The Tree of Life (ch2)

Phylogeny (ch16)

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“graduation and variety
structure…one species has
been taken and modified for
different ends”
~Charles Darwin

2
https://kaiserscience.wordpress.com/biology-the-living-environment/evolution/finches-and-evolution/
 “Thus between A & B immense gap of
relation. C & B the finest gradation, B & D
rather greater distinction. Thus genera
would be formed. - bearing relation to
ancient types with several extinct forms…”
— Charles Darwin

common ancestor

“ B
Tree of Life C B B D
• Common ancestor -
• Extant & extinct ...”
—

3
Q
Darwin’s representation of hypothetical phylogenetic relationships current

Time
Ancestor
past
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 Reconstructing phylogeny

What is phylogeny?
The history of descent of a group of taxa
The order of branching
Why “trees”?
The logic of phylogenetic inference
The history of descent from common ancestors
The data used to construct phylogenetic trees
Morphological data
Molecular data
Tracing character evolution on a given tree
Discrete data
Distance methods

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 Node
A B C D

terminal node 3

internal node Most recent common ancestor

(common ancestor) (MRCA)
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 lineage (branch)
A B C D

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 Are these trees the same?

Nodes can be rotated. Relationships among

the taxa are defined by the order of branching,
not by the linear order of the tips of the tree.

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Q

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Key elements of phylogenetic tree

Topology Branch length Root

( ) ( ) ( )

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Key elements of phylogenetic tree
Branch length Time scale
( ) Evolutionary changes

spA

spB

spC

spD

spE
100 90 80 70 60 50 40 30 20 10 Time
11 https://users.ugent.be/~avierstr/principles/phylogeny.html
Key elements of phylogenetic tree
Topology Relationship
( ) Grouping

https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/what-is-a-phylogeny/aspects-of-phylogenies/topology/
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 Key elements of phylogenetic tree
Root Direction of evolution
( ) Evolution path

unrooted

common ancestor

rooted

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https://www.megasoftware.net/mega1_manual/Phylogeny.html
Q

Q: Which of the following tree differ from the above?

https://www.chegg.com/
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Human chimpanzee bonobo

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Character to construct phylogeny
The character to construct phylogenetic trees
Morphological data
Molecular data
Requirement of characters/traits to be used
The characters in data matrices should be
independent of one another
The characters in data matrices should be
homologous
• Homologous organs
• Sequence alignment
Character vs character state
e.g. flower colour (red, blue..); beak length (<1cm, >3cm)
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 Character
• Morphology
• Anatomy
• Embryology
• Chromosomes
• Palynology
• Nucleic acids & sequences
• Genome
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18
19
 ♀ Tepal in ♂
Habit Nanophyll
inflorescence ♀ flower inflorescence

core Elatostema

Afroelatostema

Pellionia

Weddellia

Elatostematoides

Procris

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Homologous organs ( )

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SpA: TCAGACGATTGTCAGACGATTG
SpB: TCGGAGTGTCAGACGATTG
SpC: TCAGTCGATTGTCACGATTG
SpD: TCAGTCGATTGTCACGATTG
Alignment
( )
SpA: TCAGACGATTGTCAGACGATTG
SpB: TCGGAG---TGTCAGACGATTG
SpC: TCAGTCGATTGTC--ACGATTG
SpD: TCAGTCGATTGTC--ACGATTG

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 Methods used in phylogenetic analysis

Distance methods (phenetics)

UPGMA (Unweighted Pair Group Method using
Arithmetic averages) ( )
Transformed distance method ( )
Neighbor-Joining method ( )
Minimum evolution ( )
Discrete methods (cladistics)
Maximum parsimony ( )
Maximum likelihood ( )
Bayesian inference ( )

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 The principle: Occam’s razor
( )

Pluralitas non est ponenda sine necessitate.

(Entities should not be multiplied unnecessarily)

-William of Ockham
14th century

26 http://folk.uio.no/klaush/ockham.htm
 Characters

Taxon

Outgroup 0 0 0 0 0

0 1 0 0 1

Ingroup 1 1 1 1 1

0 1 1 1 1

Outgroup: A taxon that diverged from a group of other taxa

(ingroup) before they diverged from one another

https://en.wikipedia.org/wiki/Outgroup_(cladistics)
 Characters

Taxon

Outgroup 0 0 0 0 0
0 1 0 0 1
1 1 1 1 1
0 1 1 1 1

All possible trees?

