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.

Financing

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

When

What

Notes

Last day of the conference of the preceding year.

Initial website goes live

 

Includes:

●       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

Duration

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.

Timeslots

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 http://www.smbe.org/smbe/AWARDS.aspx)

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.  

Registration

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 http://www.smbe.org/smbe/MEMBERSHIP.aspx). 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.

Badges

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.

Website

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.

Programme

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.

Venue

Rooms

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.

Insurance

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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Molecular Biology and Evolution

Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life

Tue, 11 Sep 2018 00:00:00 GMT

Julie Marin and S. Blair Hedges

Patterns of Ancestral Animal Codon Usage Bias Revealed through Holozoan Protists

Wed, 29 Aug 2018 00:00:00 GMT

Abstract
Choanoflagellates and filastereans are the closest known single celled relatives of Metazoa within Holozoa and provide insight into how animals evolved from their unicellular ancestors. Codon usage bias has been extensively studied in metazoans, with both natural selection and mutation pressure playing important roles in different species. The disparate nature of metazoan codon usage patterns prevents the reconstruction of ancestral traits. However, traits conserved across holozoan protists highlight characteristics in the unicellular ancestors of Metazoa. Presented here are the patterns of codon usage in the choanoflagellates Monosiga brevicollis and Salpingoeca rosetta, as well as the filasterean Capsaspora owczarzaki. Codon usage is shown to be remarkably conserved. Highly biased genes preferentially use GC-ending codons, however there is limited evidence this is driven by local mutation pressure. The analyses presented provide strong evidence that natural selection, for both translational accuracy and efficiency, dominates codon usage bias in holozoan protists. In particular, the signature of selection for translational accuracy can be detected even in the most weakly biased genes. Biased codon usage is shown to have coevolved with the tRNA species, with optimal codons showing complementary binding to the highest copy number tRNA genes. Furthermore, tRNA modification is shown to be a common feature for amino acids with higher levels of degeneracy and highly biased genes show a strong preference for using modified tRNAs in translation. The translationally optimal codons defined here will be of benefit to future transgenics work in holozoan protists, as their use should maximise protein yields from edited transgenes.

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

Sat, 25 Aug 2018 00:00:00 GMT

Abstract
Multiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of nonsynonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.

Xenacoelomorph Neuropeptidomes Reveal a Major Expansion of Neuropeptide Systems during Early Bilaterian Evolution

Fri, 24 Aug 2018 00:00:00 GMT

Abstract
Neuropeptides are neurosecretory signaling molecules in protostomes and deuterostomes (together Nephrozoa). Little, however, is known about the neuropeptide complement of the sister group of Nephrozoa, the Xenacoelomorpha, which together form the Bilateria. Because members of the xenacoelomorph clades Xenoturbella, Nemertodermatida, and Acoela differ extensively in their central nervous system anatomy, the reconstruction of the xenacoelomorph and bilaterian neuropeptide complements may provide insights into the relationship between nervous system evolution and peptidergic signaling. Here, we analyzed transcriptomes of seven acoels, four nemertodermatids, and two Xenoturbella species using motif searches, similarity searches, mass spectrometry and phylogenetic analyses to characterize neuropeptide precursors and neuropeptide receptors. Our comparison of these repertoires with previously reported nephrozoan and cnidarian sequences shows that the majority of annotated neuropeptide GPCRs in cnidarians are not orthologs of specific bilaterian neuropeptide receptors, which suggests that most of the bilaterian neuropeptide systems evolved after the cnidarian–bilaterian evolutionary split. This expansion of more than 20 peptidergic systems in the stem leading to the Bilateria predates the evolution of complex nephrozoan organs and nervous system architectures. From this ancient set of neuropeptides, acoels show frequent losses that correlate with their divergent central nervous system anatomy. We furthermore detected the emergence of novel neuropeptides in xenacoelomorphs and their expansion along the nemertodermatid and acoel lineages, the two clades that evolved nervous system condensations. Together, our study provides fundamental insights into the early evolution of the bilaterian peptidergic systems, which will guide future functional and comparative studies of bilaterian nervous systems.

