Transcript Lecture #1: Phylogeny & the “Tree of Life”

Lecture #1: Phylogeny & the
“Tree of Life”
Phylogeny
• how do biologists classify and categorize
species?
• by understanding evolutionary relationships
• evolutionary history of a species or a group of
species = phylogeny
• phylogenies are constructed using systematics
– uses data ranging from fossils to molecules to
genes to derive evolutionary relationships
Taxonomy
• how organisms are named and classified
• the field of biology that determines phylogeny, names
organisms and places them into groups is systematics
• taxonomy = method of systematics
• biologists refer to organisms using Latin scientific names
–
–
–
–
–
binomial nomenclature
instituted in the 18th century by Carolus Linnaeus
more than 11,00 binomial names still in use today
1st part - Genus to which the species belongs (plural = genera)
2nd part – specific epithet – unique for each species
• e.g. panther = Panthera pardus
• e.g. human = Homo sapiens (“wise man”)
Taxonomy
Taxonomy
• Linnean system – grouped species
into a well organized hierarchy of
categories
– named unit at any level of the hierarchy =
taxon
– taxa = domain, kingdom, phylum, class,
order, family, genus, species
– species that are closely related – belong to
the same Genus
– related Genera are in the same family etc……
– the characters that are used to classify
organisms are determined by taxonomists
– not just physical characteristics now – but
molecular/genetics being used
Phylogeny and Taxonomy
• while the Linnean system distinguishes groups it tells us nothing
of the groups’ evolutionary relationships to each other
• proposal: that classifying organisms should be based entirely on
evolutionary relationships
– PhyloCode: a system that names groups that include a common ancestor
and all of its descendants
– changes the way taxa are defined but keeps the taxonomic names of most
species
– eliminates ranks like “family” and “class”
Morphological and Molecular Homologies
• phylogenies are inferred from both morphological and
molecular data
• phenotypic and genetic similarities due to a shared ancestry =
homologies
• homologous characteristic = characteristics of different
species that have evolved from the same origin
– similarities in the number of forelimb bones in mammals is due to
their descent from a common ancestor with the same bone structure
= morphological homology
– similarities in DNA sequences between humans and other primates is
due to their descent from a common ancestor = molecular homology
• large changes in morphological homology do NOT mean
divergence in molecular homology!!!
Morphologic Homologies
• be careful with morphological homology!
• just because two species look the same does
NOT mean there are homologous (shared
ancestor)
– e.g. Australian mole (marsupial) and a North American
mole (eutherian)
• look the same phenotypically – but a quite different in
terms of internal anatomy
• the two moles are similar due to convergent evolution
• similar environmental pressures and natural selection
produce similar (analogous) adaptations in two organisms
of different evolutionary lineages
• you have to be able to distinguish between homology
and analogy to construct a phylogenetic tree
– analogy = two structures look alike but no common descent
– e.g. bird and bat wings are analogous structures –bird and bat
wings arose independently from the forelimbs of different
ancestors
Morphologic Homologies
• homoplasy = analogous structures that arise independently
• an easy way to distinguish homology and analogy – is
complexity
– the more things that are similar in a structure between two organisms and the
more complex the structure is – the better chance the structure is homologous
– e.g. skull of humans & chimps
– but the more similar a structure is and the less complex – the more likely the
structures are analogous
– e.g. arm of a bat and bird
Molecular Homologies
• to evaluate molecular homology
requires analysis of DNA sequences
– extract the DNA, sequence the DNA and align
them in terms of similar sequences
– alignment done by powerful computer
programs that take into account deletions of
bases or additions of bases that can “shift” the
coding and non-coding sequences back or
forward
– also determine if the similarities are just a
coincidence (molecular homoplasy or analogy)
• so looking at the DNA sequences of
the Australian and N.A. moles
identifies numerous differences in
DNA sequences that can’t be aligned
– do not share a common ancestor and their
phylogenetic trees will differ
species #1
species #2
over evolutionary time
insertion of DNA bases
+ deletion of others occurs
computer programs are
still able to align these
sequences and find
commonalities
Molecular
Homology
Molecular Homology
• molecular homology is determined through molecular systematics = comparison
of nucleic acids and other molecules to deduce relatedness
• helps us create phylogenetic relationships when comparative anatomy can’t help
– e.g. molecular homologies can be found between humans and mushrooms!
