SMBE Conference guidelines

Download a PDF of the Conference Guidelines here.

Statement of diversity

SMBE has a strong commitment to diversity. Organizers should place emphasis on diversity of participants, including gender and geographic diversity, at every level of the meeting, including but not limited to the selection of plenary speakers, symposium organizers, and invited and contributed talks. Please ensure that this criterion is considered throughout the organization of the conference.

Professional Conference Organizer (PCO)

Each conference is organized jointly by SMBE’s contracted Professional Conference Organizer (PCO) and the Local Organizing Committee.  The role of the PCO is described in its contract with SMBE.

Local Organizing Committee (LOC)

The SMBE conference Local Organizing Committee should include Local Organizers and one member of SMBE Council. The role of the Council member on the LOC is to make sure the conference organizers adhere to these guidelines. Additionally, one organizer of the meeting from a previous year and one organizer of the meeting for the next year should be included for the purpose of continuity.

The LOC will be required to sign a formal agreement with SMBE agreeing to its responsibilities.

The LOC should send any presentations it makes – usually their proposal and post-conference feedback – to the SMBE Executive Administrator for archiving.


It is very important that the meeting is fully costed, with costs borne by the meeting and not by the Society.  A rolling budget should be set up with precise costs and with frequent updates on income and expenditure. The Society will provide US$100,000, which is the only funding promised by the Society. While these funds can be made available at any time and used temporarily for other expenditures (such as reserving a venue), it is understood that the US$100,000 will ultimately cover travel costs for 50 invited speakers.  In addition, in the event that a short-term loan is required for down-payments on the venue and suppliers, then this can be arranged. Be aware that this loan will be issued in US dollars and all currency change costs, as well as the danger of currency fluctuations, must be borne by the conference.

Size of conference

The conference can currently expect between 1000 and 1500 delegates, although we have seen considerable fluctuations in this number depending on factors such as convenience and cost of travel. Organizers are advised to make two alternative plans for a smaller and a larger conference - i.e. make plans for a smaller conference but include options to expand if registration numbers seem to indicate the meeting will be large. This should happen at the same location with options for a larger auditorium that can hold the entire conference. Conference attendance should be capped at 2000.

Approximate timelines




Last day of the conference of the preceding year.

Initial website goes live



●       venue

●       opportunities for sponsorship

●       composition of the organizing committee

●       contact information for the conference organizer.

10 months before the date of the conference.

Call for symposia opens

See ‘Call for symposia’ below.

9 months before the date of the conference

Call for symposia closes


8.5 months before the conference

Notification of successful Symposia


8 months before the conference

Titles and short description of all symposia, should be placed on the conference website. Note that these are sometimes worded differently from the original proposals, which sometimes contain information related to the submission process.,.


8 months before the conference

Early bird registration opens

This deadline offers discount on the registration fee. Past experience indicates that 50-75% of delegates will take advantage of this early registration deadline.

Early bird registration should be advertised to the society membership, in the society journals, through the social media, on EvolDir, etc.

7 months before the conference

Abstract submission and award applications open

6 months before the conference

Abstract submission and award applications close (though it is common to extend by one week, depending on number of submissions).

Fitch Symposium, Abstract and travel award deadlines all occur at the same time. Fitch finalists are selected first and present in a separate symposium.

2-3 weeks prior to council decision of travel awards

Deadline for symposium organizers’ talk selection

To allow inclusion of talks in symposia to be considered in selection of travel awards

2 weeks before early bird registration closes

Council decision of travel awards: award applicants notified of success or otherwise

This is essential to allow applicants time to register at Early Bird rate if they haven’t received a travel/registration award. Some individuals who do not receive funding or are not selected for a talk will not register. There can be loss of ~100 participants as a result.

4 months before the conference

Early bird registration closes, full price registration opens


2 months before the conference

Full programme available online

Until the conference begins

Full cost registration

Full cost online registration; allows delegates to submit an abstract, though as an additional encouragement to register early, it should be stipulated that late abstracts can be considered only for poster presentations.

