154 terms

Organic evolution Exam 1


Terms in this set (...)

Descent with Modification
1. All species share common ancestry
2. Changes occur through natural selection
Traits that have evolved by natural selection; inherited characteristic that increases an organism's chance of survival
Everything is perfect.

a belief that things have a set of characteristics that make them what they are, and that the task of science and philosophy is their discovery and expression; the doctrine that essence is prior to existence.

Change in the genotypic and phenotypic characteristics of groups of related organisms (populations) over generations.
-passed in the genetic material.
-can vary from simple gene frequencies in a population to macroevolution.
Evolution is NOT...
Changes in an organism due to development from zygote to adult (ontogeny)

Darwinism (refers to evolution by natural selection, although Darwin was aware of other evolutionary mechanisms)

1) Changes in an organism due to development from zygote to adult (ontogeny)
2) Darwinism
Natural Selection
A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits.

A) some variation among individuals in a population is heritable
B) some variation among individuals affects the ability of the individual to survive, grow and reproduce (the "fitness" of the organism)
C) those variations that are both heritable and improve the individual's fitness will increase in frequency in the population over generations
D) The survival and reproduction of individuals is not random; it is tied to the variation among individuals.
E) Focused on change within populations and he documented variation among individuals within a population.
Transmutation of species
view that species can change and give rise to new species
Inheritance of Acquired Characteristics
Characteristics changed as the use of them changed and these changes were passed on to the next generation. (LAMARCK)
Inheritance of acquired characteristics

the theory of evolution through the inheritance of acquired characteristics in which an organism can pass on features acquired during its lifetime
Evolution by natural selection

the theory of the evolution of species by natural selection advanced by Charles Darwin.
A modern Darwinian theory that explain new species in terms of genetic mutations

a revision of Darwin's original theory of evolution to include modern genetics
The Modern Synthesis
Developed models of evolution using discrete mutations that resulted in evolutionary change consistent with Darwin's predictions of gradual change and that discrete mutations could lead to continuous change if multiple loci affected the character.
- Mendelism and Evolutionary theory

A comprehensive theory of evolution that incorporates genetics and includes most of Darwin's ideas, focusing on populations as the fundamental units of evolution.
Local group of interbreeding organisms of the same species.
-All organisms of same group/species, which live in particular area, and have capability of interbreeding.
The amount of biological or living diversity per unit area. It includes the concepts of species diversity, habitat diversity and genetic diversity.
Change in allele frequencies in a population over generations.
Evidence that species are related by descent from common ancestors and have changed in form through time
random and along with recombination is the source of genetic variation required by evolution.
-Raw material for natural selection
-Usually deletarious
-Mutations are not dictated by environment
-Mutations occur at random
-Natural selection is not random
EX) Penicillian
Mutation rate is not the same as substitution rate
Darwin and Wallace's insights
Manuscripts with identical theories:
1) A population process: populations evolve, individuals don't
2) All organisms have a common ancestor
How do we know something in science
Direct experimentation- control confounding variables

Indirect experimentation- inference based on application of principles and laws in which we have confidence
The Scientific method
A series of steps followed to solve problems including collecting data, formulating a hypothesis, testing the hypothesis, and stating conclusions.
-Proposed species changed over time.
-Speculated life had single origin and goes
simpler -->complex

speculated on variability in a species and proposed that species changed over time
speculated that life had a single origin and that it was simpler in the past and has become more complex
-Thought fossils held the key to earlier forms of life and speculated about evolution of living forms
- *Essentialism: A line of thought that explains social phenomena in terms of natural ones
-Species have immutable essence
-Ladder of life
Ladder of Life
First system of classification. Each species on a rung as hierarchical. No evolution
Immutable essence
No evolution
Jon Ray
1686 - Recognized species and common descent

-English naturalist who classified plants based on observed similarities and differences
-Defined the term "species"
-Individuals of a species are similar as they descend from common ancestor.
(1638-86) - Recognized record of historical change
Father of geology and stratigraphy
- Recognized record of historical change
-Shark teeth
Karl Linne (Linneaus)
1735 - Early naturalists classified life's diversity

