SMBE Conference guidelines

Download a PDF of the Conference Guidelines here.
Additions to Conference Guidelines, Appendix 2, may be downloaded 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.  Please download instructions and template HERE. Applicants are required to work with SMBE’s designated PCO.


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Molecular Biology and Evolution

Withdrawn as Duplicate: The many nuanced evolutionary consequences of duplicated genes

Fri, 30 Nov 2018 00:00:00 GMT

The article 10.1093/molbev/msy216 has been withdrawn because it is a duplicate of 10.1093/molbev/msy210. The publisher regrets the error.

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

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Abstract
Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external data on phylogenies with two general methods. Method 1 allows external data to be mapped on the tree structure and used as visual characteristic in tree and data visualization. Method 2 plots the data with the tree side by side using different geometric functions after reordering the data based on the tree structure. These two methods integrate data with phylogeny for further exploration and comparison in the evolutionary biology context. Ggtree is available from http://www.bioconductor.org/packages/ggtree.

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Tue, 16 Oct 2018 00:00:00 GMT

Abstract
Adenosine deaminases (ADAs) play a pivotal role in regulating the level of adenosine, an important signaling molecule that controls a variety of cellular responses. Two distinct ADAs, ADA1 and adenosine deaminase growth factor (ADGF aka ADA2), are known. Cytoplasmic ADA1 plays a key role in purine metabolism and is widely distributed from prokaryotes to mammals. On the other hand, secreted ADGF/ADA2 is a cell-signaling protein that was thought to be present only in multicellular organisms. Here, we discovered a bacterial homologue of ADGF/ADA2. Bacterial and eukaryotic ADGF/ADA2 possess the dimerization and PRB domains characteristic for the family, have nearly identical catalytic sites, and show similar catalytic characteristics. Most surprisingly, the bacterial enzyme has a signal sequence similar to that of eukaryotic ADGF/ADA2 and is specifically secreted into the extracellular space, where it may potentially control the level of extracellular adenosine. This finding provides the first example of evolution of an extracellular eukaryotic signaling protein from a secreted bacterial analogue with identical activity and suggests a potential role of ADGF/ADA2 in bacterial communication.

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Wed, 10 Oct 2018 00:00:00 GMT

Abstract
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.

Understanding the Factors That Shape Patterns of Nucleotide Diversity in the House Mouse Genome

Mon, 08 Oct 2018 00:00:00 GMT

Abstract
A major goal of population genetics has been to determine the extent by which selection at linked sites influences patterns of neutral nucleotide diversity in the genome. Multiple lines of evidence suggest that diversity is influenced by both positive and negative selection. For example, in many species there are troughs in diversity surrounding functional genomic elements, consistent with the action of either background selection (BGS) or selective sweeps. In this study, we investigated the causes of the diversity troughs that are observed in the wild house mouse genome. Using the unfolded site frequency spectrum, we estimated the strength and frequencies of deleterious and advantageous mutations occurring in different functional elements in the genome. We then used these estimates to parameterize forward-in-time simulations of chromosomes, using realistic distributions of functional elements and recombination rate variation in order to determine whether selection at linked sites can explain the observed patterns of nucleotide diversity. The simulations suggest that BGS alone cannot explain the dips in diversity around either exons or conserved noncoding elements. A combination of BGS and selective sweeps produces deeper dips in diversity than BGS alone, but the inferred parameters of selection cannot fully explain the patterns observed in the genome. Our results provide evidence of sweeps shaping patterns of nucleotide diversity across the mouse genome and also suggest that infrequent, strongly advantageous mutations play an important role in this. The limitations of using the unfolded site frequency spectrum for inferring the frequency and effects of advantageous mutations are discussed.

Genomic Analyses of Human European Diversity at the Southwestern Edge: Isolation, African Influence and Disease Associations in the Canary Islands

