All posts by Jonathan Eisen

About 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

At @UCDavis: Assistant/Associate Professor of Grassland Ecology and Management

Assistant/Associate Professor of Grassland Ecology and Management

The Department of Plant Sciences in the College of Agricultural and Environmental Sciences at the University of California, Davis is recruiting an academic year (9-month), tenure-track Assistant/Associate Professor of Grassland Ecology and Management.

Grasslands represent some of Earth’s most expansive and diverse biomes, supporting the livelihoods of millions of people. Grasslands are sensitive to the interacting drivers of climate, grazing, and fire – and to human alteration of these natural disturbance regimes, as well as the introduction of invasive species. The conservation and sustainable use of these ecosystems in the face of rapid environmental and socio-economic change is a central challenge on the global scale.

We are seeking applicants interested in the broad study of grassland ecology to address a suite of fundamental challenges to the sustainable management of grasslands across the globe. All aspects of grassland ecology and management are of interest and will be considered in this recruitment. We are seeking a candidate interested in productive collaborations across disciplines and with grassland stakeholders. We are seeking a candidate interested in developing a dynamic grassland ecology and management teaching program at both the undergraduate and graduate levels. The successful candidate will have the opportunity to teach Ecology of Grasslands and Grazed Ecosystems (Revised PLS 135) and contribute to Principles of Rangeland Management and Ecology (PLS 130). In addition, the candidate can teach at the graduate level within their area of research expertise and contribute to graduate programs in the Ecology, International Agricultural Development, Horticulture and Agronomy graduate groups, and/or other graduate programs of interest to the individual.

Ph.D. or equivalent in ecology, rangeland science, plant sciences, or a related discipline. Demonstrated potential for excellence in research and instruction on topics relevant to grassland ecology and management.

Commensurate with qualifications and experience.

Application materials must be submitted via the following website:

The position will remain open until filled. To ensure consideration, applications should be received by 23:59 PDT October 31, 2018.

Required application materials include: 1) curriculum vitae including publication list, 2) up to three publications, 3) transcripts if the applicant is within five years of Ph.D. degree completion, 4) statement of research accomplishments, 5) statement of teaching accomplishments and philosophy, 6) statement of future research plans relevant to this position, 7) statement of contributions to diversity, and 8) the names, addresses, including e-mail, of four professional references. 9) Authorization to Release Information form. Additional inquiries should be directed to Marie Jasieniuk (masjasien) Chair of Search Committee, or Gail Taylor (gtaylor) Chair of Plant Sciences.

UC Davis is an affirmative action/equal employment opportunity employer and is dedicated to recruiting a diverse faculty community. We welcome all qualified applicants to apply, including women, minorities, veterans, and individuals with disabilities.

Ad – Grassland Ecology and Management Long Version 09-12-18.pdf

At @UCDavis: CPB Postdoctoral Fellow Search

EFFECTIVE: September 10, 2018

DEADLINE: November 1, 2018

POSTDOCTORAL FELLOW IN POPULATION BIOLOGY — The Center for Population Biology at UC Davis invites applications for a Postdoctoral Fellowship in Population Biology, broadly defined to include ecology, phylogenetics, comparative biology, population genetics, and evolution. We particularly encourage applications from candidates that have recently completed, or will soon complete, their PhD.

The position is for TWO YEARS, subject to review after one year, and can begin as early as July 1, 2019. This position is covered by a collective bargaining unit. It has a starting annual starting salary of $49,188 plus benefits, and $6,000 per annum in research support. The Fellow will be a fully participating member in the Center for Population Biology and will be expected to have an independent research program that bridges the interests of two or more CPB faculty research groups. We strongly encourage candidates to contact appropriate faculty sponsors before applying. We also ask that each Fellow propose a workshop, discussion or lecture series that they could offer to the community of population biologists at UC Davis; faculty sponsors or the Director of CPB, Artyom Kopp, can provide additional input on this aspect of the fellowship. For samples of past workshop abstracts and more information about UC Davis programs in population biology, see

ONLINE APPLICATION: Interested candidates should submit a cover letter, a CV, a short description of research accomplishments (1-2 pages), a short description of proposed research including potential faculty mentors (1-2 pages), a brief description of their proposed workshop (1 page or less), and copies of two publications, all in PDF format

Postdoc Search Ad 2018.pdf

New preprint from lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka

A new preprint has been posted from the lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia | bioRxiv

Paper was led by Laetitia Wilkins and Cassie Ettinger (Guillaume Jospin and I are co authors).  


Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. Using a shotgun metagenomics approach, we assembled population-level genomes of bacteria and archaea from two pools using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and placed them in the context of the current microbial tree of life. We highlight MAGs representing previously underrepresented archaeal phyla (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study can be considered complementary to foregoing studies in the same ecosystem as it adds more comprehensive information about phylogenetic diversity and functional potential within this highly selective habitat.

I will try to write more about it later – I am so impressed by what Laetitia and Cassie did here.  This is what we call a “reboot” project in the lab – this was data that was generated and then not turned into a paper and was just sitting there.  A while ago we started a “reboot” program to start to try to turn such data sets into papers and they adopted this data set.  The data is Solexa shotgun metagenomic data from samples from hot springs in Kamchatka (yes, Solexa, read the paper for details).  The DNA used was leftover from an old project which included a collaboration with Juergen Wiegel’s lab (and some others) that had started, at least in terms of discussions, in 2001.  Anyway – I will try to write out more on the story behind this work soon.  But please, check out the paper, and feel free to provide feedback.