-Developed the current classification scheme for organisms including binomial nomenclature
-"hierarchical scheme"
Buffon (Georges-Louis Leclerc, Comte de Buffon)
-proposed a modern definition of species based on the ability to produce fertile offspring.
-Earth formed according to laws of physics and chemistry. Supported the idea of a long time scale.
-Proposed different regions have different sets of animals and plants (Buffon's Law).
Charles Bonnet
1770 (Angel Man)
-proposed that organisms responded to natural catastrophes by evolving (kind of like natural selection) and that this evolution followed a pre-determined path (not like natural selection)
-Apes were becoming men and men were becoming angels as they evolved.
Immanuel Kant
-proposed a common origin for living things and diversification based on need in different circumstances
Cuvier (Georges Chretien Leopold Dagobert)
-founder of animal paleontology
-convinced of extinction but that evolution couldn't happen and that species couldn't change thru time.
-Catastrophism- proposed the idea that catastrophes had caused mass extinctions to explain why fossils of different strata differed and why the boundaries between strata were sharp and not gradual.

Recognized fossils resemble but are not the same as modern species
Erasmus Darwin
-Published Zoonomia, agreeing that all living things were descended from a single ancestor and that they had diversified into the various forms seen today due to competition and social interaction.
James Hutton
-Proposed gradualism: that most geological change was small (volcanoes and earthquakes were exceptions) and that the Earth was old, allowing for great change to have accumulated.
William Smith
-Proposed each layer of rock had distinct fossils, and layers that were similar age had same fossils.
-Created 1st geological map based on recognizing same layers of rock in different parts of England based on fossils in them.
Charles Lyell
-Renamed gradualism to uniformitarianism stressing that the forces of geological change seen today are the same as have been operating since the origin of the Earth, so we may understand ancient changes and predict future changes by studying current change.
Jean-Baptiste de Lamarck (1744-1829)
-Proposed separate origins for species through spontaneous generation and subsequent change by the Inheritance of Acquired Characteristics.
-More complex forms had formed earlier and had more time to become complex.
-Each species evolves toward a goal.
What sometimes happen if populations split and become isolated?
They may diverge and over vast amounts of time this can explain biodiversity and relatedness.
Thomas Malthus
-1838, Darwin read essay by this person and observed that resources are either fixed or increase linearly but that human populations using those resources increase geometrically.
-Felt shortages bound to happen once pop. caught up to amount of resource available.
-competition inevitable
Theory of Evolution
-Unifying idea explaining the life sciences and produces a tree-like model of branching common descent.
-Essential to applied sciences.
-Helps all fields to evolve thru time, like medicines evolve as bacteria evolve.
Source of Biodiveristy
When populations split and evolve traits that help the populations better adapt to the enviroment.
How species on one island has a common ancestor/relative on another island.
-That species had to branch off original as it adapted to new surroundings. Same species that evolved.
inheritance of acquired characteristics regained popularity but August Weismann demonstrated that cutting the tails off of mice never became an inherited characteristic
disagreed that the environment set the course of evolution (no mechanism proposed)
- felt that organisms progressed toward a set goal over time.
evolution occurred in discrete jumps
-"Hopeful Monsters"
Believed genetic change was discrete and sudden
claimed that genetic change was gradual and continuous
- data from multifactorial characters
Post-Synthesis: Molecular Biology
-incorporated into Darwinian theory:
-Watson and Crick, 1953 - Structure of DNA
-J. Crow and M. Kimura introduced Neutral Theory of Evolution
-wealth of discoveries about genes and genomes integrated into genetic theory (jumping genes, transposons, DNA duplications, epigenetic effects).
Mayr's Summary
-Fact 1:All species have high fertility that the pop size would have exponential increase if all individuals that were born reproduced successfully
-Fact 2: Except for minor annual and occasional major fluctuations, pops normally display stability
-Fact 3: Natural resources are limited. In a stable envir. they remain relatively constant.
-Inference 1: More individuals produced, resources not able to support, but pop size stable = fierce struggle for living among individuals of pop = survival of only a part (often very small part) of progeny of each generation.
-Inference 2: Survival in the struggle for existence isn't random but depends in part on the hereditary constitution of the surviving individuals. This unequal survival constitutes the process of natural selection.
-Fact 4: No 2 individuals are exactly the same; rather, every pop displays enormous variability.
-Fact 5: Much of this variation is heritable.
-Inference 3: Over the generations this process of natural selection will lead to a continuing gradual change of pops, that is, to evolution and to the production of new species.
Why does Darwin get the most credit for the theory?
Produced a book about evolution through natural selection and had encyclopedic data and evidence to back up statements.
Evolutionary Ideas Current in Biology
-Separation of Phenotype and Genotype

-No inheritance of acquired characteristics

-Hereditary variations are based on genes that retain their identity thru generations, they stay discrete and don't blend.

