"Phylogeny driven approaches to genomics and metagenomics": slides w/ audio from my talk at #UCDavis 1/29

Gave a talk here at UC Davis last week. Alas, not my best talk - too rushed. But, anyway, here is a video of the slideshow w/ audio. Title "Phylogeny driven approaches to genomics and metagenomics"

 

Worth a look: PhyloFacts FAT-CAT web server: ortholog identification & function prediction

Quick post.  This seems like a potentially useful resource and tool: The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

Abstract:
The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.

Sign up: SMBE Satellite Mtg. on Eukaryotic-Omics 4/29-5/2 at #UCDavis

Going to be good:

Eukaryotes | SMBE Satellite Meeting on Eukaryotic -Omics - April 29 to May 2, UC Davis Conference Center

No bias here - given that it is organized by Holly Bik in my lab and it is at UC Davis. The lineup of speakers is great and the topic is timely.  So sign up  ...

Speakers:

Rachel Adams	UC Berkeley	Groundtruthing next-gen sequencing for microbial ecology: is beta diversity robust to errors in pyrosequencing?
Nicholas A. Bokulich	UC Davis	Regional Patterns in Grape Fungal Consortia Define Wine Fermentation Communities
Sara Branco	UC Berkeley	Fungi at a small-scale: spatial zonation of fungal assemblages around single trees
C. Titus Brown	Michigan State University	Sequencing and assembly of diverse eukaryotes: like metagenomics, but much harder
Peter Countway	Bigelow Laboratory for Ocean Sciences	Title TBA
Simon Creer	Bangor University, Wales	Title TBA
Tom Delmont	Marine Biological Laboratory, Woods Hole	Phaeocystis antarctica spatiotemporal diversity, activity and its relation to prokaryotes and viruses using physiological and ‘omic approaches
Jonathan Eisen	UC Davis	The need for a phylogeny driven genomic encyclopedia of eukaryotes
Laura Eme	Dalhousie University	Large scale phylogenomic analyses of Blastocystis subtype 1 reveals a major role for lateral gene transfer in adaptation to parasitism of the human gut
Jack Gilbert	Argonne National Lab	Addressing microbial eukaryotic biogeography in home, hospitals and the world
Jean-David Grattepanche	Smith College	Title TBA
Victor Hanson-Smith	UC San Francisco	Identifying Loci of Functional Evolution in Ancestral Genes
Ian King	University of Guelph	Biomonitoring 2.0: A high-throughput genomics approach for comprehensive biological assessment of environmental change
Andrew Krohn	Northern Arizona University	Rhizosphere microbial community dynamics of drought-stressed pinyon pines (Poster)
Franck Lejzerowicz	University of Geneva	Exploring the deep-sea foraminiferal diversity by multiplexed RNA and DNA-based ultra-deep sequencing and ultra-fast bioinformatic analyses
Matthew Morgan	CSIRO Australia	Next-generation sequencing reveals the impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils
Laura Wegener Parfrey	University of Colorado, Boulder	Incorporating microbial eukaryotes into analyses of the human microbiome
Katherine Pollard	UC San Francisco	Title TBA
Dorota Porazinska	University of Florida	Discrimination of microscopic pests of agricultural importance with NGS
Thomas Richards	NHM London	Title TBA
Surya Saha	Cornell University	Composition of the Maize Endophytic Microbiome is Correlated with Maize Genotype (Poster)
Søren Sørensen	University of Copenhagen	Title TBA
Fabian Staubach	Stanford University	Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment
Sarah Stephenson	CSIRO Australia	Metagenetic examinations of benthic eukaryl estuarine communities
Joshua Stern	Georgia Institute of Technology	Searching for the Phylogenetic Place of Eukaryotes, Using Data from STORI
W. Kelley Thomas	University of New Hampshire	Title TBA
Xianfa Xie	Virginia State University	Comparative genomic study of the origin and evolution of eukaryotes

Guest post from Kimmen Sjölander about FAT-CAT phylogenomics pipeline

Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru. 

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Announcing the FAT-CAT phylogenomic annotation webserver.

