“Brachypodium genomics: The pan-genome, polyploidy and epigenetics of cold responses”
John Vogel
DOE Joint Genome Institute
Monday, March 13, 2017
4:10-5:00 PM
1022 Life Sciences
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
Round up of responses to my sign captioning request
Round up of responses to my sign captioning request
//storify.com/phylogenomics/weekly-signcaptions-contest/embed?border=false&template=grid//storify.com/phylogenomics/weekly-signcaptions-contest.js?border=false&template=grid[View the story “Weekly Sign Captioning Contest #SignCaptions #Signs #Humor ” on Storify]
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Kissing between humans and Neanderthals? Could be oral – anal contact too. Or neither.
Umm – I really do not know what to say here. There is a new incredibly exciting paper out on Neanderthal oral microbiomes.
I saw some news stories about a new study on Neanderthal oral microbiomes. And one thing caught my eye – a claim about how the data provided evidence that Neanderthal’s and humans were kissing each other.
See for example the LA Times: Vegetarian Neanderthals? Extinct human relatives hid a mouthful of surprises – LA Times
The scientists also managed to sequence the oldest microbial genome yet — a bug called Methanobrevibacter oralis that has been linked to gum disease. By looking at the number of mutations in the genome, the scientists determined it was introduced to Neanderthals around 120,000 years ago — near the edge of the time period when humans and Neanderthals were interbreeding, Weyrich said
There are a few ways to swap this microbe between species, she pointed out: by sharing food, through parental care, or through kissing.
“We really think that this suggests that Neanderthals and humans may have had a much friendlier relationship than anyone imagined,” Weyrich said. “Certainly if they’re swapping oral microorganisms — or swapping spit — it’s not these brute, rash-type encounters that people were suspecting happened during interbreeding. It’s really kind of friendly interactions.”
And Redorbit: Neanderthals were vegetarian– and probably kissed early humans
Another surprise was the discovery of the near-complete genome for Methanobrevibacter oralis, a microbe known to live between the gums and teeth of modern humans, in the dental calculus of the Neanderthals. Weyrich said that this organism is the oldest of its kind to ever be sequenced, and that its existence in Neanderthals means that it had to have been spread to humans somehow – likely through kissing, which supports the growing notion that humans and Neanderthals were known to become intimate with one another on occasion.
And the Washington Post Neanderthal microbes reveal surprises about what they ate — and whom they kissed
And there is this doozy of a quote in the Post article
“In order to get microorganisms swapped between people you have to be kissing,” Weyrich said.
And many others. Now – this seemed like it would be really hard to prove. After all, it is really hard to prove from microbiome data that two people have been kissing even when we have high quality data from many samples and even when we have data from both the possible donor and recipient. So how could one show that humans and Neanderthals were kissing with data from ancient samples and only from one of the partners in the putative exchange? Well, as far as I can tell, you cannot.
Sadly the paper is not open access and I generally avoid writing about closed access papers here. But I am making an exception here because the media has run with what I believe to be an inaccurate representation of the science.
So I went to the paper. Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. I have access to it at UC Davis but if you do not have access to it, you could search for it in SciHub (for more about SciHub see Wikipedia). I am not encouraging you to use SciHub – a site that makes papers available view what may be illegal means in some countries. But if you want to see the paper, and you have determined that you are OK with using SciHub, well, that is an option. This is a link that might get you access in SciHub, if you wanted to do that.
Anyway – I read the paper. And it really is quite fascinating. It has all sorts of interesting information and really does represent an incredible tour de force of both lab and computational work. Kudos to all involved. But alas, there is nothing in the paper about kissing. If you search in the paper for the word kiss – it is not found. The possible transfer of microbes between Neanderthal and humans is briefly discussed however.
From what I can tell, what they did here was the following:
- reconstructed a genome from their samples of Methanobrevibacter oralis subsp. neandertalensis.
- compared the genomes to other Methanobrevibacter genomes including just one other M. oralis (this one from humans)
- Inferred a
possbilepossible date range for the split between their M. oralis and that from humans
It is cool and very interesting stuff. See this figure for example.
And then based on this they write:
Date estimates using a strict molecular clock place the divergence between the M. oralis strains of Neanderthals and modern humans between 112–143 ka (95% highest posterior density interval; mean date of 126 ka) (Fig. 3b; see Supplementary Information). As this is long after the genomic divergence of Neanderthals and modern humans (450–750 ka)29, it appears that commensal microbial species were transferred between the two hosts during subsequent interactions, potentially in the Near East30.
