Discovering the Tree of Life

One of the most profound ideas to emerge in modern science is Charles Darwin's concept that all of life, from the smallest microorganism to the largest vertebrate, is connected through genetic relatedness in a vast genealogy. This "Tree of Life" summarizes all we know about biological diversity and underpins much of modern biology, yet many of its branches remain poorly known and unresolved.

To help scientists discover what Darwin described as the tree's "everbranching and beautiful ramifications," the National Science Foundation (NSF) has awarded $17 million in "Assembling the Tree of Life" grants to researchers at more than 25 institutions. Their studies range from investigations of entire pieces of DNA to assemble the bacterial branches; to the study of the origins of land plants from algae; to understanding the most diverse group of terrestrial predators, the spiders; to the diversity of fungi and parasitic roundworms; to the relationships of birds and dinosaurs.

"Despite the enormity of the task," said Quentin Wheeler, director of NSF's division of environmental biology, which funded the awards, "now is the time to reconstruct the tree of life. The conceptual, computational and technological tools are available to rapidly resolve most, if not all, major branches of the tree of life. At the same time, progress in many research areas from genomics to evolution and development is currently encumbered by the lack of a rigorous historical framework to guide research."

Scientists estimate that the 1.75 million known species are only 10 percent of the total species on earth, and that many of those species will disappear in the decades ahead. Learning about these species and their evolutionary history is epic in its scope, spanning all the life forms of an entire planet over its several billion year history, said Wheeler.

Why is assembling the tree of life so important? The tree is a picture of historical relationships that explains all similarities and differences among plants, animals and microorganisms. Because it explains biological diversity, the Tree of Life has proven useful in many fields, such as choosing experimental systems for biological research, determining which genes are common to many kinds of organisms and which are unique, tracking the origin and spread of emerging diseases and their vectors, bio-prospecting for pharmaceutical and agrochemical products, developing data bases for genetic information, and evaluating risk factors for species conservation and ecosystem restoration.

The Assembling the Tree of Life grants provide support for large multi-investigator, multi-institutional, international teams of scientists who can combine expertise and data sources, from paleontology to morphology, developmental biology, and molecular biology, says Wheeler. The awards will also involve developing software for improved visualization and analysis of extremely large data sets, and outreach and education programs in comparative phylogenetic biology and paleontology, emphasizing new training activities, informal science education, and Internet resources and dissemination.

For a list of the Assembling the Tree of Life grants, see: http://www.nsf.gov/bio/pubs/awards/atol_02.htm

Thank you so much for your reply and for pinging Nebullis!

My interest in these debates lies much more with the physics side (incl. math, information theory, cosmology, etc.) and your discussion with AndrewC has really made me curious as to intelligence and the genome itself.

As you can see from this article, it has not been easy to simulate physical intelligence: What Is Intelligence?

Give us a number, then.

It is there in the expect value.



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

motA                                                                  567   e-162
BS_motA                                                                91   1e-18
TM0676                                                                 74   1e-13
HP0815                                                                 68   6e-12
TP0725                                                                 68   6e-12
jhp0751                                                                68   6e-12
BB0281                                                                 62   3e-10
aq_1003                                                                58   6e-09
BS_ytxD                                                                43   2e-04
PH0632                                                                 31   1.1  
CT365                                                                  31   1.1  
MTH1022                                                                30   1.4  
srlE                                                                   30   1.4  
MTH924                                                                 30   1.8  
slr0301                                                                30   1.8  
HI1728                                                                 29   3.1  
Rv3689                                                                 29   4.0  
jhp0817                                                                29   4.0  
acrB                                                                   29   4.0  
BS_ylmB                                                                28   5.2  
acrF                                                                   28   5.2  
TM1385                                                                 28   6.8  
YEL031w                                                                28   6.8  
ydiS                                                                   28   6.8  
acrD                                                                   28   6.8  
yhiV                                                                   28   6.8  
AF0134                                                                 28   6.8  
Rv3091                                                                 28   8.9  
BS_braB                                                                28   8.9  
sll0537                                                                28   8.9

Notice the significant change? (Although apparently those in the know accept 10 as the cutoff for acceptance of "similarity") My phrase got 2.5. The sequence of the MOTA from the D. Vulgaris and MTH1022 when reduced to the range of 55 was IIRC ~e-05.