FAT-CAT is a new web server for phylogenomic prediction of function and ortholog identification and for taxonomic origin prediction of metagenome sequences based on HMM-based classification of protein sequences to >93K pre-calculated phylogenetic trees in the PhyloFacts database. PhyloFacts is unique among phylogenomic databases in having both broad taxonomic coverage – more than 7.3M proteins from >99K unique taxa across the Tree of Life, including targeted coverage of genomes from Eukaryotes, Bacteria and Archaea -- and integrating functional data on trees for Pfam domains and multi-domain architectures. PhyloFacts trees include functional and annotation data from UniProt (SwissProt and TrEMBL), GO, BioCyc, Pfam, Enzyme Commission and other sources. The FAT-CAT pipeline uses HMMs at all nodes in PhyloFacts trees to classify user sequences to different levels of functional hierarchies, based on the subtree HMM giving the sequence the strongest score. Phylogenetic placements within orthology groups defined on PhyloFacts trees are used to to predict function and to predict orthologs. Sequences from metagenome projects can be classified taxonomically based on the MRCA of the sequences descending from the top-scoring subtree node. Because of the broad taxonomic and functional coverage, FAT-CAT can identify orthologs and predict function for most sequence inputs. We’re working to make FAT-CAT less computationally intensive so that users will be able to upload entire genomes for analysis; in the interim, we limit users to 20 sequence inputs per day. Registered users are given a higher quota (see details online). We’d love to hear from you if you have feature requests or bug reports; please send any to Kimmen Sjölander – kimmen at berkeley dot edu (parse appropriately). 

FAT-CAT is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.

Worth a read: Jim Staley on a "Universal Species Concept" and the history of microbial species concepts

Interesting paper came up in my automated google searches for "phylogenomics": Transitioning Toward a Universal Species Concept for the Classification of all Organisms | InTechOpen.  It is by Jim Staley who has been writing a lot about microbial species concepts in the last few years.  In addition to trying to bridge the gap between bacteria/archaea and eukaryotes in terms of species concepts.  Not sure how I feel about everything in the paper but it has a really nice history of how species have been defined for bacteria. He breaks down this history into four periods

• Discovery of microorganisms,
• Advent of pure cultures and phenotypic features,
• Introduction of molecular analyses and
• Gene sequencing and genomics.

And goes through a bit of detail on each one.  He also discusses what he sees as a need for a universal species concept and even makes some suggestions about how it might be implemented.  Definitely worth a read.  

Some related posts of mine and or links of potential interest:

• Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet
• Worth a look (from arXiv): Robust estimation of microbial diversity in theory and in practice
• Mendeley collection on number of species of bacteria and archaea

Slides and slideshow w/ audio from my talk at Bay Area Illumina User's Meeting

Just quick post ... gave a talk Thursday at the Bay Area Illumina User's meeting.  I have posted my slides to Slideshare and a Video Slideshow with audio to Youtube.

"Phylogenomic approaches to microbial diversity" Talk by Jonathan Eisen at #IlluminaBayArea meeting from Jonathan Eisen

Three talks, 1.5 days at #ISMB ... phylogeny, phylogenomics, open science and more

Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the "Intelligent Systems for Molecular Biology" (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three very different talks in 1.5 days. But for now I wanted to at least get my talks posted here since I posted the slides to slideshare and recorded the audio in synch with the slides and posted these "slideshows" to YouTube. Here are the talks below:

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Talk 1 for the "Bioinformatics Open Source Conference" BOSC2012.  Was asked to talk about Open Science ... so ... I did ...

Slides: Jonathan Eisen talk on "Open Science" at #BOSC2012 #ISMB

View more presentations from Jonathan Eisen

Slideshow with audio:
 

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Talk 2 for the Student Council Symposium SCS2012. Sort of supposed to be a career guidance discussion so I geared my talk on the lines of "lessons learned" ...

Slides:Jonathan Eisen talk for #SCS2012 at #ISMB "Networks in genomics and bioinformatics: from phylogeny to Twitter"

View more presentations from Jonathan Eisen

Slideshow with audio:

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Talk 3 for the "Automated function prediction" AFP2012 satellite meeting.  I decided to talk about phylogenetic and phylogenomics approaches to functional prediction ...

Slides:Jonathan Eisen talk "Phylogneomic approaches to functional prediction"a #AFP2012 #ISMB

View more presentations from Jonathan Eisen

Slideshow with audio:

The Axis of Evol: Getting to the Root of DNA Repair with Philogeny

The Axis of Evol: Getting to the Root of DNA Repair with Philogeny 

In 2005 I wrote an essay about my time in graduate school that was potentially going to be included in a special issue of Mutation Research in honor of my PhD advisor Phil Hanawalt.  Alas, publishing my essay ran into complications in regard to the closed access policies of this journal.  So in the end, my essay was not published.  I had forgotten about it mostly until very recently.  And so I decided to convert the essay to a blog post.  The essay is sort of about what I did in grad. school and sort of about Phil ...

