Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru.
Announcing the FAT-CAT phylogenomic annotation webserver.
Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru.
Announcing the FAT-CAT phylogenomic annotation webserver.
Nice commentary / viewpoint piece in PLOS Biology last months: PLOS Biology: Evolutionary Biology for the 21st Century
Citation.Jonathan Losos, Stevan J. Arnold, Gill Bejerano, E. D. Brodie III, David Hibbett, Hopi E. Hoekstra, David P. Mindell, Antónia Monteiro, Craig Moritz, H. Allen Orr, Dmitri A. Petrov, Susanne S. Renner, Robert E. Ricklefs, Pamela S. Soltis, Thomas L. Turner (2013) Evolutionary Biology for the 21st Century. PLoS Biol 11(1): e1001466. doi:10.1371/journal.pbio.1001466
They discuss issues like Biodiversity Informatics (see Figure to the left) and evolutionary applications like evolutionary medicine, food production, sustaining biodiversity, computational algorithms, and justice. They also discuss issues like the oncoming onslaught of specimens and the need to link up with museums who have expertise in dealing with such issues. Anyway – it is worth a look. Not the most visionary of pieces ever but it has some concrete suggestions and predictions that will be of use.
A few years ago I used to post many things for the Web through Apple’s Mobile Me service. Annoyingly, Apple ended up treating this like they treat connectors and plugs for their phones and Macs. They just decided to move their online system to iCloud and deleted all the old websites through Mobile Me. Which left me in a lurch. And then I forgot about it. But I have been rediscovering how annoying this is since I had a lot of information out there on old papers and projects and now it is gone from the interwebs. So I have ben trying to re-share all of this stuff.
One way has ben to post data from old papers to Figshare. See for example:
But I also had all sorts of website related material that is annoyingly gone. And yesterday I discovered at least a simple solution to this. I can put all my old websites in my Dropbox public folder and share the link to those files with others and they work pretty well.
See for example my re-releasing of some of my April 1 and other joke websites:
Also – I have reposted some of the my old websites
|Birthday party for Darwin in 2009|
Well, I assume this was on purpose from the folks at Biomed Central but not sure. Our paper on the genome of one of Darwin’s Finches is out today in BMC Genomics: BMC Genomics | Abstract | Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence.
Abstract of the paper:
A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris.
13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin’s finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins.
These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.
There is a long long long story behind this paper. Too long for me to write up right now. I wrote up some of the story for a Figshare posting of the genome data last year.
“Darwin’s Finches” are a model system for the study of various aspects of evolution and development. In 2008 we commenced on a project to sequence the genomes of some of these species – inspired by the (then) upcoming celebration of the 200th anniversary of the birth of Charles Darwin (which was in February 2009). The project started with a brief discussion at the AGBT meeting in 2008 and then via an email conversation between Jonathan Eisen and Jason Affourtit about the possibility of a collaboration involving the 454 company (which was looking for projects to highlight the power of it’s then relatively new 454 sequencing machines). After further discussions between Jonathan Eisen, his brother Michael Eisen (who separately had become interested in Darwin’s finches) and people from 454 it was decided that this was a potentially good project for a scientific and marketing collaboration.
In these conversations it was determined that the most likely limiting factor would be access to DNA from the finches. This was largely an issue due to the fact that the Galapagos Islands (where the finches reside) are a National Park in Ecuador and also a World Heritage site. Collection of samples there for any type of research is highly regulated. Thus, Jonathan Eisen made contact with Peter and Rosemary Grant – the most prominent researchers working on the finches – and who Eisen had discussed sequencing the finch genomes in the early 2000s. In that previous conversation it was determined that the sequencing would be too expensive to carry out without a major fundraising effort. However, with the advent of “next generation” sequencing methods such as 454 the total costs of such a project would be much lower.
In the conversations with the Grants, the Grants offered to ask around to see if anyone had sufficient amounts of DNA (or access to samples), which would be needed for genome library construction. Subsequently they identified Arkhat Abzhanov from Harvard as someone who likely had samples as well as permission to do DNA-based work on them, from many of the finch species. Abzhanov offered to provide samples from three key species (large ground finch Geospiza magnirostris, large cactus finch G. conirostris and sharp-billed finch G. difficilis) and DNA was sent to Roche-454 for sequencing in July of 2008. In August, the first “test” sequence data was provided from Geospiza magnirostris. A plan was then made to generate additional data and Roche offered to do the sequencing at their center at a steep discount. Funds were raised by Jonathan Eisen, Greg Wray, Monica Riley, and others to pay for the sequencing and over the next year or so, three sequencing bursts were conducted at Roche-454. “
That is a decent summary of the background. The details on the science are in the paper. What the background does not say is that the project languished for years as we did not have funds to support the actual analysis of the genomes and it was kind of out of my normal area of expertise. Along the way, I did a poor job of communicating with some of the initial parties in the project (e.g., I did a really bad job of communicating with Greg Wray – who had provide some of the funds – and I will forever be trying to make things up to him). Anyway, thankfully Arhat eventually pulled together a group of people led by Chris Ponting to help analyze the genome and Chris led the way to the paper that is out today. Only four years after our original goal.
