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.


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

Size of conference

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

Approximate timelines




Last day of the conference of the preceding year.

Initial website goes live



●       venue

●       opportunities for sponsorship

●       composition of the organizing committee

●       contact information for the conference organizer.

10 months before the date of the conference.

Call for symposia opens

See ‘Call for symposia’ below.

9 months before the date of the conference

Call for symposia closes


8.5 months before the conference

Notification of successful Symposia


8 months before the conference

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


8 months before the conference

Early bird registration opens

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

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

7 months before the conference

Abstract submission and award applications open

6 months before the conference

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

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

2-3 weeks prior to council decision of travel awards

Deadline for symposium organizers’ talk selection

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

2 weeks before early bird registration closes

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

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

4 months before the conference

Early bird registration closes, full price registration opens


2 months before the conference

Full programme available online

Until the conference begins

Full cost registration

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

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

Post-meeting survey

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

Structure of the conference


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

Council meeting

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

Scientific content

Limit oral presentations per person

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

Presenter information

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

Plenary lectures

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

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

Special symposia

Fitch Symposium

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

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

Open Symposium

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

Faculty awards symposium

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

Parallel symposia

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

Number of symposia

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

Call for symposia

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

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

Selection of the symposia

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

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

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

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

The LOC selects the talks for the Open Symposium.


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

Selecting speakers

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

Poster sessions

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

Social events

Please provide vegetarian/vegan options with all catering.

Breaks and catering

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

Welcome reception

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

Gala Dinner  (banquet)

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

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

Awards Ceremony

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

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

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

Post-conference survey

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

Certificates of attendance

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

Post meeting reporting

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

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

Awards (see

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

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

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

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

1.     Faculty awards

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

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

2.     Fitch awards

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

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

3.     Undergraduate mentoring and diversity travel awards

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

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

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

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

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

4.     Graduate and postdoc travel awards

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

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

5.     Poster awards

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

6.     Best GBE and MBE papers awards

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

7.     Registration awards

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

8.     Carer travel awards

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

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


Payment for registration

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

Registration fees

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

Registration data

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

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

Registration should include declarations of:

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

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

Registration giveaways at the meeting

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


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

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

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

Conference website, programme, and app

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


Must include:

promotion of travel and child care awards

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

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


The timetable should ideally be available in three formats:

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

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

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

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

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

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

Additional requirements for the online programme

A participant list should be provided in the web programme.

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

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

Essential conference app features

●       Available in both iPhone and Android formats

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

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

●       Updateable and updated daily

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

●       Allow announcements

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

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

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



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

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

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

Free, secure wifi should be available throughout the venue.

Onsite child care

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

Speaker set-up

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


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

Appendix 1: SMBE policies

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

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

Appendix 2: Call for proposals for conference

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

●       North America

●       Europe

●       Rest of the World

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

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OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

Tue, 29 Jan 2019 00:00:00 GMT

We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI. Version 10 users will benefit from pipeline improvements and a completely redesigned web-interface.

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

Tue, 29 Jan 2019 00:00:00 GMT

Genetic code deviations involving stop codons have been previously reported in mitochondrial genomes of several green plants (Viridiplantae), most notably chlorophyte algae (Chlorophyta). However, as changes in codon recognition from one amino acid to another are more difficult to infer, such changes might have gone unnoticed in particular lineages with high evolutionary rates that are otherwise prone to codon reassignments. To gain further insight into the evolution of the mitochondrial genetic code in green plants, we have conducted an in-depth study across mtDNAs from 51 green plants (32 chlorophytes and 19 streptophytes). Besides confirming known stop-to-sense reassignments, our study documents the first cases of sense-to-sense codon reassignments in Chlorophyta mtDNAs. In several Sphaeropleales, we report the decoding of AGG codons (normally arginine) as alanine, by tRNA(CCU) of various origins that carry the recognition signature for alanine tRNA synthetase. In Chromochloris, we identify tRNA variants decoding AGG as methionine and the synonymous codon CGG as leucine. Finally, we find strong evidence supporting the decoding of AUA codons (normally isoleucine) as methionine in Pycnococcus. Our results rely on a recently developed conceptual framework (CoreTracker) that predicts codon reassignments based on the disparity between DNA sequence (codons) and the derived protein sequence. These predictions are then validated by an evaluation of tRNA phylogeny, to identify the evolution of new tRNAs via gene duplication and loss, and structural modifications that lead to the assignment of new tRNA identities and a change in the genetic code.