Abstract:

Phylogenomics is a field in which genome analysis and evolutionary reconstructions are integrated. This integration is important because genome data is of great value in evolutionary reconstructions, because evolutionary analysis is critical for understanding and interpreting genomic data, and because there are feedback loops between evolutionary and genome analysis such that they need to be done in an integrated manner. In this paper I describe how I developed my particular phylogenomic approach under the guidance of my Ph.D advisor Philip C. Hanawalt. Since I was the first to use the term phylogenomics in a publication, I have decided to rename the field (at least temporarily) Philogenomics.

1. Doctor of Philosophy

When I went to Stanford for graduate school, I was interested in combining evolutionary analysis and molecular biology in a way that would allow me to study molecular mechanisms through an evolutionary perspective. Although I had gone to Stanford ostensibly to work on butterfly population genetics, within two days of starting a rotation in Phil’s lab, I knew that that was where I wanted to work. This decision was somewhat traumatic, since the work on butterflies included spending the summers at 10,000 feet in the Rocky Mountains and possibly chasing butterflies like a Nabakov wanna-be all over the mountain ranges of the world. As an avid outdoor person, this was quite appealing. Nevertheless, I chose to spend 99% of my graduate work in the dingy confines of Herrin Hall, studying DNA repair. The choice of joining Phil’s lab did have one very positive affect – and that was on my relationship with my grandfather on my mother’s side. Benjamin Post was in many ways like a father to me, especially after my father passed away. He was a physicist from the “old school” and thought that most of biology was completely useless. Needless to say, when I told him I was going to graduate school in California (which he considered already one strike against me) to study butterflies, he decided I was simply a lost cause. Despite all his talk of Einstein and computers and math when I was a child, I might as well have been a poet from his point of view. To make matters worse, my grandfather was a crystallographer, and my brother was getting his Ph.D in crystallography at Harvard. When I informed my grandfather that I was going to be working on DNA repair, he seemed somewhat interested. And then I told him, my advisor, Phil Hanawalt, is relatively well known, and actually used to be considered a biophysicist. Then my grandfather really perked up. He said, “Hanawalt – is he related to Don Hanawalt?” It turns out, that my grandfather worked in the same field as Phil’s father (they both did powder diffraction) and knew him. So my grandfather said “You may not be doing real science, but at least you are doing it with the relative of a real scientist.” Thankfully, I was no longer the black sheep in the family. So, with my grandfather’s approval, I embarked on a career in DNA repair.

New openaccess paper from my lab on "Zorro" software for automated masking of sequence alignments

A new Open Access paper from my lab was just published in PLoS One: Accounting For Alignment Uncertainty in Phylogenomics. Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone.0030288

The paper describes the software "Zorro" which is used for automated "masking" of sequence alignments.  Basically, if you have a multiple sequence alignment you would like to use to infer a phylogenetic tree, in some cases it is desirable to block out regions of the alignment that are not reliable.  This blocking is called "masking."

Masking is thought by many to be important because sequence alignments are in essence a hypothesis about the common ancestry of specific residues in different genes/proteins/regions of the genome.  This "positional homology" is not always easy to assign and for regions where positional homology is ambiguous it may be better to ignore such regions when inferring phylogenetic trees from alignments.

Historically, masking has been done by hand/eye looking for columns in a multiple sequence alignment that seem to have issues and then either eliminating those columns or giving them a lower weight and using a weighting scheme in the phylogenetic analysis.

What Zorro does is it removes much of the subjectivity of this process and generates automated masking patterns for sequence alignments.  It does this by assigning confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

The software is available at Sourceforge: ZORRO – probabilistic masking for phylogenetics.  It was written primarily by Martin Wu (who is now a Professor at the University of Virginia) and Sourav Chatterji with a little help here and there from Aaron Darling I think.  The development of Zorro was part of my "iSEEM" project that was supported by the Gordon and Betty Moore Foundation.

In the interest of sharing, since the paper is fully open access, I am posting it here below the fold. UPDATE 2/9 - decided to remove this since it got in the way of getting to the comments ...

