Is there any treelikeness in prokaryotic phylogenetic history

Right now there are some very valid questions being asked about how treelike we might expect to find the history of prokaryotes.  Conflicting phylogenetic trees derived from homologs-that-look-like-orthologs are probably in large part due to horizontal (or lateral if you prefer) gene transfer.  Some might be due to hidden paralogy, poor phylogenetic models and maybe some other things, but for the most part, if we are careful about making trees, we find that the best explanation is horizontal gene transfer.

So, has this completely destroyed the phylogenetic signal for prokaryotes?  I think that on the whole the answer is yes, but are there places where we might expect treelikeness to be stronger than the confusing signal?  I think that the answer to this is yes!

We carried out a study in 2004 where we make a phylogenetic supertree from input trees that were derived from single-copy genes (these have the best chance of being true orthologs).  When we compared the input trees to the over-arching supertree, we found that, depending on the data we were looking at, we saw either a complete mess or we saw some order.

The complete mess was the data that came from a bunch of genomes that were from really, really diverse prokaryotes.

The reasonable compatibility came from genomes that were clearly more closely-related on average.

Now, we didn’t lok at really really closely related genomes (though we have elsewhere), but we know that, say, within the genus Neisseria, there is very little agreement between gene trees.

Therefore, we concluded eight years ago that a tree-like phylogeny only existed near to the tips of the prokaryotic phylogenetic history.

I’m surprised that more studies of this nature haven’t been carried out, though some have. I don’t think the answer will change though.

There is loads of disagreement between phylogenetic trees in prokaryotes and there is loads of agreement and one single answer to this question is not forthcoming.

In any case, why should we expect one single answer? Its biology, after all.

Reference:

Creevey, C.J., Fitzpatrick, D.A., Philip, G.K., Kinsella, R.J., O’Connell, M.J., Pentony, M.M., Travers, S.A.A., Wilkinson, M., and McInerney, J.O. (2004). Does a Tree-like Phylogeny Only Exist at the Tips in the Prokaryotes? Proceedings of The Royal Society of London, Biology Series271(1557):2551-8. [pdf]

Pervasive horizontal gene transfer in Chlamydia

The genome era has really taught us something impressive about the plasticity of bacterial genomes.

Gene exchange between strains of the same species and gene exchange between different species is not limited to special categories of genes and is not limited to ‘oddball’ species.  It is pervasive, frequent and it is also a public health problem.

Last week, a paper that is beautiful in its execution really highlighted the importance of gene transfer from a public health perspective.

Simon Harris and co-workers from various UK institutions, South Africa, Sweden, The Netherlands and France have published an analysis of whole genome sequences from a diverse collection of Chlamydia strains.

The work shows that using the ompA gene – which is often used for diagnosis of what kind of Chlamydia is present – is not sensible.  The history of this gene is filled with instances of gene splicing and exchange.  Other diagnostic markers have the same kind of history.

Phylogenetic trees from different markers conflict with one another, revealing that these genomes are chimaeric in many different kinds of ways.

To me this news is not surprising, merely that it is impressive.

Gene exchange defines the evolution of most ‘evolving entities’ on the planet (let’s operationally define an evolving entity as anything that is uses DNA or RNA as its genetic material and not restrict our discussion to just cellular life forms).

Gene exchange is restricted by protein-protein interactions and perhaps in sexually reproducing organisms it is restricted because only gene exchange into the single cells that are involved in reproduction are the only gene exchanges that will ever count.

Otherwise, horizontal gene transfer seems to be unstoppable and it seems to be frequent and it presents us with a significant public health problem both from the perspective of managing antibiotic resistance, but also from the perspective that this is the likely source of entirely new infectious agents.

Feel free to leave a comment below.

 

Reference:

Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW, Lewis DA, Spratt BG, Unemo M, Persson K, Bjartling C, Brunham R, de Vries HJ, Morré SA, Speksnijder A, Bébéar CM, Clerc M, de Barbeyrac B, Parkhill J, Thomson NR. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet. 2012 Mar 11. doi: 10.1038/ng.2214.

 

Also, perhaps take a look at:

McInerney, J.O., Pisani, D., Bapteste, E., and O’Connell, M.J. (2011). The Public Goods Hypothesis for the Evolution of Life on Earth. Biology Direct doi:10.1186/1745-6150-6-41. [link]

H-Index, M-Index and google citations

Today I downloaded and installed the r program for analysing Google Scholar citation metrics (you can pick it up here).

There is a lot of talk about the various metrics being used to analyse the productivity of scientists and there seems to be no really good way to do it.  A simple point-statistic doesn’t do it very well.

