over geographic distance.

Polyploidy

Large scale mutation- Duplications of entire sets of chromosomes. Humans- diploid. Many plants can be polyploid, along with self-fertilizers (autopolyploid) or hybridization of different species (allopolyploid). Errors in meiosis usually.

- Self-fertilization in plants: After first generation, 4n plants can self-fertilize, mate with 4n sibling, or backcross with parent.

- Can lead to new functions + adaptation potential (backup copies of chromosomes). Can create new species and cause genetic variation.