-Mutation is random and along with recombination is the source of genetic variation required by evolution.
-Pop is the unit of evolution. Evolution is a change in the freq. of alleles in a pop.

-Changes in gene freq. may be random/nonrandom, that is by drift/natural selection or both.

-Natural selection can account for slight and great differences among species.

-Many phenotypic characters are affected by numerous genes at diff. loci.

-Natural selection can give rise to new phenotypes by increasing the freq. of alleles that may form new combos with other genes.
Populations can accumulate genetic variation.

-Pops in diff. geographic regions differ in characteristics that have a genetic basis.

-Diff.'s b/t species and b/t pops of same species are often based on diff.'s at many genes, each w/ a small phenotypic effect.

-Species are def.'d by ability to interbreed and thus a shared gene pool. They do not interbreed with others.
Speciation usually occurs by the genetic differentiation of geographically segregated populations.

-Higher taxa arise by the prolonged, sequential accumulation of small diff.'s rather than by sudden mutational production of new "types'.

-All life forms a great 'tree of life" that has dev.'d by the branching of common ancestors

-Natural Selection, Genetic Drift, & Sexual Selection are most effective forces in evo.
Sources of Scientific Evidence
-The fossil record: transitional stages for some, supports many predictions from phylogenetic analyses.
-Phylogenetics and comparative studies in morphology, biochemistry and development. (Molecular analyses support many phylogenies based on morphology
Developmental studies reveal homologies among seemingly disparate structures. Shared developmental mechanisms reveal ancient relationships.)
-Genes and Genomes (Genomes of most organisms have similar elements. Molecular clocks can approximate times of divergence.)
Distributions of many taxa correspond to geological events that form, separate and/or connect land masses and bodies of water.
Ex: Marsupial radiation, many in Australia but also many in other regions.
Charles Darwin Timeline
-Went to Med school in Edinburgh
-Sent to Cambridge to study for clergy. Here he dev. love for natural history and worked with botany professor (John Henslow)
-1831-1836: HMS Beagle voyage with Capt. Robert Fitzroy around the world. Was ship naturalist
-After return and speciemen he collected and sent home. Came up with "Descent with modification"
-1838, Read an essay by Malthus about resources being fixed or linearly increasing but human pop usage of them increases geometrically. Inspired his Theory of Natural Selection
-1844, wrote private essay
-1858, Found Wallace wrote similar manuscript. Pub both
-1859: Pub "On the Origins of Species..."
Darwin influences
-John Henslow: Botany professor who recommended he go on HMS voyage
-Read Lyell's "Principles of Geology" to study geology
-Read "An Essay on the Principle of Population" by Thomas Malthus which inspired Theory of Natural Selection which took 20 yrs to dev.
-Alfred Russell Wallace wrote similar Manuscript with identical theory.
-Hutton and Lyell were Technically influences of Gradualism and Uniformitarianism.
Phylogenetically informative
Determine number of positions that are different
Phylogenetically uninformative
Change in position of body parts
Heterotphy Examples
-Squid eye lens proteins form lenses over light organs.
-Photosynthetic organs in stems in dry adapted species.
-Some bones bones in vertebrates, new bones can develop in connective tissue under stress "sesamoids" Panda's thumb (so 6 digits).
-Human knee cap is sesamoid.
Increasing Complexity
in the origins of eukaryotes, multicellularity, tissue formation, organs.
Decreasing Complexity
in decreases in number of structures in flowers; loss of appendages in lizards; loss of digits in tetrapods; parasites, substrate dwellers and cave dwellers
Evolutionary trends
repeated changes in the same direction.
Evolutionary trends examples
-simplification of flowers
-longer nectar spurs in columbines (better reproductive success)
-increases in size and decreases in toe number in horses
-increases in chromosome number and increases in DNA in plants.
Evolutionary radiations
divergent evolution of numerous related lineages within a relatively short time
Adaptive Radiations
Divergent evolution but when lineages become modified for different ways of life.
Genes that originate from ancestral gene duplication
Genes that diverge from a common ancestral gene
