Evolutionary History of Life

Classification Cont: What does each split on a tree represent?

- Each split on the tree represents a divergence on two evolutionary lineages from a common ancestor

(4) Sexual Reproduction Cont. Give an example of this.

- One allele is passed from each parent to their offspring; These alleles are mixed together during Prophase I in a process called crossing over - Eye color example: hazel: brown, gray, and green - done from crossing over

Cladistics Cont: When can a taxon be referred to as a clade? When can if not be referred to as a clade?

- Taxon is only a clade if it is monophyletic - If it is paraphyletic or polyphyletic then the group does not represent a clade

Various Methods of Organizing Organisms: Cell Type

1. Cell Type • Prokaryotic: - Bacteria - Archaebactria • Eukaryotic - Eukarya

Lamark's Principles

1. Tendency toward perfection - All organisms have an innate tendency towards complexity and perfection 2. Use and disuse - New ways of use led to new structures - Explanation: the more you use something, the stronger it gets; the less you use something, the weaker it gets - Individual 3. Inheritance of acquire traits - Organisms could alter the size or shape of particular organs - Explanation: inheritance of parents; mom doesn't want kidney so therefore the offspring's kidney would be smaller

Various Methods of Organizing Organisms Cont: Acquisition of Nutrients

2. Acquisition of Nutrients • Feeding (Heterotrophs) - Fungi & Animalia • Making food (Autotrophs) - Plantae • Both - Eubacteria, Archaebacteria, & Protista • Photosynthesis & Cellular a Respiration - ALL PLANTS

Various Methods of Organizing Organisms Cont: Gas Exchange

3. Gas Exchange • Method to transfer gasses such as O2 & CO2 between the organism and the environment • 2 methods - Diffusion: (Eubacteria, Archaebacteria, Protista, Fungi, Plantae) - Organ System (lungs and/or gills (Animalia)

Various Methods of Organizing Organisms Cont: Waste Remova

4. Waste Removal • Excretion of metabolic waste products • Diffusion - Lower life forms (less complex) • Organ System - Higher life forms (more complex) - Digestive system

Various Methods of Organizing Organisms Cont: Circulatory System

5. Circulatory System • Transport of nutrients, gas, etc. through the organism via Diffuson • Plantae - Xylem and phloem circulate throughout vascular tissue • Animalia - Open/closed circulatory systems

Various Methods of Organizing Organisms Cont: Dispersion

6. Dispersion • Where organisms are located throughout the environment and how they got there • Locomotion - Organisms move around • Zygotic Movement - Parental organisms is non-mobile, so seeds or seeds or spores move instead (fertilized eggs shooting through the air) • Larval Movement - Parental Organism is sedentary, so larvae move before full development (babies moving before they fully develop)

Various Methods of Organizing Organisms Cont: Support & Protection

7. Support and protection • External vs. Internal • Plantae - Cell wall - Hard vs. Soft • Animalia - Skeletons - Exo vs. Internal

Various Methods of Organizing Organisms Cont: Coordianafion of functions

8. Coordination of functions • Specialization of cells in higher life forms lead to the diversification of neurons • Bundles of neurons from nerves which combine to form the nervous system • Hormones and other neurotransmitters are used to conduct signals in the body

Various Methods of Organizing Organisms Cont: Reproduction

9. Reproduction • Asexual - Binary fission (Mitosis) - Fragmentation (Worm getting cut in half, and two worms forming) - Budding (Plants bud to make a new individual unit) • Sexual - External Vs. Internal fertilization - External: fish laying eggs - Internal: babies

Sources of Genes Variation: 4 main ways: What do these four processes alter?

Four main ways: • Formation of new alleles • Altering gene number or position - Trisomy 21 (down syndrome), Trisomy 13 (patau syndrome, etc.) • Rapid reproduction - This including the options above, result in mutations • Sexual reproduction - New (?? commemorate) of DNA • These four processes alter the existing genes, and allow for new types of phenotypes to be formed

Misconceptions of Evolution Cont:

Individuals do not involve, populations do

What is peptidoglycan?

Proteins and carbohydrate suck together

Natural Selection

• "Survival of the fittest" • Fitness - the ability to survive and reproduce • Fitness is determined by mutations and its interactions with the environment which the organism lives in • Interaction of an individuals phenotype with its environment

The Bottleneck Effect

• A massive reduction in a population can cause this effect • Certain alleles may be overrepresented in the surviving population, leading to the elimination of some genes that may have been beneficial to survival • The implications of the bottleneck effect is that even if the population recovers to its original size, there may still be low levels of gene variation • Extinction - most of them are dead - lose a lot of alleles ; influence gene flow - Tigers, Pandas, Monk Seals + Any animal on the endangered species list

