Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Amazing video from Louie Schwartzberg / Moving Art "The Beauty of Pollination" #scifoo

I met Louie Schwartzberg at the SciFoo meeting last week. He makes absolutely amazing Nature videos … here is one.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

The recursive tree of life – how a Twitter -> Blogger loop was created and broken

Earlier today I wrote a post that went something like this

Still searching for a good way to post a roundup of my twitter conversations to my blog. There don’t seem to be any good systems for doing this on Blogger. So I have, at least this week, created a Storification of my tweets and some of the associated conversations … not ideal probably but still …

I am not sure how it finished because, well, I deleted the post by accident a bit later in the day as you will see.

I do recall I posted an embedded version of this storification.

And this led to some useful responses such as

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js SO this seemed potentially interesting .. and I decided to look into IFTTT. It took a bit to figure out anything about it but at first glance it seemed not right. So I posted a response

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js So I created an IFTTT account and hacked around for a bit. I connected IFTTT to some of my social networks and then I set up two automated feeds. One that would post from Twitter to Blogger and one that would archive my Tweets to Dropbox.

 And then I ran a test. I wrote a tweet to see where it would end up and whether / how it would end up on blogger. The tweet read something like “I am testing IFTTT for autoposting my tweets to my blog” and then I went to blogger and looked to see if anything showed up there (I note – I ended up deleting this tweet later in the day – more on this in a bit). But alas it did not. At least at first. So I looked at IFTTT in more detail and something there said it usually scanned twitter every 15 minutes so it might take some time for the tweets to show up on my blog.

Meanwhile I made another test tweet that read:

Testing http://t.co/1nWox0lt again . please ignore August 12, 2012 at 09:00AM http://twitter.com/phylogenomics/status/234680659233357824 Alas I deleted this one too (again – more on this deletion frenzy in a bit).

I note – I ended up deleting this one too – but by this point I had launched the “tweet to dropbox” system at IFTTT so this tweet was archived.

And then here was the big big big mistake.  I left the house – first to go shopping and then to a wedding (of a brilliant PhD student at UC Davis).  And I shut off my phone.  After the ceremony I turned on my phone again to take some pictures.  And (of course) I checked Twitter.  And thats when I noticed something had gone horribly wrong.

This is what I saw first:

//platform.twitter.com/widgets.js “Hmm” I thought. What could that be about? First, I thought it was about all the microbe posts from yesterday. But then I saw some other posts.

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

Uh oh.  Or more like “Oh shit.”  What the $&$# was going on?  And suddenly I realized, I must still have a “blogger to twitter” autopost feature set up through blogger.  So IFTTT was posting to blogger anything I tweeted and then Blogger was posting anything there to Twitter.  A loop.  Oh no.  A loop.  Not supposed to happen to me.

So I dreadfully looked at my Twitter feed to see how many tweets had been posted in this loop.  And it was quite a few.  Oh no.  What to do?  And I panicked a bit.  I just started deleting tweets so that people would not be driven crazy by the loop (at this point I did not know how many were in the loop).  And I ended up deleting not too many but more than a few (something like ten).   I can’t embed them of course, because I deleted them.  But I do have them in my new Dropbox twitter archive.

