SMBE Conference guidelines

LOC - Local Organising Committee
SOC – Scientific Organising Committee
PCO - Professional Conference Organiser

Statement of Diversity:  SMBE has strong commitments to diversity. Organisers should place emphasis on diversity of participants, including gender and geographic, at every level of the meeting, including but not limited to the selection of plenary speakers, symposium organisers, and invited speakers. Please ensure that this criterion is considered throughout the organization of the conference.

Size of conference:  The conference can currently be expected to have between 1,000 and 1,500 delegates, although we have seen considerable fluctuations in this number depending on location (from 1000 to 1,500).  Organisers 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 to take the entire conference.  The conference attendance should be capped at 2,000.   

Scientific Organising Committee (SOC): The SMBE conference Scientific Organising Committee should include Local Organisers and one member of SMBE council. The role of the council member on the SOC is to make sure the conference organisers adhere to these guidelines. Additionally, one organiser of the meeting from a previous year and one organiser of the meeting for the next year should be included for the purpose of continuity.

Structure of the conference:  The conference has the following characteristics:

            Council Meeting: One council meeting to be held in a room that accommodates the council (10-15 members) and provides refreshments.  This meeting will usually take place the morning the first day of the conference, with the main conference starting in the late afternoon/evening with the reception and Nei lecture.

            Plenary Lectures: There should be at least 3-4 Plenary lectures.  These lectures are attended by all delegates and usually last one hour.  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.  If possible, this lecture should be arranged 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. Gender and geographic diversity is critical in the selection of plenary speakers.

There is a separate Fitch Symposium. There may also be a separate symposium for recipients of the Allan Wilson, Margaret Dayhoff, Motoo Kimura, and Service Awards.  Alternatively, these recipients should all be given the opportunity to give a lecture at the annual meeting if no special symposium for the awardees is organised.

            Parallel sessions:  The usual structure of the conference is to have no more than 4 parallel sessions (fewer than 4 is OK).  The council has decided that if there are more than four parallel sessions then delegates feel they are missing too many talks and fewer parallel sessions would restrict the diversity of the conference.  Moreover, recent experience has shown that more sessions and/or more plenary sessions put the meeting into potential financial jeopardy.  The LOC should have a mechanism to ensure that concurrent sessions stay on time and try to minimize similarity of overlapping concurrent sessions.

            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/reception). The LOC is encouraged but not required to organise Public Lectures on Evolution/Molecular Evolution either immediately before or immediately after the meeting.

Venue: 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 it is expected that approximately 80% of the delegates will attend.  Therefore, it is preferable that there is a room to hold such a number.  If this is not possible, then there should be a facility to relay the plenary lectures to another room via video link, though this is not the preferred option.  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 might wish to attend any given talk.  The rooms should be located within 1-2 min walk from each other and have seating or aisles arranged to facilitate movement between sessions. There should be a set-up room for speakers to check their presentations. The preferred presentation file format is pdf.  Apple and PC computers should be provided for presenters.  It is expected that the conference will provide morning coffee break, lunch on all days, and afternoon coffee breaks on each day, preferably with some small snack (fruit, cookies, pastry, etc.).  Please provide vegetarian/vegan options at receptions, meals, and breaks.  There should be a welcome reception on the first day and there should be an optional conference ‘gala’ dinner on one evening (the option being that delegates can choose to pay extra for this dinner or choose not to attend). Kindly ask the venue to refrain from using air freshener during the conference. Some participants are allergic to it and it exposes all participants to poor air quality.

            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 costings and with frequent updates on income and expenditure.  The Society will provide $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 $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 such a facility 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.

            Registration:  On the meeting website, SMBE members need to have the opportunity to have discounted registration. The discount for SMBE members must be at least $30, but a higher differential between member and non-member registration is allowed.  In addition to listing a price for members and non-members, the registration page needs to link to the SMBE website to give conference delegates the opportunity to join SMBE.   Finally, while most registrants will use the website, there should also be a facility to register onsite.  Students and postdocs should be given a discounted registration rate as well; the discount should be larger for graduate students than for postdocs.  Students and postdocs should clearly indicate their student or postdoc status at registration.  This also determines eligibility for certain awards.  Maintain a participant database with student or postdoc status recorded (this is essential for determining poster award eligibility, for instance), abstract numbers and titles as separate entries, and email addresses, etc.  A participant list should also be provided in the web program.

