Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

• Horizontal Gene Transfer a Hallmark of Animal Genomes? in The Scientist by Jyoti Madhusoodanan
• Humans may harbor more than 100 genes from other organisms by Sarah Williams in Science

 Here is the full text of my responses:

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"got asked by another reporter to comment on this

so - have seen the paper 

it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). "

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I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 

Without seeing the alignments I offer multiple alternative hypothesis for their findings

1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note - clustalw is a bit notorious for not producing idea alignments in some cases.
2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
5. Related to alignments they need to show which regions of alignments they excluded from phylo
6. Convergent evolution could also explain some of the patterns they observe.
7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.

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Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate - I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.

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Reporter asking what other analyses could they do

So - I don't want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 

In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.

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Reporter asking about initial impressions:

I see little here that is particularly convincing evidence for HGT ...

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My follow up email

Note - I am not saying that this is a bad paper -- just that I am not overwhelmed by their evidence and especially by what they put in the paper. 

For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don't see how they tested alternative hypotheses ...

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Some related links:

• Bacterial DNA in Human Genomes | The Scientist Magazine®
• Researchers Challenge Recent Claim That Humans Acquired 223 Bacterial Genes During Evolution
• Slideshare of slides from talk where I discuss this topic a bit

Also here are some presentations from many years ago with some discussion of HGT

Phylogenomics - talk by J. Eisen in 2000 at MBL Molecular Evolution Course from Jonathan Eisen

Talk by Jonathan Eisen for GSAC2000 on "Phylogenomics" from Jonathan Eisen

Repeated, extremely biased ratio of M:F at meetings from SFB 680 "Evolutionary Innovations" group #YAMMM

Well, this is disappointing, to say the least - there is a conference coming up in July 2015 on "Forecasting Evolution":  SFB 680 | Molecular Basis of Evolutionary Innovations at the Gulbenkian Foundation in Lisbon.

Here is the listed lineup of invited speakers:

1. Andersson (Uppsala University), (NOTE I AM ASSUMING THIS IS DAN ANDERSSON)
2. Trevor Bedford (Hutchinson Cancer Research Center), 
3. Jesse Bloom (Fred Hutchinson Cancer Research Center), 
4. Arup Chakraborty (MIT)
5. Michael Desai (Harvard University), 
6. Michael Doebeli (University of British Columbia), 
7. Marco Gerlinger (Institute of Cancer Research, London, 
8. Michael Hochberg (CRNS, Montpellier), 
9. Christopher Illingworth (Cambridge University), 
10. Roy Kishoni (Harvard University), 
11. Richard Lenski (Michigan State University), 
12. Stanislas Leibler (Rockefeller University), 
13. Marta Luksza (IAS Princeton), 
14. Luke Mahler (University of California, Davis), 
15. Leonid Mirny (MIT), 
16. Richard Neher (MPI Tuebingen), 
17. Julian Parkhill (Sanger Institute), 
18. Colin Russell (University of Cambridge), 
19. Sohrab Shah (University of British Columbia), 
20. Boris Shraiman (UCSB), 
21. Olivier Tenaillon (Inserm Paris).

For a whopping 20:1 ratio of men to women or 4.8% women. And this in a field that is just overflowing with excellent female researchers.

So I dug around a little bit.  Here is another meeting from the same group at the University of Cologne - a group known as SFB 680. SFB 680: Molecular Ecology and Evolution: Cologne Spring Meeting 2012.



Speakers:

1. Ian Thomas Baldwin, MPI Jena
2. Nitin Baliga, ISB Seattle 
3. Andrew Beckerman, University of Sheffield 
4. Joy Bergelson, University of Chicago
5. Michael Boots, University of Sheffield 
6. John Colbourne, Indiana University 
7. David Conway, LSHTM London
8. Santiago Elena, IBMCP Valencia
9. Duncan Greig, MPI Plön 
10. Bryan Grenfell, Princeton University 
11. Eddie Holmes, Pennsylvania State University 
12. Peter Keightley, University of Edinburgh
13. Britt Koskella, University of Oxford
14. Juliette de Meaux, University of Münster 
15. Thomas Mitchell-Olds, Duke University
16. Hélène Morlon, Ecole Polytechnique Paris 
17. Wayne Potts, University of Utah 
18. Michael Purugganan, New York University
19. Andrew Rambaut, University of Edinburgh 
20. Walter Salzburger, University of Basel 
21. Johanna Schmitt, Brown University
22. Ralf Sommer, MPI Tübingen
23. Miltos Tsiantis, University of Oxford 
24. Diethardt Tautz, MPI Plön 
25. Daniel Weinreich, Brown University

Session and Meeting Chairs:

1. Michael Lassig
2. Maarten Koornneef
3. Eric von Elert
4. Thomas Wiehe
5. Jonathan Howard

That would be 25:5 or 16.6% female.

And then there was this: Perspectives in Biophysics in October 2014. 