Draft post cleanup #21: Tracking progress on the vertebrate tree of life

Yet another post in my "draft blog post cleanup" series. Here is #21; from March 2010:

A very interesting paper came out recently from colleagues of mine at UC Davis:  Rapid progress on the vertebrate tree of life.  I did not know they were working on this but perhaps should have.  It has some fun/interesting analysis of the accumulation of phylogenetic knowledge over time.  For example see Figure 1

Cumulative phylogenetic information amassed for the last 16 years. The accumulation of sequences for vertebrates in GenBank (a), papers using the term 'phylogeny' or 'phylogenetics' in the Web of Science database (b) and phylogenetic resolution (measured as the proportion of nodes with at least 50% bootstrap support) in the vertebrate tree of life resulting from these research efforts (c). In all cases, the data are cumulative from the start of each analysis. Phylogenetic resolution is calculated as in Table 1. Trend lines are exponential in (a), and second order polynomial in (b) and (c).

Very nice new #PLoSGenetics paper on "Functional Phylogenomics" of Seed Plants

Update2 - 12/22 - Data available here.  Thanks to the authors for clearing things up quickly.

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Update1 -  12/19 - Data for this paper seems to be unavailable - not sure why - but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there.  Note - this is one reason that all data sets should be made available at the journal or third party sites.

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Original post:

OK never mind that the terminology of "functional phylogenomics" is a tiny bit vexing to me (long story - some other time perhaps). The paper behind it - PLoS Genetics: A Functional Phylogenomic View of the Seed Plants is very cool.

Here's what the authors did (a very coarse summary)

1. Identified sets of orthologs between plant species using the OrthologID system (which has a phylogenetic underpinning) (the data input for this appeared to have mostly been Unigene EST clusters)

Special Guest Post & Discussion Invitation from Matthew Hahn on Ortholog Conjecture Paper

I am very excited about today's post.  It is the first in what I hope will be many - posts from authors of interesting papers describing the "Story behind the paper".  I write extensive detailed posts about my papers and also have tried to interview others about their papers if they are relevant to this blog.  But Matthew Hahn approached me recently about the possibility of him writing up some details on his recent paper on the functions of orthologs vs. paralogs.  So I said "sure" and set up a guest account for him to write up his comments and details of the paper.  


For those of you who do not know, Matt is on the faculty at U. Indiana.  He was a post doc at UC Davis so I have a particular bias in favor of him.  But his recent paper has generated some controversy (I posted some links about it here).  So it is great to get some more detail from him.  In addition, I note, I am also using this approach to try and teach people how easy it is to write a blog post by getting them guest accounts on Blogger and letting them write up something with links, pictures, etc.  So hopefully we can get more scientists blogging too.


Anyway - without any further ado - here is Matt's post:

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Following Jonathan’s excellent example of how explaining the history of a project helps to illuminate how the process of science actually happens, I thought I’d start by giving a bit of history behind our study, and the paper that we recently published in PLoS Computational Biology (http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002073). And then I’ll address the critics…

How this all got started

It all started a bit more than three years ago, in the summer of 2008. Pedja (as Predrag Radivojac is known to friends) was giving a talk to a group of us on protein function prediction that he also presented as a tutorial at the Automated Function Prediction SIG at ISMB 2008. Pedja and I had already collaborated on a small project involving the evolution of phosphoryation sites, but I really had no idea about his work on function prediction, and little idea in general about how function prediction was done. Reviewing different ways to accomplish transfer-by-similarity, he eventually got around to evolutionary (phylogenomic) approaches. Here is what I remember of this specific exchange during his talk:

More on 'phylogenomics' - as in functional prediction w/ phylogeny

There is a new paper out: Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium in Briefings in Bioinformatics.

The paper is interesting and presents a new general approach to using phylogeny for functional prediction of uncharacterized genes. I am interested in this for many reasons including that I was one of, if not the first to lay this out as a concept.  In a series of papers from 1995-1998 I outlined how phylogenetic analysis could be used to aid in functional prediction for all the genes that were starting to be sequenced in genome projects without any associated functional studies (at the time, I referred to all these ESTs and other sequences as an "onslaught" - little did I know what was to come).

My first paper on this topic was in 1995: Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions.  The abstract is below:

The SNF2 family of proteins includes representatives from a variety of species with roles in cellular processes such as transcriptional regulation (e.g. MOT1, SNF2 and BRM), maintenance of chromosome stability during mitosis (e.g. lodestar) and various aspects of processing of DNA damage, including nucleotide excision repair (e.g. RAD16 and ERCC6), recombinational pathways (e.g. RAD54) and post-replication daughter strand gap repair (e.g. RAD5). This family also includes many proteins with no known function. To better characterize this family of proteins we have used molecular phylogenetic techniques to infer evolutionary relationships among the family members. We have divided the SNF2 family into multiple subfamilies, each of which represents what we propose to be a functionally and evolutionarily distinct group. We have then used the subfamily structure to predict the functions of some of the uncharacterized proteins in the SNF2 family. We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family.