This is the data for MTH1022 and the MOTA, aq_1003 in the study. The TM0676 is also from the MOTA COG.



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

MTH1022                                                               506   e-144
sll0477                                                                71   7e-13
RP309                                                                  62   5e-10
sll1404                                                                61   9e-10
slr0677                                                                60   2e-09
aq_1988                                                                58   6e-09
HP1339                                                                 48   6e-06
jhp1258                                                                48   6e-06
tolQ                                                                   47   1e-05
CT596                                                                  46   2e-05
CPn0785                                                                46   3e-05
HI0253                                                                 45   4e-05
exbB                                                                   45   4e-05
aq_1757                                                                45   5e-05
HI0385                                                                 45   7e-05
TM0676                                                                 44   1e-04
aq_1003                                                                43   2e-04
MTH671                                                                 42   4e-04
HP1445                                                                 42   6e-04
jhp1338                                                                42   6e-04
BB0281                                                                 42   6e-04
HP1130                                                                 40   0.002
jhp1058                                                                40   0.002
HP0815                                                                 37   0.018
jhp0751                                                                37   0.018
BS_ytxD                                                                33   0.20 
TP0725                                                                 33   0.26 
PH0361                                                                 30   1.7  
CT874                                                                  30   1.7  
motA                                                                   30   1.7  
Rv0545c                                                                29   2.8  
slr0531                                                                29   3.7  
sll0223                                                                29   3.7  
BS_motA                                                                28   4.9  
YNL189w                                                                28   4.9  
sfcA                                                                   28   4.9  
ftsW                                                                   28   4.9  
jhp0723                                                                28   6.3  
HP0786                                                                 28   8.3  
PH0504                                                                 28   8.3  
AF1017                                                                 28   8.3




Comparing only the 55--(Don't blame me this is what the Cognitor returns)
# >aq_1003
#           Length = 254
# 
#  Score = 39.3 bits (90), Expect = 5e-04
#  Identities = 21/46 (45%), Positives = 29/46 (62%), Gaps = 3/46 (6%)
# 
# Query: 2   PMLGLIGTVIGIWYTFRALGVNADPAAMAEGIYVALITTILGLAVA 47
#            P  G+IGT+IG+    R L    DP+A+  G+ VALITT+ G  +A
# Sbjct: 155 PAFGMIGTLIGLIQMLRNLN---DPSALGPGMAVALITTLYGAILA 197

Q: What is the Expect (E) value?

The Expect value (E) is a parameter that describes the number of hits one can "expect" to see just by chance when searching a database of a particular size. It decreases exponentially with the Score (S) that is assigned to a match between two sequences. Essentially, the E value describes the random background noise that exists for matches between sequences. For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance. This means that the lower the E-value, or the closer it is to "0" the more "significant" the match is. However, keep in mind that searches with short sequences, can be virtually indentical and have relatively high EValue. This is because the calculation of the E-value also takes into account the length of the Query sequence. This is because shorter sequences have a high probability of occuring in the database purely by chance. For more details please see the calculations in the BLAST Course.

The Expect value can also be used as a convenient way to create a significance threshold for reporting results. You can change the Expect value threshold on most main BLAST search pages. When the Expect value is increased from the default value of 10, a larger list with more low-scoring hits can be reported.

----------

BLAST 2 SEQUENCES RESULTS VERSION BLASTP 2.2.4 [Aug-26-2002] Matrix gap open: gap extension:
x_dropoff: expect: wordsize: Filter

Sequence 1	gi 15606306	flagellar motor protein MotA [Aquifex aeolicus]	Length	254	(1 .. 254)
Sequence 2	gi 21399546	MotA_ExbB, MotA/TolQ/ExbB proton channel family [Bacillus anthracis A2012]	Length	254	(1 .. 254)

NOTE:The statistics (bitscore and expect value) is calculated based on the size of nr database

Score =  138 bits (348), Expect = 9e-32
Identities = 82/237 (34%), Positives = 136/237 (56%), Gaps = 6/237 (2%)

Query: 7   IGIIAAFLLILISILIGG----SITAFINVPSIFIVVGGGMAAAMGAFPLKDFIRGVLAI 62
           +GII  F +++ +I++GG    +   F++V SI IV+GG  A  + A+   +  +   +I
Sbjct: 1   MGIIVGFAIVIAAIMLGGGGIKAFKNFLDVSSILIVIGGTTATIVVAYRFGEIKKYTKSI 60