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

Mon, 28 Jan 2019 00:00:00 GMT

Resolving the relationships of animals (Metazoa) is crucial to our understanding of the origin of key traits such as muscles, guts, and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part, this is because the genomes of deeply diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, that is, whether paralogs are excluded or included. We conclude that the placement of some deeply diverging lineages may exceed the limit of resolution afforded by the current methods based on comparisons of orthologous protein sequences, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.

A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies

Wed, 23 Jan 2019 00:00:00 GMT

New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular evolutionary patterns, and they will foster unbiased and precise dating of the tree of life.

New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

Tue, 22 Jan 2019 00:00:00 GMT

The resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

The Genome of Armadillidium vulgare (Crustacea, Isopoda) Provides Insights into Sex Chromosome Evolution in the Context of Cytoplasmic Sex Determination

Tue, 22 Jan 2019 00:00:00 GMT

The terrestrial isopod Armadillidium vulgare is an original model to study the evolution of sex determination and symbiosis in animals. Its sex can be determined by ZW sex chromosomes, or by feminizing Wolbachia bacterial endosymbionts. Here, we report the sequence and analysis of the ZW female genome of A. vulgare. A distinguishing feature of the 1.72 gigabase assembly is the abundance of repeats (68% of the genome). We show that the Z and W sex chromosomes are essentially undifferentiated at the molecular level and the W-specific region is extremely small (at most several hundreds of kilobases). Our results suggest that recombination suppression has not spread very far from the sex-determining locus, if at all. This is consistent with A. vulgare possessing evolutionarily young sex chromosomes. We characterized multiple Wolbachia nuclear inserts in the A. vulgare genome, none of which is associated with the W-specific region. We also identified several candidate genes that may be involved in the sex determination or sexual differentiation pathways. The A. vulgare genome serves as a resource for studying the biology and evolution of crustaceans, one of the most speciose and emblematic metazoan groups.

Development of the Mitochondrial Intermembrane Space Disulfide Relay Represents a Critical Step in Eukaryotic Evolution

Tue, 22 Jan 2019 00:00:00 GMT

The mitochondrial intermembrane space evolved from the bacterial periplasm. Presumably as a consequence of their common origin, most proteins of these compartments are stabilized by structural disulfide bonds. The molecular machineries that mediate oxidative protein folding in bacteria and mitochondria, however, appear to share no common ancestry. Here we tested whether the enzymes Erv1 and Mia40 of the yeast mitochondrial disulfide relay could be functionally replaced by corresponding components of other compartments. We found that the sulfhydryl oxidase Erv1 could be replaced by the Ero1 oxidase or the protein disulfide isomerase from the endoplasmic reticulum, however at the cost of respiration deficiency. In contrast to Erv1, the mitochondrial oxidoreductase Mia40 proved to be indispensable and could not be replaced by thioredoxin-like enzymes, including the cytoplasmic reductase thioredoxin, the periplasmic dithiol oxidase DsbA, and Pdi1. From our studies we conclude that the profound inertness against glutathione, its slow oxidation kinetics and its high affinity to substrates renders Mia40 a unique and essential component of mitochondrial biogenesis. Evidently, the development of a specific mitochondrial disulfide relay system represented a crucial step in the evolution of the eukaryotic cell.

Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations

Mon, 21 Jan 2019 00:00:00 GMT

Substitutions between chemically distant amino acids are known to occur less frequently than those between more similar amino acids. This knowledge, however, is not reflected in most codon substitution models, which treat all nonsynonymous changes as if they were equivalent in terms of impact on the protein. A variety of methods for integrating chemical distances into models have been proposed, with a common approach being to divide substitutions into radical or conservative categories. Nevertheless, it remains unclear whether the resulting models describe sequence evolution better than their simpler counterparts.We propose a parametric codon model that distinguishes between radical and conservative substitutions, allowing us to assess if radical substitutions are preferentially removed by selection. Applying our new model to a range of phylogenomic data, we find differentiating between radical and conservative substitutions provides significantly better fit for large populations, but see no equivalent improvement for smaller populations. Comparing codon and amino acid models using these same data shows that alignments from large populations tend to select phylogenetic models containing information about amino acid exchangeabilities, whereas the structure of the genetic code is more important for smaller populations.Our results suggest selection against radical substitutions is, on average, more pronounced in large populations than smaller ones. The reduced observable effect of selection in smaller populations may be due to stronger genetic drift making it more challenging to detect preferences. Our results imply an important connection between the life history of a phylogenetic group and the model that best describes its evolution.

