Download 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
Panthera
Speciespardus
• how organisms are named and classified
• biologists refer to organisms using Latin scientific names
–
–
–
–
–
Genus
Carnivora
Order
Class
• e.g. panther = Panthera pardus
• e.g. human = Homo sapiens (“wise man”)
• Linnean system – grouped species into a well organized
hierarchy of categories
Felidae
Family
binomial nomenclature
instituted in the 18th century by Carolus Linnaeus
more than 11,00 binomials still in use today
1st part - genus to which the species belongs (plural = genera)
2nd part – specific epithet – unique for each species
Phylum
Kingdom
Domain
– 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/genetic being
used
Panthera
Mammalia
Chordata
Animalia
Eukarya
Phylogenetic Trees
• the evolutionary history of a group of organisms
– intended to show patterns of descent NOT phenotypic similarities
• 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”
• a phylogenetic tree represents a hypothesis about evolutionary
relationships
– depicted as dichotomies or two-way branch points
– each branch point is a divergence of two evolutionary lineages from a
common ancestor
– e.g. Mephitis and Lutra
– e.g. Mustelidae and Canidae
• basal taxon = lineage that
diverges early in the history of a
group
– e.g. Felidae
• polytomy = branch point where
more than two descendant
groups emerge
Genus
• sister taxa = groups of organisms
that share an immediate
common ancestor
Panthera
pardus
(leopard)
Panthera
Family
– so Mustelidae is the common
ancestor to Mephitis & Lutra and to
their descendants the skunk and the
otter
Felidae
Order
• branch points: divides
Mustelidae into Mephitis & Lutra
Species
Phylogenetic Trees
Mephitis
mephitis
(striped skunk)
Mephitis
Lutra lutra
(European
otter)
Lutra
Mustelidae
Carnivora
Canis
familiaris
(domestic dog)
Canis
lupus
(wolf)
Canis
Canidae
• branch points: Carnivora is the common ancestor to Caniformia &
Feliformia and all of their descendents on the tree
• sister taxa = Canidae and Arctoidea; common ancestor = Canoidea
• basal taxon = Nimravidae – branched early off of Feliformia
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
– 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)
Morphological and Molecular Homologies
• phylogenies are inferred from both morphological and
molecular data
• phenotypic and genetic similarities due to a shared ancestry =
homologies
– 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
• 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
• 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
Molecular Homologies
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 analysis also helps us identify
organisms with very different phenotypes as
being closely related
– e.g. Hawaiian silversword plants – very different
phenotypic appearance throughout the islands
– but very similar in terms of their DNA sequences =
homologous
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
– molecular homologies can be found between humans and mushrooms!
• 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
• keep in mind - different genes evolve at different rates
– the evolution of ribosomal genes are slow – allows us to investigate further
back in time
– the evolution of mitochondrial genes are fast – investigation of more recent
events
•
•
as species evolve - genes duplicate
some duplicated genes found in many species do not change
significantly over the course of evolution
–
•
•
•
•
these genes retain a high level of homology over the course of their
evolution
other genes change so much – there is very little homology
left
so many species within a phylogenetic tree can share many
homologous genes and have many distinct genes
but an individual species can also possess homologous genes
as a result of their evolution
two types of homologous genes:
–
1. orthologous = genes are duplicated as species evolve
•
•
•
•
•
–
e.g. cytochrome c genes – found in humans and dogs
they show high levels of sequence alignment or homology
orthologous genes are a product of speciation
these genes can only diverge after speciation has taken place
for them to be highly homologous – rate of evolutionary change is
slow
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
Homologous
Genes
Ancestral gene
Speciation
Orthologous genes
Ancestral gene
Gene duplication
Paralogous genes
Clades & Cladistics
• inferring phylogeny from homologous characteristics = cladistics
• common ancestry is the primary criterion to classify organisms
• biologists place organisms into clades = includes the ancestral species and
all of its descendants
– “subdivision” of a phylogenetic tree
• smaller clades are nested within larger clades
– e.g. Mustelidae and Canidae are clades within the larger clade of Carnivora
• 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
Clades
• within clades you will find shared derived
characters = a character found within that 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)
• within larger clades you will find shared ancestral
characters = a character that originates within the
ancestor
– e.g. backbone – shared ancestral character to the
vertebrates: the lamprey, the tuna, the salamander, the
turtle and the leopard but NOT to the lancelet
TAXA
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
• but also the backbone is also a shared derived
Lamprey
Hinged jaws
character found within the clade of
vertebrates and not within the lancelet (cladeLancelet (outgroup) Vertebral column
chordata)
• one way to look at it is to think that shared
derived characters are unique to specific
clades
• we use shared derived characters to create the
phylogenetic tree
• so we use the shared derived character 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 character of hinged jaws to create the next etc….
– this makes the lamprey the next outgroup
Leopard
Hair
Salamander
Four walking legs
Lamprey
Paleozoic
Amniotic egg
Tuna
65.5
Turtle
251
TAXA
Cenozoic
phylogenetic trees can be constructed to also denote the amount of evolutionary
change or the time when the change happened – changing the branch length
Mesozoic
•
Vertebral column
Neoproterozoic
Lancelet (outgroup)
Millions of
years ago
542
Hinged jaws
• 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
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 – changing
the branch length
• or they can be constructed to denote the amount of genetic change
• 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
• BUT the rate of
genetic change
in fish and
humans is
different
• 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
Maximum Parsimony and
Maximum Likelihood
– 1. maximum parsimony = the tree uses
the simplest explanation consistent with
the facts
25%
15%
20%
15%
10%
• “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
15%
5%
Tree 1: More likely
Comparison of possible trees
•
5%
Tree 2: Less likely
both trees are equally parsimonius
(equally simple)
• but tree 1 assumes that the rate of change in
DNA sequences are equal – rate of change in human
• uses rather complex methods
and mushroom DNA = 20%; change in tulip DNA
• based on the differences between DNA
20%
sequences and the rate of changes in these
• which is more likely than tree 2 which assumes
sequences – equal rates of change are more likely
that the rate of change in the mushroom (5%) is
slower than that of humans (25%) and tulips (35%)
• computer programs now search for trees
maximize BOTH of these principles
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? 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.
Answer? C