Eidos

-Also known as "Essentialism

          - all species are perfect and do not need to change

-Early concept (pre-Darwin) from Western culture

- Possibility of change (evolution) not considered

           - ex.  a frog is a frog and will only be a frog

- Much of this thinking was led to the thought of a creator.  This phiosophy was only magnified by the introduction of Christianity

-"The Great Change of Being"

-ex.  Species and higher forms are seen as "fixed rungs on a ladder"

Uniformitarianism- The slow geologic process that have occurred in the past and are still occurring today

     - ex.  (erosion, mountain uplifting, etc.)

Hutton was the forebearer of Uniformitarianism.

          - introduced the concept of Deep Time, which exposes that the Earth is billions of years old

-Author of Principles of Geology

           -gradual geologic change

           -popularized the concept of uniformitarianism

-studied Demography/Ecomomics/Sociology

-Wrote The Principle of Population

         -Discussed population growth vs. limiting resources

         -Famine, disease, and war help keep population in check.

Father of Capitilism

Author of Wealth of the Nations

-laissev faire concept

    - free hand of the market

    -competition will drive the economy

Father of Modern Taxonomy

   -popularized the binomial system (genus and species)

   -developed Hierarchical Taxonomy

Developed first comprehensive theory of organic evolution

But misunderstood the mechanism of acquired charateristics

- viewed evolution as a force driving animals from simple to complex beings

(ex. bacteria<plants<animals<humans<celestial)

-Observed rich variety of geologic features and documented many deologic phenomenon which supported Lyell's rules

-Methodically collectedand categorized enormous number of specimens

- studied fossils and living organisms in great detail

-Documented biogeographic patterns that suggested common ancestry of species

Darwin's Theory of Evolution

Evolution of new species occurs via descent with modification of existing species and the mechanism for this is natural selection.

Natural Selection's 2 components

Struggle for Existence: populations can reproduce beyond resources needed to sustain them and resources become limited.  There is competition for those to get limited resources to survive.

Survival of the Fittest:  Members of a population show variation for heritable traits.  Some traits give individuals a selective advantage over others.  Over time those with this trait will become more occurant and the character of the population changes.

Fitness

Ability of an individual to produce offspring relative to other individuals in the population

Adaptation

Any trait that increases fitness

Evidence for Supporting Evolution

species have changed through time:  populations can be observed to change over time, many species have gone extinct, fossil record has trasitional forms.

        -Vestigial traits: traits one has but has no function

                                       e.g. goosebumps, tail bones

species share a common ancestor:  closely related species live in the same geographic area.

Homologous traits exist at multiple levels

-Anatomical e.g. Arm, Flipper, Wing

-Embrylogic  e.g.  similar looking embryos

-Molecualr  e.g.  use similar molecular compounds

Vertical Evolution

(definition of Paralog and Ortholog)

Evolution with a lineage through time

Ortholog: a gene in separate species that share common ancestry

Paralogs:gene copies within the same species

Horizontal Evolution

Where genes are transferred from one organism to another by means other than genes received from an ancestor

-Much rarer  than Vertical evolution

-Most common with bacteria

         -Almost certainly the way eukaryotes evolved from prokaryotic cells

Concept of a Gene

(Define locus and allele)

Region of DNA that codes for a specific polypeptide

Locus:  physical location on a specific gene on a chromosome

Allele: version of a specific gene

Hardy-Weinberg Equation

Used measure the differences in allele frequencies

      -Frequency in a population add up to 1

-Cases of changes:

     -Natural selection

      -genetic drift

       -gene flow

        -mutation

                   ^if none of the following occur it is said that the population is in equilibrium and is not evolving

Fixed vs. Lost alleles

In a Hardy-Weinberg equation....

If an allele frequency =1then it is fixed

     - unless genetic drift occurs, all offspring in the population will have this allele

If an allele frequency =0 then it is lost

     -unless genetic drift from another population enters the current population to reintroduce the allele, the current population has permenantly lost this allele

Natural Selection

Occurs when one phenotype has higher fitness

-Alleles associated with phenotpe will increase in frequency

Four different types of natural selection

-directional

-stabilizing

-disruptive

-sexual

Alleles associated with mean trait values favored

     - no change in average trait over time, but change in genetic variability due to both high and low end extrememes becoming less frequent.

ex.   Human birthweights

Alleles associated with both extremes of a trait are favored

      -Tends to increase genetic diversity

       -may result in two separate species

ex. finch beak sizes on the Galapogos islands

Sexual Selection

Results when individuals in a population differ in their ability to attract mates