 Characters

Taxon

Outgroup 0 0 0 0 0
0 1 0 0 1
1 1 1 1 1
0 1 1 1 1

Evolutionary steps = 7 7 5

The most
parsimonious tree
 A data matrix w/ molecular characters
SpA: TCAGACGATTGTCAGACCATTG
SpB: TCAGTCGACTGTCAAACCATTG
SpC: TCGGTCAATTGTCAAACGATTG
SpD: TCGGTCAATTGTCAAACGATTG

SpA SpB SpC SpD SpA SpB SpD SpC SpA SpC SpD SpB

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 A simple data matrix w/ discrete characters
For position no. 7 SpA: TCAGACGATTGTCAGACCATTG
SpB: TCAGTCGACTGTCAAACCATTG
SpC: TCGGTCAATTGTCAAACGATTG
SpD: TCGGTCAATTGTCAAACGATTG

G G A A G G A A G A A G
SpA SpB SpC SpD SpA SpB SpD SpC SpA SpC SpD SpB

G to A
SpA SpB SpC SpD

A to G

Character change (step) = 2 Character change (step) = 2 Character change (step) = 1

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 A simple data matrix w/ discrete characters
SpA: TCAGACGATTGTCAGACCATTG
SpB: TCAGTCGACTGTCAAACCATTG
SpC: TCGGTCAATTGTCAAACGATTG
SpD: TCGGTCAATTGTCAAACGATTG

G G A A G G A A G A A G
SpA SpB SpC SpD SpA SpB SpD SpC SpA SpC SpD SpB

Character change (step) = 9 Character change (step) = 9 Character change (step) = 6

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 Characters
Taxon Green leaf Wood Parallel veins Flowers
Mushroom 0 0 0 0
Cheilotheca 0 0 0 1
Agathis 1 1 1 0
Lily 1 0 1 1

Geatrum sessile
Agathis robusta

Lilium longiflorum v. formosanum

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Cheilotheca humilis
 Characters
Taxon Green leaf Wood Parallel veins Flowers
Mushroom 0 0 0 0
Cheilotheca 0 0 0 1
Agathis 1 1 1 0
Lily 1 0 1 1

Mushroom Agathis Mushroom Mushroom Agathis

Cheilotheca Lily Cheilotheca Lily Agathis Cheilotheca Lily

Evolutionary steps =

7 6 5

The most
parsimonious tree!
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 Counting evolutionary changes

Different algorithms used in parsimony

criterium:
Fitch parsimony: unordered transformation
• Fitch (1971)
• 0 <-> 1 <-> 2 <-> 0
Wagner parsimony: ordered transformation
• Kluge & Farris (1969)
• 0 -> 1 -> 2
The weighting of parsimony

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 Dollo’s Law on irreversibility
Dollo: "An organism is unable to return, even partially, to a previous stage already
realized in the ranks of its ancestors.” ( ;
)

Richard Dawkins: ”…really just a statement about the statistical improbability of

following exactly the same evolutionary trajectory twice (or, indeed, any particular
trajectory), in either direction.” ( )

Louis Dollo (1857-1931)

French-born Belgian palaeontologist

https://en.wikipedia.org/wiki/Louis_Dollo 36
 Character weighting table
Fitch parsimony Wagner parsimony
a b c d a b c d
a - 1 1 1 a - 1 2 3
b 1 - 1 1 b 1 - 1 2
c 1 1 - 1 c 2 1 - 1
d 1 1 1 - d 3 2 1 -

Dollo parsimony Tv/Ts

a b c d A C G T
a - M 2M 3M A - 5 1 5
b 1 - M 2M C 5 - 5 1
c 2 1 - M G 1 5 - 5
d 3 2 1 - T 5 1 5 -
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 Characters
Taxon Green leaf Wood Parallel veins Flowers
Mushroom 0 0 0 0
Cheilotheca 0 0 0 1
Agathis 1 1 1 0
Lily 1 0 1 1

Mushroom Agathis Mushroom Mushroom Agathis

Cheilotheca Lily Cheilotheca Lily Agathis Cheilotheca Lily

Let = 5x (character weighting)