Assessing the Response of Small RNA Populations to Allopolyploidy Using Resynthesized Brassica napus Allotetraploids

Thu, 17 Jan 2019 00:00:00 GMT

Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.

Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales

Thu, 17 Jan 2019 00:00:00 GMT

Pre-existing and de novo genetic variants can both drive adaptation to environmental changes, but their relative contributions and interplay remain poorly understood. Here we investigated the evolutionary dynamics in drug-treated yeast populations with different levels of pre-existing variation by experimental evolution coupled with time-resolved sequencing and phenotyping. We found a doubling of pre-existing variation alone boosts the adaptation by 64.1% and 51.5% in hydroxyurea and rapamycin, respectively. The causative pre-existing and de novo variants were selected on shared targets: RNR4 in hydroxyurea and TOR1, TOR2 in rapamycin. Interestingly, the pre-existing and de novo TOR variants map to different functional domains and act via distinct mechanisms. The pre-existing TOR variants from two domesticated strains exhibited opposite rapamycin resistance effects, reflecting lineage-specific functional divergence. This study provides a dynamic view on how pre-existing and de novo variants interactively drive adaptation and deepens our understanding of clonally evolving populations.

LFMM 2: Fast and Accurate Inference of Gene-Environment Associations in Genome-Wide Studies

Thu, 17 Jan 2019 00:00:00 GMT

Gene-environment association (GEA) studies are essential to understand the past and ongoing adaptations of organisms to their environment, but those studies are complicated by confounding due to unobserved demographic factors. Although the confounding problem has recently received considerable attention, the proposed approaches do not scale with the high-dimensionality of genomic data. Here, we present a new estimation method for latent factor mixed models (LFMMs) implemented in an upgraded version of the corresponding computer program. We developed a least-squares estimation approach for confounder estimation that provides a unique framework for several categories of genomic data, not restricted to genotypes. The speed of the new algorithm is several order faster than existing GEA approaches and then our previous version of the LFMM program. In addition, the new method outperforms other fast approaches based on principal component or surrogate variable analysis. We illustrate the program use with analyses of the 1000 Genomes Project data set, leading to new findings on adaptation of humans to their environment, and with analyses of DNA methylation profiles providing insights on how tobacco consumption could affect DNA methylation in patients with rheumatoid arthritis.Software availability: Software is available in the R package lfmm at

Evolution of an X-Linked miRNA Family Predominantly Expressed in Mammalian Male Germ Cells

Mon, 14 Jan 2019 00:00:00 GMT

MicroRNAs (miRNAs) are important posttranscriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during mammalian spermatogenesis are lacking. Herein, we sequenced small RNAs in highly purified mouse spermatogenic cells at different stages. We found that a family of X-linked miRNAs named spermatogenesis-related miRNAs (spermiRs) is predominantly expressed in the early meiotic phases and has a conserved testis-specific high expression pattern in different mammals. We identified one spermiR homolog in opossum; this homolog might originate from THER1, a retrotransposon that is active in marsupials but extinct in current placental mammals. SpermiRs have expanded rapidly with mammalian evolution and are diverged into two clades, spermiR-L and spermiR-R, which are likely to have been generated at least in part by tandem duplication mediated by flanking retrotransposable elements. Notably, despite having undergone highly frequent lineage-specific duplication events, the sequences encoding all spermiR family members are strictly located between two protein-coding genes, Slitrk2 and Fmr1. Moreover, spermiR-Ls and spermiR-Rs have evolved different expression patterns during spermatogenesis in different mammals. Intriguingly, the seed sequences of spermiRs, which are critical for the recognition of target genes, are highly divergent within and among mammals, whereas spermiR target genes largely overlap. When miR-741, the most highly expressed spermiR, is knocked out in cultured mouse spermatogonial stem cells (SSCs), another spermiR, miR-465a-5p, is dramatically upregulated and becomes the most abundant miRNA. Notably, miR-741−/− SSCs grow normally, and the genome-wide expression levels of mRNAs remain unchanged. All these observations indicate functional compensation between spermiR family members and strong coevolution between spermiRs and their targets.