– e.g. Hawaiian silversword plants – very different phenotypic appearance throughout
the islands
– but very similar in terms of their DNA sequences = homologous
• also allows us to reconstruct phylogenetic trees when the fossil record is absent
• so molecular biology has allowed us to add many more “branches” and “twigs”
to phylogenetic trees
• two types of homologous genes:
– 1. orthologous = genes in two (or
more) species that evolve from a
gene in a common ancestor
• e.g. cytochrome c genes – found in
humans and dogs
– they show high levels of sequence
alignment or homology
– didn’t change much from their
common ancestor
• orthologous genes are between
species
• these genes can only diverge after
speciation has taken place
• if they are highly homologous – rate of
evolutionary change is slow
• if they lose homology – rate of change
is high
Homologous
Genes
Ancestral gene
Speciation
Orthologous genes
• two types of homologous genes:
– 2. paralogous = genes are duplicated
within a species as it evolves
• e.g. olfactory receptor genes in humans –
numerous types of receptors each coded
for by different genes
• but these genes have regions of homology
when compared to one another
• paralogous genes are within a species
• these genes can diverge within a species
because they are present in more than one
copy in the genome
• result of gene duplication
• one gene stays the same
• the other “duplicated” gene has changes to
its sequence & gives rise to a new gene 
individual species evolution
Homologous
Genes
Ancestral gene
Gene duplication
Paralogous genes
Phylogenetic Trees
• the evolutionary history of a group of organisms
– intended to show patterns of descent NOT phenotypic similarities
• a phylogenetic tree represents a hypothesis about evolutionary
relationships
– depicted as branch points
– each branch point is a divergence of evolutionary lineages from a
common ancestor
Phylogenetic Trees
• THREE THINGS:
• #1: phylogenetic tress shown patterns of decent
– NOT phenotypic similarities
– closely related organisms may NOT look like each other because their
lineages evolved at different rates or faced different environmental
conditions
• #2: the sequence of branching in a tree does not indicate the
absolute age of the species
– must interpret the tree in terms of patterns of descent
– unless dates are given
• #3: do NOT assume a taxon on a tree evolved from the taxon
next to it
– instead look at the common ancestor (branch point)
Phylogenetic Trees
• basal taxon = lineage that diverges
early in the history of a group (and
has no other branch points)
– e.g. Felidae
• polytomy = many temporal based
branches
– branch point where more than two
descendant groups emerge
– cannot identify dichotomies
Genus
– e.g. Mephitis and Lutra
– e.g. Mustelidae and Canidae
Panthera Mephitis
Lutra lutra Canis
Canis
pardus mephitis
(European familiaris
lupus
(leopard) (striped skunk) otter)
(domestic dog) (wolf)
Panthera
Family
• sister taxa = groups of organisms
that share an immediate common
ancestor
Felidae
Order
– so Mustelidae is the common ancestor
to Mephitis & Lutra and to their
descendants the skunk and the otter
Species
• branch points: e.g. divides
Mustelidae into Mephitis & Lutra
Mephitis
Lutra
Mustelidae
Carnivora
Canis
Canidae
• smaller clades are nested within larger
clades
– e.g. Mustelidae and Canidae are clades within
the larger clade of Carnivora
Genus
Family
– “subdivision” of a phylogenetic tree
Panthera Mephitis
Lutra lutra Canis
Canis
pardus mephitis
(European familiaris
lupus
(leopard) (striped skunk) otter)
(domestic dog) (wolf)
Panthera
Felidae
Order
• field of biology that creates phylogenetic
trees = cladistics
• common ancestry is the primary
criterion to classify organisms
• biologists place organisms into clades =
includes the ancestral species and all of
its descendants
Species
Phylogeny & Cladistics
Mephitis
Lutra
Mustelidae
Carnivora
Canis
Canidae
Clades & Cladistics
• three types of groupings possible with a phylogenetic tree
– 1. monophyletic (“one tribe”) = ancestor (B) and all of its descendants (C – H)
– 2. paraphyletic (“beside the tribe”) = ancestor (A) and some of its descendants (I, J
K & not B – H)
– 3. polyphyletic (“many tribes”) = different ancestors and their descendants (F, G, H
& I, J, K)
Grouping 1
Monophyletic
Grouping 2
Paraphyletic
Grouping 3
Polyphyletic
• common ancestor to Caniformia and Feliformia???
