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Example of bipartition analysis for five genomes of photosynthetic bacteria(188 gene families)
total 10 bipartitions
R: Rhodobacter capsulatus, H: Heliobacillus mobilis, S: Synechocystis sp., Ct: Chlorobium tepidum, Ca: Chloroflexus aurantiacus
R: Rhodobacter capsulatus, H: Heliobacillus mobilis, S: Synechocystis sp., Ct: Chlorobium tepidum, Ca: Chloroflexus aurantiacus
Bipartitions supported by genes from chlorophyll biosynthesis pathway
Zha
xyba
yeva
, Ham
el, R
aym
ond,
and
Gog
arte
n, G
enom
e B
iolo
gy 2
004,
5: R
20
R CaH
SCtPlurality
Ca HR
SCtChl. Biosynth.
Phy
loge
netic
Ana
lyse
s of
Gen
es f
rom
ch
loro
phyl
l bio
synt
hesi
s pa
thw
ay
(ext
ende
d da
tase
ts)
R: Rhodobacter capsulatus, H: Heliobacillus mobilis, S: Synechocystis sp., Ct: Chlorobium tepidum, Ca: Chloroflexus aurantiacus
Xio
ng e
t al.
Sci
ence
, 200
0 28
9:17
24-3
0
Zha
xyba
yeva
, Ham
el, R
aym
ond,
and
Gog
arte
n, G
enom
e B
iolo
gy 2
004,
5: R
20
PROBLEMS WITH BIPARTITIONS
• No easy way to incorporate gene families that are not represented in all genomes.
• The more sequences are added, the shorter the internal branches become, and the lower is the bootstrap support for the individual bipartitions. • A single misplaced sequence can destroy all bipartitions.
Bootstrap support values for embedded quartets
+ : tree calculated from one pseudo-sample generated by bootstraping from an alignment of one gene family present in 11 genomes
Quartet spectral analyses of genomes iterates over three loops:Repeat for all bootstrap samples. Repeat for all possible embedded quartets.Repeat for all gene families.
: embedded quartet for genomes 1, 4, 9, and 10 .This bootstrap sample supports the topology ((1,4),9,10).
14
9
101
10
9
4
1
9
10
4
Zh
axy b
aye
v a e
t al. 2
00
6, G
en
om
e R
es e
ar c h
, i n p
res s
This gene family for the quartet of species A, B, C, DSupports the Topology ((A, D), B, C) with 70% bootstrap support
Iterating over Bootstrap Samples
Bootstrap support values for embedded quartets
+ : tree calculated from one pseudo-sample generated by bootstraping from an alignment of one gene family present in 11 genomes
Quartet spectral analyses of genomes iterates over three loops:Repeat for all bootstrap samples. Repeat for all possible embedded quartets.Repeat for all gene families.
: embedded quartet for genomes 1, 4, 9, and 10 .This bootstrap sample supports the topology ((1,4),9,10).
14
9
101
10
9
4
1
9
10
4
Total number of gene families containing the species quartet
Number of gene families supporting the same topology as the plurality (colored according to bootstrap
support level)
Number of gene families supporting one of the two alternative quartet topologies
Illustration of one component of a quartet spectral analyses Summary of phylogenetic information for one genome quartet for all gene
families
330 possible quartets
quartets
Num
ber
of
data
sets
685 datasets show conflicts with plurality
1128 datasets from relaxed core (core datasets + datasets with one or two taxa missing)
Quartet Spectrumof 11 cyanobacterialgenomes
PLURALITY SIGNAL
Gloeobacter
marine Synechococcus
3Prochlorococcus
2Prochlorococcus
1Prochlorococcus
Nostoc
Anabaena
Trichodesmium
Crocosphaera
Synechocystis
Thermosynechococcus
N
A
Tr
C
S
Th
G
1P
2P
3P
mS
Conflicts with plurality signal are observed in sets of orthologs across all
functional categories, including
genes involved in translation and
transcription
624/1128 ≈ 55%
Distribution of 1128 datasets in the relaxed core
212
192
441
160
123INFORMATION STORAGEAND PROCESSINGCELLULAR PROCESSESAND SIGNALINGMETABOLISM
POORLYCHARACTERIZEDNOT PRESENT IN COGS
Distribution of 624 datasets conflicting the plurality signal
127
96
249
82
70
INFORMATION STORAGEAND PROCESSING
CELLULAR PROCESSESAND SIGNALING
METABOLISM
POORLYCHARACTERIZED
NOT PRESENT IN COGS
Genes with orthologs outside the cyanobacterial phylum:Distribution among Functional Categories
(using COG db, release of March 2003)
Cyanobacteria do
not form a coherent
group (160)
Cyanobacteria do
form a coherent
group, but conflict
with plurality (294)
700 phylogenetically
useful extended
datasets
In case of the marine Synecchococcus and Prochlorococcus spp. the plurality consensus is unlikely to reflect organismal history.
