NOTOCHORD

Taxonomy is the science of grouping and naming organisms.

Taxon ( taxa-plural) is a category into which related organisms are placed
There is a hierarchy of groups (taxa) from broadest to most specific
Domain, Kingdom, Phylum, Class, Order, Family, Genus, species
Classification the grouping of information or objects based on similarities.

Gastrulation is the process in which the single-layered blastula is reorganized into a trilaminar ("three-layered")
structure known as the gastrula.
Ectoderm - hair, nails, epidermis, brain, nerves
Mesoderm - notochord (in chordates), dermis, blood vessels, heart, bones, cartilage, muscle
Endoderm - internal lining of the gut and respiratory pathways, liver, pancreas
Anamniotes: "lower vertebrates", which lay their eggs in water- fishes, amphibians
Amniotes: “higher vertebrates” which lay their eggs on land or retain the fertilized egg within the mother
The amniote embryo is the solution to reproduction in a dry environment.
Shelled eggs of reptiles and birds.
Uterus of placental mammals.
The four extraembryonic membranes are the yolk sac, amnion, chorion, and allantois.
-Cells of the yolk sac digest yolk providing nutrients to the embryo.
-The amnion encloses the embryo in a fluid-filled amniotic sac which protects the embryo from drying out.
-The chorion cushions the embryo against mechanical shocks.
-The allantois functions as a disposal sac for uric acid.
An animal with radial symmetry has body parts that radiate from a center point.
These animals meet their environment equally from all sides.
They move quite slowly.
If they are sessile, their food must float by or they must create water currents.
3. Bilateral Symmetry
Concentration of nerves and sense organs at the anterior end.
Food capturing structures are usually close to the head.
Digestive, excretory and reproductive structures are found closer to the posterior end.
A streamline body allows for faster movement.
• Coelom is a fluid-filled cavity between the intestines and the body wall of some higher animals
• It is lined with mesodermal epithelium
• A coelom can absorb shock or provide a hydroskeletal structure
Characteristics of chordates
• A. Notochord, or a rod of vacuolated cells, encased by a firm sheath that lies ventral to the neural tube in
vertebrate embryos and some adults
• B. Hollow nerve cord that lies dorsal to the notochord
• C. Pharyngeal pouches The pharyngeal pouches and slits (gill slits) are a series of paired slits in the pharynx,
serving as passageways for water to the gills. In some vertebrates, they appear only in the embryonic stages
 • D. Endostyle - elongated groove in the pharynx floor of protochordates that may develop as the thyroid gland in
chordates
Notochord
• A flexible rod-shaped body found in the embryo of all chordate
• A rod of vacuolated cells
• Formed from the mesodermal cells
• Primitive axis of the embryo
• Found ventral to the neural tube
• It becomes the nucleus pulposus of the intervertebral disc
Nerve cord
• Is a hollow cord dorsal to the notochord
• It is composed of ectodermal cells
• The dorsal nerve cord is later modified in vertebrates into the central nervous system
Pharyngial gill slits
The true gill slits are the opening to gills
The term "gill slits" has also been used to refer to the folds of skin in the pharyngeal region in embryos
They are derived from all three germ layers
Endostyle- is a longitudinal ciliated groove on the ventral wall of the pharynx which produces mucus to gather food
particles
• Deuterostomes and proteostomes
• The primitive gut that forms during gastrulation in the developing embryo is known as the archenteron
• The open end of the archenteron is called the blastopore
• Protostomes
• Deuterostomes-echinoderms—chordates-first opening become the anus
Protochordates
• Proton means first; chordate means with cord
• All marine animals
• Relatively small sized animals
• Cranium or brain box, jaws, vertebral column and paired appendages are absent.
• Dorsal tubular nerve cord, gill slits and notochord are usually present.
• Sexes may be separate or united.
• Solitary, colonial, free living, pelagic, burrowing or tube like living forms
Why are protochordates not classified as true Chordata
• Like the remaining subphylum of the chordates, the Vertebrata, the protochordates have a hollow dorsal nerve
cord, gill slits, and a stiff supporting rod, the notochord, the forerunner of the backbone.
• The protochordates differ chiefly from the vertebrates in not having a backbone.
• Recent protochordates are thought to have evolved from the same ancestral stock as that which gave rise to
the vertebrates.
General Characteristics of hemichordates
✓ Exclusively marine and soft-bodied forms
✓ Body is divisible into proboscis, collar and trunk
✓ Notochord occurs only in the anterior end of the body.
✓ Numerous paired gill slits are present.
✓ Nervous tissues lie embedded in the epidermis and occur both on the dorsal and ventral surfaces.
✓ Coelom is present
✓ Fertilization is external.
Filter feeding mechanism
Filter feeders have mucous secreting glands and numerous cilia on their proboscis
The proboscis is held out of the burrow entrance and organic particles are caught in the mucous which is swept to the
mouth by the beating of the cilia
These species can cover their mouth with their collar and thus avoid eating inorganic or otherwise undesirable materials
The digestive system is a through gut ending in a terminal anus
 Behind the mouth is a buccal cavity which leads into a pharynx which possess gill slits. These gill slits are believed to be
used primarily to assist gaseous exchange (respiration).
The Pharynx leads into an oesophagus which in turn leads to an intestine which is the main site of digestion, the
intestine leads ultimately to the anus.
Urochordates-tunicates
✓ Urochordata is the term used to refer to the presence of a notochord in the tail region, (uro=a tail;
chorde=cord).
✓ The notochord is restricted to the tail region of the larval forms of urochordates and is absent in the adults.
✓ Tunicata is the other name of this subphylum Urochordata, due to the presence of an outer leathery covering
called tunic or test in the adult (tunica – outer covering) made up of tunicin
✓ Dorsal tubular nerve cord is present in the larval forms while degenerates in the form of small ganglion in adults.
✓ A numerous gill slits are present.
✓ Sexes are united that is hermaphrodite.
Cephalochordata
• The term Cephalochordata refers to the notochord that extends the entire length of the body up to the head
region (cephalon – head; chorde – cord)
• The notochord lies on the mid dorsal region just above the alimentary canal and below the nerve cord
• No distinct head but tail present; mouth surrounded by tentacles
• the closed circulatory system is complex for so simple a chordate; flow pattern is
• remarkably similar to that of primitive fishes, although there is no heart; blood is pumped forward in the ventral
aorta by peristaltic-like contractions of the vessel wall
• Exoskeleton, head, brain, auditory organs and jaws are absent.
• Sexes are separate