Fri, 05 Oct 2018 00:00:00 GMT

Abstract
Despite the genetic resemblance of Canary Islanders to other southern European populations, their geographical isolation and the historical admixture of aborigines (from North Africa) with sub-Saharan Africans and Europeans have shaped a distinctive genetic makeup that likely affects disease susceptibility and health disparities. Based on single nucleotide polymorphism array data and whole genome sequencing (30×), we inferred that the last African admixture took place ∼14 generations ago and estimated that up to 34% of the Canary Islander genome is of recent African descent. The length of regions in homozygosis and the ancestry-related mosaic organization of the Canary Islander genome support the view that isolation has been strongest on the two smallest islands. Furthermore, several genomic regions showed significant and large deviations in African or European ancestry and were significantly enriched in genes involved in prevalent diseases in this community, such as diabetes, asthma, and allergy. The most prominent of these regions were located near LCT and the HLA, two well-known targets of selection, at which 40‒50% of the Canarian genome is of recent African descent according to our estimates. Putative selective signals were also identified in these regions near the SLC6A11-SLC6A1, KCNMB2, and PCDH20-PCDH9 genes. Taken together, our findings provide solid evidence of a significant recent African admixture, population isolation, and adaptation in this part of Europe, with the favoring of African alleles in some chromosome regions. These findings may have medical implications for populations of recent African ancestry.

FADS1 and the Timing of Human Adaptation to Agriculture

Mon, 01 Oct 2018 00:00:00 GMT

Abstract
Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced ∼8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet, or efficiency of selection due to increases in effective population size.

REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species

Wed, 26 Sep 2018 00:00:00 GMT

Abstract
Elucidating the genomic determinants of morphological differences between species is key to understanding how morphological diversity evolved. While differences in cis-regulatory elements are an important genetic source for morphological evolution, it remains challenging to identify regulatory elements involved in phenotypic differences. Here, we present Regulatory Element forward genomics (REforge), a computational approach that detects associations between transcription factor binding site divergence in putative regulatory elements and phenotypic differences between species. By simulating regulatory element evolution in silico, we show that this approach has substantial power to detect such associations. To validate REforge on real data, we used known binding motifs for eye-related transcription factors and identified significant binding site divergence in vision-impaired subterranean mammals in 1% of all conserved noncoding elements. We show that these genomic regions are significantly enriched in regulatory elements that are specifically active in mouse eye tissues, and that several of them are located near genes, which are required for eye development and photoreceptor function and are implicated in human eye disorders. Thus, our genome-wide screen detects widespread divergence of eye-regulatory elements and highlights regulatory regions that likely contributed to eye degeneration in subterranean mammals. REforge has broad applicability to detect regulatory elements that could be involved in many other phenotypes, which will help to reveal the genomic basis of morphological diversity.

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog

Tue, 25 Sep 2018 00:00:00 GMT

Abstract
We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.

Pseudogenes Provide Evolutionary Evidence for the Competitive Endogenous RNA Hypothesis

Tue, 25 Sep 2018 00:00:00 GMT

Abstract
The competitive endogenous RNA (ceRNA) hypothesis is an attractively simple model to explain the biological role of many putatively functionless noncoding RNAs. Under this model, there exist transcripts in the cell whose role is to titrate out microRNAs such that the expression level of another target sequence is altered. That it is logistically possible for expression of one microRNA recognition element (MRE)-containing transcript to affect another is seen in the multiple examples of pathogenic effects of inappropriate expression of MRE-containing RNAs. However, the role, if any, of ceRNAs in normal biological processes and at physiological levels is disputed. By comparison of parent genes and pseudogenes we show, both for a specific example and genome-wide, that the pseudo-3′ untranslated regions (3′UTRs) of expressed pseudogenes are frequently retained and are under selective constraint in mammalian genomes. We found that the pseudo-3′UTR of BRAFP1, a previously described oncogenic ceRNA, has reduced substitutions relative to its pseudo-coding sequence, and we show sequence constraint on MREs shared between the parent gene, BRAF, and the pseudogene. Investigation of RNA-seq data reveals expression of BRAFP1 in normal somatic tissues in human and in other primates, consistent with biological ceRNA functionality of this pseudogene in nonpathogenic cellular contexts. Furthermore, we find that on a genome-wide scale pseudo-3′UTRs of mammalian pseudogenes (n = 1,629) are under stronger selective constraint than their pseudo-coding sequence counterparts, and are more often retained and expressed. Our results suggest that many human pseudogenes, often considered nonfunctional, may have an evolutionarily constrained role, consistent with the ceRNA hypothesis.