Limited Evidence for Parallel Molecular Adaptations Associated with the Subterranean Niche in Mammals: A Comparative Study of Three Superorders

Mon, 20 Aug 2018 00:00:00 GMT

Abstract
Among mammals, several lineages have independently adapted to a subterranean niche and possess similar phenotypic traits for burrowing (e.g., cylindrical bodies, short limbs, and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, and the absence of light. In contrast, almost nothing is known regarding molecular adaptations in other subterranean lineages (e.g., true moles and golden moles). Therefore, the extent to which the recurrent phenotypic adaptations of divergent subterranean taxa have arisen via parallel routes of molecular evolution remains untested. To address these issues, we analyzed ∼8,000 loci in 15 representative subterranean taxa of four independent transitions to an underground niche for signatures of positive selection and convergent amino acid substitutions. Complementary analyses were performed in nonsubterranean “control” taxa to assess the biological significance of results. We found comparable numbers of positively selected genes in each of the four subterranean groups; however, correspondence in terms of gene identity between gene sets was low. Furthermore, we did not detect evidence of more convergent amino acids among subterranean species pairs compared with levels found between nonsubterranean controls. Comparisons with nonsubterranean taxa also revealed loci either under positive selection or with convergent substitutions, with similar functional enrichment (e.g., cell adhesion, immune response, and coagulation). Given the limited indication that positive selection and convergence occurred in the same loci, we conclude that selection may have acted on different loci across subterranean mammal lineages to produce similar phenotypes.

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids

Tue, 14 Aug 2018 00:00:00 GMT

Joana Isabel Meier, David Alexander Marques, Catherine Elise Wagner, Laurent Excoffier, and Ole Seehausen

Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex

Thu, 09 Aug 2018 00:00:00 GMT

Abstract
Deep coalescence and introgression make it challenging to infer phylogenetic relationships among closely related species that arose through radiative speciation events. Despite numerous phylogenetic analyses and the availability of whole genomes, the phylogeny in the Anopheles gambiae species complex has not been confidently resolved. Here we extract over 80, 000 coding and noncoding short segments (called loci) from the genomes of six members of the species complex and use a Bayesian method under the multispecies coalescent model to infer the species tree, which takes into account genealogical heterogeneity across the genome and uncertainty in the gene trees. We obtained a robust estimate of the species tree from the distal region of the X chromosome: (A. merus, ((A. melas, (A. arabiensis, A. quadriannulatus)), (A. gambiae, A. coluzzii))), with A. merus to be the earliest branching species. This species tree agrees with the chromosome inversion phylogeny and provides a parsimonious interpretation of inversion and introgression events. Simulation informed by the real data suggest that the coalescent approach is reliable while the sliding-window analysis used in a previous phylogenomic study generates artifactual species trees. Likelihood ratio test of gene flow revealed strong evidence of autosomal introgression from A. arabiensis into A. gambiae (at the average rate of ∼0.2 migrants per generation), but not in the opposite direction, and introgression of the 3 L chromosomal region from A. merus into A. quadriannulatus. Our results highlight the importance of accommodating incomplete lineage sorting and introgression in phylogenomic analyses of species that arose through recent radiative speciation events.

A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences

Tue, 07 Aug 2018 00:00:00 GMT

Abstract
Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication.

A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data

Tue, 07 Aug 2018 00:00:00 GMT

Abstract
Transposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads. Tests of the method on simulated data show that it can accurately estimate the allele frequencies of TE insertions even when the PE sequencing is conducted at a relatively low coverage (=5X). The method can also detect TE insertions under strong selection, and the detection ability increases with sample size in a population, although a substantial fraction of actual TE insertions under selection may be undetected. Application of the ML method to genomic sequencing data collected from a natural Daphnia pulex population shows that, on the one hand, most (>90%) TE insertions present in the reference D. pulex genome are either fixed or nearly fixed (with allele frequencies >0.95); on the other hand, among the nonreference TE insertions (i.e., those detected in some individuals in the population but absent from the reference genome), the majority (>70%) are still at low frequencies (<0.1). Finally, we detected a substantial fraction (∼9%) of nonreference TE insertions under selection.