Fishes
Kingdom - Animalia
Phylum - Chordata
Subphylum – Vertebrata
Superclass-Gnathostomata
Class – Pisces
▪ Skin covered in scales
▪ Ectothermic, cold blooded
▪ Soft shelled eggs that must be laid in water
▪ External fertilization
▪ All members are fully aquatic
▪ Limbs modified into fins
▪ Gas exchange through gills
▪ Lateral line
▪ Agnatha - jawless fish
▪ Cyclostomata - no jaw so the mouth cannot close, retractable teeth; Pore-like gill openings
and eel-like body - hagfish and lampreys
▪ Elasmobranchii – cartilaginous fishes, no swim bladder, teeth in several series, heterocercal (vertically
asymmetrical) tail - sharks and rays
 ▪ Osteichthyes - bony fish, ray-finned or lobe finned fishes, have swim bladder, have operculum
Rohu, catla
2. Parasitic Lampreys
• Attach to fish by sucker-like mouth and sharp teeth rasp away flesh
• Anticoagulant injected into wound to stimulate flow of blood
• Wound may be fatal to host fish
• Non-parasitic lampreys do not feed; digestive system degenerates and fish die after reproducing, within 2-3
years
Sharks
Sharks and rays are successful predators:
Sharks have a sense of smell that detect incredibly diluted substances. (one drop of blood in a mile of water)
Sharks have a “conveyor belt” of multiple rows of teeth.
They swing into place as old teeth wear out and fall away.
Unique to sharks and rays is electroreception – the ability to sense minute electricity created by muscles and nerves.
Sharks and rays have organs called ampullae of Lorenzini which you can see as visible pits near their snouts used to
detect the electrical current.
Nervous System
• central nervous system
– brain and spinal cord
• nerves connect the central nervous system with all of the organs
• sensory organs
– Eyes – focus moving closer and farther
• Nictitating membrane – reduce brightness, protect during feeding
– lateral lines – sense pressure changes, vibrations
– nostrils and olfactory sacs – smell
– taste buds – mouth, fins, skins, barbels
inner ears – hearing and balance
Gills
❖ Most fish exchange gases using gills on either side of the pharynx
❖ Consists of threadlike structures called filaments
❖ Each filament contains a capillary network that provides a large surface area for exchanging oxygen and carbon
dioxide
❖ Some fish, like sharks and lampreys, possess multiple gill openings. However, bony fish have a single gill opening
on each side. This opening is hidden beneath a protective bony cover called an operculum
Circulatory System
• two-chambered heart beneath the gills
• gas exchange takes place in gills
• oxygenated blood is carried through the arteries
• Capillaries allow oxygen and nutrients to reach the cells
• veins carry deoxygenated blood and carbon dioxide back to the heart
Scales
• Skin of most bony and cartiliginous fishes covered by scales
• These are produced from the mesoderm layer of the dermis
• The same genes involved in tooth and hair development in mammals are also involved in scale development
• Hard protective scales on their skin for protection
Swimmbladder
• Swimbladder or gas or air bladder is an internal gas-filled organ that contributes to the ability of a fish to control
its buoyancy, and thus to stay at the current water depth without having to waste energy in swimming
• Another function of the swim bladder is the use as a resonating chamber to produce or receive sound
• The Weberian apparatus is an anatomical structure that connects the swim bladder to the auditory system
Lung fishes
• Fishes having the ability to breathe air
• lungfish live only in Africa, South America and Australia
• Have lung connected to the pharynx
• Lung is a modified swim bladder
• Can survive when their pools dry up by burrowing into the mud and sealing themselves within a mucous-lined
burrow
Reproduction and Development
• Internal fertilization
• Oviparous sharks and rays lay an egg capsule immediately after fertilization that attaches to kelp with tendrils;
may take up to 2 years before mini adult hatches
• Ovoviviparous sharks retain fertilized eggs in reproductive system where they are nourished by yolk of egg;
“live” birth
• Viviparous sharks nourish embryos with maternal bloodstream; “live” birth
• Live births make it more likely more of the young survive but no other care is given after birth
Unisexual Fishes
• They produce offspring of only one type.
• It is a rare phenomenon among fishes.