So they are inferring transfer of commensal microbes based on molecular clock dating from one single M. oralis genome from Neanderthal and one from humans and a comparison of the inferred dating of their common ancestor versus the timing of supposed divergence between humans and Neanderthal. Personally it seems like a big big stretch to make that inference here. What if the dating from their analysis is off (such dating estimates are generally highly debated and unclear how accurate they are)?
But let’s just say that this is in fact good evidence for some sort of more recent common ancestry of the M. oralis found in their sample and the M. oralis found in a human than one would expect based on knowledge of Neanderthal and human common ancestry. Does that mean swapping of the microbes between humans and Neanderthal? Not at all. Maybe the M. oralis comes from food. And if it is living in some sort of food source (could be animal, or plant or something else) and it comes into both humans and Neanderthal separately, then one could easily have a way for the one found in their Neanderthal sample to have a more recent common ancestry with the one found from humans than the common ancestry of the “hosts” here.
Interestingly, the genome they used to compare to Methanobrevibacter oralis JMR01 actually came from a fecal sample and not an oral sample – see Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota. So this microbe is not solely found in the mouth and it apparently can survive transit between the mouth and another orifice, and may even be a gut resident (i.e., not just transiting).
So anyway – it seems woefully premature to conclude that the data they have here provides evidence for exchange between humans and Neanderthals of M. oralis. Could have occurred. But also could be separate colonization from similarly environmental sources.
And finally, even if we assume that the M. oralis was exchanged, which again there seems to be no good evidence for, what is to suggest that this was do due to kissing? Nothing as far as I can tell. How about sharing utensils? How about contact with fecal contaminated water (since M. oralis seems to do OK in feces)? Or I guess would could go extreme and say this could be evidence for oral anal contact between Neanderthal and humans, if we wanted to sensationalize this even more. After all, we do know many cases of microbes getting exchanged by oral – anal contact. But we don’t do we? How about we stick to what we have good evidence for and then carefully discuss possibilities, of which kissing is one, but it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best.
This There is really amazing science in this work. But the kissing claims are premature as far as I can tell (I honestly hope I am wrong and that there is more data than presented in the paper, but if there is it should be presented somewhere – or maybe I have misinterpreted the paper – but I don’t think so). If the claims are as premature as they seem to be, this is damaging in my mind to the field of microbiome science.
—————————–
UPDATE 3/10/17
Thanks to Ed Yong for updating his Atlantic article on this story to add a reference to my concerns.
He wrote
But after the paper was published, and several publications noted Weyrich’s suggestion about kissing in their headlines, Jonathan Eisen from the University of California, Davis, expressed skepticism about the claim. “Maybe the M. oralis comes from food,” he wrote in a blog post. It could have been picked up independently from the environment, or from water contaminated with feces, or from other kinds of sexual contact. A kissing route “it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best,” Eisen said.
UPDATE 2 – Made a Storify of some responses
//storify.com/phylogenomics/kissing-oral-anal-contact-or-maybe-just-maybe-neit/embed?border=false&template=grid//storify.com/phylogenomics/kissing-oral-anal-contact-or-maybe-just-maybe-neit.js?border=false&template=grid[View the story “Humans and Neanderthals – kissing, oral-anal contact, or maybe, just maybe, neither” on Storify]
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HHMI Announces New Investigator Competition
Of possible interest – was just forwarded this
Dear Colleagues,
I am pleased to share that Howard Hughes Medical Institute (HHMI) has launched a national competition to select new HHMI investigators. We invite researchers to apply who bring original and innovative approaches to the investigation of biological problems in biomedical disciplines, plant biology, evolutionary biology, biophysics, chemical biology, biomedical engineering, and computational biology. Physician scientists are encouraged to participate in the competition. We expect to appoint up to 20 new investigators.
We ask that you encourage appropriate scientists to participate in this open competition. Eligible candidates apply directly without an institutional nomination, and there are no limits on the number of applicants or awardees from any of the over 200 eligible institutions. More information about the HHMI Investigator Program and this competition may be found on our website: http://www.hhmi.org/inv2018.
In brief, candidates must meet the following eligibility criteria at the time of the application deadline:
- PhD and/or MD (or the equivalent).
- Tenured or tenure-track position as an assistant professor or higher academic rank (or the equivalent) at an eligible U.S. institution, which would become the host institution.
