Download The Business of Life Living Things: Defined Living Things

The Business of Life
•  Living Things: Parts & Emergent Properties
•  Self-Organization in the Sea
•  Reproduction: Asexual & Sexual
•  The Diversity & Unity of Living Things:
Classification & Evolution by Natural Selection
Living Things and Levels
of Organization
•  Some biologists study the parts of living
things (molecules, cells, etc): Reductionism
•  Others study the Emergent Properties The sum is greater than the parts: Holism
The Chemistry of Life
•  Living Things are mostly Water: 70-95%
•  Water is the Biological Solvent
•  Biochemistry occurs in Aqueous Solution
•  An Organisms’ Dry Weight consists
mostly of Organic Compounds:
•  Carbon-based Molecules, e.g. Proteins
Living Things: Defined
•  Living Things Consist of Cells
•  Living Things Use Energy to
•  Self-Organize
•  Grow, and
•  Reproduce (cells make cells)
•  Populations of living things may Evolve
Living Things: Parts &
Emergent Properties
•  Living things contain special molecules; but these
molecules are not alive
•  These molecules (& others) make up a cell
•  Cells can self-organize & reproduce:
Emergent Properties of Life
•  At each higher level of organization:
New Properties Emerge
Organic Compounds
•  Complex & Energy rich
•  Organisms build them up:
- Function & Storage
•  And break them down
-  Release stored energy
-  Re-use their parts
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Organic Compounds: types
•  Carbohydrates: energy & structure
•  sugars, starch, cellulose & chitin
•  Lipids: energy, membrane & hormones
•  fats & oils, phospholipids, steroids
•  Proteins: diverse and abundant
•  transport, enzymes, receptors, etc.
•  Nucleic Acids: Genetic material
•  Deoxyribonucleic acid & Ribonucleic acid
Carbohydrates: CH20
•  Glucose is an energy molecule:
•  primary fuel for aerobic respiration
•  Starch stores energy for later use
•  Cellulose & Chitin provide structure
•  Cellulose: cell wall of plants (algae), wood
•  Chitin: cell wall of fungus, exoskeleton of
arthropods - insects and crustaceans
Phospholipids are Both
Hydrophobic & Hydrophilic
- Basis of Biological Membranes
Carbohydrates: CH20
•  Carbohydrates are made of C, H & O
•  Monosaccharides are simple sugars
e.g. Glucose C6H12O6
•  Polysaccharides are complex sugars many glucose molecules bound together
e.g. Starch and Cellulose
Lipids are mostly
Hydrocarbons: H & C
•  Lipids are Hydrophobic compounds:
water is not attracted to lipids
•  Fats (oils) contain twice the energy per
weight of glucose:
•  Advantageous for mobile organisms
e.g. animals
•  Provides insulation & protection,
Example: Blubber Insulates
Proteins: Polypeptides of Amino
Acids - C, H, O, N & S
•  The most diverse & abundant organic cpds
Other Lipids are Steroids
•  Steroid Hormones: chemical messengers
•  e.g. estradiol, testosterone
•  Create the ‘traits’ of organisms:
•  The expression of genes
•  Consist of long chains of Amino Acids
•  Cholesterol is a steroid used in membranes
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Proteins: Polypeptides of Amino
Acids - C, H, O, N & S
•  Abundant and Diverse in Function:
•  Transport (hemoglobin)
•  Enzymes: catalyze chemical reactions
•  Hormones
•  Hormone Receptors
•  Structure, etc.