• Hubbs and hubbs (1932,1946) were the first to report all female population of the fish, Poecilia formosa
(commonly known as Amazon molly).
Bisexual Fishes
• In most of the fishes sexes are separate. Such fishes are called Gonochoristic fishes.
Undifferentiated gonochoristic fishes
• During initial stage of development, gonadal tissue remain in the different stage, and then develops into either
ovaries or testes.
• In Danio rerio (zebra fish), all gonads initially develop as ovaries, but in approximately half of the population,
ovarian tissue subsequently degenerates and the gonad is invaded by additional somatic cells.
• Masculinization of the gonad then proceeds to produce an initially intersexual gonad that ultimately resolves
into a normal testis.
Differentiated gonochoristic fishes
• Also termed primary gonochorism.
• Early gonad development proceeds from an indifferent gonad directly to ovary or testis.
• Example is Oncorhynchus kisutch (commonly known as Coho salmon).
Hermaphroditism
• A hermaphrodite is one in which both sex organs are present in same individual.
Migration
❖ Movements of animals in large numbers from one place to another
 ❖ In modern usage the term is usually restricted to regular, periodic movements of populations away from and
back to their place of origin
❖ The movement of the animals should be an annual or seasonal occurrence
❖ Found in crustaceans, insect, fish, amphibians, reptiles, birds and mammals
❖ A single round trip may take the entire lifetime of an individual, as with the Pacific
salmon or may a repeated round trip like birds
The animals may travel in groups along well-defined routes; or individuals may travel separately
Migration types
➢ These migrations often provide the animals with more favorable conditions of temperature, food, or water
➢ Many birds and a few bats of cold and temperate regions migrate to warmer areas during the winter
➢ The chief function of seasonal migration is to provide a suitable place for reproduction, which may not be the
place most suitable for the feeding and other daily activities of adults
➢ Hundreds of thousands of gnus (wildebeests) of E Africa take part in annual migrations to calving grounds
➢ The simplest type of regular migration is the diurnal movement of some marine microorganisms from one depth
to another in response to light changes
Fish Migrations
Mass movement between habitats
– Regular in time
– According to life history
• Oceanodromy (SW)
• Potamodromy (FW)
• Diadromy
– Anadromy (to FW to breed)
– Catadromy (to SW to breed)
– Amphidromy (not to breed, between SE &FW)
How do fish orient themselves?
• Sun position and polarized light
• Geomagnetic and geoelectric fields
• Currents (rheotaxis)
• Olfaction
• Temperature isolines
Osmoregulation in different environments
• Each species has a range of environmental osmotic conditions in which it can function:
– stenohaline - tolerate a narrow range of salinities in external environment
– euryhaline - tolerate a wide range of salinities in external environment
• short term changes: estuarine - 10 - 32 ppt, intertidal - 25 - 40
• long term changes: diadromous fishes (salmon)
Four osmoregulatory strategies in fishes
1. Isosmotic (nearly isoionic, osmoconformers)
2. Isosmotic with regulation of specific ions
3. Hyperosmotic (fresh H20 fish)
4. Hyposmotic (salt H2O fish)
Osmoconforming (no strategy) Hagfish internal salt concentration = seawater. However, since they live IN the
ocean....no regulation required!
Osmoregulation Strategies
Elasmobranchs (sharks, skates, rays, chimeras)
– Maintain internal salt concentration ~ 1/3 seawater, make up the rest of internal salts by retaining high
concentrations of urea & trimethylamine oxide (TMAO).
– Bottom line…total internal osmotic concentration equal to seawater!
– How is urea retained?
• Gill membrane has low permeability to urea so it is retained within the fish. Because internal
inorganic and organic salt concentrations mimic that of their environment, passive water influx
or efflux is minimized.
Osmotic regulation by marine teleosts...
– ionic conc. approx 1/3 of seawater
– drink copiously to gain water
– Chloride cells eliminate Na+ and Cl-
– kidneys eliminate Mg++ and SO4=
Osmotic regulation by FW teleosts
– Ionic conc. Approx 1/3 of seawater
– Don’t drink
– Chloride cells fewer, work in reverse
– Kidneys eliminate excess water; ion loss
– Ammonia & bicarbonate ion exchange mechanisms
IB 1

