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!!!

• 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

Morphologic Homologies

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

over evolutionary timeinsertion of DNA bases + deletion of others occurs

computer programs arestill able to align thesesequences and find commonalities

species #1

species #2

MolecularHomology

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

Homologous Genes

Ancestral gene

Speciation

Orthologous genes

• 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

Gene duplication

Paralogous 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

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

• branch points: e.g. divides Mustelidae into Mephitis & Lutra– so Mustelidae is the common ancestor

to Mephitis & Lutra and to their descendants the skunk and the otter

• sister taxa = groups of organisms that share an immediate common ancestor– e.g. Mephitis and Lutra– e.g. Mustelidae and Canidae

• 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

Carnivora

Pantherapardus(leopard)

Mephitismephitis(striped skunk)

Lutra lutra(Europeanotter)

Canisfamiliaris(domestic dog)

Canislupus(wolf)S

pec

ies

Gen

us

Fam

ilyO

rder

Felidae Mustelidae Canidae

Panthera Mephitis Lutra Canis

Phylogeny & Cladistics

• 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– “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

Carnivora

Pantherapardus(leopard)

Mephitismephitis(striped skunk)

Lutra lutra(Europeanotter)

Canisfamiliaris(domestic dog)

Canislupus(wolf)S

pec

ies

Gen

us

Fam

ilyO

rder

Felidae Mustelidae Canidae

Panthera Mephitis Lutra Canis

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 Paraphyletic

Grouping 2

Polyphyletic

Grouping 3

• 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??

branch points

species

TAXA

TurtleLeopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

• 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

• 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

TurtleLeopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

• 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

TAXATurtle Leopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

• we use shared derived characters to create phylogenetic trees

• 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

Droso

phila

Lanc

elet

Fish

Amph

ibia

n

BirdHum

anRat M

ouse

Cen

ozo

icM

eso

zoic

Pal

eozo

ic

65.5

251

542

Neo

pro

tero

zoic

Mil

lio

ns

of

year

s ag

o

• 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

Comparison of possible trees

15% 15% 20%

5% 5%10%

15%

25%

Tree 1: More likely 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%)

Maximum Parsimony and Maximum Likelihood

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)

• includes the cyanobacteria (blue-green algae), the spirochetes and the ancestors to mitochondria and chloroplasts

2. Archaea – prokaryotes that inhabit a wide variety of environments3. Eukarya - eukaryotes

• contains the “old” kingdoms of protists, fungi, plants and animals

• these kingdoms no longer exist!

Bacteria Eukarya Archaea

Bil

lio

n y

ear

s a

go

Origin of life

0

1

2

3

4

gene transfer

common ancestorof all life

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

• adoption of a three domain system of superkingdoms– 1. Bacteria – most of the currently

known prokaryotes (or Eubacteria)• includes the cyanobacteria (blue-

green 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!

Bacteria Eukarya Archaea

Bil

lio

n y

ear

s a

go

Origin of life

0

1

2

3

4

gene transfer

common ancestorof all life

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