Some links on "ortholog conjecture" paper and critiques of it

Recently a paper by Matt Hahn was published in PLoS Computational Biology entitled "Testing the ortholog conjecture with comparative functional genomic data from mammals."  The paper created a bit of a stir as some aspects of it call into question some of the standard assumptions made in comparative genomic analysis.

I alas do not have time to go into all the details but fortunately others have tackled this and I am posting some links here:

• Comments at Faculty of 1000 (currently available for free but not sure for how long).
• Of mice and men and meta analyses (Richard Grant discussing Michael Galperin's F1000 dissent)
• The 'Ortholog Conjecture' | The Daily Scan | GenomeWeb
• Of Mice and Men or: Revisiting the Ortholog Conjecture (Iddo Friedberg)
• Friendfeed discussion: http://friendfeed.com/erickma... (see below)

Nice review/commentary on challenges in phylogenomic analysis in PLoS Bio by Philippe et al. #fb

This one is definitely worth a read for phylogeneticists and phylogenomicists (is that a word?) out there: PLoS Biology: Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. Philippe et al. discuss some important issues in using genomes to infer phylogenies of species in this commentary/review paper.  They discuss in particular some recent studies of animal evolution but they cover a lot of useful ground here and include a good review of terminology and some of the basic issues at play.  I am personally going to have to read it in more detail to help deal with some of the issues in our recent study of novel sequences in metagenomic data.

Larry Moran on Phylogenomics, my new paper, and species

Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.

ASM Phylogenomics Notes

Well, I just gave my talk on phylogenomic and functional predictions and am going to try and catch up with blogging.

In my talk I discussed how an understanding of function and prediction of function requires an understanding of how functions have evolved.  I am trying to get my talk slides posted here but, alas, I need to deal with some Copyright issues first (OK - here is a little slideshow of my talk ... no audio sorry)

Patricia Babbitt gave a talk after mine on another aspect of phylogenomics and functional predictions.  She has done some really interesting studies (see her lab site here) of functional diversifications and the molecular level by integrating genomic, structural, biochemical and phylogenetic analyses.  She showed some really nice tools for clustering and visualization protein families that, although not phylogenetic, seemed to be very useful for the onslaught of genome data.  Unfortunately, most of her publications are not in OA journals so I cannot use any of the figures here and am not going to bother linking to the papers.

Kimmen Sjolander is talking now about her phylogenomic studies.  She is discussion "Phylofacts" which are precomputer phylogenetic trees of gene families from across the tree of life.  One great thing about her work - most of it is published in OA journals and most of her software is available for free download.

More detail on Phylofacts is available in her Genome Biology paper here.  Kimmen has done some really great work on automating phylogenomic functional predictions and this is one example.  Also see her Flower Power and Sci-Phy and Satchmo and Intrepid and Phylo builder other tools (downlaods and other information are available at her website here.)

Gretta Serres will be speaking next.  I will post on here talk soon ...  And now I am posting on it ...

She is discussing "linking metabolic diversity to protein families" os something to that effect. She discussed something I never have thought of doing which is the following - take genomes, identify the size of protein families in each genome and then cluster genomes by their similarity of the protein family size.  I assume some others must have done this but it seems like a good way to identify similar duplication pressures on distantly related organisms.  

Fear and Loathing in Boston for the ASM Meeting

OK

Here is my confession.  I hate,  I mean hate, big meetings.  If a conference has more than 200 people I start to feel icky.  And now this AM I head off to Boston for the gigantic ASM "General Meeting".  I am in part dreading the whole thing.  Anytime one needs to use an online planner to schedule which talks one might want to go to, it is not really my kind of meeting.

But, I was invited to give the "Division R" lecture.  Division R is the "Systematics and Evolutionary Microbiology" section of ASM and this year they are having a session on "Linking evolution of protein families to genome annotation efforts."  This is right up my alley as it was for genome annotation that I first started working on phylogenomic methods (and for which I coined the phrase "phylogenomics") (e.g., see my 1998 paper in Genome Research for more detail on this and see my 1995 paper on SNF2 proteins in NAR where I first discussed using evolutionary trees to predict gene function).