Age of the Earth: 4.6 billion years

Oldest rocks: 3.8 – 4.0 billion years
Oceans established > 3.8 billion years ago
Life not possible during period of heavy bombardment ~ 4.0 billion years ago
Signatures of life: 12C/13C suggests photosynthetic life existed ~ 4.0 billion years ago

Stromatolites (3.5 bill. Yr)

––Rocks with distinctive layer structure
••Look identical to living mats of microbes
––Layers of microbes and sediment
––Top layer uses photosynthesis
––Lower layers use top layer’s byproducts
Microfossils dating to 3.5 billion years ago3.5 ago
••Difficult to distinguish from mineral structuresstructures
••Analysis shows that some structures contain organic carboncarbon
--found in at least 3 sitesfound sites
Evidence in metamorphic rocks that life existed 3.85 billions years ago
Low C12/C13 fraction in rock layers suggests life
Biological processes prefer C12 to C13
Find lower fraction of C13

oReducing atmosphere on the primitive Earth. No free oxygen (O2)

oFree hydrogen (H2) and saturated hydrides (CH4, NH3 and H2O)
oEnergy for chemical reactions between these gases could come from electric discharge in storms or solar energy (no
ozone layer)
oThe Earth’s surface temperature probably hotter than today.

Assembling the cell

Organic soup was too dilute to favor the creation of complex organic molecules
Lab experiment with possible solution: When hot sand, clay or rock is placed in dilute organic solution, complex
molecules self-assemble
Organic molecules stick to surface of clay
Increases density and likelihood of reactions
Strands of RNA up to 100 bases have been produced this way
Other inorganic minerals may have also had a similar role
••Iron pyrite (fool’s gold)
––Positive charges on surface which allows organic molecules to adhere
––Formation of pyrite releases energy which could be used as fuel for chemical reactions