Evolutionary steps =
15 10 13

The most
parsimonious tree!
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 autapomorphy
( )

phylogenetic informative

synapomorphy
( )
plesiomorphy
( )
• Apomorphy ( ) A derived or specialised
character
• Synapomorphy ( ) A derived character
Characters
shared by two or more groups which originated in
Taxon their last common ancestor
0 0 0 0 0 • Autapomorphy ( ) A distinctive feature,
0 1 0 0 1 know as derived trait, that is unique to given taxon
1 1 1 1 1 • Plesiomorphy ( ) An ancestor or primitive
0 1 1 1 1
character

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 SpA: TCAGACGATTGTCAGACCATTG
SpB: TCGGTCGACTGTCAGACCATTG
SpC: TCAGTCGATTGTCA-ACGATTG
SpD: TCAGTCGATTGTCA-ACGATTG
SpE: TCAGTCGATCGTCA-ACGATTG

Parsimonious Parsimonious
uninformative informative

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 Characters

Taxon

Outgroup 0 0 0 0 0
0 1 0 0 1
1 1 1 1 1
0 1 1 1 1

Evolutionary steps = 7 7 5

The most
parsimonious tree
 Maximum likelihood

The likelihood, L, is the probability of observing

the data under a given tree and a specified
model.
L =Prob(Data | Hypothesis) or
L =Prob(Data | Tree)

data at i site

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43 Swofford et al. (1996) Molecular Systematics
 Evolutionary models

The probability will depend on the model

selection

Usually, the more complex model you select,

the better tree you will get.
Jukes & Cantor model Kimura 2-parameter model
A α G A α G
Purines

α β
α α β β
α β

Pyrimidines C T C T
α α
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 Evaluating trees

Confidence level of trees

Bootstrap (internal support, NJ, MP, ML)
Jackknife (internal support, NJ, MP, ML)
Bremer support (for parsimony)

https://www.researchgate.net/figure/Phylogenetic-tree-with-bootstrap-values-of-1-000-replicates-showing-relationships_fig2_11822744

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 Bootstrap method
resampling

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How do we use Phylogenies?

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 C4
Classification

Elatostema s.a
• Core Elatostema (C4)
• Afroelatostema (C3)
• Pellionia (C2)
• Weddellia (C1)

C3
C2
C1
Elatostematoides
Procris
48 (Tseng et al., 2019)
Clade (sister group)

monophyletic paraphyletic Polyphyletic

multiple origins and do
not share a common
A common ancestor ✓ ✓ ancestor

all descendant of that

ancestor
✓ ✘

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https://archosaurmusings.wordpress.com/2008/12/19/monophyletic-paraphyletic-and-polyphyletic/
 paraphyletic

Reptilia
(in old defination)

A phylogeny portrays relationship (common ancestry), not similarity

Polyphyletic
raptor

Cho et al. (2019)

Genome Biology
Q Monophyletic ? Paraphyletic? Polyphyletic?
Q
II. Tracing character evolution & ancestor
How the function/trait evolved

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Opsin ( ):

Dim-light animal, absorb blue (shorter wavelength)

Conger ( )

Viperfish ( )
55 https://www.britannica.com/animal/conger-eel
Biogeographic inferences

Givnish, T.J. et al. 2013. PLoS ONE. DOI: 10.1371/journal.pone.0062566 56

 Not only organism has phylogenies..
Based on Mitochondrial cytochrome b gene

Gene tree: the history of gene

copies
Haplotype: A DNA seq. that
differs from homologous
sequences

• Gene tree showing the relationship

among haplotypes (different
sequences)
• A little mixture between populations in
Mexico and USA

MacGillivray warbler
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Orthologous

• Genomes have increased in

size is gene duplication
paralogous
• Paralogous: the genes that
originate from an ancestral
gene duplication

• Orthologous: the genes that

derived from a common
ancestral gene by
phylogenetic splitting at the
organismal level (speciation)

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Q
 Gene family
Gene evolution in the globin ( )

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Comparative analysis of the evolutionary relation

Evolutionary associations
discovered by the
comparative analysis
prompt further research.

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 Estimating time of divergence
• Molecular clock: a rate of change in DNA sequences overtime, providing a basis
for dating the time of divergence of lineages if rate of change can be estimated

o
D=2rt
A B C
D is the proportion of bases pairs that differ between two
sequences
r is the rate of substitution (per site per unit time)
t is the age since the common ancestor

Calibrating using fossil evidence and estimating r and t using

regression techniques.