This is probably due to frequent gene transfer mediated by phages e.g.:
These conflicting observations are not limited to pro-karyotes. In incipient species of Darwin’s finches frequentintrogression can make some individuals characterized by morphology and mating behavior as belonging to the same species genetically more similar to a sister species (Grant et al. 2004 “Convergent evolution of Darwin's finches caused by introgressive hybridization and selection” Evolution Int J Org Evolution 58, 1588-1599).
Species evolution versus plurality consensus
Coalescence – the
process of tracing
lineages backwards
in time to their
common ancestors.
Every two extant
lineages coalesce
to their most recent
common ancestor.
Eventually, all
lineages coalesce
to the cenancestor.
t/2(Kingman, 1982)
Illustration is from J. Felsenstein, “Inferring Phylogenies”, Sinauer, 2003
Coalescence of ORGANISMAL and MOLECULAR Lineages
•20 lineages
•One extinction and one speciation event per generation
•One horizontal transfer event once in 5 generations (I.e., speciation events)
RED: organismal lineages (no HGT)BLUE: molecular lineages (with HGT)GRAY: extinct lineages
•20 lineages
•One extinction and one speciation event per generation
•One horizontal transfer event once in 5 generations (I.e., speciation events)
RED: organismal lineages (no HGT)BLUE: molecular lineages (with HGT)GRAY: extinct lineages
RESULTS:
•Most recent common ancestors are different for organismal and molecular phylogenies
•Different coalescence times
•Long coalescence time for the last two lineages
RESULTS:
•Most recent common ancestors are different for organismal and molecular phylogenies
•Different coalescence times
•Long coalescence time for the last two lineages
Time
Adam and Eve never met
Albrecht Dürer, The Fall of Man, 1504
MitochondrialEve
Y chromosomeAdam
Lived approximately
50,000 years ago
Lived 166,000-249,000
years ago
Thomson, R. et al. (2000) Proc Natl Acad Sci U S A 97, 7360-5
Underhill, P.A. et al. (2000) Nat Genet 26, 358-61
Cann, R.L. et al. (1987) Nature 325, 31-6
Vigilant, L. et al. (1991) Science 253, 1503-7
The same is true for ancestral rRNAs, EF, ATPases!
green: organismal lineages ; red: molecular lineages (with gene transfer)
Lineages Through Time Plot
10 simulations of organismal evolution assuming a constant number of species (200) throughout the simulation; 1 speciation and 1 extinction per time step. (green O)
25 gene histories simulated for each organismal history assuming 1 HGT per 10 speciation events (red x)
log
(n
umb
er o
f su
rviv
ing
line
age
s)
Bacterial 16SrRNA based phylogeny (from P. D. Schloss and J. Handelsman, Microbiology and Molecular Biology Reviews,
December 2004.)
The deviation from the “long branches at the base” pattern could be due to • under sampling• an actual radiation
• due to an invention that was not transferred• following a mass extinction