A Single Pheromone Receptor Gene Conserved across 400 My of Vertebrate Evolution

Mon, 24 Sep 2018 00:00:00 GMT

Abstract
Pheromones are crucial for eliciting social and sexual behaviors in diverse animal species. The vomeronasal receptor type-1 (V1R) genes, encoding members of a pheromone receptor family, are highly variable in number and repertoire among mammals due to extensive gene gain and loss. Here, we report a novel pheromone receptor gene belonging to the V1R family, named ancient V1R (ancV1R), which is shared among most Osteichthyes (bony vertebrates) from the basal lineage of ray-finned fishes to mammals. Phylogenetic and syntenic analyses of ancV1R using 115 vertebrate genomes revealed that it represents an orthologous gene conserved for >400 My of vertebrate evolution. Interestingly, the loss of ancV1R in some tetrapods is coincident with the degeneration of the vomeronasal organ in higher primates, cetaceans, and some reptiles including birds and crocodilians. In addition, ancV1R is expressed in most mature vomeronasal sensory neurons in contrast with canonical V1Rs, which are sparsely expressed in a manner that is consistent with the “one neuron–one receptor” rule. Our results imply that a previously undescribed V1R gene inherited from an ancient Silurian ancestor may have played an important functional role in the evolution of vertebrate vomeronasal organ.

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Mon, 24 Sep 2018 00:00:00 GMT

Abstract
The rate of molecular evolution varies widely among species. Life history traits (LHTs) have been proposed as a major driver of these variations. However, the relative contribution of each trait is poorly understood. Here, we test the influence of metabolic rate (MR), longevity, and generation time (GT) on the nuclear and mitochondrial synonymous substitution rates using a group of isopod species that have made multiple independent transitions to subterranean environments. Subterranean species have repeatedly evolved a lower MR, a longer lifespan and a longer GT. We assembled the nuclear transcriptomes and the mitochondrial genomes of 13 pairs of closely related isopods, each pair composed of one surface and one subterranean species. We found that subterranean species have a lower rate of nuclear synonymous substitution than surface species whereas the mitochondrial rate remained unchanged. We propose that this decoupling between nuclear and mitochondrial rates comes from different DNA replication processes in these two compartments. In isopods, the nuclear rate is probably tightly controlled by GT alone. In contrast, mitochondrial genomes appear to replicate and mutate at a rate independent of LHTs. These results are incongruent with previous studies, which were mostly devoted to vertebrates. We suggest that this incongruence can be explained by developmental differences between animal clades, with a quiescent period during female gametogenesis in mammals and birds which imposes a nuclear and mitochondrial rate coupling, as opposed to the continuous gametogenesis observed in most arthropods.

Successive Domain Rearrangements Underlie the Evolution of a Regulatory Module Controlled by a Small Interfering Peptide

Fri, 07 Sep 2018 00:00:00 GMT

Abstract
The establishment of new interactions between transcriptional regulators increases the regulatory diversity that drives phenotypic novelty. To understand how such interactions evolve, we have studied a regulatory module (DDR) composed by three MYB-like proteins: DIVARICATA (DIV), RADIALIS (RAD), and DIV-and-RAD-Interacting Factor (DRIF). The DIV and DRIF proteins form a transcriptional complex that is disrupted in the presence of RAD, a small interfering peptide, due to the formation of RAD–DRIF dimers. This dynamic interaction result in a molecular switch mechanism responsible for the control of distinct developmental processes in plants. Here, we have determined how the DDR regulatory module was established by analyzing the origin and evolution of the DIV, DRIF, and RAD protein families and the evolutionary history of their interactions. We show that duplications of a pre-existing MYB domain originated the DIV and DRIF protein families in the ancestral lineage of green algae, and, later, the RAD family in seed plants. Intraspecies interactions between the MYB domains of DIV and DRIF proteins are detected in green algae, whereas the earliest evidence of an interaction between DRIF and RAD proteins occurs in the gymnosperms, coincident with the establishment of the RAD family. Therefore, the DDR module evolved in a stepwise progression with the DIV–DRIF transcription complex evolving prior to the antagonistic RAD–DRIF interaction that established the molecular switch mechanism. Our results suggest that the successive rearrangement and divergence of a single protein domain can be an effective evolutionary mechanism driving new protein interactions and the establishment of novel regulatory modules.

Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo

Sat, 01 Sep 2018 00:00:00 GMT

Abstract
A driving hypothesis of evolutionary developmental biology is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here, we have tested Darwin’s “selection opportunity” hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a “developmental constraint” hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and postembryonically. To distinguish between adaptation and relaxation hypotheses, we investigated the evidence of positive selection on protein-coding genes in relation to their expression over development, in fly Drosophila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. First, we found that genes specifically expressed in late development have stronger signals of positive selection. Second, over the full transcriptome, genes with evidence for positive selection trend to be expressed in late development. Finally, genes involved in pathways with cumulative evidence of positive selection have higher expression in late development. Overall, there is a consistent signal that positive selection mainly affects genes and pathways expressed in late embryonic development and in adult. Our results imply that the evolution of embryogenesis is mostly conservative, with most adaptive evolution affecting some stages of postembryonic gene expression, and thus postembryonic phenotypes. This is consistent with the diversity of environmental challenges to which juveniles and adults are exposed.