Either on the penultimate day of the meeting or up to two days later

Post-meeting survey

To be emailed to all meeting participants and able to run on a computer OR phone 

Structure of the conference


The preferred conference length is at 3.5 days with the acceptable range from 3 to 4 days (not counting the day of the council meeting/opening reception). The LOC is encouraged but not required to organize Public Lectures on Evolution/Molecular Evolution either immediately before or immediately after the meeting.

Council meeting

One council meeting to be held in a room that accommodates the council plus outside participants (about 16 people altogether).  Light breakfast, lunch, and all day coffee, tea, and light refreshments should be provided. This meeting will usually take place on the first day of the conference, starting at 8 or 9 am and must end at least 15 minutes before the Nei lecture. The main conference usually begins in the late afternoon/early evening with the Nei lecture, followed by the opening reception.

Scientific content

Limit oral presentations per person

Each person is limited to one oral presentation (either invited or contributed) for the entire annual SMBE meeting. If the same person is invited to several symposia, the person is given a choice of in which symposium s/he would like to present.

Presenter information

Each presenter should have clear instructions on where their presentation is going to be held, when they have been allocated a speaking time, and how to upload their slides.

Plenary lectures

There should be 3-4 plenary lectures, which are attended by all delegates, and usually last one hour. The number of plenary lectures should be limited to keep costs down and maximize  the number of multi-speaker symposia. Refer to the ‘Statement of Diversity’ above in the selection of plenary speakers. 

One of these plenary lectures is the Nei Lecture, named in honour of Professor Masatoshi Nei, and is given by the President of the society. Usually this lecture takes place near the beginning of the conference. SMBE has funds for this lecture to be published in MBE. The other plenary lectures are invited by the LOC and the invitees are usually fully funded in terms of the registration fee, travel and accommodation by the meeting.

Special symposia

Fitch Symposium

The Fitch Symposium occurs as an exclusive event when no other events or symposia are taking place.

Graduate students and postdocs in their first year of their first postdoc are eligible to apply to present their work in the Fitch Symposium, which is a plenary symposium, again attended by all delegates at the conference. A committee is convened each year by the Past-President to select the 8 talks from the submitted abstracts. The President-Elect will moderate the Fitch Symposium. The President will convene a committee to select the winner.

Open Symposium

The LOC is strongly encouraged to include an Open Symposium at which ground-breaking work not covered by the accepted symposium topics can be presented, Faculty award recipients can present, and potentially to allow more student/postdoc talks accepted.

Faculty awards symposium

There may also be a separate symposium for recipients of the Allan Wilson, Margaret Dayhoff, Motoo Kimura, and Community Service Awards.  Recipients of these awards should all be given the opportunity at the meeting, either in an ordinary symposium, or the special symposium, or in slots set aside for them in the Open Symposium.  The Council members responsible for these awards should be informed of the latest dates that lectures can incorporated into the programme.

Parallel symposia

The LOC should have a (usually audible) mechanism to ensure that concurrent sessions stay on time and try to minimize similarity in content or theme of overlapping concurrent sessions.

Number of symposia

There should be approximately 20-30 symposia, usually with no more than four parallel sessions (fewer than four is fine). SMBE Council considers that if there are more than four parallel sessions then delegates feel they are missing too many talks, while fewer parallel sessions restrict the diversity of the conference. Moreover, recent experience has shown that more sessions and/or additional plenary speakers can put the meeting into financial jeopardy.

Call for symposia

The call for symposia should indicate that if a symposium is selected, the invited speakers will have all or most of their registration fee, accommodation, and travel covered by the conference (at the level of approximately $2000 per invited speaker against receipts; adjusted reimbursement for intra- and intercontinental travel is allowed. This $2000 support for invited speakers should be maintained by the LOC under all circumstances.

A list of at least two confirmed invited speakers per symposium should be requested in response to the call for symposia.

Selection of the symposia

Most symposia are selected by the LOC on the basis of proposals and depending on whether the same topics were covered by symposia at recent SMBE meetings.

Symposia should reflect the broad diversity of interests in the SMBE community, not simply the most popular topics. Symposium organizers select abstracts for talks, taking speaker diversity into consideration (see Statement of diversity above) as well as diversity of career stage (student/postdoc/junior/senior investigators).