I have been a birder and an evolutionary biologist for many many many years. Thus this is kind of a cool project for me. When I was in the Galapagos in 2002 I dreamed of doing a project like this – and even started doodling Darwin’s finches all over the place – including on some of the styrofoam cups we sent down to the bottom of the ocean on the outside of the Alvin sub as part of a deep sea research cruise I went on. See below:
|Me, in the Galapagos in 2002|
|Me in the Galapagos in 2002|
|Me, today, w/ Darwin’s finch art|
Was browsing through this paper (largely due to my interest in sequencing genomes of novel organisms): Genome Biology | Abstract | Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.
And I found they found something very interesting. “We identified two rhodopsins both with C-terminal histidine kinase and response regulator domains with homology to the sensory rhodopsins of the green algae that represent candidates for light sensors in Ac (Figure 3).” Seems they found some homologs of the proteorhodopsin / halorhodopsin family of proteins which I have been interested in for years. Check out Figure 3:
Every couple of months there is a new group of organisms that is found to have a member of this gene family. See for example: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea for papers in which I was involved where Rhodopsins were part of the story. Also see the Venter et al. Sargasso paper: PDF. Anyway – just a quick post for those out there interested in rhodopsins and the like …
Call for participants: Evolutionary Biology of the Built Environment Working Group. Details copied from the announcement pasted below:
|My tribute to Carl Woese 12/30/12|
Sadly, Carl Woese has passed away. I am collecting some links and posts about him here in his memory. He was without a doubt the person who most influenced my career as a scientist.
News stories about Woese’s passing
Some of my posts about Woese
Storification of Tweets and other posts about his passing //storify.com/phylogenomics/rip-carl-woese.js?template=slideshow[View the story “RIP Carl Woese” on Storify]
Other posts worth reading about Woese’s passing
|My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast.|
People not Projects.
It is such a simple concept. But it is so powerful. I first became aware of this idea as it relates to funding scientific research in regard to the Howard Hughes Medical Institute’s Investigator program. Their approach (along with a decent chunk of money) has helped revolutionize biomedical science. And thus I was personally thrilled to see the introduction of this concept in the area of Marine Microbiology a few years back with the Gordon and Betty Moore Foundation’s “Marine Microbiology Initiative Investigator” program. Launched in 2004 it helped revolutionize marine microbiology studies in the same way HHMI’s investigator program revolutionized biomedical studies.
The first GBMF MMI Investigator program ran from 2004 -2012. And the people supported were pretty darn special:
Now I am I suppose a little biased in this because at the same time GBMF launched this program they also put a bunch of money into the general area of Marine Microbiology and I have been the recipient of some of that money. For example, I got a small amount of money as part of the GBMF Funded work at the J. Craig Venter Institute on the Sargasso Sea and Global Ocean Sampling metagenomic sequencing projects and also had a subcontract from UCSD/JCVI to do some work as part of the “CAMERA” metagenomic database project. I ended up being a coauthor on a diverse collection of papers associated with these projects including Sargasso metagenome and this review, and GOS1, GOS2 and my stalking the 4th domain paper.
I am also a bit biased in that I have worked with many of the people on the initial MMI Investigator list some before, some after the awards including papers with Jen Martiny, Ed Delong, Alex Worden and Ginger Armbrust, and Mary Ann Moran.
But perhaps most relevant in terms of possible bias towards the Gordon and Betty Moore Foundation is that in 2007 my lab received funds through the MMI program for a collaborative project with Jessica Green and Katie Pollard for our “iSEEM” project on “Integrating Statistical, Ecological and Evolutionary analyses of Metagenomic Data” (see http://iseem.org) which was one of the most successful collaborations in which I have ever been involved. This project produced something like a dozen papers and many major new developments in analyses of metagenomic data including 16S copy correction, sifting families, microbeDB, PD of metagenomes, WATERs, BioTorrents, AMPHORA. and STAP. This project just ended but Katie Pollard and I just got additional funds from GBMF to continue related work.