Founder Effect: Isolation

• A small population becomes isolated, & establishes a new population with a different gene pool from the source population • Accounts for high frequency of certain inherited disorders, due to the small existing gene pool • Frequency of alleles that affect traits may be extremely higher or lower than their counterpart in the source population • Isolation

Darwin and The Origin of Species

• Although Darwin was not the first person to propose the theory of evolution, he is widely considered the first person to "perfect" the theory of evolution • Darwin began his explanation of evolution by abandoning the idea of a species as perfect and unchanging, but rather argued for natural variation and natural and artificial selection (eat something → artificial selection)

(1) Formation of New Alleles

• Arise from mutations (or a change in the nucleotide sequences) in a sequence of DNA • Only new alleles formed in gametes will be passed on to the next generation, but a majority of the mutations occur in somatic cells • An example of this is sickle cell anemia - A disease that affects the formation of healthy red blood cells; heterozygous people who have sickle cell anemia can repel malaria)

Organization of Domains/Kingdoms

• Based on similarities & differences • Can include large features like cell type, or cell structure • Can include small features like body type or mode of acquiring nutrition

(4) Sexual Reproduction

• Because of the random fertilization, independent assortment, and crossing over principles, we see larger amounts of genetic variation in populations that multiply via sexual reproduction • This allows existing alleles to combine in unique ways that were never seen before, & even allow new combinations of traits and genes to be created

Plantae Cont.

• Cellulose cell walls • Terrestrial biosphere depends on plants - primary producers • Important source of oxygen • Grouped into non-vascular (no transport) and vascular (transport component); seedless & seed producing

Fungi Cont.

• Decomposers • Some are parasitic • Source of a variety of food sources (bread and beer); used for antibiotics and chemicals, responsible for spoilage and crop loss

3 Problems With Lamark's Theory

• Did not know how traits are inherited - Study of genetics wasn't fully formulated • Did no know behavior did not have an effect an inheritable characteristics • Thought that organisms made a conscious choice to become more complex and evolved

Difference between eubacteria & archaebacteria?

• Difference in cell wall (E does have peptidoglycan & A doesn't have peptidoglycan)

Homologous Vs. Analogous Cont: How does knowing the difference between the two, help? What are analogous structure that evolve independently called?

• Differentiating between the two is one of the most important aspects in constructing phylogenies • Analogous structures that evolve independently are called homoplasies

Phylogenetic Trees: What are divergences? What are the three different types of "groups" in a phylogenetic tree?

• Divergences are branch points on the tree • A lineage that evolved early & remains unbranched is called a basal taxon, while groups that share a recent divergence from the same branch are called sister taxa (sister taxa is more related bc they share a common ancestor) • When a divergence occur with more than two new lineages this is called polytomy

Classification: least to most specific

• Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (Donkey Kong Plays Clash Of Fame while Going Swimming)

What are the kingdoms?

• Eubacteria and eukaryotes are divided into 5 kingdoms - Monera - Protista - Fungi - Plantae - Animalia • Archaebacteria is considered its own kingdom • Eukarya: least diverse • Archae: middle • Bacteria: most diverse

What is Protista?

• Eukaryotic • Protozoa - microscopic, heterotrophic, mobile (cila, flagella, or pseudopodia), important component of zooplankton, some parasitic • Algae - photosynthetic; red or brown pigment in addition to chlorophyll; important part of marine and freshwater environments bc of oxygen production • Slime and water molds - heterotrophic, reproduction via spores, aquatic and terrestrial with various modes of acquiring nutrution

Fungi

• Eukaryotic, heterotrophic • Absorbs nutrients after enzyme digestion • Body composed of hyphae (it forms masses called mycelium) • Chitin cell wall (also found in bugs)

Plantae

• Eukaryotic, multicellular • Photosynthetic • Multicellular reproduction organs • Alternation of generations

Animalia

• Eukaryotic, multicellular, heterotrophic • Exhibit tissue differentiation and complex organ systems • Movement by muscular contraction • Have specialized nervous tissue to coordinate responses to stimuli

Influences on Evolution: Variations

• Genetic variation is the representation of different phenotypic variations • Variation at the whole gene level (gene variability) can be quantified as the average percentage of loci that are heterozygous • Variation at the molecular level of DNA (nucleotide variability), but very little changes lead to phenotypic variation

Homologous Vs. Analogous

• Homologous refers to something that changed from similar structures over time, while analogous refers to structures that evolved to be similar due to similar environments

Homologous & Analogous Structure Examples

• Homologous: structures that are similar in origin (bone structures) - Whale and Human • Analogous: structures that phenotypically look the same, but aren't the same in origin (bone structures) - Fish and Whale - Bird & Bat - Snakes & Eels

Ingroups Vs. Outgroups

• Ingroups represent the species or groups of species that remain in the line • Outgroups represent the species or group of species that diverge from the common lineage • Useful for figuring out common traits

Lamark

• Jean-Baptiste Lamark was a scientist that started to analyze how organisms adapted to their environments • Proposed that by selective use or disuse, organisms acquired or lost certain traits during their lifetime • Lamark had three main ideas that influenced future scientists

Dichotomous Key

• Key - consist of a series of choices that lead to the correct item • Dichotomous - "divided into two parts" • If steps are followed correctly, organisms will always be able to be identified using this key (if applicable)

Classification

• Known as taxonomy • Groups are decided by common features • One method of classification is a cladogram

Animalia Cont.