Symposium proposals should include a summary of the topic, why it is timely for the SMBE meeting, and which speakers have been invited and confirmed. If there are two or more proposals on the same topic, the LOC has a choice of selecting one proposal or merging two or more proposals. Merging two or more symposia either reduces the number of invited speakers that can be supported by SMBE or the number of slots available for contributed talks and is therefore discouraged.

Each symposium organizer can only select one talk from her/his own research group. That includes his/her own talk. In the event of too few submissions, exceptions to this rule may permit one additional talk from the organizer’s group, after consultation with the LOC.

The LOC selects the talks for the Open Symposium.


Recent conferences have settled on a structure where a ‘unit’ of time is 15 minutes. This includes time for questions (usually, 12 minutes for the talk and 3 minutes for questions and movement between rooms). This makes it especially important to have rooms in close proximity to each other. Invited speakers can be allocated 15 or 30 mins. It is also prudent to remind symposium organizers that delegates frequently move between symposia, so it is useful to allow one minute of moving time between talks (if adequate for travel between rooms) within the allocated 15 minutes and to be sure that the layout of seating is conducive to movement between rooms.. Some symposium organizers may choose to use the first 15 minutes to provide an overview of the study area at the beginning, but this is subject to time availability.

Selecting speakers

Each symposium of contributed talks will select its preferred speaker list from the list of contributed talk abstracts. It is best if a delegate is allowed to submit their abstract to more than one symposium (though logistically, it is probably best to restrict this to two symposia). When the symposium organizers are given their list of abstracts and delegates who wish to speak in their symposium, they can choose their preferred list of speakers. However, the exact details of this process are to be worked out by the LOC. In the end, the LOC will match delegates and symposia and communicate to both the symposium organizers and the delegates the outcome of this process. This decision should be reached before Early Bird registration closes as it affects many scientists’ travel funding, and no later than 4 months before the conference.

Poster sessions

Poster presenters frequently feel that they do not get adequate opportunity to present their work, so it is important that each poster presenter is given enough time both to talk to other delegates and to have the posters visible (at breaks, etc.). Poster sessions should have accompanying refreshments and each poster should have at least two sessions when they are available to be seen. Although not always possible, it is desirable to have sufficient space that all posters can be viewed throughout the meeting, so that participants (and poster judges) have plenty of opportunity for viewing. The website should also indicate when posters can go up. Poster space should only be made available to participants who have registered and sent payment, to minimize “no-shows.”

Social events

Please provide vegetarian/vegan options with all catering.

Breaks and catering

It is expected that the conference will provide morning coffee break, lunch on all days, afternoon coffee breaks on each day, preferably with some small snack (fruit, cookies, pastry, etc.), and poster sessions.

Welcome reception

This typically provides ample snacks, enough for all participants, in addition to at most one or two drink tickets. Additional drinks can usually be purchased at the bar.

Gala Dinner  (banquet)

Delegates can choose to pay extra for this dinner or choose not to attend.

This is the preferred venue for distributing awards, and awardees present at the meeting, including all Fitch participants, should have free Gala tickets. A few venues include an after-dinner speaker, and some venues include dancing Drink tickets may be provided at registration for the Gala, with additional drinks available for purchase.

Awards Ceremony

The preferred venue for the Awards Ceremony (which lasts about 20 minutes) is the Gala Dinner.

If the awards are not distributed at the Gala Dinner, then 20-30 minutes should be set aside for an Awards Ceremony in the middle of the last morning (to allow enough time for decisions to be made on poster prizes and to maximize attendance). This ceremony is usually combined with an invitation to the next meeting (10-15 minutes), but the Gala is the preferred venue for awards.

While not all poster participants typically attend the Gala, due to cost, unless it is covered in registration, not all participants attend a separate Awards Ceremony, due to other choices on the last day, including packing and checking out of the hotel.

Post-conference survey

Each delegate should be invited to evaluate the conference, either using a paper form that can be dropped into a box onsite or an online form that can be completed either on a computer or smart phone.  The survey should be organized by the PCO and its content checked by the SMBE Council representative before distribution.

Certificates of attendance

Some delegates will require a certificate of attendance for their home institutions or for funding agencies that have supported their travel. These certificates should be provided on request and made available at the conference venue or sent after the meeting.

Post meeting reporting

Meeting organizers are required to provide a summary document to the Council after the

meeting, including the diversity statistics of the meeting participants, (gender, geography, and career stage).