• consider the Caniformia branch of the tree - example of a sister
taxa??
• consider the common ancestor Feloidea - example of a basal taxon
evolving from this clade??
species
branch points
• when examining a
phylogenetic tree you will find
shared derived characteristics
= a character found within a
clade but not necessarily
within their shared common
ancestor
– e.g. hair – shared derived
character for mammals (the
leopard) but NOT for reptiles
(the turtle)
– one way to look at it is to think
that shared derived
characteristics are unique to
specific clades
TAXA
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
• BUT when examining a tree you will
also find shared ancestral
characteristics = a character that
originates within the ancestor
– e.g. vertebral column – shared
ancestral character to the
vertebrates: the lamprey, the tuna,
the salamander, the turtle and the
leopard but NOT to the lancelet
• but you could also consider the
vertebral column to be a shared
derived characteristic found within
the lamprye( vertebrates) and not
within the lancelet (chordates)
TAXA
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
• so we use the shared derived characteristic of a vertebral column to
determine the first branch point
– the lancelet (no vertebral column) is called the outgroup and the remaining organisms
are the ingroup
• use the derived characteristic of hinged jaws to create the next etc….
– this makes the lamprey the next outgroup
• we use shared derived
characters to create
phylogenetic trees
TAXA
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
65.5
Millions of
years ago
Neoproterozoic
542
Paleozoic
251
Mesozoic Cenozoic
• phylogenetic trees can be constructed to also denote the
amount of evolutionary change or the time when the change
happened – by changing the branch length
• common
ancestor of the
fish and the
human arose
542 MYA!!
• so there has
been 542
million years of
evolution for
both the fish
and the human
Maximum Parsimony and Maximum Likelihood
•
•
•
•
you are analyzing data for 50 species
there are 3x1076 different ways to arrange these specific into a tree!
with DNA sequencing it gets more complicated
you can narrow the possible trees by using the principles of
– 1. maximum parsimony = the tree uses the simplest explanation consistent
with the facts
• “Occam’s razor” = if you have several theories based on facts, the one that is the simplest is
likely to be right!
• in other words = “KISS” – keep it simple stupid!
– 2. maximum likelihood = the tree reflects the most likely sequence of
evolutionary events
• uses rather complex methods
• proposes that the tree with equal rates of change is more likely
• computer programs now search for trees maximize BOTH of these
principles
Maximum Parsimony and Maximum Likelihood
25%
15%
15%
20%
15%
10%
5%
Tree 1: More likely
Comparison of possible trees
5%
Tree 2: Less likely
• how do we arrange a human, a tulip and a
mushroom on a phylogenic tree based on
their DNA sequences??
• two possible trees given
• both trees are equally parsimonius
(equally simple)
• remember equal rates of changes are
more likely!!
• so tree 1 assumes that the rate of change
in DNA sequences between all three
species are equal – rate of change in
human and mushroom DNA = 20%; change
in tulip DNA 20%
• which is more likely than tree 2 which
proposes rates of change for the
mushroom (5%), for humans (25%) and
tulips (35%)
From Kingdoms to Domains
• earliest taxonomists just had two kingdoms: Plants and
Animals
• with the discovery of bacteria – things got a bit more
complicated
• but bacteria were classified as plants since they were
found to have a cell wall
• since algae underwent photosynthesis – considered
plants also
• fungi also classified as plants – despite having nothing
in common with plants
• organisms that consumed were considered animals –
including single celled organisms like protozoans
• in 1969: five-kingdom classification system – Robert
Whittaker
– recognized the existence of two fundamental cell types:
prokaryotes and eukaryotes
– created a separate kingdom for prokaryotes and divided up
the eukaryotes
– 1. Monera - prokaryotic
– 2. Protista – unicellular organisms including algae
– 3. Fungi
– 4. Plantae
– 5. Animalia
– based on the nutritional requirements and methods of
these domains
•
•
•
•
plants = autotrophs
fungus and animals = heterotrophs
fungus = decomposers
animals = digestors within the body
• recently the application of
molecular analysis to this
classification has resulted in a
reclassification
• adoption of a three domain system
1. Bacteria – most of the currently
known prokaryotes (or Eubacteria)
2. Archaea – prokaryotes that
inhabit a wide variety of
environments
3. Eukarya - eukaryotes
• contains the “old” kingdoms of
protists, fungi, plants and animals
• these kingdoms no longer exist!
