not just for his or her own self, family or not just for his or her own self, family or nation, but for the benefit of all mankind.

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Wallaceburg District Secondary School - Science Department 1

I believe that to meet the challenge of the I believe that to meet the challenge of the next century, human beings will have to next century, human beings will have to develop a greater sense of universal develop a greater sense of universal responsibility. Each of us must learn to work responsibility. Each of us must learn to work

not just for his or her own self, family or not just for his or her own self, family or nation, but for the benefit of all mankind.

nation, but for the benefit of all mankind.

His Holiness the Dalai Lama, speech? in 1994 His Holiness the Dalai Lama, speech? in 1994

SBI3U 1.04 Genetic SBI3U 1.04 Genetic

Phylogeny Phylogeny

Just funny Just funny

http://www.kfdunn.com/vector/g_expression.htm

How do we use genetics to How do we use genetics to

infer relationships?

• • First what are the First what are the – – The tools? The tools?

– – The methods? The methods?

–

– The theories? The theories?

(Merck 2005)

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What we need before we can What we need before we can

use genetics use genetics

• • Homology review: similarity due to Homology review: similarity due to common descent

common descent

• • How do we assess homology of DNA How do we assess homology of DNA sequences?

sequences?

• • Levels of homology Levels of homology – – Locus(Location) Locus(Location) – – Allele (branch) Allele (branch) –

– Nucleotide position (order) Nucleotide position (order)

Fishbein Fishbein, M. (2003a)., M. (2003a).

Example number 1 Example number 1

Things we need to do the Things we need to do the

analysis analysis

http://www- 03.ibm.com/ibm/history/exhib its/vintage/vintage_4506VV1 001.html

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Simple Sequence Alignment Simple Sequence Alignment

Taxon 1 GTACGTTG Taxon 2 GTACGTTG Taxon 3 GTACGTTG Taxon 4 GTACATTG Taxon 5 GTACATTG Taxon 6 GTACATTG

Simple Sequence Alignment Simple Sequence Alignment

Taxon 1 GTACG GTTG Taxon 2 GTACG GTTG Taxon 3 GTACG GTTG Taxon 4 GTACA ATTG Taxon 5 GTACA ATTG Taxon 6 GTACA ATTG

Simple Sequence Alignment Simple Sequence Alignment

Taxon 1 GTACGTTG Taxon 2 GTACGTTG Taxon 3 GTACGTTG Taxon 4 GTACATTG Taxon 5 GTACATTG Taxon 6 GTACATTG

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DNA Sequence Data Matrix DNA Sequence Data Matrix

G G T T T T A A C C A A T T G G T6 T6

G G T T T T A A C C A A T T G G T5 T5

G G T T T T A A C C A A T T G G T4 T4

G G T T T T G G C C A A T T G G T3 T3

G G T T T T G G C C A A T T G G T2 T2

G G T T T T G G C C A A T T G G T1 T1

C8 C8 C7 C7 C6 C6 C5 C5 C4 C4 C3 C3 C2 C2 C1 C1

Slightly Less Simple Slightly Less Simple Sequence Alignment Sequence Alignment

Taxon 1 AGAGTGAC Taxon 2 AGAGTGAC Taxon 3 AGAGTGAC Taxon 4 AGAGGAC Taxon 5 AGAGGAC Taxon 6 AGAGGAC

Slightly Less Simple Slightly Less Simple Sequence Alignment Sequence Alignment

Taxon 1 AGAGT TGAC Taxon 2 AGAGT TGAC Taxon 3 AGAGT TGAC Taxon 4 AGAGGAC Taxon 5 AGAGGAC Taxon 6 AGAGGAC

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Slightly Less Simple Slightly Less Simple Sequence Alignment Sequence Alignment

Taxon 1 AGAGTGAC Taxon 2 AGAGTGAC Taxon 3 AGAGTGAC Taxon 4 AGAG−GAC Taxon 5 AGAG−GAC Taxon 6 AGAG−GAC