•  Organisms need Nitrogen for Proteins
Nucleic Acids & The Flow of
Genetic Information
•  DNA is made of Four Nucleotides: ATGC
•  Genes are specific Sequences of DNA
•  Genes code for Proteins
- which create the traits of organisms
•  A specific sequence of DNA nucleotides is
transcribed into messenger RNA (mRNA)
•  The mRNA is then translated to a specific
sequence of amino acids => Protein
Nucleic Acids: DNA & RNA
C, H, O, N & P
•  Deoxyribonucleic acid & Ribonucleic acid
•  DNA is is the Genetic Material:
•  Handed down from cell to cell, and
•  From generation to generation
•  Organisms need Phosphorus & Nitrogen
•  for their nucleic acids
The Flow of Genetic
Information
DNA

Inheritance: cellcell, parentoffspring
Gene Expression: within cells
DNA

RNA

Proteins
Chemical Energy
Organisms Use Energy
•  Organisms must Harvest Energy from the
environment, because •  Organisms continuously Use Energy
(efficiently; Harness Energy) to –
•  Self-Organize, Grow & Reproduce
•  Chemical energy is the form of energy
used by organisms in their activities
•  Metabolism: the sum of an organisms
chemical reactions
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Sunlight & Photosynthesis:
Energy for Life on Earth
•  Photosynthesis traps the energy of
the sun (photons) and uses that
energy to make (synthesize) sugars
and other energy compounds
Photosynthesis:
6 CO2 & 6 H2O → C6H12O6 & 6 O2
Carbon Dioxide & Water → Sugar & Oxygen
Recall: Sugar is an organic compound
Giant Kelp: Macrocystis
•  Photosynthetic organisms are called
Autotrophs: self-feeding
•  They can harvest the energy of the sun and
transform it into chemical energy
•  Plants & Algae are Autotrophs
Chemical Energy & Cellular Work:
ATP → ADP & Pi
•  Organisms release the stored energy in
their molecules to make ATP:
Adenosine Tri-Phosphate
•  ATP is the energy currency of the cell the right amount of energy for cell
movement, transport & chemical synthesis
•  Organisms use either Anaerobic and/or
Aerobic Respiration to make ATP
Autotrophs & Heterotrophs
•  Autotrophs can transform solar
energy into chemical energy - the
energy contained in chemical bonds
•  Heterotrophs: Other-feeding, are
organisms that must consume ‘others’
for their chemical energy: herbivores,
carnivores and decomposers
Aerobic Respiration
C6H12O6 & 6 O2 → 6 CO2 & 6 H2O
Organic Cpd & Oxygen → Carbon Dioxide & Water
•  Aerobic Respiration:
•  Requires Oxygen
•  Produces 18x the ATP vs. anaerobic respiration
•  Efficient Harnessing of Chemical Energy!
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The Living Processes of Organisms:
Metabolism - Occurs in Cells
The Living Processes of Organisms:
Metabolism - Occurs in Cells
Cell Parts: Plasma membrane, DNA & Cytoplasm
•  Plasma membrane: a fence with gates - protects
the organized living cell from the chaos of the
universe
•  DNA: the genetic material (HQ) - directions to
make proteins
•  Cytoplasm:
•  Cytosol: semi-liquid matrix
•  Organelles: cell bodies with special function
Prokaryotic Cells
Pro-before, Karyo-Nucleus
•  Prokaryote cells are Ancestral
•  They lack a nucleus: their DNA is ‘naked’
•  They are relatively small & simple, without
membrane-bound organelles
Eukaryotic Cells:
Endosymbionts
•  Two of the most important organelles in
Eukaryotes are:
1.  Mitochondria - the site of Aerobic
Respiration
2.  Chloroplasts - the site of Photosynthesis
•  These organelles are bacteria!
Eukaryotic Cells:
Eu-true, Karyo-Nucleus
•  Eukaryotes are Derived, more recently evolved
•  Eukaryotic Cells have a true nucleus - their
DNA is enclosed in membrane
•  They are relatively large & complex, with many
membrane-bound organelles
The Endosymbiotic Theory
•  An ancestral Eukaryote engulfed an aerobic
bacterium & did not completely digest it!
•  Endosymbiosis evolved
•  Later: a photosynthetic bacteria, was engulfed
e.g. Prochloron
•  New symbiosis
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Why are Cells so Small?
•  Prokaryotic cells average 1-10 microns
•  Eukaryotic cells average 10-100 microns
Cell Size is Limited by Surface Area
Levels of Organization:
Organismal Biology & Ecology
Cells need adequate Membrane
(surface area) to meet the needs
of their Cytoplasm (volume)
•  Cells need new sources of energy & nutrients
•  Cells need to release their wastes
•  Cells exchange matter & energy across their
membranes
•  As a cell increases in size, volume increases
faster than surface area
•  Eukaryotic cells can be larger due to their
abundant internal membranes
Sponge: a simple, multicellular animal
•  Many organisms are unicellular
•  Larger organisms are multicellular:
•  Cells make-up tissues
•  Tissues make-up organs
•  Organs make-up organ systems
•  Our Focus: Whole organisms and above
•  Populations: groups of the same species
•  Communities: groups of different species
•  Ecosystems: communities, energy & nutrients
Organismal Level
Sponge: a simple, multicellular animal
Population Level
A Population of mussels: Mytilus
•  Population: members of the same species living in the same
area, with the opportunity to interact
•  Patterns: density & dispersion, age structure, sex ratio, etc.