complete extra sets of chromosomes occurs commonly in plants and occasionally in animals.
Gregor Mendel (1822-1884)
Theory of particulate inheritance
What is the Evidence for Evolution?
1) Microevolution (change in allele frequencies)
2) Speciation
3) Macroevolution (large dramatic evolutionary change)
4)Evidence of common ancestry
5)The earth is old
Evidence of Microevolution
1) Selective breeding
2) Direct observations of natural populations
3) Vestigial structures
Selective Breeding
EX) Illinois long term selection experiment on Maize where they selected certain desired traits
Direct Observations of Natural Populations
EX) Soapberry bugs
*To find new hosts
Vestigial structures
functionless versions of a structure resulting from an evolutionary reduction from a more elaborate functional character
EX) Pelvic bones in whales
Evidence of speciation
Contemporary evidence that species share common ancestors (ring species)
Ring Species
Ring species is a connected series of neighboring populations that can interbreed with relatively closely related populations, but for which there exist at least two "end" populations in the series that are too distantly related to interbreed.
Law of succession
Extinct forms are similar to extant forms in each biogeographical province
Evidence that species change through time
-Transitional forms
Ex) Horses fore feet and hind feet. From having multiple digits to only one
Ex) Tiktallik- intermediate between fish and amphibians
=Possession by two or more species of a trait derived with or without modification from their common ancestor
=Similarity resulting from common ancestry.
**Homologies reflect shared ancestry, Homoplasious characters do not
-evolve once on the tree
Molecular homology
-Possession by two or more species of a trait that has not been derived from their common ancestor
-character state similarity not due to common descent
**Convergent evolution: independent evolution of similar trait
**Evolutionary reversals: reversion back to an ancestral character state
-independently evolve 2 or more times on the tree
Convergent Evolution
-Similarity of traits gained through independent evolutionary pathways
-Evolution toward similar characteristics in unrelated species
Parallel Evolution
-Similarity of traits gained through evolution from the same underlying developmental mechanism
-related species evolve after similarly diverging from common ancestry
EX) Mangrove physiology
*Abscisic acid confers salt tolerance and causes seed to germinate on plant
*Underlying developmental physiology and gene regulation is the same for different mangroves
Reversal Evolution
-Similarity of traits that occurs when one taxon reverts to an ancestral character state and shares it with a taxon that got it directly from a common ancestor
-EX) newest species did not get it from its predecessor, but straight from its oldest ancestor
-EX) Lower jaw teeth in frogs
*Most modern frogs have no teeth in lower jaw
*Their ancestor had these teeth
-Old earth
-Geological processes that occur now operate at similar rates in the past
-James hutton and Charles Lyell
i. Younger strata are deposited on older strata
ii. Lava & sedimentary rocks are laid down in horizontal strata, so non-horizontal bending or tipping occurred after these strata were formed
iii. Intrusions and boulders are younger than host rocks.
iv. Early fossils are simpler than more recent fossils. Recent fossils are most similar to present day organisms. Strata in different regions can be related by fossil similarity
=The earth must be older than 6,000 years
Modern Radiometric dating
=Based on the property that unstable isotopes of naturally-occurring elements decay at a constant rate
=Half-life- Time for ½ of the parent isotope to decay into daughter isotopes; can be determined empirically
=Must assume the original ratio of parent and daughter isotopes; some of these can be predicted from recently formed volcanic rock (e.g. Potasium K-40 & Argon-Ar-40)
=Decay rates unaffected by the environment and act as natural clocks
=Initial ratios confirmed by observation of newly formed rock
=Ratios of
Indicate that moon rocks & meteorites are ~4.6 b.y. old
Determining the relationships within and among groups
The classification of organisms into a hierarchical series of groups emphasizing their historical relationships
Sister taxa
groups that share an immediate common ancestor
A group of species that includes an ancestral species and all its descendants.
a branch point from which more than two descendant groups emerge
Ancestral state