Integrating Embryonic Development and Evolutionary History to Characterize Tentacle-Specific Cell Types in a Ctenophore

Thu, 30 Aug 2018 00:00:00 GMT

Abstract
The origin of novel traits can promote expansion into new niches and drive speciation. Ctenophores (comb jellies) are unified by their possession of a novel cell type: the colloblast, an adhesive cell found only in the tentacles. Although colloblast-laden tentacles are fundamental for prey capture among ctenophores, some species have tentacles lacking colloblasts and others have lost their tentacles completely. We used transcriptomes from 36 ctenophore species to identify gene losses that occurred specifically in lineages lacking colloblasts and tentacles. We cross-referenced these colloblast- and tentacle-specific candidate genes with temporal RNA-Seq during embryogenesis in Mnemiopsis leidyi and found that both sets of candidates are preferentially expressed during tentacle morphogenesis. We also demonstrate significant upregulation of candidates from both data sets in the tentacle bulb of adults. Both sets of candidates were enriched for an N-terminal signal peptide and protein domains associated with secretion; among tentacle candidates we also identified orthologs of cnidarian toxin proteins, presenting tantalizing evidence that ctenophore tentacles may secrete toxins along with their adhesive. Finally, using cell lineage tracing, we demonstrate that colloblasts and neurons share a common progenitor, suggesting the evolution of colloblasts involved co-option of a neurosecretory gene regulatory network. Together these data offer an initial glimpse into the genetic architecture underlying ctenophore cell-type diversity.

GBE | Most Read

Genome Biology & Evolution

IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing

Mon, 19 Nov 2018 00:00:00 GMT

Matthew Jobin, Haiko Schurz, and Brenna M. Henn

Effect of Collapsed Duplications on Diversity Estimates: What to Expect

Fri, 26 Oct 2018 00:00:00 GMT

Abstract
The study of segmental duplications (SDs) and copy-number variants (CNVs) is of great importance in the fields of genomics and evolution. However, SDs and CNVs are usually excluded from genome-wide scans for natural selection. Because of high identity between copies, SDs and CNVs that are not included in reference genomes are prone to be collapsed—that is, mistakenly aligned to the same region—when aligning sequence data from single individuals to the reference. Such collapsed duplications are additionally challenging because concerted evolution between duplications alters their site frequency spectrum and linkage disequilibrium patterns. To investigate the potential effect of collapsed duplications upon natural selection scans we obtained expectations for four summary statistics from simulations of duplications evolving under a range of interlocus gene conversion and crossover rates. We confirm that summary statistics traditionally used to detect the action of natural selection on DNA sequences cannot be applied to SDs and CNVs since in some cases values for known duplications mimic selective signatures. As a proof of concept of the pervasiveness of collapsed duplications, we analyzed data from the 1,000 Genomes Project. We find that, within regions identified as variable in copy number, diversity between individuals with the duplication is consistently higher than between individuals without the duplication. Furthermore, the frequency of single nucleotide variants (SNVs) deviating from Hardy–Weinberg Equilibrium is higher in individuals with the duplication, which strongly suggests that higher diversity is a consequence of collapsed duplications and incorrect evaluation of SNVs within these CNV regions.

From De Novo to “De Nono”: The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates

Mon, 22 Oct 2018 00:00:00 GMT

Abstract
The evolution of novel protein-coding genes from noncoding regions of the genome is one of the most compelling pieces of evidence for genetic innovations in nature. One popular approach to identify de novo genes is phylostratigraphy, which consists of determining the approximate time of origin (age) of a gene based on its distribution along a species phylogeny. Several studies have revealed significant flaws in determining the age of genes, including de novo genes, using phylostratigraphy alone. However, the rate of false positives in de novo gene surveys, based on phylostratigraphy, remains unknown. Here, I reanalyze the findings from three studies, two of which identified tens to hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered approach. Most putative de novo genes discovered in these investigations are no longer included in recently updated mouse gene sets. Using a combination of synteny information and sequence similarity searches, I show that ∼60% of the remaining 381 putative de novo genes share homology with genes from other vertebrates, originated through gene duplication, and/or share no synteny information with nonrodent mammals. These results led to an estimated rate of ∼12 de novo genes per million years in mouse. Contrary to a previous study (Wilson BA, Foy SG, Neme R, Masel J. 2017. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth. Nat Ecol Evol. 1:0146), I found no evidence supporting the preadaptation hypothesis of de novo gene formation. Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes.