Awards (see

SMBE provides several types of pre-conference awards, which should be administered via the conference abstract submission system. It is essential that time is allowed for awardees to be chosen and applicants notified before Early Bird registration closes so that attendees can make informed financial decisions about registration options and travel.

Those receiving awards that include registration and travel need to pay in the first instance and will then be reimbursed by SMBE.  This applies to all but recipients of Registration-only awards, who need  a code to put in to the online registration system to avoid payment.

SMBE-appointed committees select the recipients of travel awards.  All award applicants should be SMBE members.

SMBE’s Faculty, Best Paper, Fitch, and best poster awards are presented at the Awards Ceremony. All awardess, including all eight Fitch presenters, attending the meeting are eligible for free Gala Dinner tickets.

1.     Faculty awards

Faculty award-winners are reimbursed for registration and travel to the meeting.

Recipients of these awards should all be given the opportunity to present talks at the meeting, either in an ordinary symposium or the special symposium or in slots set aside for them in the Open Symposium.  The Council members responsible for these awards should be informed of the latest dates that lectures can be incorporated  into the programme.

2.     Fitch awards

All those selected to present in the Fitch Symposium are eligible for a free Gala Dinner ticket, and will be reimbursed for travel and accommodation.

The Council will appoint two separate committees, one to review the initial applicants to the Fitch symposium and another to determine the winner among the 8 finalists (see timeline above). Banquet tickets should be reserved for the 8 finalists.

3.     Undergraduate mentoring and diversity travel awards

Award-winners are reimbursed for registration and a contribution toward travel to the meeting.

10 undergraduate mentoring and diversity awards are available each year to undergraduate students that submit abstracts. The total value of each of  these awards is $1500 to $2000, depending whether intercontinental travel is involved. This covers registration, with the rest intended for travel.   Registration fees are to be charged directly to SMBE, so that students do not have to pay themselves (the amount of registration cost being deducted from the final value of their award, and the award recipients informed at time of notification of the value of their award to be used for travel and lodging).

One or two SMBE Councillors assigned by the Council will take charge of this selection, with a recommended bias towards funding those selected to give oral presentations, keeping the Statement of Diversity in mind.

The process consists of finding a mentor for each student so that they can be guided through the conference. In addition, a dinner should be arranged for all 10 students, their 10 mentors and the Council members who organize the activity. The conference organizers should reserve 10 banquet tickets for the awardees (to be charged to SMBE) and liaise with the Councillors in order to find an appropriate restaurant for the mentoring dinner, which is usually on the first full day.). The Councillors will send the list of awardees and their details to the meeting organizers and the PCO so that they can be registered automatically.

All undergraduate awardees should present their posters in the same poster session and their posters grouped together.

4.     Graduate and postdoc travel awards

Award-winners are reimbursed for registration and travel to the meeting.

SMBE provides graduate and postdoc travel awards for the purpose of enhancing gender and geographic diversity. The awards are chosen from eligible applicants who are SMBE members and who have expressed a desire to be considered for such awards. The Past-President, usually in conjunction with the LOC, will head a committee to determine the awards.

5.     Poster awards

The poster prizes will be decided by a committee convened by the President-Elect. Poster prizes consist of up to 9 prizes of $500 each, to be distributed in the 3 categories of postdoc, graduate student, and undergraduate prizes (it does not have to be 3 each).

6.     Best GBE and MBE papers awards

Award recipients receive registration waivers, travel awards to attend the meeting, and a Gala ticket.

7.     Registration awards

These are registration only awards, and there are usually more of these than awards that include travel.

8.     Carer travel awards

SMBE provides additional travel awards for our members who are also primary carers (for example caring for children or dependent adults, including adult children with a disability or an elderly relative). This award can be used in the manner of choosing of the awardee, for example for procuring child care or dependent care at home (e.g., flying a relative to help at home while the delegate is at the meeting; hiring a professional). Priority will be given to early-career scientists and according to need (e.g., younger children, disabled children or adults).

Information about Carer Travel Awards should be included in emails promoting conference registration and applications should be through the registration system. The decision on who is granted an award will be made by a committee of at least one person designated by Council. It shall be noted that people in need of an early decision can email a request to the organizers and/or council member in charge of the Carer Travel Award process.  