So sure – I am biased. But the program is simply great. In the eight years since the initial grants the Gordon and Betty Moore Foundation has helped revolutionize marine microbiology. And a lot of this came from the Investigator program and it’s emphasis on people not projects. I note – the Moore Foundation has clearly decided that this “people not projects” concept is a good one. A few years ago they partnered with HHMI to launch a Plant Sciences Investigator Program which I wrote about here.
It was thus with great excitement that I saw the call for applications for the second round of the MMI Investigator program. I certainly pondered applying. But for many reasons I decided not to. And today the winners of this competition have been announced and, well, it is an very impressive crew:
Some of the same crowd as the previous round. Some new people. Some people not there from the previous round. All of them are rock stars in their areas especially if one takes into account how senior they are (the more junior people are stars in development). And all have done groundbreaking work in various areas relating to marine microbiology. The organisms covered here run the gamut including viruses, bacteria, archaea, and microbial eukaryotes. The areas of focus covered range from biogeochemistry to ecosystem modeling with everything in between. It really is an impressive group. Delong pioneered metagenomics and helped launch studies of uncultured microbes in the oceans. Karl has led the Hawaii Ocean Time series and done other brilliant work. Sullivan and Rohwer and pushing the frontiers of viral studies in the oceans. Allen, Armbrust, and Worden are among the leaders in genomic studies of microbial eukaryotes in the marine environment. Dubilier, Bidle, Fuhrman and
Follows Stocker (double listed Follows in original post …) – though they focus on very different aspects of marine microbes – are helping lead the charge in understanding interactions across the domains of life in the marine environment. Orphan, Saito, Deutsch, Follows and Pearson are on the cutting edge of biogeochemical studies and trying to link experimental studies of microbes to biogeochemistry of oceans.
This article has been revised to reflect the following correction:
Correction: November 29, 2012
An earlier version of this article misstated the title of Charles Darwin’s classic book on the subject of evolution. It is “On The Origin of Species,” not “On the Origin of the Species.”
Today the outermost twigs and buds of the Tree of Life are occupied by mammals and birds, while at the base of the trunk lie the most primitive phyla — Porifera (sponges), Platyhelminthes (flatworms), Cnidaria (jellyfish).
The mystery of life is not concealed in the higher animals,” Kubota told me. “It is concealed in the root. And at the root of the Tree of Life is the jellyfish.
Hydrozoans, he suggests, may have made a devil’s bargain. In exchange for simplicity — no head or tail, no vision, eating out of its own anus — they gained immortality.
As an aside, the article is littered with painful other statements like
It is possible to imagine a distant future in which most other species of life are extinct but the ocean will consist overwhelmingly of immortal jellyfish, a great gelatin consciousness everlasting.
You might expect that biotech multinationals would vie to copyright its genome; that a vast coalition of research scientists would seek to determine the mechanisms by which its cells aged in reverse; that pharmaceutical firms would try to appropriate its lessons for the purposes of human medicine; that governments would broker international accords to govern the future use of rejuvenating technology. But none of this happened.
He cited this as an example of a phenomenon he calls the Small’s Rule: small-bodied organisms are poorly studied relative to larger-bodied organisms. There are significantly more crab experts, for instance, than hydroid experts.
Saw this tweet a few minutes ago:
The title of the paper took me a reread or two to understand. But once I got what they were trying to say I was intrigued. And so I went to the paper: PLOS Genetics: A Novel Human-Infection-Derived Bacterium Provides Insights into the Evolutionary Origins of Mutualistic Insect–Bacterial Symbioses. And it is loaded with interesting tidbits. First, the first section of the results details the history of the infection in a 71 year old male and his recovery and the isolation and characterization of a new bacterial strain. Phylogenetic analysis revealed this was a close relative of the Sodalis endosymbionts of insects.
And then comparative genomics revealed a bit more detail about the history of this strain, it’s relatives, and some of the insect endosymbionts. And plus, it allowed the authors to make some jazzy figures such as
And this and other comparative analyses revealed some interesting findings. As summarize by the authors
Our results indicate that ancestral relatives of strain HS have served as progenitors for the independent descent of Sodalis-allied endosymbionts found in several insect hosts. Comparative analyses indicate that the gene inventories of the insect endosymbionts were independently derived from a common ancestral template through a combination of irreversible degenerative changes. Our results provide compelling support for the notion that mutualists evolve from pathogenic progenitors. They also elucidate the role of degenerative evolutionary processes in shaping the gene inventories of symbiotic bacteria at a very early stage in these mutualistic associations.
The paper is definitely worth a look.