The Expansion of Inosine at the Wobble Position of tRNAs, and Its Role in the Evolution of Proteomes

Thu, 27 Dec 2018 00:00:00 GMT

The modification of adenosine to inosine at the first position of transfer RNA (tRNA) anticodons (I34) is widespread among bacteria and eukaryotes. In bacteria, the modification is found in tRNAArg and is catalyzed by tRNA adenosine deaminase A, a homodimeric enzyme. In eukaryotes, I34 is introduced in up to eight different tRNAs by the heterodimeric adenosine deaminase acting on tRNA. This substrate expansion significantly influenced the evolution of eukaryotic genomes in terms of codon usage and tRNA gene composition. However, the selective advantages driving this process remain unclear. Here, we have studied the evolution of I34, tRNA adenosine deaminase A, adenosine deaminase acting on tRNA, and their relevant codons in a large set of bacterial and eukaryotic species. We show that a functional expansion of I34 to tRNAs other than tRNAArg also occurred within bacteria, in a process likely initiated by the emergence of unmodified A34-containing tRNAs. In eukaryotes, we report on a large variability in the use of I34 in protists, in contrast to a more uniform presence in fungi, plans, and animals. Our data support that the eukaryotic expansion of I34-tRNAs was driven by the improvement brought by these tRNAs to the synthesis of proteins highly enriched in certain amino acids.

Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach

Wed, 05 Dec 2018 00:00:00 GMT

We present a new phylogenetic approach, selection on amino acids and codons (SelAC), whose substitution rates are based on a nested model linking protein expression to population genetics. Unlike simpler codon models that assume a single substitution matrix for all sites, our model more realistically represents the evolution of protein-coding DNA under the assumption of consistent, stabilizing selection using a cost-benefit approach. This cost–benefit approach allows us to generate a set of 20 optimal amino acid-specific matrix families using just a handful of parameters and naturally links the strength of stabilizing selection to protein synthesis levels, which we can estimate. Using a yeast data set of 100 orthologs for 6 taxa, we find SelAC fits the data much better than popular models by 104–105 Akike information criterion units adjusted for small sample bias. Our results also indicated that nested, mechanistic models better predict observed data patterns highlighting the improvement in biological realism in amino acid sequence evolution that our model provides. Additional parameters estimated by SelAC indicate that a large amount of nonphylogenetic, but biologically meaningful, information can be inferred from existing data. For example, SelAC prediction of gene-specific protein synthesis rates correlates well with both empirical (r=0.33–0.48) and other theoretical predictions (r=0.45–0.64) for multiple yeast species. SelAC also provides estimates of the optimal amino acid at each site. Finally, because SelAC is a nested approach based on clearly stated biological assumptions, future modifications, such as including shifts in the optimal amino acid sequence within or across lineages, are possible.

GBE | Most Read

Genome Biology & Evolution

Evolution of Sex Chromosome Dosage Compensation in Animals: A Beautiful Theory, Undermined by Facts and Bedeviled by Details

Sat, 13 Apr 2019 00:00:00 GMT

Liuqi Gu and James R. Walters

Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae

Fri, 05 Apr 2019 00:00:00 GMT

The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived “nucleomorph” genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2′-O methylation of rRNA (but not snRNA). In B. natans, we found the previously undetected 5S rRNA as well as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18–21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.

Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer

Sat, 23 Mar 2019 00:00:00 GMT

The Chinese forest musk deer (Moschus berezovskii; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered. To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes. Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies. Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD. FMD-specific missense mutations were found in two PSGs (MHC class II antigen DRA and ADA) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases. Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion. Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD. Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species.