DNA Sequence Data Matrix DNA Sequence Data Matrix

C C A A G G

− − G G A A G G A A T6 T6

C C A A G

− G

− G G A A G G A A T5 T5

C C A A G G

− − G G A A G G A A T4 T4

C C A A G G T T G G A A G G A A T3 T3

C C A A G G T T G G A A G G A A T2 T2

C C A A G G T T G G A A G G A A T1 T1

C8 C8 C7 C7 C6 C6 C5 C5 C4 C4 C3 C3 C2 C2 C1 C1

Alignment Gaps Alignment Gaps

• • Gaps are inserted to maximize Gaps are inserted to maximize homology across nucleotide positions homology across nucleotide positions

• • Gaps are hypothesized indels Gaps are hypothesized indels

• • Inserting a gap assumes that an indel Inserting a gap assumes that an indel event is a better explanation of the event is a better explanation of the differences among sequences than differences among sequences than nucleotide substitution

nucleotide substitution

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AGAGTGAC AGAGTGAC AGAGTGAC AGAG−GAC AGAG−GAC AGAG−GAC Taxon 1 AGAGTGAC

Taxon 2 AGAGTGAC Taxon 3 AGAGTGAC Taxon 4 AGAGGAC Taxon 5 AGAGGAC Taxon 6 AGAGGAC

3 substitutions 0 indels

0 substitutions 1 indels

Ambiguous Alignment with a Ambiguous Alignment with a

Single

Single- -Base Base Indel Indel

Taxon 1 GGTCAG Taxon 2 GGCCAA Taxon 3 AGCTAA Taxon 4 AGCAA Taxon 5 AGCAA Taxon 6 AGCAA

Ambiguous Alignment with a Ambiguous Alignment with a

Single

Single- -Base Base Indel Indel

Taxon 1 GGTCAG Taxon 2 GGCCAA Taxon 3 AGCTAA Taxon 4 AGCAA Taxon 5 AGCAA Taxon 6 AGCAA

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Ambiguous Alignment with a Ambiguous Alignment with a

Single

Single- -Base Base Indel Indel

Taxon 1 GGTCAG GGTCAG Taxon 2 GGCCAA GGCCAA Taxon 3 AGCTAA AGCTAA Taxon 4 AG−CAA AGC−AA Taxon 5 AG−CAA AGC−AA Taxon 6 AG−CAA AGC−AA

4 substitutions 1 indels

4 substitutions

1 indels

_FishbeinFishbein, M. (2003a)., M. (2003a).

More Ambiguous Alignment More Ambiguous Alignment

with a Single

with a Single- -Base Base Indel Indel

Taxon 1 AAGGTT Taxon 2 AAGGTT Taxon 3 AAGAT Taxon 4 AACGTT Taxon 5 AACGTT Taxon 6 AACGTT

More Ambiguous Alignment More Ambiguous Alignment

with a Single

with a Single- -Base Base Indel Indel

Taxon 1 AAGGTT Taxon 2 AAGGTT Taxon 3 AAGAT Taxon 4 AACGTT Taxon 5 AACGTT Taxon 6 AACGTT

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A More Ambiguous Alignment A More Ambiguous Alignment

T 1 AAG−GTT AAG−GTT AAG−GTT T 2 AAG−GTT AAG−GTT AAG−GTT T 3 AAGA−−T AAG−A−T AAGA−−T T 4 AAC−GTT AA−CGTT AA−CGTT T 5 AAC−GTT AA−CGTT AA−CGTT T 6 AAC−GTT AA−CGTT AA−CGTT

1 substitution 2 indels (1 bp, 2bp)

1 substitution 3 indels (1bp, 1bp, 1bp)

1 substitution 3 indels (1 bp, 1 bp, 2bp)

Here is an example (#2) of Here is an example (#2) of how it is done (simply put) how it is done (simply put)

Example Example

Taxon 1 GTAA G-GTTTT G Taxon 2 GTAA G-GTTTT G Taxon 3 GTAA GA--TTTG Taxon 4 GTAA C -GTTTT G Taxon 5 GT--- TTG Taxon 6 GT--- TTG Taxon 7 GT--- TTG Taxon 8 GTA--- TTG Taxon 9 GTAA C -GTTTT G