Payment for registration

The online registration system should accept all major credit and debit cards using the conventional inputting mechanism.  Credit card fees charged to the conference should be less than 3% per transaction.

Registration fees

SMBE members receive discounted registration. The discount for SMBE members must be at least $30, but a higher differential between member and non-member registration is allowed. Students and postdocs should be given a further discounted registration rate as well; the discount should be larger for graduate students than for postdocs.  The conference registration page should allow conference delegates the opportunity to join SMBE on the spot, e.g. by linking to the SMBE website membership page in a new window (currently Finally, while most registrants will use the website, it should also be possible to register onsite (‘walk-ins’).

Registration data

Registration data, including lists of delegates, should only be given to SMBE officials and used for SMBE business.  Third parties, including organizers of future conferences, should not be given the lists without express permission from SMBE.

This determines eligibility for certain awards and allows SMBE to maintain a participant database with student or postdoc status recorded (this is essential for determining poster and travel award eligibility, for instance). The conference organizers must maintain a database of participants with this information, as well as abstract numbers and titles as separate entries, email addresses, affiliations, etc.

Registration should include declarations of:

·  career stage (faculty, postdoc, graduate student, undergraduate, other)

gender,(with both a write-in option for non-gender conforming participants who prefer to specify and the option omit             this question).

Registration giveaways at the meeting

Printed conference material should be kept to a minimum. Sponsors should be encouraged to provide advertisements and information on the conference website or app or instead of printed flyers.


Each delegate should be provided with a badge. This must not include advertising promotion for any journal or society other than MBE/GBE and SMBE, though non-journal sponsors may sponsor lanyards. It is desirable to have badges that designate Editors and Associate Editors of the journals (sometimes provided by the MBE EiC) as well as a separate designation for Council members, and/or speakers, though this is the option of the organizers.

Other swag (bags, bottles, USB thumb drives, etc.)

Should be kept to a minimum to reduce environmental impact and should avoid advertising for journals directly competing with society journals.  

Conference website, programme, and app

SMBE conference promotion should consider environmental impact and minimize the use of printed materials.


Must include:

promotion of travel and child care awards

SMBE policies on harassment and broadcasting (text in Appendix to this document)

All images either posted online or used in emails related to the conference should be approved by the Council liaison and take gender balance and other demographic issues into consideration, regarding the people shown in the images. When possible, images from previous SMBE meetings should be used.


The timetable should ideally be available in three formats:

●       “at-a-glance” format, simply detailing the session/symposia times and locations.

●       a more detailed version with each speaker shown in column format so that parallel talks are on the same row. This helps         participants plan their schedule. Once the meeting starts, it should be updated live online (or at least daily), since changes       do arise.

●       a detailed online-only booklet with each speaker listed along with all co-authors, affiliations, and abstract.

Be sure that all authors are visible in the complete online program, not just the presenting author, since many people choose to attend a talk based on the laboratory or senior author. It is helpful if this information can be provided in column format.

The programme should include SMBE policies on harassment and broadcasting (text in Appendix) and an email contact to report any violations of these policies. 

The most updated printed or printable conference programme should be the version with concurrent sessions in columns and concurrent talks in rows to make it easy to choose a path.

Additional requirements for the online programme

A participant list should be provided in the web programme.

The entire conference program, complete with timetables, should be made available for download to laptops or mobile devices, usually in PDF or Excel format.

The online programme should also contain all the logistical details for the conference, including the best and most cost-effective means of ground and air transportation to the meeting location.

Essential conference app features

●       Available in both iPhone and Android formats

●       Useable offline, since many travelers do not have a data plan and some hotels charge fees for wifi. Wifi quality can also be unreliable at large meeting venues.

●       If possible should not require registration (unless necessary for those who want  to customize it, for example to create a personalized program)

●       Updateable and updated daily

●       Include first author name, surname, and talk title, hyperlinked to abstract with all authors.

●       Allow announcements

●       Include SMBE policies on harassment and social media (text in Appendix) with quick email link to report violations

●       Include quick link so that a poster presenter can invite another meeting participant to her/his poster. (This should not require composing an email each time.)