Evidence of Polygenic Adaptation to High Altitude from Tibetan and Sherpa Genomes

Thu, 18 Oct 2018 00:00:00 GMT

Abstract
Although Tibetans and Sherpa present several physiological adjustments evolved to cope with selective pressures imposed by the high-altitude environment, especially hypobaric hypoxia, few selective sweeps at a limited number of hypoxia related genes were confirmed by multiple genomic studies. Nevertheless, variants at these loci were found to be associated only with downregulation of the erythropoietic cascade, which represents an indirect aspect of the considered adaptive phenotype. Accordingly, the genetic basis of Tibetan/Sherpa adaptive traits remains to be fully elucidated, in part due to limitations of selection scans implemented so far and mostly relying on the hard sweep model.In order to overcome this issue, we used whole-genome sequence data and several selection statistics as input for gene network analyses aimed at testing for the occurrence of polygenic adaptation in these high-altitude Himalayan populations. Being able to detect also subtle genomic signatures ascribable to weak positive selection at multiple genes of the same functional subnetwork, this approach allowed us to infer adaptive evolution at loci individually showing small effect sizes, but belonging to highly interconnected biological pathways overall involved in angiogenetic processes.Therefore, these findings pinpointed a series of selective events neglected so far, which likely contributed to the augmented tissue blood perfusion observed in Tibetans and Sherpa, thus uncovering the genetic determinants of a key biological mechanism that underlies their adaptation to high altitude.

Moraxella catarrhalis Restriction–Modification Systems Are Associated with Phylogenetic Lineage and Disease

Thu, 18 Oct 2018 00:00:00 GMT

Abstract
Moraxella catarrhalis is a human-adapted pathogen, and a major cause of otitis media (OM) and exacerbations of chronic obstructive pulmonary disease. The species is comprised of two main phylogenetic lineages, RB1 and RB2/3. Restriction–modification (R-M) systems are among the few lineage-associated genes identified in other bacterial genera and have multiple functions including defense against foreign invading DNA, maintenance of speciation, and epigenetic regulation of gene expression. Here, we define the repertoire of R-M systems in 51 publicly available M. catarrhalis genomes and report their distribution among M. catarrhalis phylogenetic lineages. An association with phylogenetic lineage (RB1 or RB2/3) was observed for six R-M systems, which may contribute to the evolution of the lineages by restricting DNA transformation. In addition, we observed a relationship between a mutually exclusive Type I R-M system and a Type III R-M system at a single locus conserved throughout a geographically and clinically diverse set of M. catarrhalis isolates. The Type III R-M system at this locus contains the phase-variable Type III DNA methyltransferase, modM, which controls a phasevarion (phase-variable regulon). We observed an association between modM presence and OM-associated middle ear isolates, indicating a potential role for ModM-mediated epigenetic regulation in OM pathobiology.

Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications

Tue, 18 Sep 2018 00:00:00 GMT

Abstract
Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs.

Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions

Sat, 15 Sep 2018 00:00:00 GMT

Abstract
Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.

Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments

Wed, 12 Sep 2018 00:00:00 GMT

Abstract
The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary process. In this study, our objectives were 1) to better understand the qualitative concordance between conclusions drawn from analyses of differential expression and changes in genic sequence and 2) to quantitatively test whether differentially expressed genes were enriched for sites putatively under positive selection within gene regions. To achieve this, we compared populations of fish (Poecilia mexicana) that have independently adapted to hydrogen-sulfide-rich environments in southern Mexico to adjacent populations residing in nonsulfidic waters. Specifically, we used RNA-sequencing data to compare both gene expression and DNA sequence differences between populations. Analyzing these two different data types led to similar conclusions about which biochemical pathways (sulfide detoxification and cellular respiration) were involved in adaptation to sulfidic environments. Additionally, we found a greater overlap between genes putatively under selection and differentially expressed genes than expected by chance. We conclude that considering both differential expression and changes in DNA sequence led to a more comprehensive understanding of how these populations adapted to extreme environmental conditions. Our results imply that changes in both gene expression and DNA sequence—sometimes at the same loci—may be involved in adaptation.