Some sticky issues

• Short branches and ortholog/paralog inference

• Short branches and rearrangement

• Species tree

• Multiple roots

Very short branches imply non-binary nodes

FA HA1MA1 HA2CA2CA1

FA HA1MA1 HA2CA2CA1

Alternate Hypotheses

FA HA1MA1 HA2CA2CA1 FA HA1MA1 HA2CA2CA1

FA HA1 MA1 HA2CA2CA1FA HA1 MA1 HA2CA2CA1

Each alternate hypothesis yields a different set of orthologs

FA HA1 MA1 HA2CA2CA1

FA HA1MA1 HA2CA2CA1

D

FA HA1MA1 HA2CA2CA1

D

All three are orthologs

Orthologs: (MA1,CA1)

Paralogs: (HA1,CA1), (HA1,MA1)

Orthologs: (HA1,CA1)

Paralogs: (MA1,CA1), (HA1,MA1)

Some sticky issues

• Short branches and ortholog/paralog inference

• Short branches and rearrangement

• Species tree

• Multiple roots

CA1

HA2CA2

HA1

FA CA1HA2CA2 HA1FA

FA HA1 HA2CA2CA1

Hypothesis 1:

FAHA1 HA2CA2CA1

Hypothesis 2:D D

Rearrangement will prefer hypothesis 1, but is that a better choice?

Some sticky issues

• Short branches and ortholog/paralog inference

• Short branches and rearrangement

• Species tree

• Multiple roots

Baldauf, Science 2003

General agreement on unrooted Eukaryotic tree

Dictyostelium

AnimalsFungi

Plasmodium

Plants

Cavalier-Smith’s root

Arisue’s root

Some sticky issues

• Short branches and ortholog/paralog inference

• Short branches and rearrangement

• Species tree

• Multiple roots

Beta Crystalin familyCrybB2

Crybb2

CrybB1

CrybA2

CrybA4

CrybA3

CrybA1

Notung: All bold branches have the

same score

Ruvinsky and Silver, Genomics, 1997

Beta Crystalin family

Ruvinsky and Silver:

Root provided by biochemical information

acidic basicA2 A3 A1 B3B1A4 B2