Query: 63  KKAFLWKPPDLNDVIETIGEIASKVRKEGILALEGDIELYYQKDPLLGDMIRMLVDGIDI 122
                 +  DL  + +   + + K +K G+L+LE D E     +P +   IR+++ G D 
Sbjct: 61  FTVLHRREEDLEQLTDLFVDFSKKSKKHGLLSLEVDGEQV--DNPFIQKGIRLMLSGYDE 118

Query: 123 NDIKATAEMALAQLDEKMSTEVAVWEKLADLFPAFGMIGTLIGLIQMLRNLNDPSALGPG 182
            ++K      +     ++    A+ +K+ D  PA+GMIGTLIGLI ML+NL D S +G G
Sbjct: 119 EELKEVLMKDVETEVYELRKGAALLDKIGDFAPAWGMIGTLIGLIIMLQNLQDTSQIGTG 178

Query: 183 MAVALITTLYGAILANAFAIPVANKLKKAKDMEVLVKTIYIEAIEKIQKGENPNVVK 239
           MAVA++TTLYG++LAN  AIP+A K+ +  +     K   IEAI ++ +G+ P+ +K
Sbjct: 179 MAVAMLTTLYGSVLANMIAIPLAEKVYRGIEDLYTEKKFVIEAISELYRGQIPSKLK 235

CPU time:     4.58 user secs.	    0.58 sys. secs	    5.16 total secs.

Lambda     K      H
   0.321    0.141    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 604
Number of Sequences: 0
Number of extensions: 59
Number of successful extensions: 3
Number of sequences better than 300.0: 1
Number of HSP's better than 300.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1
length of query: 254
length of database: 396,279,676
effective HSP length: 123
effective length of query: 131
effective length of database: 396,279,553
effective search space: 51912621443
effective search space used: 51912621443
T: 9
A: 40
X1: 16 ( 7.4 bits)
X2: 129 (49.7 bits)
X3: 129 (49.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.7 bits)

Yes. So you demonstrated that they are very alike. Did anthrax come from Aquifex aeolicus or is it the other way? Or was the gene for MOTA transferred from a flagellar bug to Anthrax? From the entry for the Anthrax bug

Protein-coding genes were predicted using GeneMarkS program (kindly provided by M. Borodovsky). Conserved domains were detected using reverse-position-specific BLAST search against the NCBI conserved domain database (CDD). Functional annotation is based on CDD assignments, it has not yet been subject to manual review. Method: conceptual translation.

Yes. So you demonstrated that they are very alike. Did anthrax come from Aquifex aeolicus or is it the other way? Or was the gene for MOTA transferred from a flagellar bug to Anthrax?

Anthrax and A. aeolicus have very similar proton transport systems, in the form of motA, ExdB/ExbB, and TolQ/TolR. In the absence of more information, we cannot say what the exact relationship bewteen the two is, but we cannot rule out the hypothesis that they are related somehow. What did you expect?

Heh. If you need extra help, here's your cheat sheet - a lower E-value indicates a more significant match - i.e., the closer the E-value is to 0, the less likely the match is due to random chance. So for post 1146, an E-value of 2e-04 is indicates that a random match between MTH1022 and motA is rather unlikely. But an E-value of 2.5 indicates that a random match between MTH1022 and the string "imadethesethingssmartlyinfiveyearsintheskyfindthesecret" is rather more likely, and hence not as significant.

Soooooo, one match is significant, and the other is not. So here's the pop-quiz: What can we say about the relationships (if any) between motA and MTH1022, and motA and the string "imadethesethingssmartlyinfiveyearsintheskyfindthesecret"?

Actually, I meant "what did you expect me to say?" rather than "what did you expect to find?" ;)

I would make a stronger statement, there is a relationship, presently unknown. We can rule out the no relationship verdict.

I would agree. As I said before, we can try to make some educated guesses about the relationship by using the degrees of difference to try and place them in a relative taxonomy. That's not conclusive, of course, but it can point us in a productive direction. And we can compare our results to morphological/cladistic taxonomies, to give us another factor in deciding the relationship.

And eventually, we can accumulate enough evidence to begin to lean in one direction or another about what the relationship is - do they share common ancestry? Did one of them just scarf up the genes from the other? Maybe they both obtained the same gene from a third source?

We'll make a materialist out of you yet.... ;)

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