Bio 112 Exam 1

Fact

An observation that has been repeatedly confirmed and for all practical purposes is accepted as “true”

Hypothesis

A tentative statement about the natural world leading to deductions that can be tested

Theory

A well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences and tests hypotheses

Pattern of a scientific theory

A statement that summarizes a series of observations about the natural world; the what

Process of a scientific theory

A mechanism that produces the pattern or set of observations; the how

Typological thinking

The idea that every organism is an example of a perfect essence that is unchanging. Acknowledged that individuals of a species vary slightly, but deemed them as trivial deviations around the perfect essence. Introduced by Plato

Scale of nature

An organization of typological thinking in which species are organized into a sequence based on increased size and complexity. Introduced by Aristotle

Change through time

Lamarack built on scale of nature and claimed that organisms originate at the bottom of the scale by spontaneous generation, then evolve by moving up the scale over time to continuously progress and produce larger and more complex species.

Common ancestry

Darwin and Wallace introduced the idea that all species are related by a common ancestor

Population thinking

The idea that variation among individuals in a population is key to understanding the nature of the species

Patterns (2) of the theory of evolution

Species change over time

Species are related by common ancestry

Collectively: evolution

Major process of theory of evolution

Natural selection - Differential survival and reproductive success

Vestigial trait

A reduced or incompletely developed structure with no function, or reduced function, but is clearly similar to functioning organs/structures in ancestral or closely related species

Four main evidences for evolution

Sedimentary rocks and rocks derived from episodic lava flows are used to age fossils

Extinction (proves species aren’t static)

Resemblances found between fossils and living species

Vestigial traits

Genetic homology

Similarity in DNA nucleotide sequences, RNA nucleotide sequences, or amino acid sequences from a common ancestor

Developmental homology

Similarity in developmental structures of processes; similarity in embryonic form due to common ancestry

Structural homology

Similarity in adult morphology (form) due to a common ancestor

Homology

The study of likeness; A similarity that exists in a species due to common ancestry

Internal consistency

The observation that data from independent sources agree in supporting predictions made by a theory

Artificial selection

To choose certain individuals with desirable traits to reproduce and manipulate the composition of the population

Darwin’s 4 postulates for evolution by natural selection

1. Variation exists among individuals within a population
2. Some trait differences are heritable
3. Survival and reproductive success are highly variable
4. The subset of individuals that survive and produce the most offspring are not random

Fitness

The ability of an individual to produce surviving, fertile offspring

Natural selection

Differential success in reproduction; produces adaptations in organisms that fit the environment; increases the frequency of alleles that contribute to reproductive success in a certain environment

Adaptation

A heritable trait that increases the fitness of an individual in a particular environment relative to others lacking that trait

Explain how evolution caused drug resistance

The original population contained individuals with the heritable ability to resist a chemical compound. Susceptible individuals died and the alleles related to resistance increased in frequency

Acclimatization

A change in an individual’s phenotype that occurs in response to a change in natural environmental conditions; Phenotype changes NOT passed down to offspring

Limitations of natural selection

1. Non-adaptive traits; Vestigial traits don’t increase the fitness of individuals, but they are not adaptive structures, they exist because they were present in ancestral population
2. Fitness trade-offs; A compromise between 2 traits that can’t be optimized simultaneously
3. Genetic constraints; Selection on 1 trait may cause a change in another strait
4. Historical constraints; All traits evolve from previous traits
5. Environmental constraints; Natural selection occurs in context of changing environments

Mechanisms/processes of evolution

1. Natural selection
2. Genetic drift
3. Gene flow
4. Mutation

Genetic drift

Causes allele frequencies to change randomly/by chance; Most pronounced in small populations; Can lead to random loss or fixation of alleles

Gene flow

Occurs when individuals leave 1 population, join another, and breed; Tends to equalize allele frequencies between both populations

Mutation

Modifies allele frequencies by continually introducing new alleles; Changes the primary structure of DNA and increases genetic diversity

Hardy-Weinberg Equilibrium

Allele frequencies: p+q=1

Genotype frequencies: p^2+2pq+q^2=1

Acts as a null hypothesis for the study of evolutionary processes

Five assumptions of Hardy-Weinberg Principle

1. Random mating; Assumes gametes combine at random and individuals don’t choose mates
2. No natural selection; Assumes all members of parent population survive and contribute equal number of gametes to the gene pool
3. No genetic drift; Assumes alleles are picked in their exact frequencies p and q. Acts as if population is infinitely large
4. No gene flow; Assumes no new alleles are added by immigration and none are lost through emigration
5. No mutation; Assumes no new alleles are introduced

Four modes of natural selection

1. Directional selection; Changes the average value of a trait (phenotype) in 1 direction
2. Stabilizing selection; Reduces the variation in a trait by reducing both extremes
3. Disruptive selection; Increases variation in a trait by eliminating phenotypes near the average value and favoring extreme phenotypes
4. Balancing selection; Maintains variation in a trait because no phenotype has a distinct advantage

Founder effect

A type of genetic drift in which a change in allele frequencies occurs when a group of individuals immigrates to a new area and a new population is established

Genetic bottleneck

A type of genetic drift in which a sudden reduction in population size occurs, reducing the diversity of alleles present in the population

Point mutation

A change in a single base pair in DNA; Could result in a polypeptide with a novel amino acid sequence or in a change in regulation of the expression of other genes

Chromosome-level mutation

A change in the number or composition of chromosomes; Can cause gene duplication (increase the number of copies of a gene)

Lateral (horizontal) gene transfer

The transfer of genetic information from one species to another

Phylogeny

The branching evolutionary history of species or taxonomic groups (groups of organisms)