- More than 3, but no more than 12, years of post-training, professional experience. To meet this requirement, the applicant’s professional appointment(s) must have begun no earlier than June 1, 2005, and no later than September 1, 2014.
- Principal investigator on one or more active, national peer-reviewed research grants with an initial duration of at least three years, such as an NIH R01 grant. Mentored awards, career development and training grants do not qualify. Multi-investigator grants may qualify.
The deadline for submission of all application materials is June 27, 2017, at 3:00 p.m., Eastern Time.
The HHMI review process will include evaluation of applications by distinguished scientists, leading to the selection of semifinalists by early 2018. Following further review, finalists will be selected in the spring of 2018, with appointments to begin as early as September 1, 2018. Institutions with finalists who have not previously hosted an HHMI investigator will be required to enter into a collaborative agreement with HHMI.
HHMI welcomes a diverse and broad applicant pool. Individuals from gender, racial and ethnic groups underrepresented in biomedical research at the career stages targeted by this program are encouraged to apply. As an equal opportunity employer, HHMI does not discriminate on the basis of race, color, sex, religion, national origin, disability, age or any other characteristic protected under applicable law.
We appreciate your help in distributing this announcement to colleagues at your institution.
With best regards,
Erin
Erin K O’Shea PhD
President
Howard Hughes Medical Institute
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Today at #UCDavis-Nipam Patel “The Evolution of Animal Diversity: Insights from Emerging Model Systems”
Nipam Patel from UC Berkeley
The Evolution of Animal Diversity: Insights from Emerging Model Systems
4:10 in 100 Hunt Hall.
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Postdoctoral Fellowship in Marine Biodiversity: Hakai & Smithsonian MarineGEO
was forwarded this announcement
Postdoctoral Fellowship in Marine Biodiversity
Application review begins March 27, 2017
The Hakai Institute and the Smithsonian Institution’s MarineGEO program seek candidates for a Postdoctoral Fellow based at the University of British Columbia to lead a detailed assessment and analysis of biodiversity in coastal benthic habitats of the Calvert Island Marine Station on the Central Coast of British Columbia. Details below and here: https://www.hakai.org/marinegeopostdoc
The position is part of an ongoing research program aiming to understand nearshore biodiversity of this unique region. We seek a Postdoctoral Fellow to lead a detailed biological inventory of this region (‘BioBlitz’), and develop research that takes advantage of this inventory and existing biological datasets to advance our comparative understanding and quantitative estimates of biodiversity in the North Pacific region.
The Fellow’s time will be split equally between leading the “BioBlitz” and complementary biodiversity research, with data analysis/manuscript preparation stemming from these two activities.
BioBlitz
The Fellow will lead the BioBlitz in the summer of 2017, an intensive field characterization and analysis of biodiversity along Calvert Island’s shorelines and representative habitats of British Columbia’ Central Coast region. The BioBlitz will be conducted in collaboration with the Hakai Institute’s group of researchers (Nearshore Marine Ecology, Oceanography, Geospatial groups) and with a team of experts from the BC region, Smithsonian Institution, and around the world. There are two key components of the BioBlitz:
• A two-week, detailed inventory of representative nearshore habitats: seagrass meadows, soft sediment substrates, intertidal rocky reef and kelp forests. These inventories will complement and add taxonomic resolution to on-going interannual and seasonal monitoring of indicator species and functional diversity in these habitats. The Fellow will have the opportunity to specialize in particular methods or habitats of their interest, but will work with a much larger team of taxonomic generalists and specialists to broadly cover the nearshore environment.
• Analysis and comparison of benthic subtidal rocky reef biodiversity using standardized settlement plates (Autonomous Reef Monitoring Structures, ARMS). ARMS have been deployed to sample differences in community structure between kelp forests (dominated by both Nereocystis and Macrocystis kelps) and de-forested urchin barrens in near proximity to the Calvert Island Research Station.
Together, these BioBlitz components aim to integrate taxonomic descriptions of species with genetic analyses and community-level data. Ultimately, this will produce an unprecedented level of understanding and baseline of habitat-associated marine biodiversity in the Northeast Pacific.
Proposed Research
In conjunction with the BioBlitz, there is considerable scope for independent research employing the BioBlitz collections data, and taking advantage of existing nearshore habitat monitoring datasets (seagrass, kelp, soft sediment, rocky intertidal datasets) and oceanographic/atmospheric data.