A Genome-Wide Association Study of Skin and Iris Pigmentation among Individuals of South Asian Ancestry

Thu, 21 Mar 2019 00:00:00 GMT

South Asia has a complex history of migrations and is characterized by substantial pigmentary and genetic diversity. For this reason, it is an ideal region to study the genetic architecture of normal pigmentation variation. Here, we present a meta-analysis of two genome-wide association studies (GWASs) of skin pigmentation using skin reflectance (M-index) as a quantitative phenotype. The meta-analysis includes a sample of individuals of South Asian descent living in Canada (N = 348), and a sample of individuals from two caste and four tribal groups from West Maharashtra, India (N = 480). We also present the first GWAS of iris color in South Asian populations. This GWAS was based on quantitative measures of iris color obtained from high-resolution iris pictures. We identified genome-wide significant associations of variants within the well-known gene SLC24A5, including the nonsynonymous rs1426654 polymorphism, with both skin pigmentation and iris color, highlighting the pleiotropic effects of this gene on pigmentation. Variants in the HERC2 gene (e.g., rs12913832) were also associated with iris color and iris heterochromia. Our study emphasizes the usefulness of quantitative methods to study iris color variation. We also identified novel genome-wide significant associations with skin pigmentation and iris color, but we could not replicate these associations due to the lack of independent samples. It will be critical to expand the number of studies in South Asian populations in order to better understand the genetic variation driving the diversity of skin pigmentation and iris color observed in this region.

Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation

Tue, 19 Mar 2019 00:00:00 GMT

PIWI proteins and their guiding Piwi-interacting (pi-) RNAs direct the silencing of target nucleic acids in the animal germline and soma. Although in mammal testes fetal piRNAs are involved in extensive silencing of transposons, pachytene piRNAs have additionally been shown to act in post-transcriptional gene regulation. The bulk of pachytene piRNAs is produced from large genomic loci, named piRNA clusters. Recently, the presence of reversed pseudogenes within piRNA clusters prompted the idea that piRNAs derived from such sequences might direct regulation of their parent genes. Here, we examine primate piRNA clusters and integrated pseudogenes in a comparative approach to gain a deeper understanding about mammalian piRNA cluster evolution and the presumed gene-regulatory role of pseudogene-derived piRNAs. Initially, we provide a broad analysis of the evolutionary relationships of piRNA clusters and their differential activity among six primate species. Subsequently, we show that pseudogenes in reserve orientation relative to piRNA cluster transcription direction generally do not exhibit signs of selection pressure and cause weakly conserved targeting of homologous genes among species, suggesting a lack of functional constraints and thus only a minor significance for gene regulation in most cases. Finally, we report that piRNA-producing loci generally tend to be located in active genomic regions with elevated gene and pseudogene density. Thus, we conclude that the presence of most pseudogenes in piRNA clusters might be regarded as a byproduct of piRNA cluster generation, whereas this does not exclude that some pseudogenes nevertheless play critical roles in individual cases.

Sex-Biased Gene Expression and Dosage Compensation on the Artemia franciscana Z-Chromosome

Wed, 13 Mar 2019 00:00:00 GMT

Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.

Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster

Mon, 11 Mar 2019 00:00:00 GMT

Codon usage patterns are affected by both mutational biases and translational selection. The frequency at which each codon is used in the genome is directly linked to the cellular concentrations of their corresponding tRNAs. Transfer RNA abundances—as well as the abundances of other potentially relevant factors, such as RNA-binding proteins—may vary across different tissues, making it possible that genes expressed in different tissues are subject to different translational selection regimes, and thus differ in their patterns of codon usage. These differences, however, are poorly understood, having been studied only in Arabidopsis, rice and human, with controversial results in human. Drosophila melanogaster is a suitable model organism to study tissue-specific codon adaptation given its large effective population size. Here, we compare 2,046 genes, each expressed specifically in one tissue of D. melanogaster. We show that genes expressed in different tissues exhibit significant differences in their patterns of codon usage, and that these differences are only partially due to differences in GC content, expression levels, or protein lengths. Remarkably, these differences are stronger when analyses are restricted to highly expressed genes. Our results strongly suggest that genes expressed in different tissues are subject to different regimes of translational selection.