Sidney Fox (1950’s) demonstrated that polymerization of amino acids can occur
hot areas (volcanoes/pools) could concentrate amino acids in order to make polypeptides
in the lab, he made polymers of 200+ amino acids called thermal proteinoids
when placed in water they can cluster together in bodies called proteinoid microspheres that automatically form two-
layer membranes, grow, and even take up molecules from the surrounding environment
When present in certain concentrations in aqueous solutions, proteinoids form small structures called microspheres or
protocells. This is because some of the amino acids . incorporated into proteinoid chains are more hydrophobic than
others, and so proteinoids cluster together like droplets of oil in water. Many argue that these are not themselves alive
in the traditional sense, but these structures exhibit many of the characteristics of cells accepted as living cells:
a film--like outer wall.
osmotic swelling and shrinking.
budding.
 binary fission (dividing into two daughter microspheres).
streaming movement of internal particles.
What was the source of the ribonucleotide
The sugar found in the backbone of both DNA and RNA, ribose, has been particularly problematic, as the most
prebiotically plausible chemical reaction schemes yield only a small amount of ribose mixed with a diverse assortment of
other sugar molecules.
These difficulties have led some scientists to hypothesize that RNA was preceded by other RNA-like molecules that were
more stable and readily synthesized under prebiotic conditions.
Based on analyses of meteorites, such as the Murchison meteorite, other scientists contest that some components of
RNA may have formed in space and arrived on Earth rather than being formed de novo on the Earth.
PNA
Large RNA molecules are inherently fragile and can easily be broken down into their constituent nucleotides with
hydrolysis. Even without hydrolysis RNA will eventually break down from background radiation. (Pääbo 1993, Lindahl
1993).
A proposed alternative to RNA in an "RNA World" is the peptide nucleic acid, PNA. PNA is more stable than RNA and
appears to be more readily synthesised in prebiotic conditions, especially where the synthesis of ribose and adding
phosphate groups are problematic
In Cech’s words
“We both found that RNA could fold into complex shapes and catalyze biochemical reactions, a function previously
thought to be restricted to protein enzymes. Thus, RNA was sometimes an active participant in the chemistry of life, not
just a passive messenger. We named these RNA enzymes "ribozymes
1980 : T. Cech studied the rRNA genes in Tetrahymena
- 4 ribosomal RNAs
- 2 primary transcripts. One is processed into 3 separate rRNAs
• A few seconds after transcription, a 413nt intron is removed from the 6400nt primary transcript
RNAse P is a ribozyme
• in prokaryotes and organelles of eukaryotes
• size in E. coli: 377-nucleotide RNA component (125 kD)
+ 119-amino acid polypeptide (14 kD)
• The RNA portion is essential for the cleaving activity of the
tRNA precursor (pTyr), but the protein is necessary to cleave at least another precursor RNA
Structure of the ribosome
When the structures of the two ribosomal subunits had been obtained at high resolution, it was clear that a radical
change in the boundary conditions of ribosome research had occurred. One finding that initially caught considerable
attention was that the peptidyl-transferase centre, where peptide bond formation is catalyzed seemed to lack ribosomal
protein components. In fact, there was no visible peptide chain within 18Å from the identified peptidyl-transferase
centre (Nissen et al., 2000), which by many was taken as the ultimate proof of previous suggestions, e.g. (Noller et al.,
1992), that the ribosome is a ribozyme, i.e. an enzyme deriving its catalytic power from RNA and not protein.
Membrane Formation
First organisms had simple metabolism
••Atmosphere was O22 free, must have been anaerobic
••Probably chemoheterotrophs
––Obtained nutrients from organic material
––Obtained nutrients from inorganic material
••Modern archaea appear to be close to the root of the tree of lifethe life
••Obtaining energy from chemical reactions involving hydrogen, sulfur and iron compounds (all abundant on early
Earth)
••Natural selection probably resulted in rapid diversification
••Modern DNA has enzymes that reduce the rate of mutations
••RNA is not so lucky, more likely to have copying errors
••Higher mutation rate in early evolution than now
Photosynthesis
Most important new metabolic process evolved graduallygradually
••Organisms that lived close to ocean surface probably developed means of absorbing sunlight (UV in
particular)(particular)
••Once absorbed, developed method of turning it into energyinto energy
––Modern organisms of purple sulfur bacteria and green sulfur bacteria much like early photosynthetic microbes, use
H2S instead of H2O for photosynthesismicrobes, photosynthesis
Although the first photosynthetic organisms may have also used hydrogen sulfide as a source of hydrogen, those that
used water would have had a virtually unlimited supply.
As they removed hydrogen from water, they would have released free oxygen gas into the atmosphere—a process that
would have had a dramatic effect.
The accumulation of oxygen gas, which is very reactive, would have been toxic to many of the anaerobic organisms on
Earth.
While these photosynthetic cells prospered, others would have had to adapt to the steadily increasing levels of
atmospheric oxygen or perish.
Some of the oxygen gas reaching the upper atmosphere would have reacted to form a layer of ozone gas, having the
potential to dramatically reduce the amount of damaging ultraviolet radiation reaching Earth.
At the same time, the very success of the photosynthetic cells would have favoured the evolution of many
heterotrophic organisms.
Rise of O22
Rise of O2 would have created a crisis for life
O2 reacts with bonds of organic materials
Surviving species avoided effects of O2 because they lived or migrated to underground locations
Many anaerobic microbes found in such locales today
OO22 is highly reactive
••All initial O22 would react with rock and minerals in water
••OO22 could not accumulate in atmosphere until surface rock was saturated
••Rocks 2Rocks 2--3 bill. old called banded iron formations, show atmosphere had <1% of current amount of O22
••Rock evidence suggests that O22 amounts in atmosphere began to rise about 2.0 bill. ago
••Clear evidence of O22 near current levels appears only 200 million yr ago
––Find charcoal (fossil fuel)
––Indicates enough O22 in atmosphere for fires to burning
Early Eukaryotes
Fossil evidence dates to 2.1 bill. ago
••Dates to when O22 rising in atmosphere
••DNA evidence suggests that prokaryotes and eukaryotes separated from common ancestor much earlier
••OO22 played a key role in eukaryote evolution
––Cells can produce energy more efficiently using aerobic metabolism than anaerobic metabolism
––Adaptations of aerobic organisms could develop adaptations that required more energy that would be available for
anaerobic organisms

IB 2

How do fossils form?

Most fossils form when organisms that die become buried in sediment.
Some remains that become buried in sediments are actually changed to rock. These are called petrified fossils.
Sometimes the remains dissolve and a hollow space is created, this space is called a mold. This mold becomes filled with
hardening minerals, forming a cast.
Some organisms have been preserved in substances other than sediment…like ice. Ex. mammoths
A fossil may be:
an original skeleton or shell;
a mold or cast;
material that has replaced the once living thing;
traces such as footprints or worm tubes
What are the fossil types?
Body fossils – actual parts of an organism, unaltered or altered bones, shells, leaf imprints
Trace fossils – evidence of life that is not a body fossil tracks, burrows, casts
What are the modes of fossil preservation for body fossils
Unaltered Original Material - original, unaltered material from the living organism unaltered bone or shell
Encrustations or entombments – material is trapped inside coating such as amber
Unaltered Mummification - quickly dried material
Refrigeration – material is trapped inside ice and tissue is preserved

What are the modes of fossil preservation?