Using this diverse dataset and collaboration, applicants will propose research questions (1-page document) pertaining to, but not limited to:
• spatial scaling of biodiversity
• habitat connectivity and complexity
• functional and taxonomic diversity; relationships to ecosystem services
• drivers of change in benthic diversity
Research may focus on either specific habitats or taxa, or address comparative, cross-habitat questions. The proposed research should contribute to biodiversity knowledge of the Northeast Pacific region, with global context and comparative relevance through Smithsonian’s MarineGEO global network.
The Fellowship
The Fellow will be supervised by Margot Hessing-Lewis (Hakai Institute), Patrick Martone (UBC Botany) and Mary O’Connor (UBC Zoology), with residency at the University of British Columbia (UBC). They will collaborate closely with other scientists from the Hakai Institute, the Smithsonian Institution (Washington D.C.) and UBC (Biodiversity Research Center and Beatty Biodiversity Museum, Institute for Oceans and Fisheries).
The candidate must have a Ph.D. in biology, marine science, or other appropriate field, experience in marine field ecology, and clear evidence of research achievement and promise. Because the project involves a collaborative partnership, strong organizational, communication, writing, and people skills are essential. Advanced quantitative skills, including analysis of genomic datasets and taxonomic expertise, or community biodiversity data are also a plus.
To Apply
Applications should include (1) a current Curriculum Vitae; (2) a one-page summary of relevant career goals, interests, experience and publications; (3) a one-page proposal of research questions relevant to the stated goals of the research program; and (4) names and full contact information (postal address, email address, and phone number) for two references (we will contact them directly to request letters of recommendation).
Please submit your application electronically as a single PDF document to the three supervisors listed below with the file name and email subject heading ‘Hakai MarineGEO Postdoc application – SURNAME’ with your surname in capital letters.
The position is a Mitacs Accelerate Post Doc, available immediately for up to two years, contingent on satisfactory progress. The stipend is $55,000 per year, plus Mandatory Employment Related Benefits. Additional funds for research and travel related to the BioBlitz will also be provided.
Review of applications will begin on March 27, 2017 and will continue until the position is filled.
The two-year position will start in Spring 2017. Specific start dates will be negotiated with the successful candidate. The BioBlitz is planned for August 2017.
Project supervisors
Dr. Margot Hessing-Lewis
margot
Hakai Institute: https://www.hakai.org/
Dr. Patrick Martone
Patrick.martone
http://www3.botany.ubc.ca/martone/
Dr. Mary O’Connor
oconnor
http://oconnorlab.weebly.com/people.htm
2017_Hakai-MarineGEO_postdoc_ad_final.pdf
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FORCE11 Scholarly Communications Institute 7/30 – 8/4
Just got this by email. Could be of interest to some.
|
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At #UCDavis 3/8 Miriam Martin on “Improving student learning in microbiology through peer-to-peer instruction & a collaboratively-designed intro course”
MIC 291: Selected Topics in Microbiology
Work-in-Progress Seminars
Dr. Miriam Martin
(Dept. of Microbiology & Molecular Genetics)
"Improving student learning in microbiology through peer-to-peer instruction and a collaboratively-designed introductory course"
Wednesday, March 8, 2017
4:10 pm
1022 Life Sciences
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3/9 at #UCDavis Harvey Karten – could be good but “Evolutionary Connectomics?” Noooooooooooooooooooo #BadomicsWord
Just got this by email:
Looks possibly very interesting but "Evolutionary Connectomics" — that is a #Badomics Word / phrase
https://phylogenomics.blogspot.com/p/my-writings-on-badomics-words.html
Reminder next week…
Ted Jones History of Neuroscience Lecture announcement…
Dr. Harvey Karten will be presenting “Evolutionary Connectomics”
Thursday, March 9th at 4pm at the Center for Neuroscience, Rm 113.
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Blast form the past – videos from 2002 research cruise at the Galapagos Rift
OK it is only 15 years after the fact but am posting some videos from the 2002 Galapagos Rift Expedition I went on May 24 – June 4, 2002. It was the cruise honoring the 25th Anniversary of the discovery of deep sea hydrothermal vent ecosystems.
For more information see the web site from Dive and Discover
- Mission & Objectives
- Daily Updates
- Mail Buoy
- Scientists & Crew
- Interviews
- Hot Topics
- Slideshows
- Videos
Here is a playlist with all my videos, some from the cruise and some from the Galapagos Islands where the cruise started / stopped. I have not edited any of the videos – just digitized everything from the tapes and posted them. Apologies if anything is, well, inappropriate for any reason.
Jonathan Eisen's Lab 