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Even for the Fast-Melting Arctic, 2016 Is 'Uncharted Territory' - Washington Post

Featured News - Mon, 05/16/2016 - 16:53
One of the best-established ideas about global warming is that it will hit the Arctic the hardest, creating a feedback loop as melting ice leaves more dark ocean to absorb more energy. It's part of a concept called “Arctic amplification." Already this year, the Arctic has exceeded 4 degrees Celsius above average. Chris Mooney discussed the changes with Lamont's Marco Tedesco.

Dumping Iron in the Pacific Ocean Won't Fix Our Climate - Gizmodo

Featured News - Mon, 05/16/2016 - 16:51
Scientists have discovered a major problem with one popular geoengineering scheme that entails dumping iron into the ocean to fuel algae that can soak up carbon dioxide: Basically, the plan is not supported by the geologic record, at least not in the equatorial Pacific. The study was led by Lamont's Gisela Winckler and Robert Anderson.

Phylogenetic placement re-re-visited

Chasing Microbes in Antarctica - Fri, 05/13/2016 - 15:48

Disclaimer: I banged this out fast from existing scripts to help some folks, but haven’t tested it yet.  Will do that shortly, in the meantime, be careful!


I use phylogenetic placement, namely the program pplacer, in a lot of my publications.  It is also a core part of of the paprica metabolic inference pipeline.  As a result I field a lot questions from people trying to integrate pplacer into their own workflows.  Although the Matsen group has done an excellent job with documentation for pplacer, guppy, and taxtastic, the three programs you need to work with to do phylogenetic placement from start to finish (see also EPA), there is still a steep learning curve for new users.  In the hope of bringing the angle of that curve down a notch or two, and updating my previous posts on the subject (here and here), here is a complete, start to finish example of phylogenetic placement, using 16S rRNA gene sequences corresponding to the new tree of life recently published by Hug et al.  To follow along with the tutorial start by downloading the sequences here.

You can use any number of alignment and tree building programs to create a reference tree for phylogenetic placement.  I strongly recommend using RAxML and Infernal.  After a lot of experimentation this combination seems to be produce the most correct topologies and best supported trees.  You should be aware that no 16S rRNA gene tree (or any other tree) is absolutely “correct” for domain-level let alone life-level analyses, but nothing in life is perfect.  While you’re installing software I also recommend the excellent utility Seqmagick.  Finally, you will need a covariance model of the 16S rRNA gene to feed into Infernal.  You can find that at the Rfam database here.

The workflow will follow these steps:

  1. Create an alignment of the reference sequences with Infernal
  2. Create a phylogenetic tree of the alignment
  3. Create a reference package from the alignment, tree, and stats file
  4. Proceed with the phylogenetic placement of your query reads

Create an alignment of the reference sequences

The very first thing that you need to do is clean your sequence names of any wonky punctuation.  This is something that trips up almost everyone.  You should really have no punctuation in the names beyond “_”, and no spaces!

tr " -" "_" < hug_tol.fasta | tr -d "%\,;():=.\\*[]\"\'" > hug_tol.clean.fasta

Next create an alignment from the cleaned file.  I always like to degap first, although it shouldn’t matter.

## Degap seqmagick mogrify --ungap hug_tol.clean.fasta ## Align cmalign --dna -o hug_tol.clean.align.sto --outformat Pfam hug_tol.clean.fasta ## Convert to fasta format seqmagick convert hug_tol.clean.align.sto hug_tol.clean.align.fasta

Build the reference tree

At this point you should have a nice clean DNA alignment in the fasta format.  Now feed it to RAxML to build a tree.  Depending on the size of the alignment this can take a little bit.  I know you’ve read the entire RAxML manual so of course you are already aware that adding additional cpus won’t help…

raxmlHPC-PTHREADS-AVX2 -T 8 -m GTRGAMMA -s hug_tol.clean.align.fasta -n ref.tre -f d -p 12345

I like having a sensibly rooted tree; it’s just more pleasing to look at.  You can do this manually, or you can have RAxML try to root the tree for you.

raxmlHPC-PTHREADS-AVX2 -T 2 -m GTRGAMMA -f I -t RAxML_bestTree.ref.tre -n root.ref.tre

Okay, now comes the tricky bit.  Clearly you’d like to have some support values on your reference tree, but the Taxtastic program that we will use to build the reference tree won’t be able to read the RAxML stats file if it includes confidence values.  The work around is to build a second tree with confidence values.  You will feed this tree to Taxtastic with the stats file from the tree we already generated.