•  Processes: density-dependent effects: intraspecific
competition, crowding, disease, etc.
An Intertidal Community
•  Community: populations of different species living in
the same area, with the opportunity to interact
•  Patterns: species richness, biodiversity
•  Processes: interspecific interactions •  Competition
•  Predation
•  Symbiosis:
•  Mutualism
•  Parasitism
•  Commensalism
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Limiting Resources
•  Populations & Communities can be limited by
necessary resources that are in short supply
•  A resource in short supply may:
•  Affect survival and reproduction
•  Limit population size or Species richness
•  Nitrogen and Phosphorus are two limiting
nutrients: photosynthetic organisms
•  Food and Shelter may limit animals
Salinity, Diffusion & Osmosis
•  Diffusion is the passive movement of substances
from an area of high activity (concentration) to an
area of lower activity (concentration)
•  Diffusion continues until Equilibrium is reached
Osmoregulation &
Osmoconformers
Self-Organization in the Sea
Organisms have two alternate ‘strategies’:
1. Conform to their environment: allow their
internal environment (cells) to be determined
by the environment outside their body/cells
2. Regulate their internal environment to maintain
Homeostasis: a constant internal state,
regardless of the environment
•  Regulation (self-organization) costs energy, but
•  Provides benefits: better control of metabolism
Osmosis: Diffusion of Water
•  Osmosis is the diffusion of water
•  Water flows passively across cell membranes
•  Osmosis can threaten living things
Osmoregulators I
•  Osmoregulation: managing water & salt balance
•  Osmoconformers allow their internal water & salt
concentrations to match the water around them
•  Hagfish are Osmoconformers:
They live on the ocean floor, conditions are fairly
constant: internal water concentration equals
external water concentration (some salts vary)
•  Sharks (Class Chondrichthyes) maintain an
internal water concentration similar to the external
water concentration
•  But their salt levels are lower than sea water
•  Sharks retain urea in their blood - to balance their
concentrations of salt (NaCl) to water
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Osmoregulators II
•  Bony marine fish (Class Osteichthyes)
- maintain their internal salts at 14 ppt
- vs the 35 ppt salinity of sea water
Temperature as Environment
•  Temperature affects metabolism
•  Limits survival & distribution of organisms (freeze)
•  Bony marine fish actively:
- drink sea water,
- pump NaCl from their gills &
- excrete concentrated urine
Sea Turtles secrete salty tears
Thermoregulation
Poikilotherms vs Homeotherms
•  Temperature affects metabolism:
The chemical reactions of living things
•  An increase of 100C doubles metabolic rates
•  Poikilotherms (ectotherms)- are conformers,
‘cold-blooded’ (externally heated)
•  Homeotherms (endotherms) - are regulators,
maintain a constant warm body temperature
‘warm-blooded’ (internally heated)
•  Poikilotherms do not ‘spend’ energy to be warm,
but they are less active in cold temperatures
vs. homeotherms (e.g. fish vs. otter)
•  Homeotherms spend 97% of their energy budget
on being warm!
but their higher body temperature allows for
greater activity: feeding, metabolism, etc.
•  Why does the early bird get the worm?