Bateman-Trivers: Sexual selection acts more strongly on males

                -female choice

                -male-male competition

- mating calls, mating rituals, courtship acts, physical attributes, or even a Nuptial Gift, which is a gift (such as food) one brings to the other to please.

ex. zebra finches orange bills

Balancing Polymorphism

(define and name the two mechanisms)

Maintains "less fit" alleles in a population

Heterozygote Advantage:  Heterozygotes have higher fitness in some cases.  Will maintain less fit alleles in a population

     -ex. sickle cell anemia

Negative Frequency Dependent Selection: Rare individuals have hagher fitness

      -ex. scale eating fish with slanted mouths, non-rewarding orchids that get pollinated

Genetic Drift

Natural Selection is driven by the environment

-it is random with respect to fitness

-most pronounced in small populations

-over time can lead to lost fixation of alleles

Founder Effect vs. Genetic Bottleneck

Founder Effect: The loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population.

ex. a seed that randomly starts a new population away from its donor

Genetic Bottleneck: an event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing.

       -Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size.

       - leads to increased genetic homogeneity.

Gene Flow

The movement of alles from one population to another

     -Immigration/Emmigration

      -Equalizes allele frequences between populations

Genetic Diversity

-Decreased in donor population

-Increased in recipient population

Gene flow is a great "homogenizer" of alleles

        -only when gene flow is reduced can we get speciation

Mutation

Random production of a new allele

    -Increases genetic diversity

    -usually due to damage or replication errors of DNA

    -mutation rates are extremely low, however there are vast amounts of mutations in a genome

Most mutations lower fitness

   -Natural selection will increase the frequency of mutated alleles given they increase fitness and decrease ones that lower fitness

Inbreeding

Mating between relatives

   -ex of non-random mating

   -increases homozygosity in genotypes

   -Does not alter allele frequencies in gene pool, but alters genotype frequencies

Inbreeding depression

   -Homozygous recessive genotypes often lower in fitness

Speciation

Formation of new species from ancestral species

    -genetic isolation and genetic divergence

Species Concept

Biological, Morphological, Phylogenetic, Ecological

Evolutionary Independent populations

     -Distinguished by common characteristics which are shared AMONGST members of species  or set them APART from other species

Biological- Members of a species can interbreed and produce VIABLE offspring

   -however can't apply to fossils or asexual organisms

Morphological- Based on different morphology

      -used most commonly with fossils and asexual organisms

       -however it is subjective. Intra-species morphological variation often greater than that of inter-species variation 

              ^e.g. Female and male ducks = intra species

Phylogenetic- based on ancestral analysis

             -  Look at the "end" of the branch and the "tip" of a species

           - very strong foundation and applicable however few thorough phylogenies are available

Ecological- based on environmental context.  Each species occupies a unique niche.

           -gets difficult to characterize niche because technically no two organisms can occupy the exact same niche.

Reproductive Isolation

(Prezygotic vs Post-zygotic)

Reasons why one species cannot or will not reproduce with other species

Prezygotic- zygote is never formed.

            -Possible diruptions include: temporal, spatial, and behavioral  situations.

             -gametic barriers

             -Mechanical incompatibility

post-zygotic- zygote is formed but is not viable

    -hybrid viability: zygote fails to survive

     -Hybrid survives but is sterile and cannot reproduce

              ^ex.  Mule

Allopatric Speciation

Population becomes geographically isolated and gene flow ceases between the separated population and the original.

      - Natural selection, Genetic Drift, and mutation all play a part in the genetic divergence of the separated specie. 

Dispersal-  Small # of individuals disperse to new habitat and founder effect increases likelihood of genetic drift.

           -different environment creates selective pressure (especially prevelent in islands)

Vicariance-  (Barrier forms) Large population split into 2 or more subpopulations. 

     -usually due to emerging geographic barrier

      - new population is now genetically isolated.

Sympatric Speciation

Speciation without geographic isolation

    -natural selection overwhelms geneflow

     -sympatric population mechanisms that reduce gene flow

           ^e.g. prezygotic disruptions (spacial, temporal, and behavioral isolation)

Polyploidy-  speciation in a single generation

ex. hawthorne trees, fall and spring mating crickets.

Hybrids

Formed when isolated populations reconnect

    -if viable hybrids form, but they may have lower fitness than one or both parent species

    -if sufficient genetic divergence has occurred, the two populations cannot make viable offspring

Hybrid Zones

Area of OVERLAP where interbreeding of separate species occur

If hybrid fitness is lower then there are narrow hybrid zones and selection favors the populations separate traits

If hybrid fitness is higher then it can result in the extinction of the species with lower fitness.