A state characteristic of an ancestor shared with related groups.
Derived state
state that evolved after the ancestral state in this lineage
Reading a Phylogentic Tree
-Ancestral closer to the root (beginning of tree, usually right side)
-Derived is closer to the terminal node (the end of the tree, usually left side)
-Nodes are the actual species,
-Taxa can be rotated around nodes and still depict the same relationships
-Some trees may be unrooted
-Some trees indicate rates of evolution based on branch length
Monophyletic groups
A group of organisms that forms a clade, which consists of all the descendants of a common ancestor
Paraphyletic groups
is a group of organisms that includes an ancestor but not all of its descendants.
-a group composed of members that do not share a common ancestor
philosophies of Classification
1) Artificial- Do not reflect evolutionary relationships
**plants classified by flower color, wildlife classified by habitat type
2) Phenetics- assignment of relationships based on overall similarity
**EX) used all shared characters, those that share the most traits will be grouped together
3) Cladistics- Use only synapomorphies reflect descent from a single common ancestor
Methods of classification
1. Neighbor Joining -uses a similarity matrix to construct the phylogeny
2. Maximum Parsimony -accepts the tree with the least amount of homoplasy; requires searching of "tree space."
3. Maximum likelihood, Bayesian, coalescent
**used for molecular data
**use an underlying model of the evolutionary process to determine the most likely relationships
the ancestral trait state, usually in reference to a derived trait state
new traits found on the tree
shared ancestral states
unique derived characters
-In this comparison feathers arean autapomorphy for birds (compared to frogs and turtles)
Shared traits derived from an evolutionary ancestor common to all members of a group
=How are characters defined as a synapomorphies vs sympleisiomorphies?
=How we decide if a trait is ancestral or derived ?
By comparison with an outgroup
Steps in Phylogeny construction
(Wagner trees, a type of neighbor joining tree)
1) build character matrix
2) Determine matrix of shared character states )
(phenetic approach) or shared derived character states (cladistic approach)
3)Build tree by linking taxa and nodes with the most similarities (pheneticist) or synapomorphies (cladist)
-Branching evolution occurs when a new species branches out from a parent species
change within a species
Maximum Parsimony
Choose the tree with the fewest steps
Alleles in a population...
Coalesce (fuse together) to a common ancestor
-Factors that affect coalescent time
*Random variation
*Natural selection
Incomplete lineage sorting
diversity in the common ancestor of three or more species does not coalesce with the same topology as the species tree
Gene trees and species trees do not always match...
Data from multiple genes used in phylogeny construction
Building a phylogeny with genetic data
-Each nucleotide a potentially informative character
-But, homoplasy common
*Only four possible character states
-Genes differ in rate of evolution
*Slowly evolving genes useful for distantly
related species
*Rapidly evolving genes useful for closely
related lineages
Common methods with Genetic data and trees
-Maximum parsimony
*Simplest explanation favored
_Distance matrix (e.g. neighbor joining)
*Clusters taxa based on genetic distance
-Maximum likelihood
*Finds most likely tree given specific model of
molecular evolution
-Bayesian methods
*Looks at probability that a tree is correct given a
specific model of molecular evolution
Genetic Case studies
Forensic Science
Numbers of Giraffe species
Biogeographic trends
**Hawaiian crickets
Origin of whales
the first whales evolved over 50 million years ago, and the ancestor of both these groups was terrestrial.
Tumor cells in dogs
Canine transmissible venereal tumor (CTVT) is an unusual form of cancer because the infectious agent is not a virus or bacterium but the tumor cells themselves, which are passed from one dog to another during coitus
Origin of human clothing use
For instance, based on genetic skin-coloration research, humans lost body hair around one million years ago—an ideal time to start wearing clothes for warmth. ... They hypothesized that body lice must have evolved to live in clothing, which meant that they weren't around before humans started wearing clothes
Biogeography of the Seychelles Chameleon
Through Oceanic Dispersal
Molecular Clocks