Altered Permineralization – pores in tissue are filled by minerals
Replacement – replacement of tissue with minerals
Altered Carbonization – tissue material is decomposed or reduced to a film of carbon

More on trace fossils

• Mold – reproduction of the inside or outside surface of a living thing
• Cast – duplicate of the original organism; usually formed by replacement of inside of living thing
• Burrows or borings – Spaces dug out by living things and preserved as is or filled in
• Gastroliths – smooth stones from abdominal cavity of dinosaurs
• Coprolites – fossilized excrement; usually preserved by replacement
• Tracks – impressions of passage of living things

Molecular Evolution
• Molecular evolution address two broad range of questions:
• 1. Use DNA to study the evolution of organisms, e.g.
• population structure, geographic variation and phylogeny
• 2. Use different organisms to study the evolution process of DNA
Reveal dynamics of evolutionary processes.
Indicate chronology of change.
Identify phylogenetic relationships.
Sequence Alignments
Matching nucleotides are interpreted as unchanged since a common ancestor.
Substitutions, insertions, and deletions can be identified.
Gaps inserted to maximize the similarity between aligned sequences indicate occurrence of insertions and deletions
(indels).

Optimal alignment
• Many alignments are possible between sequences, and algorithms typically maximize the matching number of
amino acids or nucleotides, invoking the smallest possible number of indel events.
Substitutions
• When DNA sequences diverge, they begin to collect mutations. The number of substitutions (P) found in an
alignment is widely used in molecular evolution analysis.
Number of substitutions
• If the alignment shows few substitutions, a simple count is used.
• If many substitutions occurred, it is likely that a simple count will underestimate the substitution events, due to
the probability of multiple changes at the same site.
Jukes and Cantor Model
• They assumed that each nucleotide is equally likely to change into any other nucleotide, and created a
mathematical model to describe multiple base substitutions.
• K= -(3/4)*ln (1-(4/3)*P)
• P= observed number of substitutions over the total number of sites.
• K=distance between sequence x and sequence y expressed as the number of changes per site corrected
for multiple substitutions at the same site
Pseudogenes
• Highest rate of evolution is that of nonfunctional pseudogenes, which no longer code for proteins.
• What advantage pseudogenes provide for evolution of multiple gene families?
Coding sequences with high rates of nonsynonymous substitution
• Major histocompatibility complex (MHC) in mammals
– If there is evolutionary pressure for diversity, substitutions become advantageous.
– MHC is involved in immune function where diversity favors fewer individuals vulnerable to an infection
by any single virus.
– Viruses utilize error-prone replication coupled with diversifying selection.
– Both viruses and MHC complex rapidly evolves due to natural selection for diversification.
Ribosomal RNAs
• Sequences of rRNA regions that interact and provide for ribosomal function by pairing will be subject to
mutation at the same rates as sequences that do not pair.
 • However, mutations that disrupt pairing will be selected against, since such mutations will alter ribosomal
function and become detrimental to fitness.
Mitochondrial DNA (mtDNA)
• Mammalian mitochondrial genome contains a circular, double-stranded mtDNA about 15000 bp long (1/10000
of the nuclear genome, encoding 2 rRNAs, 22 tRNAs, and 13 proteins).
• The average synonymous substitution rate in mammalian mitochondria is 5.7 x 10-8/site/year, 10 times higher
than the synonymous substitutions in nuclear genes.
• The higher rates of mutation in mtDNA are likely to be due to:
• The higher error rate during replication and repair. DNA polymerases have no proofreading ability.
• Higher concentrations of mutagens such as free radicals resulting from metabolic processes.
• Less selective pressure because there are many of them within the cell; changes are less detrimental.