Biophysical Inference of Epistasis and the Effects of Mutations on Protein Stability and Function

Thu, 02 Aug 2018 00:00:00 GMT

Abstract
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. The essential function of many proteins that fold into a specific structure is their ability to bind to a ligand, which can be assayed for thousands of mutated variants. However, binding assays do not distinguish whether mutations affect the stability of the binding interface or the overall fold. Here, we introduce a statistical method to infer a detailed energy landscape of how a protein folds and binds to a ligand by combining information from many mutated variants. We fit a thermodynamic model describing the bound, unbound, and unfolded states to high quality data of protein G domain B1 binding to IgG-Fc. We infer distinct folding and binding energies for each mutation providing a detailed view of how mutations affect binding and stability across the protein. We accurately infer the folding energy of each variant in physical units, validated by independent data, whereas previous high-throughput methods could only measure indirect changes in stability. While we assume an additive sequence–energy relationship, the binding fraction is epistatic due its nonlinear relation to energy. Despite having no epistasis in energy, our model explains much of the observed epistasis in binding fraction, with the remaining epistasis identifying conformationally dynamic regions.

Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Thu, 02 Aug 2018 00:00:00 GMT

Abstract
The rate of recombination impacts on rates of protein evolution for at least two reasons: it affects the efficacy of selection due to linkage and influences sequence evolution through the process of GC-biased gene conversion (gBGC). We studied how recombination, via gBGC, affects inferences of selection in gene sequences using comparative genomic and population genomic data from the collared flycatcher (Ficedula albicollis). We separately analyzed different mutation categories (“strong”-to-“weak,” “weak-to-strong,” and GC-conservative changes) and found that gBGC impacts on the distribution of fitness effects of new mutations, and leads to that the rate of adaptive evolution and the proportion of adaptive mutations among nonsynonymous substitutions are underestimated by 22–33%. It also biases inferences of demographic history based on the site frequency spectrum. In light of this impact, we suggest that inferences of selection (and demography) in lineages with pronounced gBGC should be based on GC-conservative changes only. Doing so, we estimate that 10% of nonsynonymous mutations are effectively neutral and that 27% of nonsynonymous substitutions have been fixed by positive selection in the flycatcher lineage. We also find that gene expression level, sex-bias in expression, and the number of protein–protein interactions, but not Hill–Robertson interference (HRI), are strong determinants of selective constraint and rate of adaptation of collared flycatcher genes. This study therefore illustrates the importance of disentangling the effects of different evolutionary forces and genetic factors in interpretation of sequence data, and from that infer the role of natural selection in DNA sequence evolution.

Within-Gene Shine–Dalgarno Sequences Are Not Selected for Function

Wed, 01 Aug 2018 00:00:00 GMT

Abstract
The Shine–Dalgarno (SD) sequence motif facilitates translation initiation and is frequently found upstream of bacterial start codons. However, thousands of instances of this motif occur throughout the middle of protein coding genes in a typical bacterial genome. Here, we use comparative evolutionary analysis to test whether SD sequences located within genes are functionally constrained. We measure the conservation of SD sequences across Enterobacteriales, and find that they are significantly less conserved than expected. Further, the strongest SD sequences are the least conserved whereas we find evidence of conservation for the weakest possible SD sequences given amino acid constraints. Our findings indicate that most SD sequences within genes are likely to be deleterious and removed via selection. To illustrate the origin of these deleterious costs, we show that ATG start codons are significantly depleted downstream of SD sequences within genes, highlighting the constraint that these sequences impose on the surrounding nucleotides to minimize the potential for erroneous translation initiation.