            Symposium structure: Recent conferences have settled on a structure where a ‘unit’ of time is 15 minutes.  This means that contributed talks can be scheduled to last 15 minutes, including time for questions (usually, 12 minutes for the talk and 3 minutes for questions and movement between rooms).  Invited speakers can then be allocated time slots of 15 or 30 min.  It is also prudent to advise symposium organisers that delegates frequently move between symposia, so it can be useful to allow one minute of moving time between talks within the allocated 15 minutes. It is also often helpful to assign symposia organisers 15 minutes to provide an overview of the study area at the beginning, but this is subject to time availability.

            Contributed speakers:  Each symposium will decide its preferred speaker list from the list of contributed speakers.  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 organisers are given their list of delegates who wish to speak in their symposium, they can select their preferred list of speakers.  However, the exact details of this process are to be worked out by the SOC.  In the end, the SOC will match delegates and symposia and communicate to both the symposium organisers and the delegates the outcome of this process.  This decision should be reached no later than 3 months before the conference.

            Limit of presentations per person: A 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 has a choice of in which symposium s/he would like to present.

On-Site Child Care:  Organisers will arrange for on-site (in the same building as the conference) childcare, as this is an issue of great importance to the members of the Society.  SMBE will help defray the cost of childcare.  Please communicate early and often with the Society as to the costs, barriers and opportunities for child care.

            Badges: Each delegate should have a badge.  In addition, it is desirable to have badges that clearly delineate Editors and Associate Editors of the journals as well as a separate designation for Council members.

            Poster sessions:  Poster presenters frequently feel that they do not get ample opportunity to present their work, so it is important that each poster presenter is given enough time to talk to other delegates.  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 would be 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.

            Conference app:  A conference app should be made available in both iPhone and Android formats. The app should have an option via which any poster presenter should be able to invite another meeting participant to her/his poster. It is best if the app and files can be used offline, since many travelers do not have a data plan and some hotels charge exorbitant fees for wifi.  Wifi quality can also be unreliable at large meeting venues. Apps that let you create a personalized schedule are quite useful.

            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.

            Evaluation form:  Each delegate should be invited to evaluate the conference, either using a paper form that can be dropped into a box on-site or an online form that can be filled in by each delegate.

            Certificate of Attendance:  Many delegates will require a certificate of attendance for their home institutions or for funding agencies that might have underwritten their travel.  These certificates should be available at the conference venue.

            Fitch Symposium: Graduate students and post-docs in their first year of their first post-doc 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 decide on 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.

Conference Swag should be kept to a minimum to reduce environmental impact.

Awards: SMBE provides several awards. Applications for these awards will be handled on the SMBE website and are not the responsibility of the organiser. However, the LOC should advertise these awards on its website (both the registration webpage and abstract submission form) and is asked to provide some help for the organization of these awards (details below):   

1.         Undergraduate mentoring and diversity program: 10 undergraduate and diversity awards are available each year to undergraduate students that submit abstracts.  The value of these awards is $1,500 to $2,000.  One or two SMBE Councillors assigned by the Council will take charge of this section.  It consists of finding a mentor for each student so that they can be guided through the conference and in addition, there is a dinner for all 10 students, their 10 mentors and the council members who organise the activity. The conference organisers 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 dinner. The registration fees of the awardees are to be charged directly to SMBE, so that students do not have to pay by themselves (the amount of registration cost being deduced from their award). The Councillors will send the list of awardees to the meeting organisers so that they can get registered.  All undergraduate awardees present their posters in the same poster session and next to each other.

2.         Graduate and Postdoc Travel Awards:  SMBE provides graduate and postdoc travel awards, with an expressed purpose of enhancing gender and geographic diversity.  The awards are culled from applicants that have expressed a desire to be considered for such awards.  The Past-President, usually in conjunction with the SOC, will head a committee to determine the awards.

3.         Child-Travel Awards:  Council will be enacting awards for travel for an accompanying child (children).  This award can also be used for procuring child-care at home (e.g., flying a grandparent to help at home while the delegate is at the meeting). Priority will be given to early career scientists (graduate students and postdocs).

4.         Fitch Award:  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 timing below).  Banquet tickets should be reserved for the 8 finalists (to be paid by SMBE).

5.         Poster Awards:  The poster prizes will be decided by a committee convened by the Council and headed by the President-Elect.  Poster prizes consist of at least one Postdoc prize and at least one student prize.