Reproduction
Asexual Reproduction
•  Organisms are made of Cells
•  Reproduction is the making of new cells
- To create a new, separate individual
•  Asexual reproduction: reproduction without ‘sex’
- Produces Clones: genetically identical
•  Sexual reproduction: mixes genetic material
- Makes new cells/individuals with
- Unique Genomes: combinations of genes
•  Many organisms produce ‘clones’ - offspring with
identical genetic material (DNA/chromosomes)
1.  A mother cell replicates its DNA (chromosomes)
2.  Then divides into two daughter cells
3.  Each daughter cell is genetically identical to the
mother cell and its ‘sister’
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Binary Fission
•  Prokaryotes (Bacteria & Archaea) reproduce by
- Binary Fission ‘split in two’
- Creates two genetically - identical offspring
Mitosis
•  Eukaryotes undergo Mitosis:
- Creates two genetically-identical cells
•  Eukaryotes can be unicellular or multicellular
•  In multicellular forms the new cell produces
more identical cells to become a multicellular
individual - genetically-identical to its parent
Mitosis & Asexual Reproduction
Examples:
- Unicellular Dinoflagellate
- Budding in a multicellular coral
- Rhizomes in a multicellular plant
Sexual Reproduction Creates
New Genetic Combinations
Sexual Reproduction requires a complex life cycle.
•  At some stage in a sexual life cycle:
Cells have two copies of each chromosome:
- Diploid cells (2n)
- one from each parent via fertilization
•  At another stage in a sexual life cycle:
Cells have only one copy of each chromosome
- Haploid cells (n)
- via Meiosis
Sexual Life Cycles Alternate:
Meiosis (2n→n) & Fertilization (n+n→2n)
•  Meiosis: Is the process in which a diploid cell
(2n) divides to produce four haploid cells (n) spores or gametes: eggs & sperm
•  Fertilization is the coming together of:
two haploid cells (n) - egg & sperm
creates a new diploid cell (2n) - a zygote
Fertilization Creates a Zygote:
a Genetically Unique Diploid Cell
Diagrams of Human and Algal Life
Cycles: with Meiosis & Fertilization
•  Sexual Life Cycles create new, unique Genomes
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Three Types of Sexual Life Cycles:
- All: Alternate Meiosis & Fertilization
- Difference: Mitosis
Three Types of Sexual Life Cycles in
Multicellular Organisms
All Alternate Meiosis & Fertilization
Key
Haploid (n)
n
Gametes
n
Mitosis
n
n
MEIOSIS
Spores
2n
(a) Animals
2n
Mitosis
Mitosis
n
n
MEIOSIS
Diploid
multicellular
organism
Mitosis
n
n
FERTILIZATION
Zygote
Haploid unicellular or
multicellular organism
Haploid multicellular organism
(gametophyte)
Diploid (2n)
Gametes
n
n
Spores
Gametes
n
FERTILIZATION
MEIOSIS
2n
Diploid
multicellular
organism
(sporophyte)
Difference: Mitosis can occur in diploid cells,
haploid cells, or both to produce
Mitosis
n
n
2n
Zygote
2n
Mitosis
(b) Plants and some algae
FERTILIZATION
Zygote
(c) Most fungi and some protists
Reproduction & Survival
Multicellular Diploids (e.g. animals)
Multicellular Haploids (e.g. fungi)
Multicellular Diploids & Haploids (e.g. plants)
Mating Behavior & Anisogamy
•  In Evolutionary Terms: Survival is
meaningless without Reproduction
•  Many species ‘pair spawn’ - a male & female
come together to join their gametes
•  Natural Selection has strongly influenced:
Mating patterns
•  The differences between the sexes affects
their relative mating strategies
•  Females make eggs:
few, large, non-motile, energy rich
•  Males make sperm:
many, small, motile, few added nutrients
‘cheap’
•  Many Marine Organisms Broadcast spawn:
release many gametes directly into the water often on a daily or lunar cycle, e.g. Tridacna
Anisogamy Theory
A(n)-not, without; Iso-the same; Gamy-gametes
•  Anisogamy Theory refers to the different gametes
made by the sexes, and predicts ‘syndromes’ of
their mating behavior
•  ‘Female syndrome’: because females make few,
large, energy rich eggs - they should be choosy
•  ‘Male syndrome’: because males make many,
small, ‘cheap’ sperm - they should be eager
Anisogamy & Sexual Selection
•  Anisogamy Theory predicts:
•  Females should be Choosy - pick one best mate
•  Males should be Eager - mate with anything
(nearly) that moves
•  Sexual Selection refers to this difference in
selection on the sexes, due to Anisogamy
•  Males tend to be large, colorful, armed - To attract females and compete with males
•  Females tend to be smaller and drab
- They can choose from many available males
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Live Birth & Maternal Care
Parental Care
Successful reproduction includes offspring
survival
In pair-spawning species, the fertilized egg, or
zygote, may be cared for by a parent.