Evidence for a Unique DNA-Dependent RNA Polymerase in Cereal Crops

Tue, 24 Jul 2018 00:00:00 GMT

Abstract
Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.

Rapid Viral Symbiogenesis via Changes in Parasitoid Wasp Genome Architecture

Tue, 24 Jul 2018 00:00:00 GMT

Abstract
Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of the genus Fopius, this recent acquisition allows an unprecedented opportunity to examine early endogenization events. Massive amounts of virus-like particles (VLPs) are produced in wasp ovaries. Unlike most endogenous viruses of parasitoid wasps, the VLPs do not contain DNA, translating to major differences in parasitism-promoting strategies. Rapid changes include genomic rearrangement, loss of DNA processing proteins, and wasp control of viral gene expression. These events precede the full development of tissue-specific viral gene expression observed in older associations. These data indicate that viral endogenization can rapidly result in functional and evolutionary changes associated with genomic novelty and adaptation in parasitoids.

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent

Mon, 23 Jul 2018 00:00:00 GMT

Abstract
The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation of the multispecies coalescent, using transmodel Markov chain Monte Carlo to calculate the posterior probabilities of different species trees. BPP is suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here, we provide a practical guide to the use of BPP in species tree estimation. BPP is a command-line program that runs on linux, macosx, and windows. This protocol shows how to use both BPP 3.4 (http://abacus.gene.ucl.ac.uk/software/) and BPP 4.0 (https://github.com/bpp/).

Novel Bioinformatics Approach Identifies Transcriptional Profiles of Lineage-Specific Transposable Elements at Distinct Loci in the Human Dorsolateral Prefrontal Cortex

Fri, 20 Jul 2018 00:00:00 GMT

Abstract
Expression of transposable elements (TE) is transiently activated during human preimplantation embryogenesis in a developmental stage- and cell type-specific manner and TE-mediated epigenetic regulation is intrinsically wired in developmental genetic networks in human embryos and embryonic stem cells. However, there are no systematic studies devoted to a comprehensive analysis of the TE transcriptome in human adult organs and tissues, including human neural tissues. To investigate TE expression in the human Dorsolateral Prefrontal Cortex (DLPFC), we developed and validated a straightforward analytical approach to chart quantitative genome-wide expression profiles of all annotated TE loci based on unambiguous mapping of discrete TE-encoded transcripts using a de novo assembly strategy. To initially evaluate the potential regulatory impact of DLPFC-expressed TE, we adopted a comparative evolutionary genomics approach across humans, primates, and rodents to document conservation patterns, lineage-specificity, and colocalizations with transcription factor binding sites mapped within primate- and human-specific TE. We identified 654,665 transcripts expressed from 477,507 distinct loci of different TE classes and families, the majority of which appear to have originated from primate-specific sequences. We discovered 4,687 human-specific and transcriptionally active TEs in DLPFC, of which the prominent majority (80.2%) appears spliced. Our analyses revealed significant associations of DLPFC-expressed TE with primate- and human-specific transcription factor binding sites, suggesting potential cross-talks of concordant regulatory functions. We identified 1,689 TEs differentially expressed in the DLPFC of Schizophrenia patients, a majority of which is located within introns of 1,137 protein-coding genes. Our findings imply that identified DLPFC-expressed TEs may affect human brain structures and functions following different evolutionary trajectories. On one side, hundreds of thousands of TEs maintained a remarkably high conservation for ∼8 My of primates’ evolution, suggesting that they are likely conveying evolutionary-constrained primate-specific regulatory functions. In parallel, thousands of transcriptionally active human-specific TE loci emerged more recently, suggesting that they could be relevant for human-specific behavioral or cognitive functions.

Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea)

Thu, 19 Jul 2018 00:00:00 GMT

Abstract
Transcriptome-based exon capture methods provide an approach to recover several hundred markers from genomic DNA, allowing for robust phylogenetic estimation at deep timescales. We applied this method to a highly diverse group of venomous marine snails, Conoidea, for which published phylogenetic trees remain mostly unresolved for the deeper nodes. We targeted 850 protein coding genes (678,322 bp) in ca. 120 samples, spanning all (except one) known families of Conoidea and a broad selection of non-Conoidea neogastropods. The capture was successful for most samples, although capture efficiency decreased when DNA libraries were of insufficient quality and/or quantity (dried samples or low starting DNA concentration) and when targeting the most divergent lineages. An average of 75.4% of proteins was recovered, and the resulting tree, reconstructed using both supermatrix (IQ-tree) and supertree (Astral-II, combined with the Weighted Statistical Binning method) approaches, are almost fully supported. A reconstructed fossil-calibrated tree dates the origin of Conoidea to the Lower Cretaceous. We provide descriptions for two new families. The phylogeny revealed in this study provides a robust framework to reinterpret changes in Conoidea anatomy through time. Finally, we used the phylogeny to test the impact of the venom gland and radular type on diversification rates. Our analyses revealed that repeated losses of the venom gland had no effect on diversification rates, while families with a breadth of radula types showed increases in diversification rates, thus suggesting that trophic ecology may have an impact on the evolution of Conoidea.

Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments

Mon, 16 Jul 2018 00:00:00 GMT

Abstract
Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.

Evolution on the Biophysical Fitness Landscape of an RNA Virus

Thu, 28 Jun 2018 00:00:00 GMT

Abstract
Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics that propagates millions of independent small viral subpopulations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction, an atypical case in evolution. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs between molecular traits of viral proteins shape viral evolution.

Duplication of hsp-110 Is Implicated in Differential Success of Globodera Species under Climate Change

Thu, 28 Jun 2018 00:00:00 GMT

Abstract
Managing the emergence and spread of crop pests and pathogens is essential for global food security. Understanding how organisms have adapted to their native climate is key to predicting the impact of climate change. The potato cyst nematodes Globodera pallida and G. rostochiensis are economically important plant pathogens that cause yield losses of up to 50% in potato. The two species have different thermal optima that may relate to differences in the altitude of their regions of origin in the Andes. Here, we demonstrate that juveniles of G. pallida are less able to recover from heat stress than those of G. rostochiensis. Genome-wide analysis revealed that while both Globodera species respond to heat stress by induction of various protective heat-inducible genes, G. pallida experiences heat stress at lower temperatures. We use C. elegans as a model to demonstrate the dependence of the heat stress response on expression of Heat Shock Factor-1 (HSF-1). Moreover, we show that hsp-110 is induced by heat stress in G. rostochiensis, but not in the less thermotolerant G. pallida. Sequence analysis revealed that this gene and its promoter was duplicated in G. rostochiensis and acquired thermoregulatory properties. We show that hsp-110 is required for recovery from acute thermal stress in both C. elegans and in G. rostochiensis. Our findings point towards an underlying molecular mechanism that allows the differential expansion of one species relative to another closely related species under current climate change scenarios. Similar mechanisms may be true of other invertebrate species with pest status.

Specificity of the DNA Mismatch Repair System (MMR) and Mutagenesis Bias in Bacteria

Mon, 25 Jun 2018 00:00:00 GMT

Abstract
The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extremophile bacterium Deinococcus radiodurans ΔmutS1 and the model soil bacterium Pseudomonas fluorescens wild-type and MMR (Methyl-dependent Mismatch Repair-deficient) strains, we report the mutational features of these two important bacteria. We find that P. fluorescens has one of the highest MMR repair efficiencies among tested bacteria. We also discover that MMR of D. radiodurans preferentially repairs deletions, contrary to all other bacteria examined. We then, for the first time, quantify genome-wide efficiency and specificity of MMR in repairing different genomic regions and mutation types, by evaluating the P. fluorescens and D. radiodurans mutation data sets, along with previously reported ones of Bacillus subtilis subsp. subtilis, Escherichia coli, Vibrio cholerae, and V. fischeri. MMR in all six bacteria shares two general features: 1) repair efficiency is influenced by the neighboring base composition for both transitions and transversions, not limited to transversions as previously reported; and 2) MMR only recognizes indels <4 bp in length. This study demonstrates the power of mutation accumulation lines in quantifying DNA repair and mutagenesis patterns.

Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera

Tue, 19 Jun 2018 00:00:00 GMT

Abstract
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that interspecies hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of coevolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter. Here we describe many such candidates encoded by the Heterochromatin Protein 1 (HP1) gene family across Diptera, an insect Order that encompasses dramatic episodes of heterochromatic sequence turnover. Using BLAST, synteny analysis, and phylogenetic tree building across 64 Diptera genomes, we discovered a staggering 121 HP1 duplication events. In contrast, we observed virtually no gene duplication in gene families that share a common “chromodomain” with HP1s, including Polycomb and Su(var)3-9. The remarkably high number of Dipteran HP1 paralogs arises from distant clades undergoing convergent HP1 family amplifications. These independently derived, young HP1s span diverse ages, domain structures, and rates of molecular evolution, including episodes of positive selection. Moreover, independently derived HP1s exhibit convergent expression evolution. While ancient HP1 parent genes are transcribed ubiquitously, young HP1 paralogs are transcribed primarily in male germline tissue, a pattern typical of young genes. Pervasive gene youth, rapid evolution, and germline specialization implicate heterochromatin-encoded selfish elements driving recurrent HP1 gene family expansions. The 121 young genes offer valuable experimental traction for elucidating the germline processes shaped by Diptera’s many dramatic episodes of heterochromatin turnover.

GBE | Most Read

Genome Biology & Evolution

Highlight: The Evolutionary Arsenal of Aphids

Sat, 13 Oct 2018 00:00:00 GMT

Nature provides countless examples of evolutionary arms races, in which species develop adaptations and counter-adaptations in a struggle for survival and reproduction. Such arms races are common between predator and prey or between parasite and host. Understanding this coevolutionary process can aid in our ability to develop necessary countermeasures, such as overcoming bacterial resistance to antibiotics.

Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae

Tue, 18 Sep 2018 00:00:00 GMT

Abstract
Gene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, using the Solanaceae family as a model and Pfam domain families as a proxy for gene families, we investigated variation in gene family sizes across species and the likely factors contributing to the variation. We found that genes in highly variable families have high turnover rates and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high- and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggest that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.

Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution

Tue, 18 Sep 2018 00:00:00 GMT

Abstract
Endogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41–15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10−8 to 8.07 × 10−8 and 4.72 × 10−8 to 1.42 × 10−7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.

New Perspectives on the Evolutionary History of Vitellogenin Gene Family in Vertebrates

Tue, 18 Sep 2018 00:00:00 GMT

Abstract
Vitellogenin (Vtg) is a glycolipophosphoprotein produced by oviparous and ovoviviparous species and is the precursor protein of the yolk, an essential nutrient reserve for embryonic development and early larval stages. Vtg is encoded by a family of paralog genes whose number varies in the different vertebrate lineages. Its evolution has been the subject of considerable analyses but it remains still unclear. In this work, microsyntenic and phylogenetic analyses were performed in order to increase our knowledge on the evolutionary history of this gene family in vertebrates. Our results support the hypothesis that the vitellogenin gene family is expanded from two genes both present at the beginning of vertebrate radiation through multiple independent duplication events occurred in the diverse lineages.