The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system for posting tweets to… http://t.co/xtuELMBb
August 12, 2012 at 09:06AM
http://twitter.com/phylogenomics/status/234682399693352962
– – – – –
The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting tweet to blogger system from IFTTT http://t.co/THhFkG7S
August 12, 2012 at 09:06AM
http://twitter.com/phylogenomics/status/234682401337524224
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system for posting… http://t.co/LKd976jR
August 12, 2012 at 09:22AM
http://twitter.com/phylogenomics/status/234686366678654976
– – – – –
The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting tweet to blogger… http://t.co/bOVmkEB0
August 12, 2012 at 09:22AM
http://twitter.com/phylogenomics/status/234686368612245505
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please ignoreTesting… http://t.co/EGWmjifq
August 12, 2012 at 09:37AM
http://twitter.com/phylogenomics/status/234690113525915648
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing an http://t.co/1nWox0lt IFTTT system… http://t.co/h8iOJFey
August 12, 2012 at 09:37AM
http://twitter.com/phylogenomics/status/234690132605804545
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/1nWox0lt again . please… http://t.co/RYKpNwdE
August 12, 2012 at 09:51AM
http://twitter.com/phylogenomics/status/234693721545920512
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing http://t.co/iXtneMx2… http://t.co/Ueg9mK2F
August 12, 2012 at 10:07AM
http://twitter.com/phylogenomics/status/234697523661512705
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: Testing… http://t.co/lwELrRso
August 12, 2012 at 10:21AM
http://twitter.com/phylogenomics/status/234701228347633664
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/Vz9GDrUI
August 12, 2012 at 10:36AM
http://twitter.com/phylogenomics/status/234704905246494721
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/PcTqp1mg
August 12, 2012 at 10:51AM
http://twitter.com/phylogenomics/status/234708632443441152
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/YecKMslQ
August 12, 2012 at 11:05AM
http://twitter.com/phylogenomics/status/234712346797428736
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/T2rE2shW
August 12, 2012 at 11:21AM
http://twitter.com/phylogenomics/status/234716246023745536
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/lYFK57gx
August 12, 2012 at 11:35AM
http://twitter.com/phylogenomics/status/234719738536796160
– – – – –
The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree of Life: The Tree… http://t.co/7X0Bypuj
August 12, 2012 at 11:50AM
http://twitter.com/phylogenomics/status/234723474831204352
– – – – – 

Oooh – that was bad.  But how to control it?  I first tried to unlink the IFTTT app from Twitter from inside Twitter.  That is, I tried to remove the permissions the IFTTT app had to post/read my twitter feed.  But Twitter seems to not provide access to applications control from a mobile device.  Crap.
So then I tried to log on to Google Blogger and unlink it from IFTTT.  Also no success.  Seems that many systems default to mobile options and do not provide access to full features no matter what.  
So then I called up my brother and thankfully he was there and after telling him my Twitter password (risky I know .. given my families tendency for pranks) – he deactivated the IFTTT access to Twitter.  Phew.  That hopefully would break the loop.  But to be safe I decided to check Blogger.  And Oh man- there were a lot of posts there too.  That was going to drive people crazy I am sure just as all the tweets did.  So I kind of panicked again and deleted all the IFTTT posts.  And I even accidentally deleted the post that launched all of this (see above).  Uggh.  I don’t like it when people delete posts but I needed to get control of this loop.  I figured, even if the IFTT Twitter -> Blogger system kept going – because it apparently only checked Twitter every 15 minutes I could keep the loop under control by monitoring Twitter and Blogger and deleting any posts before they got reposted somewhere else. 
So – while sitting at the wedding reception I did exactly this.  And it seemed under control.  So I posted to Twitter to apologize and tell people things seemed better.

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js So – seemed under control – sort of. And then I made the mistake of looking at Facebook. Oh no. Autofeeds there up the wazoo too. I am going to delete those later. What a nightmare. And it could have ben much worse if I did not catch it at the wedding. Because now I have to head to Berkeley for a birthday party for my brother’s kids. Hopefully – the loop is broken. And I have only one think left to say. The tree of life. The tree of life. The tree of life. The tree of life ….