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Planctomycetes and Eukaryotes are both interesting, but not specifically related

We have finally published our analysis of the relationships between Planctomycetes, Verrucomicrobia and Chlamydia (the so-called PVC group) and Eukaryotes.  In other words, we have shown that these two groups of organisms share superficial similarities, but have no close relationship.  The manuscript has been published in BioEssays and you can access it here [1].

If you take a look at two papers in particular [2,3] – though there are many more on the subject – you can see that thousands of eukaryotic genes can trace their origins to prokaryotic taxa, but there has been no systematic large-scale study to date that has been able to show that any appreciable number of genes group eukaryotes and PVC bacteria together to the exclusion of all other taxa.

This is the gold-standard test.  Can we use careful reconstruction of the evolutionary histories of large numbers of genes to infer the prokaryotic ancestry of eukaryotes?  To a certain extent, we can.  However, it is fraught with difficulties, both in modeling evolutionary history and also incorporating horizontal gene transfer, which tends to obscure the histories somewhat.

Nonetheless, when we actually carried out these analyses, we can see clear patterns emerge.  We can see that there is a large component of the eukaryotic cell that is specifically linked to organisms that are in the alpha-proteobacterial group.  We can see a large component that is specifically associated with the archaebacteria and we can see a large component associated with the cyanobacteria.

The fine-grained placement of these eukaryotic genes is very difficult and I feel that more work needs to be done in this area, but nonetheless, one other thing emerges: There is no strong association between PVC bacteria and eukaryotes.

Right now, as far as the data is concerned (and remember, the data wins, not our pre-conceived notions or our preferences – we have to do science, after all) there is no specific link between PVC bacteria and eukaryotes.

Which is why it is annoying when people ignore the evidence and put forward claims that only look at part of the data [4].

A number of papers have tried to claim that PVC bacteria are in some way intermediate between bacteria and eukaryotes.  This is nonsense. Emboldened with this kind of success, the authors have gone off on a tangent claiming that this in some way validates ideas about autogenous evolution of the eukaryote cell (that the eukaryote cell arose first without any fusion event) and so on.

The problem for these other scientists and their claims is that the real evidence is out there, it has been published and it is very difficult to get around.  Several labs from several countries have looked at these data and there is no real problem with interpreting the data – the phylogenetic signals linking eukaryotes to prokaryotes are easy to find and they link eukaryotes to three main lineages – cyanobacteria, alpha-proteobacteria and archaebacteria.  All other linkages can be explained by small amounts of horizontal gene transfer of some kind.

Finding endocytosis-like processes in Planctomycetes is great [5].  This is indeed an interesting feature of a bacterium.  Does it automatically follow that by studying this bacterium, we will know more about eukaryotes?  Not necessarily.  It might, but it is not a logical conclusion that it will.  Consider, for instance, a birds wing and the wing of a jumbo jet.  Nothing about a birds wing will tell you how a jumbo jet’s wing works.  Engineers gave up at a very early stage when they tried to make aeroplanes with flapping wings.  The two entities both are used for flight, but it is not logical to say that studying one might provide an insight into the other.  The only insights we might get will be dull and uninformative for the most part.

So, if you want to study eukaryote endocytosis, then study it in eukaryotes – there are plenty eukaryotes.

I say it again: PVC bacteria are not specifically related to eukaryotes.  You can find more detail in the paper.

References

1. McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, et al. Planctomycetes and eukaryotes: A case of analogy not homology. Bioessays 2011; 33:810-7.

2. Pisani D, Cotton JA, McInerney JO. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol 2007; 24:1752-60.

3. Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, et al. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 2004; 21:1643-60.

4. Devos DP, Reynaud EG. Evolution. Intermediate steps. Science 2010; 330:1187-8.

5. Fuerst JA, Sagulenko E. Protein uptake by bacteria: An endocytosis-like process in the planctomycete Gemmata obscuriglobus. Commun Integr Biol 2010; 3:572-5.

 

 

Clans, clades and unrooted trees

A few years back, Mark Wilkinson at The Natural History Museum, London came up with the idea that we should really have a more precise language for groups that we can see on unrooted trees.

The problem stemmed from the fact that on an unrooted tree a clade is not defined.

A clade is a monophyletic group, a collection of organisms or taxa that can trace their roots to a single common ancestor.

Naturally this means that we have clades within clades within clades.

All cellular life might be considered a clade, but this seems a little trivial and uninformative.

