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

SpeciesPantherapardus

PantheraGenus

FamilyFelidae

CarnivoraOrder

MammaliaClass

PhylumChordata

KingdomAnimalia

EukaryaDomain

Taxonomy• how organisms are named and classified• biologists refer to organisms using Latin scientific names

– 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

• e.g. panther = Panthera pardus• e.g. human = Homo sapiens (“wise man”)

• 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/genetic being

used

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

Phylogenetic Trees• branch points: 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– e.g. Felidae

• polytomy = branch point where more than two descendant groups emerge

Carnivora

Pantherapardus(leopard)

Mephitismephitis(striped skunk)

Lutra lutra(Europeanotter)

Canisfamiliaris(domestic dog)

Canislupus(wolf)

Sp

ecie

sG

enu

sF

amil

yO

rder

Felidae Mustelidae Canidae

Panthera Mephitis Lutra Canis

• 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!!!

• 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

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• 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

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– 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

Homologous Genes

Ancestral gene

Speciation

Orthologous genes

Ancestral gene

Gene duplication

Paralogous genes

• 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

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 Paraphyletic

Grouping 2

Polyphyletic

Grouping 3

Clades

TAXA

TurtleLeopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

• 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

• but also the backbone is also a shared derived character found within the clade of vertebrates and not within the lancelet (clade 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

• phylogenetic trees can be constructed to also denote the amount of evolutionary change or the time when the change happened – changing the branch length

TAXA

TurtleLeopard

Hair

Amniotic egg

Four walking legs

Hinged jaws

Vertebral column

Salamander

Tuna

Lamprey

Lancelet (outgroup)

Droso

phila

Lanc

elet

Fish

Amph

ibia

nBird

Human

Rat Mou

se

Cen

ozo

icM

eso

zoic

Pal

eozo

ic

65.5

251

542

Neo

pro

tero

zoic

Mill

ion

s o

fye

ars

ago

• 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

• 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

Droso

phila

Lanc

elet

Fish

Amph

ibia

nBird

Human

Rat Mou

se

Cen

ozo

icM

eso

zoic

Pal

eozo

ic

65.5

251

542

Neo

pro

tero

zoic

Mill

ion

s o

fye

ars

ago

• 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

Droso

phila

Lanc

elet

Fish

Amph

ibia

nBirdHum

anRat

Mou

se

• BUT the rate of genetic change in fish and humans is different

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• based on the differences between DNA sequences

and the rate of changes in these sequences – equal rates of change are 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

• 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 and mushroom DNA = 20%; change in tulip DNA 20%• which is more likely than tree 2 which assumes that the rate of change in the mushroom (5%) is slower than that of 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 – 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? 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