Turning Vice into Virtue: Using Batch-Effects to Detect Errors in Large Genomic Data Sets

Mon, 10 Sep 2018 00:00:00 GMT

Abstract
It is often unavoidable to combine data from different sequencing centers or sequencing platforms when compiling data sets with a large number of individuals. However, the different data are likely to contain specific systematic errors that will appear as SNPs. Here, we devise a method to detect systematic errors in combined data sets. To measure quality differences between individual genomes, we study pairs of variants that reside on different chromosomes and co-occur in individuals. The abundance of these pairs of variants in different genomes is then used to detect systematic errors due to batch effects. Applying our method to the 1000 Genomes data set, we find that coding regions are enriched for errors, where ∼1% of the higher frequency variants are predicted to be erroneous, whereas errors outside of coding regions are much rarer (<0.001%). As expected, predicted errors are found less often than other variants in a data set that was generated with a different sequencing technology, indicating that many of the candidates are indeed errors. However, predicted 1000 Genomes errors are also found in other large data sets; our observation is thus not specific to the 1000 Genomes data set. Our results show that batch effects can be turned into a virtue by using the resulting variation in large scale data sets to detect systematic errors.

Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae

Fri, 07 Sep 2018 00:00:00 GMT

Abstract
Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0–3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.

Predicting Evolution of the Transcription Regulatory Network in a Bacteriophage

Sat, 01 Sep 2018 00:00:00 GMT

Abstract
Prediction of evolutionary trajectories has been an elusive goal, requiring a deep knowledge of underlying mechanisms that relate genotype to phenotype plus understanding how phenotype impacts organismal fitness. We tested our ability to predict molecular regulatory evolution in a bacteriophage (T7) whose RNA polymerase (RNAP) was altered to recognize a heterologous promoter differing by three nucleotides from the wild-type promoter. A mutant of wild-type T7 lacking its RNAP gene was passaged on a bacterial strain providing the novel RNAP in trans. Higher fitness rapidly evolved. Predicting the evolutionary trajectory of this adaptation used measured in vitro transcription rates of the novel RNAP on the six promoter sequences capturing all possible one-step pathways between the wild-type and the heterologous promoter sequences. The predictions captured some of the regulatory evolution but failed both in explaining 1) a set of T7 promoters that consistently failed to evolve and 2) some promoter evolution that fell outside the expected one-step pathways. Had a more comprehensive set of transcription assays been undertaken initially, all promoter evolution would have fallen within predicted bounds, but the lack of evolution in some promoters is unresolved. Overall, this study points toward the increasing feasibility of predicting evolution in well-characterized, simple systems.

Convergent Plastome Evolution and Gene Loss in Holoparasitic Lennoaceae

Wed, 29 Aug 2018 00:00:00 GMT

Abstract
The Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one of the last remaining independently evolved lineages of parasitic angiosperms lacking a published plastome. In this study, we present the assembled and annotated plastomes of two species spanning the crown node of Lennoaceae, Lennoa madreporoides and Pholisma arenarium, as well as their close autotrophic relative from the sister family Ehretiaceae, Tiquilia plicata. We find that the plastomes of L. madreporoides and P. arenarium are similar in size and gene content, and substantially reduced compared to T. plicata, consistent with trends seen in other holoparasitic lineages. In particular, most plastid genes involved in photosynthesis function have been lost, whereas housekeeping genes (ribosomal protein-coding genes, rRNAs, and tRNAs) are retained. One notable exception is the persistence of a rbcL open reading frame in P. arenarium but not L. madreporoides suggesting a nonphotosynthetic function for this gene. Of the retained coding genes, dN/dS ratios indicate that some remain under purifying selection, whereas others show relaxed selection. Overall, this study supports the mounting evidence for convergent plastome evolution in flowering plants following the shift to heterotrophy.

Genetic and Molecular Basis of Feather Diversity in Birds

Wed, 29 Aug 2018 00:00:00 GMT

Abstract
Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.

Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes

Sat, 25 Aug 2018 00:00:00 GMT

Abstract
Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these, and three additional aphid genome assemblies (Acyrthosiphon pisum, Diuraphis noxia, and Myzus persicae), we show that aphid genomes consistently encode similar gene numbers. We compare gene content, gene duplication, synteny, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites. Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth. Putative effector repertoires, originating from duplicated and other loci, have an unusual genomic organization and evolutionary history. We identify a highly conserved effector pair that is tightly physically linked in the genomes of all aphid species tested. In R. padi, this effector pair is tightly transcriptionally linked and shares an unknown transcriptional control mechanism with a subset of ∼50 other putative effectors and secretory proteins. This study extends our current knowledge on the evolution of aphid genomes and reveals evidence for an as-of-yet unknown shared control mechanism, which underlies effector expression, and ultimately plant parasitism.

Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus

Sat, 25 Aug 2018 00:00:00 GMT

Abstract
The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.

Mobile Elements Shape Plastome Evolution in Ferns

Sat, 25 Aug 2018 00:00:00 GMT

Abstract
Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.

Conotoxin Diversity in Chelyconus ermineus (Born, 1778) and the Convergent Origin of Piscivory in the Atlantic and Indo-Pacific Cones

Mon, 30 Jul 2018 00:00:00 GMT

Abstract
The transcriptome of the venom duct of the Atlantic piscivorous cone species Chelyconus ermineus (Born, 1778) was determined. The venom repertoire of this species includes at least 378 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. A total of three individuals were sequenced showing considerable intraspecific variation: each individual had many exclusive conotoxin precursors, and only 20% of all inferred mature peptides were common to all individuals. Three different regions (distal, medium, and proximal with respect to the venom bulb) of the venom duct were analyzed independently. Diversity (in terms of number of distinct members) of conotoxin precursor superfamilies increased toward the distal region whereas transcripts detected toward the proximal region showed higher expression levels. Only the superfamilies A and I3 showed statistically significant differential expression across regions of the venom duct. Sequences belonging to the alpha (motor cabal) and kappa (lightning-strike cabal) subfamilies of the superfamily A were mainly detected in the proximal region of the venom duct. The mature peptides of the alpha subfamily had the α4/4 cysteine spacing pattern, which has been shown to selectively target muscle nicotinic-acetylcholine receptors, ultimately producing paralysis. This function is performed by mature peptides having a α3/5 cysteine spacing pattern in piscivorous cone species from the Indo-Pacific region, thereby supporting a convergent evolution of piscivory in cones.

Genes Involved in Drosophila melanogaster Ovarian Function Are Highly Conserved Throughout Evolution

Fri, 27 Jul 2018 00:00:00 GMT

Abstract
This work presents a systematic approach to study the conservation of genes between fruit flies and mammals. We have listed 971 Drosophila genes involved in female reproduction at the ovarian level and systematically looked for orthologs in the Ciona, zebrafish, coelacanth, lizard, chicken, and mouse. Depending on the species, the percentage of these Drosophila genes with at least one ortholog varies between 69% and 78%. In comparison, only 42% of all the Drosophila genes have an ortholog in the mouse genome (P < 0.0001), suggesting a dramatically higher evolutionary conservation of ovarian genes. The 177 Drosophila genes that have no ortholog in mice and other vertebrates correspond to genes that are involved in mechanisms of oogenesis that are specific to the fruit fly or the insects. Among 759 genes with at least one ortholog in the zebrafish, 73 have an expression enriched in the ovary in this species (RNA-seq data). Among 760 genes that have at least one ortholog in the mouse; 76 and 11 orthologs are reported to be preferentially and exclusively expressed in the mouse ovary, respectively (based on the UniGene expressed sequence tag database). Several of them are already known to play a key role in murine oogenesis and/or to be enriched in the mouse/zebrafish oocyte, whereas others have remained unreported. We have investigated, by RNA-seq and real-time quantitative PCR, the exclusive ovarian expression of 10 genes in fish and mammals. Overall, we have found several novel candidates potentially involved in mammalian oogenesis by an evolutionary approach and using the fruit fly as an animal model.