And since the meeting is in Boston (where I was born), I agreed to go.  Add I am sure I will see some great things there.  But travel and I do not agree well right now and I am I guess dreading the whole thing.  If you want to learn more about phylogenomics go to the division R session (Kimmen Sjolander, Patricvia Babbitt, and Margrethe Serres are also talking). And I will try to blog from the meeting but we shall see ...

Oakley Keeping his Eye on Evolution

I saw an interesting talk today and thought I would post on it. I was not expecting to be able to go to the talk as I was supposed to be at a workshop in San Francisco but had to bail on it because my kids have been sick. But I did go in to Davis for a brief spell to go to a seminar by Todd Oakley who gave a talk here today.

It was a generally insightful phylogenomic tour of the evolution of opsins and eyes in animals. He also mentioned a paper he had recently in PLoS One on Animal Opsin evolution. This is from the work of his graduate student David Plachetzki and it does a nice job of doing "phylogenomic" analysis in the way I think of phylogenomics -- that is -- a integration of evolutionary and genomic analyses. (NOTE - I think it is kind of lame that people use the term phylogenomics, which I coined by the way, to refer to "using genomes to infer evolutionary trees). It is a paper worth checking out if you are interested in the origin of novelty.

I am putting links here to some of their figures and embedding them in this blog because, well, I can since PLoS One uses a broad Creative Commons license. For example - see Figure 6 from their paper below (the citation is Plachetzki DC, Degnan BM, Oakley TH (2007) The Origins of Novel Protein Interactions during Animal Opsin Evolution. PLoS ONE 2(10): e1054. doi:10.1371/journal.pone.000105).

Figure 6. Ancestral state reconstruction of G protein-binding interactions for each metazoan opsin-mediated phototransduction cascade obtained by simulated mutational mapping [64] (see methods).For each class of opsin, the P value of the reconstructed ancestral G α interactions is represented in pie graphs. Ancestral G protein interactions in phototransduction cascades mediated by ciliary, rhabdomeric and G_o opsins can be significantly resolved (P>0.95) but the ancestral states of the rhabdomeric+G_o, and cnidops clades are equivocal. ML state reconstructions shown for each node as colored branches. Red, G_i/t; Blue, G_q; Green, G_o; Black, no G protein interaction (as is the case for RGR/Retinochrome opsins); Grey, equivocal reconstruction from ML. Reconstructed ancestral amino acid motifs of the 4th cytoplasmic loop region of opsin are shown along branches in logos. Maximum vertical height scales to P = 1.0. We obtained clear reconstructed states for most of the residues in a conserved tripeptide motif (residues 310, 311 and 312, horizontal bar) for the ciliary, rhabdomeric and G_o /RGR nodes. For the most part, the remainder of the residues in can be unequivocally reconstructed to the level of Dayhoff classes. B = HRK, X = LIVM, J = GATSP, Z = DENQ..

























See also Figure 2

"Figure 2. Unrooted metazoan-wide phylogeny of opsins, new cnidarian genes in bold, branches proportional to substitutions per site. Circles at nodes indicate Bayesian posterior probabilities (White = 1.0, Red>0.90, Blue>0.80, Green>0.70, Yellow>0.60, Black>0.50). cil = ciliary, rh = rhabdomeric."

Phylogenomics makes the big time --- University of Manitoba seeking a "Chair" in Phylogenomics

Now I know Phylogenomics has hit the big time.

University of Manitoba is looking for a chair in the emerging area of phylogenomics. See below. PS - Good job phylogenomics. You have made it.


From their ad:

UNIVERSITY OF MANITOBA – CANADA RESARCH CHAIR – TIER II
Phylogenomics Chair, Department of Biological Sciences, Faculty of Science
Position # 06661 and 06662

The University of Manitoba is seeking applications or nominations for a Canada Research Chair established by the Government of Canada to enable Canadian Universities to foster world-class research excellence (http://www.chairs.gc.ca). Our Strategic Research Plan (http://www.umanitoba.ca/admin/vp_research/research_chairs.html) identifies a Tier II Chair in the Faculty of Science in the area of Phylogenomics as a priority.

The emerging field of Phylogenomics uses an exciting comparative approach to research that integrates the study of the evolution of species using genomic data and the study of genome function using phylogenetic data, and can powerfully inform a broad spectrum of biological research