Punctuated Equilibrium vs Gradualism

Punctuated Equilibrium: Change occurs in short bursts

                       -long periods of little change

                       -predicts new species to appear rapidly

                       -fossil record tends to support this idea

Gradualism:  Genetic change is continuous and accumulates through time

              -leads to changes in phenotype and new species

              -predicts transitional forms

              -Molecualr data tends to support gradualism

Evolutionary-Developmental Biology

(EvoDevo)

An interdisciplinary approach that attempts to explain radical development of body plans

ex.  Paleontology, anatomy, molecular bio, genetics, developmental bio etc.

Homoeotic Genes

(Hox Genes)

Regulates development alon an axis (such as a dorsal fin)

   -can be specific to a body region

   -are turned on/off by their own regulating gene

   -the more hox genes = the more complex the body plan

Gene duplication (paralogs) mutations produce more Hox genes

Paedomorphosis

Retention of laraval Juvenile characteristics in adult

    ex. plankton

can lead to new body plans

Allometric Growth

Differences in growth rates

     -ex chimp skulls vs human skulls

-Genes promoting skull growth suppressed as chimp grows and genes promoting jaw growth continue

BMP4 Gene

(gremlin)

A gene that causes tissue to degenerates 

Ex.   Chicken feet have BMP4 but ducks feet do not, the result= ducks have webbed feet

Ubx Gene

causes abdominal leg growth

ex insects such as centipedes, it is a good mutation

in flies it causes  a second pair of wings to form on the thorax which lowers their fitness by causing them to become less aerodynamic.

Hoxd-11

a.k.a sonic hedgehog gene.

regulates the directon of the embryonic limb bud

can for either fin or limb depending on how much is expressed

Ortholog relationship with different species

Many structures such as eyes, wings, legs are similar in organisms and genes that direct their development are evolutionarily related

   - Orthologs

Ex.  Eyes in insects and mammals

Pax-6 gene creats a normal eye in mice

experiment: transplants of fly DNA for eyes onto mice limb

Phylogenies

(Components of phylogentic trees)

An Evolutionary history for a group of organisms

   - typically depicted as a tree

Branch-populations through time

Nodes-forks where ancestors splits into two or more descendents

         - polytongy is when it splits in 2 or more groups, also called a star phlogeny

Tips-extinct or existing species

      ^  tips can rotate on the node and it won't affect the information presented

Sister Taxa- when two nodes emerge on a adjacent or the same branch they are known as sister taxa.

     -   the one closest to the base of the root is more related to the ancestor

root: the common ancestor

Different Stages of Phylogenies

(Mono, Poly, Para)

Monophyletic group-  (Just Right) ancestor and all its descendants

Polyphyletic group- (Too many) groups of species with different common ancestors (not evolutionarily correct)

Paraphyletic- (Too Little)  Group with common ancestor but only some of its descendats are listed

Adaptive Radiations

Appear in phylogenies as polytomies (star phylogenies)

Three potential mechanisms

-Colonization event

      -habitat unoccupied by competitors is cololnized by a species which quickly radiates to exploit the new resources.

      -  ex.  after a mass extinction, or a newly discovered area

Morphological Innovation-  Allows new resources to be exploited

    - ex.  flowers, feathers, and mouth part modifications

       -ex.  Insects and Larvae do not directly compete with each other

Mass Extinctions- Removes major competitors from the system and allows surviving species to exploit resources that were previously unavailable

Fossils

(4 basic types)

A physical trace of an organism that lived in the past

    -can be dated using radioisotopes 

4 basic types of fossils

organically preserved

compressed carbon rich films

casts

permineralized (ex petrified wood)

Fossil Biases

(limitations)

Habitat Bias-  Burrowing organisms and organisms with good climate conditions will be more likely to leave behind fossils

Taxonomy bias-  organisms with harder parts in their anatomy are more likely to leave fossils

Temporal bias-  older organisms have greater chance their fossils gets destroyed by natural harm

Abundance bias-  the more organisms of that species the greater chance fossils will be left behind.

Molecular Clock

Mutation rate is constand and mutations are neutral

   -can use these neutral mutations to estimate time of divergence for lineages

    -reletionship should be linear.

Cons

-Generation times

-mutation affected by selection

-species specific differences in mutation rates

Cladistics

Tool for estimating phylogeny

   -cladogram= considers pathways of evolution and selects most plausible tree

           -considers shared vs non-shared traits

sympleisomorphry- trait shared with ancestor

synapomorphy-derived trait (not shared with ancestor)

ingroup- organisms of a taxonic group that shares synapomorphy

outgroup-closest ancestor of ingroup but lacks synapomorphy

Problems with Cladistics

Convergent evolution- same trait but independetly derived

     -ex wings,0 flippers, eyes, etc

Reverse mutations-base pair substitution can revert

- can confuse the cladistic scoring of a matrix

            - solution: maximum parsimony = the simplest  explanation is the right one.