1. Konstantin Doubrovinski
2. Tobias Bollenbach
3. Stefano Pagliara
4. Damien Faivre
5. Ingmar Schön
6. Kurt Schmoller
7. Max Ulbrich
8. Florian Rehfeld
9. Steffen Sahl
10. Timo Betz
11. Alexandre Persat

And this Evolutionary Genomics 2011

1. Rubén Alcázar (MPI for Plant Breeding Research, Cologne)
2. John Baines (Christian-Albrechts-University, Kiel)
3. Thomas Bataillon (University of Aarhus)
4. Frank Chan (MPI for Evolutionary Biology, Plön)
5. George Coupland (MPI for Plant Breeding Research, Cologne)
6. Susanne Foitzik (Johannes Gutenberg-University, Mainz)
7. Isabel Gordo (Instituto Gulbenkian, Lisbon)
8. Oskar Hallatschek (MPI for Dynamics and Self-Organization, Göttingen
9. Jonathan Howard (University of Cologne)
10. JinYong Hu (MPI for Plant Breeding Research, Cologne)
11. Jeffrey Jensen (University of Massachusetts, Medical School, Worchester)
12. Michael Lässig (University of Cologne)
13. Dirk Metzler (Ludwig-Maximilians-University, Munich)
14. Ville Mustonen (Welcome Trust Sanger Institute)
15. John Parsch (Ludwig-Maximilians-University, Munich)
16. Frank Rosenzweig (University of Montana, Missoula)
17. Christian Schlötterer (University of Veterinary Medicine, Vienna)
18. Shamil Sunyaev (Brigham & Women's Hospital and Harvard Medical School) 
19. Karl Schmid (University of Hohenheim)
20. Ana Sousa (Instituto Gulbenkian, Lisbon)
21. Diethard Tautz (MPI for Evolutionary Biology, Plön)
22. Xavier Vekemans (University of Lille)

Session and Meeting Chairs

• Wolfgang Stephan
• Michael Lässig
• Berenike Maier
• Wolfgang Stephan
• Peter Pfaffelhuber
• Juliette de Meaux

For a 19:3 ratio or 13.6 % women for the speakers and if you include session chairs it comes to 23:5 or 18 % female total.

And Evolutionary Innovations in 2010. 

Invited speakers:

1. R. Bundschuh (Ohio State University), 
2. C. Callan (Princeton University),
3. A. Clark (Cornell University), 
4. J. Colbourne (Indiana University),
5. E. Dekel (Weizmann Institute),
6. L. Hurst (University of Bath), 
7. S. Elena (Universidad Polytecnica de Valencia), 
8. E. Koonin (National Center for Biotechnology Information), 
9. M. Kreitman (University of Chicago),
10. S. Leibler (Rockefeller University, New York and Institute for Advanced Study, Princeton),
11. T. Lengauer (Max Planck Institute for Informatics), 
12. S. Maerkl (Ecole Polytechnique de Lausanne), 
13. C. Marx (Harvard University), 
14. L. Mirny (Massachusetts Intitute of Technology), 
15. V. Mustonen (Sanger Institute), 
16. C. Pal (Biological Research Center, Szeged),
17. D. Petrov (Stanford University), 
18. B. Shraiman (Kavli Institute for Theoretical Physics, Santa Barbara),
19. S. Sunyaev (Harvard University), 
20. D. Tautz (Max-Planck-Institute for Evolutionary Biology)

Plus session chairs 

1. Johannes Berg
2. Siegfried Roth
3. Wolfgang Werr
4. Martin Lercher

And addition speakers not listed on their invited speakers page:

1. Michael Lassig
2. Ruben Alcazar
3. Juliette de Meaux
4. Joachim Krug

For a whopping ratio of 27:1 or 3.6 %

The only meeting from them I could find with a decent / non massively skewed ratio was the following very small one: Evolution of Development

1. Cassandra Extavour
2. Angela Hay
3. Felicity Jones
4. Nicolas Gompe
5. Kristen Panfillio
6. Christiane Kiefer

This is a nice case.  But it really seems like an exception in a long list of meetings with a much smaller representation of female speakers than one would expect based on the researchers in the fields.   I think the SFB680 seriously need to consider what is causing these biases and they should do something about it.

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See this page for other posts of mine on this and related topics.

A distasteful & disgraceful "Are there limits to evolution?" meeting at the University of Cambridge #YAMMM

Well, I saw this Tweet the other day

Another for @phylogenomics's list of YAMMMs (Yet Another Mostly Male Mtg). Ratio = 1F speaker to 23M speakers. http://t.co/qgEfwtBS2B
— Hopi Hoekstra (@hopihoekstra) September 16, 2014

And though there was a bit of a discussion on Twitter I felt I had to follow up with a blog post. When I saw the post I was at a conference (Lake Arrowhead Microbial Genomes) where I could get Twitter access but for some reason very little web access. So I could not dig around until now (I am home). 

This meeting is a complete disgrace and an embarassment for the field of evolutionary biology, for the University of Cambridge which is hosting the meeting, and for the Templeton Foundation which is sponsoring it.

Why do I say this? Well, pretty simple actually. The meeting site lists the Invited Keynote speakers for the meeting.  Notice anything?  How about I help you by bringing all the pictures together.

Notice anything now?  How about I help you some more by masking out the men and not the women.

Impressive no?  25 speakers - 23 of them male.  I guess that means there are no qualified female speakers who coudl discuss something about evolution right?  It would be worth reading "Fewer invited talks bu women in evolutionary biology symposia" to get some context.  What an incredible, disgusting, distasteful and disgraceful meeting.  

I recommend to everyone who was considering going to this meeting - skip it.  Also consider writing to the University of Cambirdge and the Templeton Foundation to express your thoughts about the meeting.  This certainly is a fine example of Yet Another Mostly Male Meeting (YAMMM).  Well, maybe I should word that differently - this is a disgusting example of a YAMMM.  

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For more on this and related issues

Posts on Women in STEM

Also see

See meeting w/ severely bad speaker gender ratio but don't feel comfortable posting?send me details & I will post phylogenomics@me.com
— Jonathan Eisen (@phylogenomics) September 19, 2014