Phylogenetic Trees

What Is a Tree?
A tree is an acyclic connected graph that consists of a collection of nodes (internal and external) and branches
connecting them so that every node can be reached by a unique path from every other branch.
features
 Internal nodes represent taxonomic units such as species or genes; the external nodes, those at the ends of the
branches, represent living organisms.
 The lengths of the branches usually represent an elapsed time, measured in years, or the length of the branches
may represent number of molecular changes (e.g. mutations) that have taken place between the two nodes.
 Sometimes, the lengths are irrelevant and the tree represents only the order of evolution. [In a dendrogram,
only the lengths of horizontal (or vertical, as the case may be) branches count].
 Finally the tree may be rooted or unrooted.
 Root: origin of evolution
 Leaves: current organisms, species, or genomic sequence
 Branches: relationship between organisms, species, or genomic sequence
 Branch length: evolutionary time (in cladogram, it doesn't represent time)
Rooted / Unrooted trees
❑ Rooted tree: directed to a unique node
❑ (2 * number of leaves) - 1 nodes,
❑ (2 * number of leaves) - 2 branches
❑ Unrooted tree: shows the relatedness of the leaves without assuming ancestry at all
❑ (2 * number of leaves) - 2 nodes
❑ (2 * number of leaves) - 3 branches
More tree types
❑ Unrooted tree
❑ Rooted tree
❑ Cladograms: Branch length have no meaning
❑ Phylograms: Branch length represent evolutionary change
❑ Ultrametric: Branch length represent time, and the length from the root to the leaves are the same
Example of how to construct a cladogram:
❑ 1. Select your species for which you want to make a cladogram. These are called the ingroup. They have shared
primitive and derived characters.
❑ 2. Select an outgroup → a species that is closely related to the species under study, the outgroup has a shared
primitive character that is common to all species.
❑ 3. Construct a character table and tabulate the data. → The more shared characters, the more closely related
are the species.
❑ 4. Construct a cladogram based on the number of shared characters.
❑ The outgroup here, the lancelet has a notochord, the shared primitive character. The ingroup is five vertebrates
❑ One of the newest quantitative methods is to compare the nucleotide (or amino acid) sequence in a particular
segment of DNA common to all the organisms to be included in the study.
 ❑ Those organisms that show the greatest number of nucleotide sequence differences are considered to have
diverged from a common ancestor (following separate evolutionary paths) the greatest number of years ago
Maximum Parsimony and Maximum Likelihood
 Systematists can never be sure of finding the single best tree in a large data set.
◦ Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood.
 The principle of parsimony helps systematists reconstruct phylogeny
 a. Phylogenies can be extremely complicated.
 b. The principle of parsimony states that a theory about nature should be the simplest explanation that is
consistent with facts.
 c. A phylogenetic tree is a hypothesis. There may be many possible trees, but the simplest one is probably the
most accurate.
Basic Procedure for building biological trees
 Start with TWO sequences and add the rest of the sequences one at a time.
 Each new sequence becomes a leaf of the tree (meaning, nothing further can be attached to this point).
Choose the place carefully and take into account the score information we obtained
Distance Matrix methods
❑ Calculate all the distance between leaves (taxa)
❑ Based on the distance, construct a tree
❑ Good for continuous characters
❑ Not very accurate
❑ Fastest method
❑ UPGMA
❑ Neighbor-joining
UPGMA
❑ Abbreviation of “Unweighted Pair Group Method with Arithmetic Mean”
❑ Originally developed for numeric taxonomy in 1958 by Sokal and Michener
❑ Simplest algorithm for tree construction, so it's fast!
This method follows a clustering procedure:
(1) Assume that initially each species is a cluster on its own.
(2) Join closest 2 clusters and recalculate distance of the joint pair by taking the average.
(3) Repeat this process until all species are connected in a single cluster
Neighbour Joining
This algorithm does not make the assumption of molecular clock and adjust for the rate variation among branches. It
begins with an unresolved star-like tree. Each pair is evaluated for being joined and the sum of all branches length is
calculated of the resultant tree.
The pair that yields the smallest sum is considered the closest neighbors and is thus joined .A new branch is inserted
between them and the rest of the tree and the branch length is recalculated. This process is repeated until only one
terminal is present.

Ants

What are ants?

•Any of various social insects of the family Formicidae, characteristically having wings only in the males and fertile
females and living in colonies that have a complex social organization.
Ants are hugely successful ecologically speaking and are common in almost all terrestrial habitats.
•There are about 10,000 known species which is more than twice the total number of mammal species.
•In some rainforests, the dry weight of ants and termites is about four times the dry weight of all the other land animals
combined!
Generally, single ants behave in a simple way. Indeed, alone, an ant is perhaps not really an ant at all!
•Even though ant brains are always small, between species, the sizes can differ several orders of magnitude. The
number of neurons can be as little as 10,000!
Individual units do not gather, store or process information to a great extent.
•Information is dealt with at the collective level due to an interaction between the units.
•The colony/network IS the organism.
•The behavior of ants develops due to a network of chemicals in their colonies.
Connectivity
•The main and most essential difference lies in the connectivity.
•Contact between ants => short/transient
•Synaptic connections => long-term
•As a consequence, memory in ant colonies is limited (chemicals can lead to longer-term type memories but this
strategy seems to reduce the possible number of memories that can be stored).
How to Ants Communicate?
•High level of self organization.
•Collective ‘intelligence’.
•E.g. in army ants, the swarm behaves like a single entity even though there is no central control.
•The (inseminated) female creeps under a stone or wood to make the initial nest. If the situation allows, the entrance is
closed off. She then lays about one egg every day.
•An egg changes to a larva within about 25 days. After some 10 days, the larva forms a white cocoon.
•About 60 days after the eggs are laid, the first worker is born.
•With a gradual increase in the number of workers, the nest grows. About 2,000 ants live in a single nest of the
Camponotus japonicus ant.
•After the growing period (usually several years) the first sexuals are born. In a given region, the sexuals of the colonies
in that region often fly out at the same time so that there is a high probability for a male to meet a female during her
nuptial flight.
•When the queen dies the colony will usually not survive since workers do not reproduce
•Ants secrete substances called pheromones, which are chemical messages detected by other ants through sense
organs or the antennae.This process called chemoreception , is the primary communication vehicle that facilitates mate
attraction ,kin and non kin recognition.
•Ants send tactile signals by touching and stroking each other’s bodies with their antennae and forelegs.

