Intro
Phylogeny
Terminology
Interpretation
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Intro
Phylogeny
Terminology
Interpretation
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Today
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Fast heuristics for database search Multialignment
Introduction to phylogeny
Intro
Phylogeny
Terminology
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Intro
Phylogeny
Terminology
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Phylogeny
Carl Woese and the evolution of 16S ribo RNA.
Ernst Haeckel (1834–1919)
Intro
Phylogeny
Terminology
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Intro
Phylogeny
Terminology
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Species phylogeny
Phylogeny: Gene/protein families
0.93 1.00 0.78 0.84 0.95 0.95 0.86 0.97 0.54
0.99 0.54 0.96 1.00
0.71
0.99
0.95 0.78 0.91 1.00 0.77 0.96 0.94 0.87 0.97
0.96 0.95 0.51
0.65 0.99 0.94 0.93 0.99
0.90
0.91
1.00
0.94
1.00 0.91 1.00
Ptr592874 PttMAP20 At5g37478_alt Os09g13650.1 AT3G01015.1 AT5G15510.1 Ptr668651 Ptr546644 Os12g38790.1 Os03g11400.1 AT5G44270.1 AT1G03780.2 Ptr75311 Ptr594654 Os07g32390.1 Ptr566133 PttMAP20−H1 Ptr564928 Os03g58480.1 BIP116 Os07g08790.1 Ptr653406 PttMAP20−H2 Ptr667581 Os11g36340.1 AT2G35880.1 Os02g10690.1 BIP118 Os06g40450.1 AT4G32330.1 AT2G25480.1 Ptr654148 Ptr578210 Ptr691617 Ptr658207 Ptr354840 Ptr355005 AT3G26050.1 Ptr564607 Ptr658783 AT1G70950.1 Os11g38010.1 AT3G23090.1 Ptr595399 Ptr85496 Q84ZT9_WAVE−DAMPENED2 AT3G04630.1 AT1G54460.1 TPX2_HUMAN Q9CT36_MOUSE Q805A9_CHICK Q6NUF4_XENLA
• Three species • One clade marked: Share motif (”KLEEK”) • Numbers: Reliability
Intro
Phylogeny
Terminology
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Intro
Phylogeny
Terminology
KLEEK
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Biogeography: History of Gondwana
Biogeography: History of Gondwana
Swenson et al, 2001 Swenson et al, 2001
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Terminology
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Intro
Phylogeny
Terminology
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Pretty = good
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Goals of this course
Understand techniques for phylogeny Know how to reconstruct trees Understand value of reliability among trees Interpret results Applications
Phylogeny Terminology Interpretation Next time
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• Bad method • Doubtful alignment • Good start?
Intro Phylogeny Terminology Interpretation Next time Intro
Terminology
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Example tree: Unrooted
l l l l l l D D D D D D
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Nodes, vertices, branchpoints Edges between nodes Leafs: the ”extant” nodes Rooted and unrooted trees In rooted trees: All nodes but the leaves have children Branch lengths: Proportional to evolution or not?
Phylogeny Terminology Interpretation Next time Intro
e e e e e e e e e e e
Intro
Phylogeny
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Example tree: Maybe rooted
33 333 rr rr rr rr rr ¨¨ r¨¨ rr rr rr r
Intro Phylogeny Terminology Interpretation Next time Intro
Example tree: Same again
Phylogeny
Terminology
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Branchlengths
• Length b proportional to average number of • • • •
Molecular clock
mutations b = tλ, time × speed of evolution λ is the rate of evolution Compare distance, time, and speed λ varies over
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• Dubious assumption: Evolution has a
constant rate
• Works for some data • Pseudogenes? • Introns? • Reasonable in 3rd codon position
time ”space” sequence
Intro
Phylogeny
Terminology
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Intro
Phylogeny
Terminology
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Newick format
• Notation for tree structure, formally (for
Newick with branchlengths
((a:0.5, b:1.5):0.3, (c:0.4, d:1.7):0.5);
computers) and informally (discussion)
• Simply put: • One string a is a tree with one leaf. • Two trees T1 and T2 can be put together to a larger tree using parenthesis: (T1 , T2 ) • One tree is terminated with semicolon: (a, b); • Example: ((a, b), (c, d)) means
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a
Intro Phylogeny
b
c
d
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Terminology
Many children
((a, b, c), (d, e, f, g));
Intro
Phylogeny
Terminology
How interpret relationships?
Old assignment: What is correct? 1. Seal is more related to horse than whale. 2. Seal is more related to whale than horse 3. Seal is as related to horse as to whale
(From Science)
4. Seal is related to whale, but not horse
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Methods for reconstructing trees
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Unrooted trees: Three children at ”root”
(((a, b), c), d, ((e,f) ,g));
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Intro
Phylogeny
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How interpret relationships?
Old assignment: What is correct? 1. Horse is more related to chicken than mouse. 2. Horse is more related to mouse than chicken. 3. Horse is as related to mouse as to chicken. 4. Horse is related to chicken, but more closely related to mouse.
(From Science)
Interpretation
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