• Major consumers in almost all ecosystems • Show great variety of forms and function • Complexity of systems increased over time - Nervous systems, brain development, and circulatory systems

Artificial Selection: Mankind has been...

• Mankind has been artificially selecting organisms with specific traits for the benefit of man rather than the survival of the species • Species like sheep, crops, and dogs have been selected for specific traits and bred until those traits were dominantly expressed • By artificial selection, mankind was able to produce a wide range of plants and animals that looked very different than their ancestors

(2) Altering Gene Number or Position

• Most of the time large changes in the chromosomes create negative effect of the organism that experiences it • In rare cases, the rearrangement can be beneficial (in the case of linking DNA segments that produce a positive effect) - Ol factory receptor: something that allows us to smell - Truffle: fungus that grow in the ground • Some duplications such as the genes that play a role in detecting odor, play a positive role in fitness

Classification Cont.

• Organisms are named bionomially based upon the genus and species - Binomial Nomenclature is a process of naming organisms based on their genus or species) • Visually shown on a phylogenetic tree and labeled by taxa (or taxon; groups among the tree)

Cladogram

• Original classification was based less upon factual relationships and more upon different characteristics • Many different classification trees could be formed with the same organisms • A solution to this was a cladogram, or a method using derived characteristics to classify organisms

What is archaebacteria?

• Prokaryotic, unicellular, microscopic • Cell wall does not contain peptidoglycan • Differs biochemically, from eubacteria (composure of their cell wall) • Inhabits sewage, swamps, animal guts, salty environments, and hot habitats

What is eubacteria (good bacteria)?

• Prokaryotic, unicellular, microscopic, cell wall made of peptidoglycan • Mostly decomposers, but some bacteria are parasitic, autotrophic, or nitrogen fixating • Important in food industry, medical industry, and personal hygiene

Three Key Points of Phylogenetic Trees

• Show patterns of descent, not phenotypes • Branching does not necessarily indicate the actual ages of the organisms • Taxon on phylogenetic trees did not evolve from the taxon next to it, but rather they share a common ancestor - whales and humans

Homologous Structures

• Similarities in bone arrangement and number can prove to be just as helpful in identifying divergences as DNA • DNA sequences can also be called homologous if they descended from a common ancestor • Very easily confused with analogous structures

Various Methods of Organizing Organisms Cont: The 5 Kindgdoms

• The 5 kingdoms are a result of various methods of classification, but usually cell type - Monera (prokaryotes) - Protista (single celled eukaryotes) ; Amoeba - Fungi (fungus and related organisms) - Plantae (plants) - Animalia (animals)

Phylogeny

• The evolutionary history of a species or a group of species • To be able to study phylogenies, we must use systematics, a discipline that focuses on classifying organisms and determining their evolutionary relationships • Response for showing evolutionary relationships between organism

Domains

• The most general groups of organization are called domains • Three domains - Bacteria (Eubacteria) - Archae - Eukarya

Genetic Drift

• The probability of deviation from the predicted result increases as the number of individuals (or sample size) decrease • Chance events can cause allele frequency to fluctuate unpredictability from one generation to the next • Two main effects that affect genetic draft - the founder effect and the bottleneck effect

(3) Rapid Reproduction

• The speed in which organisms allow some populations to experience more genetic variation is the same amount of time • Because prokaryotes and viruses multiply at a quicker rate, they often experience more mutations and would experience quicker mutations allowing them to become resistant to antibiotics and other treatments

Natural Selection Cont.

• To both artificial and natural selection, only certain individuals or a population produce new individuals • To artificial selection, the trait being selected for, contribute to the fitness of that organism • Over time, natural selection results in changes in the inherited characteristics of a population and the change increase a species' fitness in its environment • Positive mutations → passed on ; Negative mutations → passed on and the species eventually may die

Cladistics

• Using ancestry to classify organisms • Separated into groups called clades - Represents an ancestral species and all descendants

Misconceptions of Evolution Cont: What can we examine? How can we examine this? What are the three main events that influence allele frequency?

• We can examine microevolution, the smallest unit of evolution - To do this, we can examine the change in allele frequency • Three main events that influence this are natural selection, genetic draft, and gene flow