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Delimit Ambiguous Region Delimit Ambiguous Region

Taxon 1 G TAA G-GTTTT G Taxon 2 G TAA G-GTTTT G Taxon 3 G TAA GA--TTT G Taxon 4 G TAA C -GTTTT G Taxon 5 G T--- TTG Taxon 6 G T--- TTG Taxon 7 G T--- TTG Taxon 8 G TA--- TTG Taxon 9 G TAA C -GTTTT G

Delimit Ambiguous Region Delimit Ambiguous Region

Taxon 1 AA G-GTT Taxon 2 AA G-GTT Taxon 3 AA GA--T Taxon 4 AAC-GTT Taxon 5 --- Taxon 6 --- Taxon 7 --- Taxon 8 A --- Taxon 9 AAC-GTT

Remove Gaps Remove Gaps

Taxon 1 AA G GTT Taxon 2 AA G GTT Taxon 3 AA GAT Taxon 4 AAC GTT Taxon 5

Taxon 6 Taxon 7

Taxon 8 A

Taxon 9 AAC GTT

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Recode Ambiguous Region Recode Ambiguous Region

State Taxon 1 AAG G TT 0 Taxon 2 AAG G TT 0 Taxon 3 AAG AT 1 Taxon 4 AAC GTT 2

Taxon 5 3

Taxon 6 3

Taxon 7 3

Taxon 8 A 4

Taxon 9 AAC GTT 2

_FishbeinFishbein, M. (2003a)., M. (2003a).

Recoded Matrix Recoded Matrix

Taxon 1 GTAA G-GTTTTG 0 Taxon 2 GTAA G-GTTTTG 0 Taxon 3 GTAA G A--TTT G 1 Taxon 4 GTAA C-GTTTT G 2 Taxon 5 GT--- TTG 3 Taxon 6 GT--- TTG 3 Taxon 7 GT--- TTG 3 Taxon 8 GTA---TTG 4 Taxon 9 GTAA C-GTTTT G 2

Recoded Matrix Recoded Matrix

Taxon 1 GTTTG 0

Taxon 2 GTTTG 0

Taxon 3 GTTTG 1

Taxon 4 GTTTG 2

Taxon 5 GTTTG 3

Taxon 6 GTTTG 3

Taxon 7 GTTTG 3

Taxon 8 GTTTG 4

Taxon 9 GTTTG 2

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Questions?

I hope so!

Here is a genetic trait moving Here is a genetic trait moving through selective breeding of through selective breeding of

a plant a plant

From Judd et al. (2002), Plant Systematics

SO how does this help SO how does this help

• • There are some major problems There are some major problems

– – Gene expression does not necessarily confer Gene expression does not necessarily confer with morphological data

with morphological data

– – Methodologies are still being developed Methodologies are still being developed – – Huge holes in information Huge holes in information

–

– Are we even right? Are we even right?

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Knowledge links Knowledge links

Overview

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References References

•

• FishbeinFishbein, M. (2003a). Retrieved Aug. 09, 2005, from http://www2., M. (2003a). Retrieved Aug. 09, 2005, from http://www2.msstatemsstate..eduedu/~zg3/docs/S03_Lecture09./~zg3/docs/S03_Lecture09.pptpptWeb site: Web site:

http://www2.

http://www2.msstatemsstate..eduedu/~zg3/docs/S03_Lecture09./~zg3/docs/S03_Lecture09.pptppt. .

•• Judd et al. (2002), Plant Judd et al. (2002), Plant SystematicsSystematics

•

• Merck and Company, (2005). Retrieved Aug. 09, 2005, fromMerck and Company, (2005). Retrieved Aug. 09, 2005, fromTHeTHeMerck Manual The second home edition Web site: Merck Manual The second home edition Web site:

http://www.

http://www.merckmerck.com/.com/mmhemmhe/sec01/ch002/ch002a.html/sec01/ch002/ch002a.html