Phylogenetic Inferences

Uses phylogenies to understand  evolutionary history and process

ex selfing in phlox plants-  most phlox plants are incapable  of selfing but 3 species do.  Maximum parsimony would say that are monophyletic but molecular analysis says they are polyphyletic

Ratite Evolution-  Ratite = Lare flightless birds that can be related to emu, ostrich, etc.  Biogeographies and molecular data both conflict each other.

Whale Evolution- whales don't have an astralagus.  But a whale ancestor fossil was found with an astralagus.

Primordial Soup

(3 theories)

Reducing Atmosphere- (Miller- 1953)

Atmosphere of early Earth was low in 02 but rich in H2, NH3, CH4, H2O vapor, and energy

     -formed organic molecules that accumulated in the worlds oceans.

Extraterrestrial-  Organic compounds delivered via asteroids/meteorites

Deep Sea Vent-  Organic compounds formed at hydrothermal vents rich in H2, S, and NH3

  - H2O temperature suitable for organic chemistry

Step 2 -  clay surfaces may have served as templates against which the first RNA or amino acid polymers were formed

Step 3-  Formation of protobionts

               -were not considered "alive" because they had no genetic material

               -   consisted of a simple boundry with polymers inside doing enzymatic action that included replication

         - common protobionts are coacervates, microspheres, liposomes

Step 4 -  New protobionts with enhanced enzymatic or replicating abilities were formed and favored through an evolutionary jump.

    - a mutation may have created an RNA  molecule that could both store info and have a catalytic role.

 Step 5- an RNA world to DNA world

    - this allowed separation of information and catalytic functions

       -originally RNA did both but DNA is more stable (double-helix) and proteins were better catalysts.

The Four Major Eons

Hadean- formation of Earth, primordial soup and protobionts

Archean- origin of life, radiation of prokaryotes

Proterozoic- origin and radiation of eukaryotes, simple multicellular organisms

        ^ These three eons make up the Precambrian Era

Phanerozoic- radiation and diversification of multicellular organisms

The Cambrian Explosion

(and the 3 fossil formations)

The rapid appearance and diversification of phyla at the start of paleozoic

   -565 mya simple multicellular organisms appear

   - within 40 million years of this almost all major plant/animal phyla appear

1. Duoshaunto Fossils- formation of around 580-579 mya Found in Southern China

           -microscopic fossils, likely all filter feeders (tiny sponges/embryos)

2. Eidacaran Fossils- 560-540 mya found in southern Australia

           -Sponges, Jellies, combjellis, burrows, and tracks.

           -  NO hard shells, limbs or heads with feeding appendages

3.  Burgess Shale Fossils- Found in Canada 525-515 mya

            -abundant sponges, jellies, combjellies, and brand new animals with eyes, mouths, limbs, shells, and feeding appendages.

             -Almost every modern phyla present!

Milestones of the Paleozoic Era

(First era of the Pherozoic)

-Cambrian Explosion

-first vertebrates, fishes, diversify

           -the invasion of land, first reptiles, amphibians, insects

-Extensive fern forest

          -first gymnosperms

Permian Extinction (90%  of all species extinct!)

Milestones of the Mesozoic Era

(also known as the age of...)

a.k.a. Age of the Reptiles

First dinosaurs and mammals

   -dinosaurs radiate and dominate (mostly in Jurassic era)

Gymnosperms radiate

First flowering plants

Mass extinction at the end of Cretaceous (believed to be caused by an E.T. impact)

Milestones of the Cenozoic Era

(also known as the age of....)

Also known as the Age of the Mammals

Radiation of Mammals

   -Appearance of hominids

Radiation of flowering plants/insects

Mass Extinctions

Defined as when 60% or more of species are lost in 1 million years

                       -Random and episodic

                        -sets up for adaptive radiation

Background Extinction sets refers to normal extinction rate pre-humans

Cretaceous Extinction

65 mya

a.k.a. K-T Event

 85% species lost big losers: dinosaurs and marine reptiles

     -reptiles, mammals, birds, amphibians survive

- cause massive meteor impact in Yucatan

Permian Extinction

Permian extinction occured circa 250 mya

     - Largest of all extinctions 96% of species

     - Thought to be caused when Laurussia collided with Gondwana to form Pangea.  Large Volcanic eruption caused mass extinction

          -Eruption could have had great impact on rapid climate shifts.