Critical assumption: Constant rate of substitutions
D = 2rt
t = D/2r
*t is the time since divergence between the species' common ancestor
*D is the proportion of base pairs that differ between two sequences
*r is the rate of base pair substitution per million years
*"2" represents the two diverging lineages
Rate constancy assumption does not always hold.
Compression fossil
fossil that has been compressed in sedimentary rock
Impression fossil
Imprint of organism produced during fossilization
Permineralized fossil
Structures are buried in sediments and dissolved minerals precipitate into the cells
unfilled spaces formed after remains decay after being buried in dedient
When molds are filled with new material that hardens
Unaltered remains
Preserved traces of organisms such as mummies, organisms embedded in amber, dried dung, etc
Bias in the fossil record
=Geographical bias - most fossils from lowland and marine habitats; areas where decays is fast generate fewer fossils
=Taxonomic bias - most fossils are marine, but only 10% of current taxa are marine; organisms that lack hard parts do not fossilize
=Temporal bias - sediment formation varies episodically
Early earth
-No free oxygen
-Mostly methane and ammonia, and water
Oparin-Haldane model
RNA arose first
1. RNA does it all
a. enzyme
b. information storage
c. possesses genotype & phenotype
2. Machinery to process RNA into proteins is
highly conserved and built around RNA
molecules (e.g. tRNA, rRNA).
3. ATP & GTP are currency of bioenergy
- both are ribonucleoside triphosphates
(building blocks of RNA)
Plesiomorphies of extant organisms
i. all life uses DNA and protein
ii. all life shares the same 20 amino acids
iii. all life shares the same basic genetic code
Fossil stromatolites from Saratoga Spring, New York. Stromatolites are among the oldest fossils of life, some dating to 3.5 bya
Proterozoic Eon (Pre-Cambrian)
-Concentration of free oxygen increases
-3.4 bya first photosynthetic bacteria arise
-Ancestors of extant cyanobacteria
-Presence of oxygen greatly increased potential efficiency of metabolism (respiration, krebs cycle)
**First Eukaryotic fossils
*origin of mitochondria and chloroplasts
Ediacarian Period 635 - 541 mya
-Last period of proterozoic
- Organized, differentiated multicellular
-Sizes larger than centimeters
-Almost all forms of symmetry
-Perhaps first embyros
-Diversification coincided with large increases in atmospheric oxygen
Phanerozoic Eon
Know the periods and ears of their dates
(picture in email)
The Cambrian Explosion 540 MYA
-Most Major animal groups appear
-Mollusks, Arthropods, Chordates, etc....
-Burgess Shale
**Complex bilaterally symmetric organisms
-Molecular clock suggests that major animal groups diverged from a common ancestor
-Small shelly fauna (calcium phosphate)
-First Jawless fishes arise
*gills used for respiration not feeding
*Bony heads
-Earliest animal fossils with shells
-May have influenced the cambrian explosion
Ediacaren Period 541 mya
Mass extinction of Ediacaran biota; first trilobites arise, (Neo-proterozoic eon)
Evolutionary innovation of seeds
-Protective coat
-food supply for the embryo
-potentially dormat for long periods
-water not required for fertilization
-Four Limbs vertically beneath the body
-Teeth more specialized than Pelycosaurs
-Arose in the early Permian 275 mya
-Oldest Mammal fossil is 125 MYA
-Radiation of mammals occurs 65 MYA
-3 extant groups
*Monotremes, Placentals, Marsupials
variant form of a gene; variant nucleotide sequences at a particular locus; sometimes distinguished from other alleles by its effect on phenotype
the genetic constitution of an individual organism at one or more loci singled our for discussion; the complete hereditary or genetic constitution of an individual
one of the sequences of a gene or DNA segment that can be distinguished from homologous sequences by molecular methods such as DNA sequencing
Genetic variation
When phenotypes of different genotypes differ in the same environment
Environmental variation
Results when phenotypes of the same genotype differ across environments
Phenotypic plasticity
the ability to develop different phenotypes in different environments
can block translation
chromosome site occupied by a particular gene; often used to refer to the gene itself
Duplication of the entire genome
Genetic Load
reduction in mean fitness of a population resulting from the presence of all deleterious alleles
The substitution rate
The rate of fixation of new mutation in a population

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