We generally think that a clade should be defined in some way.  The most usual definition is that all members of a clade might share a ‘uniquely derived’ character or feature.  They would have what we call a synapomorphy for that feature – all members of the clade would have this feature and those organisms that lacked the feature could not be members of that clade.  Vertebrates, for instance, all have vertebrae and we consider that vertebrates all form a single clade.  Strawberries are not vertebrates, in part, because they lack vertebrae (also we might imagine there are other reasons).

 

 

However, one point to make is that a clade can really only be defined on a rooted phylogenetic tree. An unrooted tree cannot have clades because the direction of evolution is not defined.

A ‘clan’

Therefore, Mark proposed that we use the word ‘clan’ in order to identify a group on an unrooted tree that might – given some particular rooting – be a clade if the tree was rooted.  Essentially a clan is defined by a split on the unrooted tree, as long as we ignore the trivial splits that separate the terminal taxa from the rest of the tree.

Then we had the issue of what to call the unrooted equivalent of a sister-group.  We settled on ‘adjacent group’, which seemed sensible. Click on the figure in order to see it full-sized.

So far there have been no objections to this new terminology and in fact it seems to have caught on a little.  At the end of this blog post I will put a few manuscripts that have explored this terminology a little further.

Please leave a comment.

 

 

Reference:

Of clades and clans: terms for phylogenetic relationships in unrooted trees Wilkinson Mark ; McInerney James O. ; Hirt Robert P. Foster, Peter G ; Embley T. Martin TRENDS IN ECOLOGY & EVOLUTION  Volume: 22   Issue: 3   Pages: 114-115   DOI: 10.1016/j.tree.2007.01.002   Published: MAR 2007

http://www.ncbi.nlm.nih.gov/pubmed/17239486

 

Some further reading:

Of woods and webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli Beauregard-Racine Julie; Bicep Cedric; Schliep Klaus; et al. BIOLOGY DIRECT  Volume: 6     Article Number: 39   DOI: 10.1186/1745-6150-6-39   Published: JUL 20 2011

Telling the whole story in a 10,000-genome world Beiko Robert G. BIOLOGY DIRECT  Volume: 6     Article Number: 34   DOI: 10.1186/1745-6150-6-34   Published: JUN 30 2011

Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe Triponez Y.;Buerki S.; Borer M.; et al. MOLECULAR ECOLOGY  Volume: 20   Issue: 11   Pages: 2442-2463   DOI: 10.1111/j.1365-294X.2011.05096.x   Published: JUN 2011

Clades, clans, and reciprocal monophyly under neutral evolutionary models Zhu Sha; Degnan James H.; Steel Mike THEORETICAL POPULATION BIOLOGY  Volume: 79   Issue: 4   Pages: 220-227   DOI: 10.1016/j.tpb.2011.03.002   Published: JUN 2011

Characterization of a regulatory unit that controls melanization and affects longevity of mosquitoes An Chunju; Budd Aidan; Kanost Michael R.; et al. CELLULAR AND MOLECULAR LIFE SCIENCES  Volume: 68   Issue: 11   Pages: 1929-1939   DOI: 10.1007/s00018-010-0543-z   Published: JUN 2011

Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees Schliep Klaus; Lopez Philippe; Lapointe Francois-Joseph; et al. MOLECULAR BIOLOGY AND EVOLUTION  Volume: 28   Issue: 4   Pages: 1393-1405   DOI: 10.1093/molbev/msq323   Published: APR 2011

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi Slot Jason C.; Rokas Antonis CURRENT BIOLOGY  Volume: 21   Issue: 2   Pages: 134-139   DOI: 10.1016/j.cub.2010.12.020   Published: JAN 25 2011

Evolution of Patchily Distributed Proteins Shared between Eukaryotes and Prokaryotes: Dictyostelium as a Case Study Andersson Jan O. JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY  Volume: 20   Issue: 2   Pages: 83-95   DOI: 10.1159/000324505   Published: 2011

On the need for integrative phylogenomics, and some steps toward its creation Bapteste Eric; Burian Richard M. BIOLOGY & PHILOSOPHY  Volume: 25   Issue: 4   Pages: 711-736   DOI: 10.1007/s10539-010-9218-2   Published: SEP 2010

Mitochondrial DNA variation in Arctic charr (Salvelinus alpinus (L.)) morphs from Loch Rannoch, Scotland: evidence for allopatric and peripatric divergence Verspoor E.; Knox D.; Greer R.; et al. HYDROBIOLOGIA  Volume: 650   Issue: 1   Pages: 117-131   DOI: 10.1007/s10750-010-0106-1   Published: AUG 2010