UPDATE: My brother did indeed make use of my Twitter password, the bastard

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Interested in MiSeq Illumina sequencing of low diversity libs – read this

Everyone -if you are interested in using the Illumina MiSeq to sequencing low diversity libraries – read this … Sequencing low diversity libraries on Illumina MiSeq from THE Nick Loman.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

History of the Lake Arrowhead Microbial Genomes meetings

Recommended meeting for those interested in microbial diversity and/or microbial genomics: Microbial Genomics – ARROWHEAD 2012

Among the reasons to go:

And if you want to know more about past meetings see below:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Lake Arrowhead past meeting notes

Posting notes and notebooks from past Lake Arrowhead genomes meetings

Notes and materials from MARS Sample Handling Workshops 2000-2001 #Curiosity

I had the pleasure of serving as a panel member for some NASA sponsored “Mars Sample Handling Workshops” in 2000-2001 and thereabouts.  I have all these materials still from those meetings and in light of the Mars Curiosity Rover landing and other recent activities I thought it would be good to share them.  Most/all are public domain materials but not all are easy to find so I thought I would post them here.  Note – I have done no clean up of scans – will do so at some point. Enjoy.

 

 

Courtesy employee notice regarding annual systemwide payroll disclosure

Just received this … seemed to be something that should be shared publicly.

Wow – Google Scholar "Updates" a big step forward in sifting through the scientific literature

I logged on to Google Scholar a few minutes ago and discovered something very new

This “updates” thing was not there earlier in the day.  So I clicked on the link and got to this page: Scholar Updates: Making New Connections – Google Scholar Blog where James Connor from Google reports

Since Google Scholar launched nearly eight years ago, we’ve been helping people find the research they’re looking for.  But often the spark for discovery comes from making a new connection or looking in a direction that you hadn’t yet considered and that — before your aha! moment — you wouldn’t have known to look for.  Today we hope to start fostering these new connections with Scholar Updates. 

We analyze your articles (as identified in your Scholar profile), scan the entire web looking for new articles relevant to your research, and then show you the most relevant articles when you visit Scholar.  We determine relevance using a statistical model that incorporates what your work is about, the citation graph between articles, the fact that interests can change over time, and the authors you work with and cite.  You don’t need to configure updates or enter any queries.  We’ll notify you about new updates by displaying a preview on the homepage and highlighting a bell icon on search results pages: …

To get article updates relevant to your work, all you need to do is create a public Scholar profile. Article updates will automatically start to appear within a few days. 

Wow.  Completely awesome if it works well.  So, well, let’s see if it works well.  For me the system recommends the following

Evolutionary Diversity of the Mitochondrial Calcium UniporterAG Bick, SE Calvo… – Science, 2012 

REGEN: Ancestral Genome Reconstruction for BacteriaK Yang, LS Heath… – Genes, 2012

Both have some relevance to me.  The first one is about evolution of a gene family and has a line in the abstract that clearly might have driven the automated suggestion: “Here, we characterize the phylogenomic distribution of the uniporter’s membrane-spanning pore subunit (MCU) and regulatory partner (MICU1).” But, well, I am not too interested in this paper.  Not really my thing.