## Generate confidence scores for tree raxmlHPC-PTHREADS-AVX2 -T 8 -m GTRGAMMA -f J -p 12345 -t RAxML_rootedTree.root.ref.tre -n conf.root.ref.tre -s hug_tol.clean.align.fasta

Now we can use the alignment, the rooted tree with confidence scores, and the stats file without confidence scores to create our reference package.

taxit create -l 16S_rRNA -P hug_tol.refpkg --aln-fasta hug_tol.clean.align.fasta --tree-stats RAxML_info.ref.tre --tree-file RAxML_fastTreeSH_Support.conf.root.ref.tre

Align the query reads

At this point you have the reference package and you can proceed with analyzing some query reads!  The first step is to align the query reads in exactly the same fashion as the reference sequences.  This is important as the alignments will be merged later.

## Clean the names tr " -" "_" < query.fasta | tr -d "%\,;():=.\\*[]\"\'" > query.clean.fasta ## Remove any gaps seqmagick mogrify --ungap ## Align cmalign --dna -o query.clean.align.sto --outformat Pfam query.clean.fasta

Now we use the esl-alimerge command, included with Infernal, to merge the query and reference alignments.

## Merge alignments esl-alimerge --outformat pfam --dna -o query.hug_tol.clean.align.sto query.clean.align.sto hug_tol.refpkg/hug_tol.clean.align.sto ## Convert to fasta seqmagick convert query.hug_tol.clean.align.sto

Phylogenetic placement

Now we’re on the home stretch, we can execute the phylogenetic placement itself!  The flags are important here, so it’s worth checking the pplacer documentation to insure that your goals are consistent with mine (get a job, publish some papers?).  You can probably accept most of the flags for the previous commands as is.

pplacer -o query.hug_tol.clean.align.jplace -p --keep-at-most 20 -c hug_tol.refpkg query.hug_tol.clean.align.fasta

At this point you have a file named query.hug_tol.clean.align.jplace.  You will need to use guppy to convert this json-format file to information that is readable by human.  The two most useful guppy commands (in my experience) for a basic look at your data are:

## Generate an easily parsed csv file of placements, with only a single placement reported for each ## query read. guppy to_csv --point-mass --pp -o query.hug_tol.clean.align.csv query.hug_tol.clean.align.jplace ## Generate a phyloxml tree with edges fattened according to the number of placements. guppy fat --node-numbers --point-mass --pp -o query.hug_tol.clean.align.phyloxml query.hug_tol.clean.align.jplace

New Mercury Maps Showcase Planet's Striking Features -

Featured News - Mon, 05/09/2016 - 12:00
The first global digital-elevation model of Mercury reveals a striking landscape of basins and lava plains. Lamont Director Sean Solomon was principal investigator on the MESSENGER mission and discussed the data MESSENGER captured.

Slow-Motion Earthquakes May Also Lead to Tsunamis - Business Standard

Featured News - Fri, 05/06/2016 - 10:26
Slow-motion earthquakes or "slow-slip events" can rupture the shallow portion of a fault that also moves in large, tsunami-generating earthquakes. A new study involving Lamont's Spahr Webb examines a slow-slip event off New Zealand.

Maureen Raymo Elected to National Academy of Sciences - National Academy of Sciences

Featured News - Tue, 05/03/2016 - 16:21
Marine geologist and paleoceanographer Maureen Raymo was among 84 scientists elected for membership in the National Academy of Sciences, one of the highest honors awarded to engineers and scientists in the United States.