At @ucdavis: Marine aquaculture recruitment seminars

Forwarding this:

This week VetMed will be hosting two of the three candidates for the Marine Aquaculture Science faculty position. All are invited to the recruitment seminars which will be held in 1041 Valley Hall from 12-1 on Tuesday and Thursday.

CMSI will be hosting an afternoon meet & greet with coffee and dessert from 2:15-3:15.

The recruitment seminar flyers for the two candidates are attached.

Colleen Burge
June 12 12:00 – 1:00 (1041 Valley Hall): Seminar- “Host-Pathogen Interactions in a Changing Ocean: from Disease Emergence to Solutions"
2:15 – 3:15 (1347 Storer Hall): Meet & greet with CMSI faculty, staff, postdocs and students

Jan Lovy
June 14 12:00 – 1:00 (1041 Valley Hall): Seminar- “Research on microparasites affecting wild and farmed fish: From the farm to a laboratory disease model to gain insights on host-pathogen interactions"
2:15 – 3:15 (1347 Storer Hall): Meet & greet with CMSI faculty, staff, postdocs and students

Thu 5/31 at UC Davis: Rachel Sollman on Spatial capture-recapture: a flexible framework to study wildlife populations


This week’s Ecology and Evolution Seminar series will be given by Rahel Sollmann, from the WFCB department here at UC Davis. For more about Rahel’s research, click here.

Her talk, titled: "Spatial capture-recapture: a flexible framework to study wildlife populations" will be tomorrow, Thursday, May 31 at 4:10 pm in Everson Hall.

UCB IB Dept Lecturer Pool for “General Biology”

Lecturer Positions in General Biology – BIO 1B

Department of Integrative Biology

University of California, Berkeley

The Department of Integrative Biology at UC Berkeley is generating an applicant pool of qualified temporary full or part-time lecturers to teach the General Biology laboratory class, BIO 1B (, should the need arise. The pool will remain in place for one calendar year; those interested in remaining in the pool after the year must reapply. Appointments may be renewable based on need, funding, and performance. Positions range from 50% – 100%, depending on the number of sections taught. Vacancies may arise during Fall, Spring, or Summer.

The laboratory class currently covers three major sections: Evolution, Ecology, and Organismal Diversity. Exercises include investigations into population genetics, phylogenetic relationships, macroevolution, predator/prey interactions, competition, bioindicators, and structure and function of organisms. BIO 1B is a gateway course to the major field of Integrative Biology that consists of three one-hour lectures and one four-hour combined discussion and lab each week. The class has 48 sections with a maximum of 18 students in each section. Lecturers will be required to lead one discussion and lab per week, create quizzes, grade assignments, attend a Friday instructional meeting, be familiar with lecture, proctor exams, hold office hours and complete other instructional duties as assigned. Senior lecturers mentor new hires and Graduate Student Instructors (GSIs).

Minimum Basic Qualifications (by time of application): The completion of all Ph.D. degree requirements except the dissertation is required at the time of application.

Additional Qualifications (by start date): A Ph.D. or equivalent degree in biology or a closely related discipline is required by the time of appointment. Experience teaching a college-level course (previously employed as a graduate student instructor, teaching assistant, lecturer, etc.) of the biological sciences is also required.

Preferred Qualifications: Experience working with computer-based phylogenetic programs and familiarity with online course and grading systems is preferred. Preference will be given to those with experience teaching a class similar to UC Berkeley’s Bio 1B lab courses.

Minimum full-time annual salary is $53,402. Salary is commensurate with experience and education.

Appointments for fall semesters are usually reviewed in May and finalists are selected once funding is confirmed for the next academic year. Spring semester appointments are reviewed in September. Reviews for Summer are in January.

Application requirements to apply: Cover letter, curriculum vitae, statement of teaching philosophy, student evaluations of teaching, and names and email addresses of three references. One miscellaneous teaching document is optional. Please include career highlights in the cover letter that specifically address the subject matter of our course. The CV should include teaching experience with a listing of dates, courses, units, and title (Lecturer, Graduate Student Instructor/Teaching Assistant, Guest Lecturer, etc.). Statement of Teaching Philosophy should be no more than three pages. Student evaluations of teaching should include all respondents (quantitative and qualitative). For those with considerable teaching experience, complete student evaluations of teaching from the last three courses taught will suffice. The cover letter, CV, and complete student teaching evaluations are very important. To receive full consideration, please ensure your application is complete by the time of review. To apply:


Letters of recommendation may be requested of finalists. If reference letters are later solicited by the Department, they will be treated as confidential per University of California policy and California state law. Please refer potential referees, including when letters are provided via a third party (i.e., dossier service or career center), to the UC Berkeley statement of confidentiality

( prior to submitting their letters.

The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see: The department is interested in candidates who will contribute to diversity and equal opportunity in higher education through their teaching.

Bio 1B Lecturer Pool Ad for 2018-2019v2.pdf