●        Include, if possible, the ability to create a personalized schedule, selecting talks and/or abstracts to attend, by clicking on (such as “liking” or saving to schedule) either the talk title, speaker name, or abstract from any of its views.  This may include the option to set reminders. Reminders, alerts, or notifications (for example of poster sessions closing or a talk about to start) should always be inaudible.



The conference venue should have at least one room that can hold at least 80% of delegates. Past experience indicates that for the plenary talks approximately 80% of the delegates will attend. Therefore, it is preferable that there is a room to hold this number. If this is not possible, then there should be a facility to relay the plenary lectures to another comfortable room via video link.

The venue should additionally have enough rooms for all parallel sessions and these should be sufficiently large to accommodate approximately one third of the conference, given the difficulty in predicting the numbers of delegates that attend any given talk. The rooms should be located no more than a 1-2 min walk from each other and have seating or aisles arranged to facilitate movement between sessions.

Kindly ask the venue to refrain from using air freshener during the conference in all locations, including registration desk and lobbies. Some participants are allergic to it and it exposes all participants to poor air quality.

Free, secure wifi should be available throughout the venue.

Onsite child care

Organizers will arrange for onsite (in the same building as the conference) child care, as this is an issue of great importance to the members of the Society. SMBE will help defray the cost of child care. Please communicate early and often with the Society as to the costs, barriers and opportunities for child care. Ideally the onsite location should be no more than a 5 minute walk from the sessions but not right next to a room where there are talks. Parents need quick access but the sound level can be that of a play-room setting.

Speaker set-up

There should be a set-up room for speakers to check their presentations. The preferred presentation file format is pdf, but ideally both Powerpoint and Keynote should be accepted. Both modern (current OS) Apple and PC computers should be provided for presenters.


The LOC is responsible for liaising with SMBE and the PCO to ensure that all insurance requirements are met.

Appendix 1: SMBE policies

Policy on harassment, discrimination and liability
SMBE and the Annual Meeting organizers are dedicated to providing a safe, hospitable, and productive environment for all attendees. Accordingly, the SMBE Annual Meeting prohibits all forms of discrimination and harassment. Behaviour that undermines the integrity of intellectual discourse and interactions will not be tolerated. This applies to all conference participants, including staff, volunteers, and attendees. If a participant engages in harassing or discriminatory behaviour, the SMBE Annual Meeting organizers reserve the right to take action ranging from a simple warning to the offender to expulsion from the conference. If you have a question or concern about this policy or would like to report an incident involving yourself or another person, please contact any member of the Local Organizing Committee or email [email address for the appropriate year’s conference PCO]. We take such issues seriously and will maintain your confidentiality (unless legally compelled otherwise). Neither SMBE nor the SMBE Annual Meeting organizers shall be responsible for any defamatory, offensive, or illegal conduct of Meeting participants, and shall not be held liable for personal injury, property damage, theft or damage of any kind suffered by the participants at or in connection with the SMBE Annual Meeting.

Broadcasting policy
The SMBE Annual Meeting supports the communication and discussion of science. Information presented at the Meeting (in oral or poster format) may be reported and discussed by attendees and science writers via blogs, Twitter, or other formats, unless any of the authors requests otherwise. We do request that communications are respectful and do not directly reproduce visual materials (e.g., no posting of photos of slides or posters) unless permission is obtained from the presenter or if they have already made this information freely available in an open-source forum. If a presenter does not want information from his/her presentation to be photographed at all, or broadcast, they should make this clear in their talk/poster and we ask that attendees respect this. If you have questions or concerns about this policy, or would like to report an abuse of it, please contact any member of the Local Organizing Committee or email [email address for that year’s conference PCO].

Appendix 2: Call for proposals for conference

The President-Elect issues a call for proposals five years (e.g. call issued in 2017 for meeting in 2021) before the conference year, following the rotation below:

●       North America

●       Europe

●       Rest of the World

Applicants will be required to submit written proposals following a standard template to SMBE Council.  Applicants are required to work with SMBE’s designated PCO.

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Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation

Thu, 22 Feb 2018 00:00:00 GMT

Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1–5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.

Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure

Wed, 21 Feb 2018 00:00:00 GMT

The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = πN/πS) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (Ne) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus—two mouse subspecies with different Ne. Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small Ne (M. m. musculus) was three times higher than that observed for that with large Ne (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population.

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention

Wed, 21 Feb 2018 00:00:00 GMT

Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21–22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions. Here, we define a deterministic model that represents the propagation of active TEs, aspects of the host response and the accumulation of silenced TEs. We describe general properties of the model and also fit it to biological data in order to explore two questions. The first is why two overlapping pathways are maintained, given that both are likely energetically expensive. Under our model, RdDM silenced TEs effectively even when the initiation of silencing was weak. This relationship implies that only a small amount of RNAi is needed to initiate TE silencing, but reinforcement by RdDM is necessary to efficiently counter TE propagation. Second, we investigated the reliance of the host response on rates of TE deletion. The model predicted that low levels of deletion lead to few active TEs, suggesting that silencing is most efficient when methylated TEs are retained in the genome, thereby providing one explanation for the large size of plant genomes.

Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

Wed, 21 Feb 2018 00:00:00 GMT

There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.

Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism

Wed, 14 Feb 2018 00:00:00 GMT

Human infection with the gastrointestinal pathogen Campylobacter jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analyzed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multihost (ecological generalist) ST-21 and ST-45 clonal complexes (CCs). Combined nucleotide and amino acid sequence analysis identified 12 human-only amino acid KPAX clusters among polyphyletic lineages within the common disease causing CC21 group isolates, with no such clusters among CC45 isolates. Isolate sequence types within human-only CC21 group KPAX clusters have been sampled from other hosts, including poultry, so rather than representing unsampled reservoir hosts, the increase in relative frequency in human infection potentially reflects a genetic bottleneck at the point of human infection. Consistent with this, sequence enrichment analysis identified nucleotide variation in genes with putative functions related to human colonization and pathogenesis, in human-only clusters. Furthermore, the tight clustering and polyphyly of human-only lineage clusters within a single CC suggest the repeated evolution of human association through acquisition of genetic elements within this complex. Taken together, combined nucleotide and amino acid analysis of large isolate collections may provide clues about human niche tropism and the nature of the forces that promote the emergence of clinically important C. jejuni lineages.

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

Wed, 14 Feb 2018 00:00:00 GMT

Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small. Here, we took advantage of methods for culturing H. defensa outside of aphids to generate complete genomes and transcriptome data for four strains of H. defensa from the pea aphid Acyrthosiphon pisum. Chosen strains also spanned the breadth of the H. defensa phylogeny and differed in strength of protection conferred against parasitoids. Results indicated that strains shared most genes with roles in nutrient acquisition, metabolism, and essential housekeeping functions. In contrast, the inventory of mobile genetic elements varied substantially, which generated strain specific differences in gene content and genome architecture. In some cases, specific traits correlated with differences in protection against parasitoids, but in others high variation between strains obscured identification of traits with likely roles in defense. Transcriptome data generated continuous distributions to genome assemblies with some genes that were highly expressed and others that were not. Single molecule real-time sequencing further identified differences in DNA methylation patterns and restriction modification systems that provide defense against phage infection.

Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome

Thu, 08 Feb 2018 00:00:00 GMT

Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth’s cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was >90%. Three genomic islands were identified in the E. antarcticum B7 genome. These islands contained genes involved in flagella biosynthesis and chemotaxis, as well as enzymes for carotenoid biosynthesis. Clustering of cold shock proteins by Ka/Ks ratio suggests the occurrence of a positive selection over these genes. Neighbor-joining clustering of complete genomes showed that the E. sibiricum was the most closely related to E. antarcticum. A total of 92 genes were shared between Exiguobacterium and Psychrobacter. A reduction in the genomic content of E. antarcticum B7 was observed. It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. In our study, eight genomes of Exiguobacterium and Psychrobacter were compared and analysed. Psychrobacter showed higher genomic plasticity and E. antarcticum B7 presented a large decrease in genomic content without changing its ability to grow in cold environments.

The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity

Tue, 06 Feb 2018 00:00:00 GMT

Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Mon, 05 Feb 2018 00:00:00 GMT

Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.

An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae

Sat, 03 Feb 2018 00:00:00 GMT

Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.