In fishes, fathers often care for eggs until
hatching.
The Unity and Diversity of Life
•  Over 2 million living species have been
named & many others are known from the
fossil record
•  Despite this great diversity, evidence
indicates that all organisms, living & dead,
are related.
•  We all come from a common ancestor!
Hierarchical Classification
•  Internal fertilization occurs in many groups.
•  Mothers often retain the young until hatching
(birth).
•  Mammals provide much parental care before and
after birth, e.g. milk & protection.
•  Mostly Maternal Care!
Classifying Life
•  Carolus Linneaus introduced a System of
Classification that is still used today
•  It consists of a series of nested sets
•  From Kingdom to species
•  Each grouping was made by shared characters:
e.g. Chordates have a notochord and
Mammals have mammary glands
The Classification System today
Includes ‘Domain’
Each species has a
unique binomial:
Genus species
e.g Panthera pardus
A species is a group of
organisms that can
successfully reproduce
with each other
Figure 25.8
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Classification & Evolution
The Theory of Evolution by
Natural Selection
•  Linnaeus grouped organisms by their common
characteristics. He did not accept evolution
•  The Theory of Evolution states that populations
of living things change over time
•  Scientists today see these same groups as
relatives - descended from a common ancestor
•  Darwin called this ‘Descent with Modification’
•  Why do mammals share mammary glands?
Their common ancestor evolved the trait, so the
living descendants share the trait
Charles Darwin: Feb. 12, 1812
•  Darwin was brought up to be a Doctor
•  He was also a great Naturalist
•  He ended up with a degree in Natural Theology:
The study of nature to demonstrate how perfectly
the world was made by the creator
•  Many scientists had ideas of evolution prior to
Darwin, but Darwin discovered the mechanism:
Natural Selection
Darwin & the Voyage of the Beagle: 1831-1836
•  Darwin knew the organisms of Temperate England
•  Organisms of Tropical S. America were different
•  Organisms of Temperate S. America?
•  Then – Galapagos Islands and Darwin’s Finches
•  After graduating, he was destined for the clergy,
but was hastily placed on board the HMS Beagle
just before its departure in the spring of 1831
Darwin’s ‘Dangerous Idea’
•  Darwin found groups of similar organisms were
found in localized regions: Biogeography
•  This regionalization suggested they had
evolved from a common ancestor in that region
•  He proposed Natural Selection as a mechanism
that could create new, better forms, adapted for
their particular environments
 Darwin’s Theory of Evolution by
Natural Selection * Part I.
  Observation 1. Populations have tremendous
reproductive potential.
  Observation 2. Populations tend to be stable.
  Observation 3. Resources are limited. (Malthus 1798)
  Inference 1. Production of excess offspring leads to a
struggle for existence; only a fraction of the offspring
born will survive to reproduce.
•  After Ernst Mayr. 1982
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 Darwin’s Theory of Evolution by
Natural Selection * Part II.
  Observation 4. Individuals vary within a population.
  Observation 5. Much of this variation is heritable.
  Inference 2. Some variants will be better able to
survive and reproduce in their environment.
  Inference 3. The reproductive differential between
variants in the population will lead to a gradual
change in the population, with favorable traits
(adaptations) accumulating over the generations.
* After Ernst Mayr. 1982
Further Support for Evolution
•  Comparative Anatomy
•  Comparative Embryology
•  Artificial Selection
•  DNA - the hereditary material
•  Evolution is a fact: e.g. Guppies
- 100’s of other published studies
•  Problems of poor design
Adaptation
•  The Theory of Evolution by Natural Selection
suggests a process that creates new types of
organisms, better ADAPTED to survive and
reproduce in their environments
•  Adaptations are:
•  New Features
•  They provide a performance advantage
•  They have been shaped by natural selection
Evolution
•  Evolution defined:
Any change over time in a
population’s appearance or
genetic structure
Evolution: Theory & Fact
•  The Theory of Evolution by Natural Selection is
the unifying theme of biology
•  It explains a great deal about living things
•  It has been well tested and not disproven
•  It generates ideas in biology
•  Evolution has also been directly observed by
scientists: Populations were observed to change
over time. In these cases, evolution is a fact.