1
Billion years ago
• includes the cyanobacteria (bluegreen algae), the spirochetes and
the ancestors to mitochondria and
chloroplasts
0
Bacteria
Eukarya
gene transfer
2
3
common ancestor
of all life
4
Origin of life
Archaea
Team Problems
• Question: The correct sequence from the most to the
least comprehensive of the taxonomic levels listed here
is
– A) family, phylum, class, kingdom, order, species, and
genus.
– B) kingdom, phylum, class, order, family, genus, and
species.
– C) kingdom, phylum, order, class, family, genus, and
species.
– D) phylum, kingdom, order, class, species, family, and
genus.
– E) phylum, family, class, order, kingdom, genus, and
species.
Answer? B
• Question: If organisms A, B, and C belong to the
same class but to different orders and if
organisms D, E, and F belong to the same order
but to different families, which of the following
pairs of organisms would be expected to show
the greatest degree of structural homology?
–
–
–
–
–
A) A and B
B) A and C
C) B and D
D) C and F
E) D and F
Answer? E
• QUESTION) Hawaiian silverswords have very different
phenotypes as you travel from island to island.
• On the basis of their morphologies, how might
Linnaeus have classified the Hawaiian silverswords?
– A) He would have placed them all in the same species.
– B) He probably would have classified them the same way
that modern botanists do.
– C) He would have placed them in more species than
modern botanists do.
– D) He would have used evolutionary relatedness as the
primary criterion for their classification.
– E) Both B and D are correct.
From Kingdoms to Domains
• earliest taxonomists just had two kingdoms: Plants and
Animals
• with the discovery of bacteria – things got a bit more
complicated
• but bacteria were classified as plants since they were
found to have a cell wall
• since algae underwent photosynthesis – considered
plants also
• fungi also classified as plants – despite having nothing
in common with plants
• organisms that consumed were considered animals –
including single celled organisms like protozoans
• in 1969: five-kingdom classification system – Robert
Whittaker
– recognized the existence of two fundamental cell types:
prokaryotes and eukaryotes
– created a separate kingdom for prokaryotes and divided up
the eukaryotes
– 1. Monera - prokaryotic
– 2. Protista – unicellular organisms including algae
– 3. Fungi
– 4. Plantae
– 5. Animalia
– based on the nutritional requirements and methods of
these domains
•
•
•
•
plants = autotrophs
fungus and animals = heterotrophs
fungus = decomposers
animals = digestors within the body
• recently the application of
molecular analysis to this
classification has resulted in a
reclassification
– some prokaryotes can differ
dramatically from each other – as
much as they differ from plants and
animals
– construction of phylogenetic trees
based on molecular data
– 1. Bacteria – most of the currently
known prokaryotes (or Eubacteria)
• includes the cyanobacteria (bluegreen algae), the spirochetes and the
ancestors to mitochondria and
chloroplasts
– 2. Archaea – prokaryotes that inhabit
a wide variety of environments
– 3. Eukarya - eukaryotes
• contains the “old” kingdoms of
protists, fungi, plants and animals
• these kingdoms no longer exist!
1
Billion years ago
• adoption of a three domain system
of superkingdoms
0
Bacteria
Eukarya
gene transfer
2
3
common ancestor
of all life
4
Origin of life
Archaea
Team Problems
• Question: The correct sequence from the most to the
least comprehensive of the taxonomic levels listed here
is
– A) family, phylum, class, kingdom, order, species, and
genus.
– B) kingdom, phylum, class, order, family, genus, and
species.
– C) kingdom, phylum, order, class, family, genus, and
species.
– D) phylum, kingdom, order, class, species, family, and
genus.
– E) phylum, family, class, order, kingdom, genus, and
species.
Answer? B
• Question: If organisms A, B, and C belong to the
same class but to different orders and if
organisms D, E, and F belong to the same order
but to different families, which of the following
pairs of organisms would be expected to show
the greatest degree of structural homology?
–
–
–
–
–
A) A and B
B) A and C
C) B and D
D) C and F
E) D and F
Answer? C