Relative Mutation Rates in Nucleomorph-Bearing Algae

Mon, 11 Mar 2019 00:00:00 GMT

Chlorarachniophyte and cryptophyte algae are unique among plastid-containing species in that they have a nucleomorph genome: a compact, highly reduced nuclear genome from a photosynthetic eukaryotic endosymbiont. Despite their independent origins, the nucleomorph genomes of these two lineages have similar genomic architectures, but little is known about the evolutionary pressures impacting nucleomorph DNA, particularly how their rates of evolution compare to those of the neighboring genetic compartments (the mitochondrion, plastid, and nucleus). Here, we use synonymous substitution rates to estimate relative mutation rates in the four genomes of nucleomorph-bearing algae. We show that the relative mutation rates of the host versus endosymbiont nuclear genomes are similar in both chlorarachniophytes and cryptophytes, despite the fact that nucleomorph gene sequences are notoriously highly divergent. There is some evidence, however, for slightly elevated mutation rates in the nucleomorph DNA of chlorarachniophytes—a feature not observed in that of cryptophytes. For both lineages, relative mutation rates in the plastid appear to be lower than those in the nucleus and nucleomorph (and, in one case, the mitochondrion), which is consistent with studies of other plastid-bearing protists. Given the divergent nature of nucleomorph genes, our finding of relatively low evolutionary rates in these genomes suggests that for both lineages a burst of evolutionary change and/or decreased selection pressures likely occurred early in the integration of the secondary endosymbiont.

Resolving Phylogenetic Relationships for Streptococcus mitis and Streptococcus oralis through Core- and Pan-Genome Analyses

Thu, 07 Mar 2019 00:00:00 GMT

Taxonomic and phylogenetic relationships of Streptococcus mitis and Streptococcus oralis have been difficult to establish biochemically and genetically. We used core-genome analyses of S. mitis and S. oralis, as well as the closely related species Streptococcus pneumoniae and Streptococcus parasanguinis, to clarify the phylogenetic relationships between S. mitis and S. oralis, as well as within subclades of S. oralis. All S. mitis (n = 67), S. oralis (n = 89), S. parasanguinis (n = 27), and 27 S. pneumoniae genome assemblies were downloaded from NCBI and reannotated. All genes were delineated into homologous clusters and maximum-likelihood phylogenies built from putatively nonrecombinant core gene sets. Population structure was determined using Bayesian genome clustering, and patristic distance was calculated between populations. Population-specific gene content was assessed using a phylogenetic-based genome-wide association approach. Streptococcus mitis and S. oralis formed distinct clades, but species mixing suggests taxonomic misassignment. Patristic distance between populations suggests that S. oralis subsp. dentisani is a distinct species, whereas S. oralis subsp. tigurinus and subsp. oralis are supported as subspecies, and that S. mitis comprises two subspecies. None of the genes within the pan-genomes of S. mitis and S. oralis could be statistically correlated with either, and the dispensable genomes showed extensive variation among isolates. These are likely important factors contributing to established overlap in biochemical characteristics for these taxa. Based on core-genome analysis, the substructure of S. oralis and S. mitis should be redefined, and species assignments within S. oralis and S. mitis should be made based on whole-genome analysis to be robust to misassignment.

The Molecular Basis of Freshwater Adaptation in Prawns: Insights from Comparative Transcriptomics of Three Macrobrachium Species

Wed, 06 Mar 2019 00:00:00 GMT

Elucidating the molecular basis of adaptation to different environmental conditions is important because adaptive ability of a species can shape its distribution, influence speciation, and also drive a variety of evolutionary processes. For crustaceans, colonization of freshwater habitats has significantly impacted diversity, but the molecular basis of this process is poorly understood. In the current study, we examined three prawn species from the genus Macrobrachium (M. australiense, M. tolmerum, and M. novaehollandiae) to better understand the molecular basis of freshwater adaptation using a comparative transcriptomics approach. Each of these species naturally inhabit environments with different salinity levels; here, we exposed them to the same experimental salinity conditions (0‰ and 15‰), to compare expression patterns of candidate genes that previously have been shown to influence phenotypic traits associated with freshwater adaptation (e.g., genes associated with osmoregulation). Differential gene expression analysis revealed 876, 861, and 925 differentially expressed transcripts under the two salinities for M. australiense, M. tolmerum, and M. novaehollandiae, respectively. Of these, 16 were found to be unannotated novel transcripts and may be taxonomically restricted or orphan genes. Functional enrichment and molecular pathway mapping revealed 13 functionally enriched categories and 11 enriched molecular pathways that were common to the three Macrobrachium species. Pattern of selection analysis revealed 26 genes with signatures of positive selection among pairwise species comparisons. Overall, our results indicate that the same key genes and similar molecular pathways are likely to be involved with freshwater adaptation widely across this decapod group; with nonoverlapping sets of genes showing differential expression (mainly osmoregulatory genes) and signatures of positive selection (genes involved with different life history traits).