Phylogenic tree

A simplified diagram of phylogeny

Outgroup

A taxon that is not part of the taxonomic group of concern, but is closely related

Node

A point within the tree where a branch splits into 2 or more branches; represents the most recent common ancestor of the descendant groups

Polytomy

A node that depicts an ancestral branch splitting into 3 or more descendant branches

Character/trait

Any heritable genetic, morphological, physiological, developmental, or behavioral characteristic that varies among the taxa being studied

Monophyletic group

Any group that forms an evolutionary unit including an ancestral population and all of its descendants

Paraphyletic group

Includes an ancestral population and some of its descendants, but not all

Polyphyletic group

Shares similar traits but does not include most recent common ancestor

Homology

Similarity due to common ancestry

Homoplasy

Similarities not based on common ancestry; Traits evolved independently in 2 or more different lineages

Parsimony

Assumes that the most correct phylogenetic tree is the one with the fewest steps

Evolutionary distance

Method for determining correctness of phylogenic tree; Acknowledges that more rapid evolutionary change can occur in some branches

Maximum likelihood/Bayesian analysis

Complex mathematical model for phylogenic trees that requires more information; Produces precise estimates of evolutionary history with more statistical power

Fossil record

The total collection of fossils

Limitations of the fossil record

1. Habitat bias
2. Taxonomic bias
3. Temporal bias
4. Abundance bias

Habitat Bias

Burial in sediment is crucial to fossilization, so organism that live in areas where sediments are actively deposited are more likely to form fossils

Taxonomic Bias

Organisms with hard portions such as shells or bones are more likely to leave fossils

Temporal Bias

Recent fossils are more common than ancient fossils

Abundance Bias

There are more fossils of common species or organisms that are abundant, widespread, and present on Earth for a longer period of time

Adaptive Radiation

Occurs when a single lineage rapidly produces many descendant species with a wide range of adaptive forms

Cambrian Explosion

A period of about 50 million years in which life forms became much larger and more complex and many different traits emerged in organisms (adaptive radiation)

Causes of Cambrian Explosion

1. High oxygen levels; Increased aerobic respiration supported larger bodies and more active movements
2. Diversification of algae; Larger and more nutrient-rich photosynthetic organisms produced oxygen and served as a higher quality food source, making more energy and mass available for growth, reproduction, and diversification
3. Evolution of predation; Evolution of predation caused natural selection for shells, hard exoskeletons, rapid movement, etc.
4. New niches beget new niches; Once animals could move and use new resources, availability to exploit new niches created more new niches, driving speciation and ecological diversification
5. New genes, new bodies; Hox genes are important for organizing the development of body in diverse animals by signaling where cells are in he embryo. Increased number of hox genes allowed larger and more complex bodies to evolve

Microbiome

A community of microbes that naturally inhabits a particular area and encompasses all of the contained genetic material

Microbes

Microscopic organisms

Pathogens

Bacteria that causes diseases

Koch’s postulates to establish a causative link between a microbe and a disease

1. Microbe must be present in individuals suffering from the disease and absent from healthy individuals
2. Microbe must be isolated and grown in a pure culture away from the host organism
3. If microbe from pure culture is injected into a healthy individual, disease symptoms should appear
4. Microbe must be isolated from diseased experimental individual and again grown on a pure culture to examine its size, shape, and color to be the same as the original microbes’

Bioremediation

The use of living organisms (Bacteria or Archaea) to degrade environmental pollutants

Enrichment culture

Based on establishing a specified set of growing conditions. Cells that thrive under these conditions increase in numbers enough to be isolated and studied

Metagenomics

Used to catalog all genes present in a mixed community of prokaryotes; Based on extracting and sequencing DNA fragments and comparing sequences with known genes to identify species and investigate biological processes

Transformation

When bacteria or archaea naturally take up DNA from the environment that has been released by cell lysis or secreted

Transduction

When viruses pick up DNA from 1 prokaryotic cell and transfer it to another cell

Conjugation

When genetic information is transferred by direct cell-to-cell contact

Plasmid transfer via conjugation

A conjugation tube forms between 2 prokaryotic cells and a plasmid (a small circular piece of DNA) is copied in 1 cell and transferred to another

Recombination via conjugation

Occurs when a plasmid that has been integrated into the main bacterial chromosome is copied and transferred with genes from the main bacterial chromosome through a conjugation tube, resulting in a new combination of alleles on receiving chromosome

Morphological diversity in bacteria

1. Size
2. Shape; filaments, spheres (cocci), rods (bacilli), or spirals can be arranged in chains or clusters
3. Motility; flagella spin to allow bacteria to swim ahead or tumble. Bacteria can also glide to creep along surfaces

Gram-positive cells

Have a plasma membrane surrounded by a cell wall with extensive peptidoglycan

Gram-negative cells

Have a plasma membrane surrounded by a cell wall that has 2 components: a thin, gelatinous later with peptidoglycan and an outer phospholipid bilayer

3 ways in which bacteria and archaea acquire energy to produce ATP

1. Phototrophs; Use light energy to excite electrons, ATP produced via phosphorylation


2. Chemoorganotrophs; Oxidize organic molecules with high potential energy, ATP produced by cellular respirator or fermentation


1. Chemolithotrophs; Oxidize inorganic molecules with high potential energy, ATP produced by cellular respiration where inorganic compounds act as an electron donor

2 ways bacteria and archaea obtain building-block compounds with carbon-carbon bonds

1. Autotrophs; Synthesize their own compounds from simple starting materials
2. Heterotrophs; Absorb ready-to-use organic compounds produced by other organisms