Inside West Virginia's Battle Over Teaching Climate Change - Climate Wire

Featured News - Fri, 04/29/2016 - 12:00
In a coal state struggling with environmental regulations and a fiscal crisis, teaching climate science has hit a nerve. Climate Wire spoke with Lamont Special Research Scientist Kim Kastens.

No Way the Great Barrier Reef Was Bleached Naturally - Washington Post

Featured News - Fri, 04/29/2016 - 11:20
Climate change dramatically upped the odds of severe coral bleaching of the Great Barrier Reef, researchers say. Lamont's Adam Sobel discussed the findings with the Washington Post.

Video: Peter deMenocal on Why Climate Matters - Talks@Columbia

Featured News - Thu, 04/28/2016 - 17:22
Climate change is one of the most complex and difficult challenges facing the world, and one of the most divisive. In this video, Lamont's Peter deMenocal discusses how climate is changing today and why.

Robotic Laboratories Fan Out to Study the Seas - Scientific American

Featured News - Thu, 04/28/2016 - 17:15
"They look like R2-D2 in swim floaties, but they could revolutionize ocean science." Lamont's Kyle Frischkorn writes about the new wave of marine robots.

Killer Landslides: The Lasting Legacy of the Nepal Earthquake - Scientific American

Featured News - Mon, 04/25/2016 - 12:33
A year after a devastating earthquake triggered killer avalanches and rock falls in Nepal, scientists are wiring up mountainsides to forecast hazards. Scientific American talks with Lamont's Colin Stark.

New York City Leads Investment in Climate Change Preparation - CCTV

Featured News - Fri, 04/22/2016 - 12:00
CCTV talked with Lamont's Klaus Jacob about how New York City is bracing for the effects of climate change and whether it is doing enough.

What Is the Climate Innovation Gap? - PBS SciTech Now

Featured News - Thu, 04/21/2016 - 12:00
Over the last decade, federal spending on research and development as a percentage of our country’s GDP has been declining. PBS SciTech Now talks with Lamont's Peter deMenocal.

Fate of World's Coasts Rests on Melting Ice - Scientific American

Featured News - Thu, 04/21/2016 - 12:00
Lamont's Maureen Raymo talks about the value of determining the heights of prehistoric shorelines for projecting future sea level rise.

This Is How Surfers Are Helping Fund Climate Science - Climate Central

Featured News - Wed, 04/20/2016 - 12:00
The World Surf League has created a unique partnership with climate scientists at Lamont that could help the sport, the ocean and spur a new research model.

The Mad Dash to Figure Out the Fate of Peatlands - Smithsonian Magazine

Featured News - Wed, 04/20/2016 - 12:00
As the planet’s peat swamps come under threat, the destiny of their stored carbon remains a mystery. Lamont's Jonathan Nichols takes the Smithsonian on a tour of the challenge.

Ice a Surprising Heat Source on Jupiter's Europa - Cosmos Magazine

Featured News - Mon, 04/18/2016 - 16:44
Constant gravitational pressures on the icy surface of Jupiter’s moon Europa generate much more heat than previously thought, which may force a rethink about the chemistry of the liquid water ocean below the surface, says Lamont's Christine McCarthy.

Di che colore è la Groenlandia? - La Repubblica

Featured News - Sun, 04/17/2016 - 12:00
In a column appearing in Italy's La Repubblica, Lamont's Marco Tedesco discusses the darkening of Greenland and how that contributes to a cycle of melting. The column is written in Italian.

What Loss of Snowpack Means for Water Supplies - The Desert Sun

Featured News - Thu, 04/14/2016 - 10:30
Global warming will require big changes in how we management water, the Desert Sun writes. “In general, what a measure like this is telling us is that our historical reliance on snow is untenable in a future climate," said Lamont's Justin Mankin.

It’s April, and Scientists Are Already Stunned by Greenland’s Melting - Washington Post

Featured News - Wed, 04/13/2016 - 09:11
The vast Greenland ice sheet is seeing a record-breaking level of melt for so early in the season. “The potential implications, in terms of runoff and so on, they alter the memory of the snowpack, the potential implications can be big either for the same season or future seasons,” said Lamont's Marco Tedesco.



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