Speciation

What is a species?
Typological Species Concept: species are a 'type' of organism…Plato
"Species are as many as were created in the beginning by the Infinite." (Linnaeus, 1758)
Biological Species Concept
•Species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from
other such groups (Mayr, 1940).
•What do you do with asexual organisms, and what do you do with organisms that occasionally form hybrids with one
another? Other difficulties include:
•What is meant by “potentially interbreeding
•Fossils---for example, it is not really possible (or very meaningful!) to figure out whether a trilobite living 300 million
years ago would have interbred with its ancestor living 310 million years ago.
Evolutionary Species
•Evolutionary species concept: A species is a single lineage of ancestor-descendant populations which maintain its
identity from other such lineages and which has it own evolutionary tendencies and historical fate (Simpson, 1961;
Wiley, 1981).
Phylogenetic Species
•A species is the smallest diagnosable cluster of individual organisms within which there is a parental pattern of ancestry
and descent (Cracraft 1983).
Isolating mechanisms
Premating and postmating barriers
Premating barriers prevent mating or egg fertilization if members of different species try to mate.
Postmating barriers prevent the development of viable progeny
Postmating
a. Reduced hybrid viability
- Abort development of hybrid at some embryonic stage.
b. Reduced hybrid fertility
- Meiosis doesn’t produce fertile gametes in vigorous hybrids. donkey + horse = mule (sterile hybrid)
c. Hybrid breakdown
- First-generation hybrids are fertile, but they cannot produce fertile offspring in the next generation (e.g. different
species of cotton).
Modes of speciation
Allopatric speciation
• reproductive isolation occurs in complete geographic isolation (no gene flow).
Parapatric speciation
• reproductive isolation occurs without complete geographic isolation (some gene flow).
Sympatric speciation
Reproductive isolation evolves with complete geographic overlap.

Macroevolution
= large scale evolution at & above species level
Microevolution = small scale evolution at the population level
Platy fish and swordtail: F2hybrids show higher probability of contracting cancer.
Platyfish/swordtail inviability has been localised to an X-linked oncogene and receptor for tyrosine kinase with an
autosomal inhibitor in Platyfish, where the system generates spots. There is no inhibitor in the swordtail, with
consequent melanoma in the F2 generation

Why is the X chromosome so often implicated in hybrid infertility?

it appears that most alleles causing hybrid sterility and inviability are recessive
advantageous recessives will be fixed faster on the X chromosome
Tempo of Speciation
1) Gradualism (gradualistic speciation) = gradual, step-by-step evolutionary change
Species showing very little evolutionary change:
E.g.:Coelacanth (Latimeria) - 250 myr, rediscovered 1938
Horseshoe crab
Dawn-Redwood Tree (Metasequoia)
Maidenhair Tree (Ginkgo)
2) Punctuated Equilibrium = rapid evolutionary change during speciation followed by relatively long periods of stasis
(no change).

How can rapid speciation (resulting in punctuated equilibrium) occur?

1) Founder principle or population bottleneck
2) Major environmental change, new niches open up.
- both can accelerate evolutionary change

Invertebrates

Phylum
You need a body plan
How do you define the body plan?
–Levels of organization
–Body symmetry
–Differentiation of germ layers
–Formation of body cavities
–Patterns of embryonic development
–Segmentation
–Cephalization
–Limb formation
1. Endoderm: the innermost germ layer, develops into linings of the digestive tract and much of the respiratory system
2. Mesoderm: the middle layer, gives rise to the muscles and much of the circulatory, reproductive, and excretory organ
systems
3. Ectoderm: the outermost layer, produces sense organs, nerves, and the outer layer of skin

Cephalization
Animals with bilateral symmetry typical exhibit cephalization- the concentration of sense organs and nerve cells at their
anterior end
•The most successful animals including arthropods and vertebrates exhibit pronounced cephalization
•Insect and vertebrate embryos heads are formed by fusion and specialization of several body segments during
development
–As the segments fuse the external and internal parts combine in ways that concentrate sense organs in the head, such
as the eyes
–Nerve cells that process information and “decide” what an animal should do are also found in the head
–Animals with a head move in a head first direction because this way the concentration of sense organs and nerve cells
come in contact with the new environment first