But paper number 2 seems a bit closer to my heart: REGEN: Ancestral Genome Reconstruction for Bacteria.  And bonus – it is freely available.  And so, well, I read over it.  And it is definitely related to what I do and I probably would not have seen it without this notification.  Cool.
So I give Scholar Updates a 1.5 / 2 score which translates to a 7.5 out of 10.  Not bad.  But could be better.  So I clicked on the “See all Updates” link to see what else was there.  And this was a pleasant surprise.  Here is what I got (showing the first page).
50 papers in all with the “Top” selection selected at the top of the page.  And some even come with a comment like Cites A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea or 
The first 25 of the papers are listed below:
  1. Defining the human microbiome
  2. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities
  3. VIROME: a standard operating procedure for analysis of viral metagenome sequences
  4. Complete Genome Sequence of Paenibacillus strain Y4. 12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park
  5. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
  6. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov.
  7. Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.
  8. Complete genome sequence of Pyrobaculum oguniense
  9. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT)
  10. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness
  11. Complete genome sequence of the aromatic-degrading deep-terrestrial-subsurface alphaproteobacterium Novosphingobium aromaticivorans type strain (F199 T), …
  12. Complete genome sequence of Thauera aminoaromatica strain MZ1T
  13. Non-contiguous finished genome sequence and description of Anaerococcus vaginalis
  14. Non-contiguous finished genome sequence and description of Alistipes senegalensis sp. nov.
  15. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton
  16. Predicting kinase-substrate interactions in the era of proteomics
  17. REGEN: Ancestral Genome Reconstruction for Bacteria
  18. Targeted recovery of novel phylogenetic diversity from next-generation sequence data
  19. A call for an international network of genomic observatories (GOs)
  20. Large and linked in scientific publishing
  21. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
  22. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics
  23. Ultrafast clustering algorithms for metagenomic sequence analysis
  24. IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project
  25. Microbiomes
  26. Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan‐Vavilov Deep
  27. Distance-Decay diversity patterns of phyllosphere bacteria on Tamarisk trees across the Sonoran Desert
  28. Exposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure
  29. Reconstruction of Ribosomal RNA Genes from Metagenomic Data
  30. Genome Sequence of the Unclassified Marine Gammaproteobacterium BDW918
  31. Surprising results on phylogenetic tree building methods based on molecular sequences
  32. Road map of the phylum Actinobacteria
  33. Building non-coding RNA families
  34. Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures
  35. Metagenomic microbial community profiling using unique clade-specific marker genes
  36. Unlocking the potential of metagenomics through replicated experimental design
  37. Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem
  38. Minimizing the average distance to a closest leaf in a phylogenetic tree
  39. Parallel-META: efficient metagenomic data analysis based on high-performance computation
  40. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains
  41. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)
  42. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15T
  43. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)
  44. Evolutionary Diversity of the Mitochondrial Calcium Uniporter
  45. Phylogenetic Clustering Reveals Selective Events Driving the Turnover of Bacterial Community in Alpine Tundra Soils
  46. A comparative evaluation of sequence classification programs
  47. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)
  48. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as …
  49. Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4T)
  50. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)
And well, I’ll be damned.  I kind of want to read almost all of them.  Son based on the top 50 I would give Scholar Updates a score of something like 47/50 or 9.4 / 10.  Many have complained about the limited developments in Google Scholar over the years but this is definitely a nice development.  I hope it means Google will be putting more effort into other developments.
Now – off to read some papers.  And if you do not have a Google Scholar page – you should definitely think about making one now as this is how you open up this feature.

———————–
UPDATE 1 8/9 1:45 AM

Just noticed that now in the top of the page when I go to Google Scholar there is also now a link to “Updates”

UPDATE 2: 8/9 10 AM – Some other posts about this

UPDATE 3: 8/9 10 AM – Other stuff from around the web about this

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Silly microbiologist, genomes are for mutualists

New paper in PLoS Genetics of possible interest: PLoS Genetics: Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medica.

The abstract does an OK job with the technical details:

Abstract:
The symbiosis between rhizobial bacteria and legume plants has served as a model for investigating the genetics of nitrogen fixation and the evolution of facultative mutualism. We used deep sequence coverage (>100×) to characterize genomic diversity at the nucleotide level among 12 Sinorhizobium medicae and 32 S. meliloti strains. Although these species are closely related and share host plants, based on the ratio of shared polymorphisms to fixed differences we found that horizontal gene transfer (HGT) between these species was confined almost exclusively to plasmid genes. Three multi-genic regions that show the strongest evidence of HGT harbor genes directly involved in establishing or maintaining the mutualism with host plants. In both species, nucleotide diversity is 1.5–2.5 times greater on the plasmids than chromosomes. Interestingly, nucleotide diversity in S. meliloti but not S. medicae is highly structured along the chromosome – with mean diversity (θπ) on one half of the chromosome five times greater than mean diversity on the other half. Based on the ratio of plasmid to chromosome diversity, this appears to be due to severely reduced diversity on the chromosome half with less diversity, which is consistent with extensive hitchhiking along with a selective sweep. Frequency-spectrum based tests identified 82 genes with a signature of adaptive evolution in one species or another but none of the genes were identified in both species. Based upon available functional information, several genes identified as targets of selection are likely to alter the symbiosis with the host plant, making them attractive targets for further functional characterization.