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The molecular clock of cytochrome c

63 Raven et al. (2005) Biology. Fig. 1.15

Difficulties in phylogenetic analysis
 Difficulties in phylogenetic analysis

Scoring characters is difficult

Alignment problem
Character independency
Homoplasy is very common
Variation of substitution rate among sites
Rate variance among lineages
Gene tree and species tree might be different
Hybridization and horizontal gene transfer
Methodological concerns

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Different alignments among genes

SpA: TCAGACGATTGTCAGACGATTG
SpB: TCGGA-G--TGTCAGACGATTG
SpC: TCAGTCGATTGTCA--CGATTG
SpD: TCAGTCGATTGTCA--CGATTG

SpA: TCAGACGATTGTCAGACGATTG
SpB: TCGGAG---TGTCAGACGATTG
SpC: TCAGTCGATTGTC--ACGATTG
SpD: TCAGTCGATTGTC--ACGATTG

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 Difficulties in phylogenetic analysis

Scoring characters is difficult

Homoplasy is very common
Variation of substitution rate among sites
Rate variance among lineages
Gene tree and species tree might be different
Hybridization and horizontal gene transfer
Methodological concerns

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 Homoplasy ( )
Pellionia scabra

© D. S. Lin

Elatostema cyrtandrifolium

http://bruce0342.blogspot.tw/2014/11/blog-post_25.html 68 © J. Y. Huang
Description of homoplastic character states

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Evolutionary reversal

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 Convergent evolution in birds

Hummingbirds
(Family Trochilidae
Erythrina
)

Sunbirds (Family
Nectariniidae
Aloe
)

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 Difficulties in phylogenetic analysis

Scoring characters is difficult

Homoplasy is very common
Variation of substitution rate among sites
Rate of molecular evolution
Rate variance among lineages
Gene tree and species tree might be different
Hybridization and horizontal gene transfer
Methodological concerns

72
 The probability for the changes in DNA are
different among sites

73 Freeman & Herron (2004) Evolutionary analysis Fig. 6.21

• Mitochondrial gene COI
• Different substitution rate in different positions
• Use different models for different positions

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 Difficulties in phylogenetic analysis

Scoring characters is difficult

Homoplasy is very common
Variation of substitution rate among sites
Rate variance among lineages and sites
Evolutionary radiation
Gene tree and species tree might be different
Hybridization and horizontal gene transfer
Methodological concerns

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Adaptive radiation

• Fast speciation rate

• Few character
difference
• Incomplete lineage
sorting

cichlid fish

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 Difficulties in phylogenetic analysis

Scoring characters is difficult

Homoplasy is very common
Variation of substitution rate among sites
Rate variance among lineages
Gene tree and species tree might be different
Incomplete lineage sorting
Hybridization, horizontal gene transfer,
introgression
Methodological concerns

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Species tree Gene tree

• Gene tree may not be

equal to species tree

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• complete lineage sorting

Gene tree = species tree

https://genetics.thetech.org/ask-a-geneticist/incomplete-lineage-sorting
• incomplete lineage sorting ( )

gene tree = species tree

https://genetics.thetech.org/ask-a-geneticist/incomplete-lineage-sorting
 Difficulties in phylogenetic analysis

Scoring characters is difficult

Homoplasy is very common
Variation of substitution rate among sites
Rate variance among lineages
Gene tree and species tree might be different
Hybridization and horizontal gene transfer
Methodological concerns

81
Horizontal gene transfer of the algal nuclear gene psbO to the

photosynthetic sea slug Elysia chlorotica

Algal 1

Algal 2

Sea slug

82 (Rumpho et al., 2008)

 Hybrid ?

E. platyphyllum E. lineolatum var. majus

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84
 (D)
(S)
(H)
(B)
(M)

(A)

●: E. lineolatum var. majus ♢: E. platyphyllum ★: hybrid

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E. lineolatum var. majus ♂
♀

E. playphyllum ♂
♀

nrITS cpDNA

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87
 Difficulties in phylogenetic analysis

Scoring characters is difficult

Homoplasy is very common
Variation of substitution rate among sites
Rate variance among lineages
Gene tree and species tree might be different
Hybridization and horizontal gene transfer
Methodological concerns

88
UPGMA Maximum parsimony tree

89