Phylogenetic Hypotheses
•  Modern Classification systems hypothesize
the branching of descendants from common
ancestors: Phylogenetic Hypotheses
•  Cladistics is a modern school of classification
that uses only shared, derived characters
(often adaptations) to suggest relationships
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Convergent Evolution:
•  Separate evolutionary events shaped by the
same selective forces produce similar responses
- Torpedo shape for hydrodynamic efficiency
We now group organisms into three
Domains vs. the old five Kingdom system
Domain Bacteria: prokaryotic
Domain Archaea: prokaryotic
Domain Eukarya: eukaryotic
Archaea & Eukarya are sister groups
Marine ‘Lifestyles’
•  Plankton: wanderers, drift in the water
column; unable to swim against currents
•  Nekton: swimmers, able to direct their
movement in the ocean, swim against currents
Hierarchical Classification &
Systematics
  Carolus Linnaeus created a classification
system (1748) still used today. He grouped
species in increasingly broad categories of
nested sets
  Kingdom, Phylum, Class, Order, Family,
Genus & specific epithet
•  Benthos: bottom-dwellers, may be
permanently attached to the sea floor, or
otherwise bottom-associated
Binomial Nomenclature
  Linnaeus also created the Scientific Binomial
 the two-part scientific name of a species
 Genus species (specific epithet)
 Underlined or italicized:
 Homo sapiens, or
  Homo sapiens
Phylogentic Systematics
  Since the time of Darwin, systematists have
organized groups (taxa) based on their
hypothesized evolutionary relationships
  Phylogenetic systematics has been shaped by
 Cladistics: a school of systematics which uses only
shared, derived characteristics to identify related
groups, or ‘clades’ of organisms (clade = a branch)
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Linking Classification and Phylogeny
  Systematists depict evolutionary relationships
in branching ‘phylogenetic trees’
  Each branch point, or ‘node’
Represents their most recent common
ancestor and the divergence of two groups
  ‘Deeper’ branch points
Represent progressively greater amounts
(time) of divergence
Cladistics
  Clades
 Can be nested within larger clades, but not
all groupings or organisms qualify as clades
 A ‘good’ clade consists of a common
ancestor and all of its descendants
= A Monophyletic Group (one tribe)
Pleisiomorphies
  A shared ancestral character: Pleisiomorphy
 Is a homologous structure that predates the
branching of a particular clade from other
members of that clade
 Is shared beyond the taxon we are trying to
define
 In cladistics, is called a ‘pleisiomorphic
character’ or a ‘pleisiomorphy’
  Phylogenetic systematics informs the construction
of phylogenetic trees based on shared
characteristics
  A cladogram
  Is a depiction of patterns of shared characteristics
among taxa
  A clade within a cladogram
  Is defined as a group of species that includes an
ancestral species and all its descendants
  Cladistics
  Is the study of resemblances among clades
Shared Derived vs. Shared
‘Primitive’ Characteristics
  In cladistic analysis ‘Clades’ are defined by
their evolutionary novelties, or shared
derived characters: ‘Synapomorphies’
  Synapomorphies are:
 Evolutionary novelties evolved uniquely within a
particular clade: usually an Adaptation
 Often used to name groups (taxa): e.g.
mammary glands define members of Class
Mammalia
Outgroups
  Systematists use a method called
outgroup comparison
 To differentiate between shared derived
and shared ancestral character states
 Synapomorhphies vs. Pleisiomorphies
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  As a basis of comparison we need to
designate an outgroup
 A species or group of species that is closely
related to the ingroup, the various species we
are studying
  Outgroup comparison
 Is based on the assumption that homologies
present in both the outgroup and ingroup must
be ancestral characters - ‘pleisiomorphies’ -that
predate the divergence of both groups from a
common ancestor
  The outgroup comparison enables us to
focus on just those characters that were
derived at the various branch points in
the evolution of a clade
  I.e. Synapomorphies:
Shared derived characters
Phylogenetic Trees and Timing
  Any chronology represented by the
branching pattern of a phylogenetic tree
 Is relative rather than absolute in terms of
representing the time of divergences
Recall: Phylogenetic trees
= Phylogenetic Hypotheses
 Logical, provisional explanations: they attempt
to explain the distribution of characters and
character states based on evolutionary
relationships
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