I think the author summary is a bit more, well, friendly:

Facultative mutualisms are relationships between two species that can live independently, but derive benefits when living together with their mutualistic partners. The facultative mutualism between rhizobial bacteria and legume plants contributes approximately half of all biologically fixed nitrogen, an essential plant nutrient, and is an important source of nitrogen to both natural and agricultural ecosystems. We resequenced the genomes of 44 strains of two closely related species of the genus Sinorhizobium that form facultative mutualisms with the model legme Medicago truncatula. These data provide one of the most complete examinations of genomic diversity segregating within microbial species that are not causative agents of human illness. Our analyses reveal that horizontal gene transfer, a common source of new genes in microbial species, disproportionately affects genes with direct roles in the rhizobia-plant symbiosis. Analyses of nucleotide diversity segregating within each species suggests that strong selection, along with genetic hitchhiking has sharply reduced diversity along an entire chromosome half in S. meliloti. Despite the two species’ ecological similarity, we did not find evidence for selection acting on the same genetic targets. In addition to providing insight into the evolutionary history of rhizobial, this study shows the feasibility and potential power of applying population genomic analyses to microbial species.

I have highlighted the section dissing pathogen studies …

As with every good paper, it starts with a tree

Figure 1. Neighbor-joining trees showing relationships among 32 S. meliloti (blue squares) and 12 S. medicae (red circles). 
A) chromosomes, B) pSymA and pSMED02, and C) pSymB and pSMED01. Trees were constructed using sequences from coding regions only. The length of the branch separating S. medicae from S. meliloti strains is shown at a scale that is 5% of the true scale. The 24-strain S. meliloti group is marked by asterisks. All branches had 100% bootstrap support unless otherwise indicated. Branches with <80% bootstrap support were collapsed into polytomies. An identical tree with strain identifications is provided as Figure S2.

The tree lays out the phylogeny of the strains sequenced in this study.  And it provides the main framework for much of the rest of the paper.  
Some comments:
  • The genomes were sequenced to ~ 100x coverage with on an Illumina GAIIx.
  • Reads were then aligned to reference genomes of close relatives of the sequenced strains.
  • These alignments were then used for various comparative and population genetic analyses
  • As far as I can tell no de novo assemblies were done
  • I am quite confused about their methods for detecting putative regions that have undergone horizontal gene transfer:
    • In the methods: “We identified genes likely to have experienced recent horizontal gene transfer by comparing the ratio of polymorphisms that were shared between species to fixed differences between species. Based on the whole-genome distribution of this ratio (Figure S3) we identified putatively transferred genes as those with a ratio of shared polymorphisms to fixed differences >0.2.”
    • Not sure how/why this should work.  Not saying it is a bad idea – I just don’t really understand it.
  • They also examine various population genetic parameters including possible selection, SNPs, Tajima’s D, and more. 
It is worth a read.  They summarize their various findings with:

Population genetic analyses of nucleotide diversity segregating within Sinorhizobium medicae and S. meliloti have provided unprecedented insight into the evolutionary history of these ecologically important facultative symbionts. While previous analyses have detected evidence for horizontal gene transfer between these species, our data reveal that gene transfer is restricted almost exclusively to plasmid genes and that the plasmid regions that show evidence of transfer have less interspecific divergence than other genomic regions. Interestingly, nucleotide variation segregating within a 24-strain subpopulation of S. meliloti is highly structured along the chromosome, with one half of the chromosome harboring approximately one-fifth as much diversity as the other. The causes of the difference between the two chromosome halves may be a selective sweep coupled with extensive hitchhiking, if this is correct it would suggest that bouts of strong selection may be important in driving the divergence of bacterial species. Finally, we’ve identified genes that bear a signature of having evolved in response to recent positive selection. Functional characterization of these genes will provide insight into the selective forces that drive rhizobial adaptation.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Curiosity on Mars

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–