6.         Additional Awards:  SMBE has enacted additional awards that will be presented at the meeting.  No additional work will be required by meeting organisers, but it is important to keep in mind that the President and other Council members will need to award the Fitch Prize and a number of additional awards in front of meeting delegates. Preferably the best venue for this is the gala banquet.

Approximate timelines:

Initial website goes live: Last day of the conference of the preceding year.  This will provide information about the venue, opportunities for sponsorship, the composition of the organising committee, contact information for the conference organiser.

Call for symposia opens: Call opens 10 months before the date of the conference and closes nine months before the date of the conference.  Symposium proposals should include a summary of the topic and why this topic is timely for the SMBE meeting. A list of already confirmed invited speakers (2 per symposium) should also be included. A 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 $2,000 per invited speaker against receipts; adjusted reimbursement for intra- and intercontinental travel is allowed). These promises should be kept by the LOC under all circumstances. If there are two or more proposals on the same topic, the SOC has a choice of selecting one proposal or merging two or more proposals. Merging two or more symposia does either reduce the number of invited speakers that can be supported or the number of slots available for contributed talks.

Call for Symposia closes: Call closes approximately 9 months before the conference.

Selection of the Symposia: The symposia are selected by the SOC on the basis of proposals and depending on whether the same topics were subject to symposia at recent SMBE meetings. There should be approximately 20-30 symposia, reflecting the broad diversity of interests of the SMBE community, not simply the most popular topics. Additionally, the SOC is strongly encouraged to have an Open Symposium at which ground-breaking work not covered by the accepted symposia can be presented and potentially more student/postdoc talks are accepted.

       Notification of successful Symposia: Approximately 8.5 months before the conference.

       Registration opens: 8 months before the conference.  At this time, the titles of all symposia, as well as a short description of the symposia should be placed on the conference website.  The registration opening should be advertised to the society membership, on the society journals and through the social media, on EvolDir, etc.  Registration and payment for the meeting should be separate from Abstract submission.

       Early Registration deadline:  The early registration deadline should be 5 months before the conference.  This deadline offers discount on the registration fee.  Past experience indicates that 50-75% of delegates will take advantage of this early registration deadline.

       Selection of talks for Symposia and Fitch Prize:

- Fitch Symposium, Abstract and travel award deadlines all occur at the same time. Abstracts are handled by Allen Press. All award applicants should be SMBE members.

- Fitch finalists are selected first and present in a separate symposium.

- Symposium organisers select abstracts for talks, taking diversity into consideration (it is good to include some graduate students and postdocs, and of course to take gender/geographic diversity into account).  A symposium organiser cannot select more than one talk from her/his own research group.  The SOC selects talks for the Open Symposium.

- The SMBE-appointed committee selects the recipients of travel awards, with a recommended bias towards funding those selected to give oral presentations, keeping gender and geographical diversity in mind.  

- Symposium organisers will be given a deadline of talk selection that must be adhered to, no less than 2 weeks prior to council decision of travel awards. Council will take these decisions into account when awarding travel grants. Therefore, all talk decisions must occur 2-3 weeks prior to the deadlines for council to make award decisions.

- Early bird Registration deadline happens next.

Late registration deadline: The late registration deadline should be full cost and allows delegates to submit an abstract, though as an additional encouragement to register early, it might be stipulated that late abstracts can be considered only for poster presentations.

Conference timetable:  The final conference timetable should be made publicly available as soon as possible, preferably at least two months before the conference.

Timetable and conference program:  The entire conference program, complete with timetables should be made available for download to laptops or mobile devices.  The timetable should ideally be available in three formats: an “at-a-glance” format, simply detailing the session/symposia times and locations, a more detailed version with each speaker listed and finally a very detailed version with each speaker listed along with their abstract and all authors.  The online program should also contain all the logistical details for the conference. It is desirable to provide a printable conference program with concurrent sessions in columns and concurrent talks in rows to make it easy to choose a path. Be sure that all authors are visible in the complete program, not just the presenting author, since many people choose to attend a talk based on the lab or senior author.

Meeting organisers are required to provide a summary document to the Council after the meeting, including the statistics of the meeting participants (gender, student/participant).

Download a PDF of the Conference Guidelines here.

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Molecular Biology and Evolution

Jawing Away: Bahama Pupfish Study Identifies Candidate Genes Driving Food-Niches


<span class="paragraphSection">Within the salty lakes of the Bahama’s San Salvador Island is an amazing diversity of fishes that may rival Charles Darwin’s finches in the Galapagos.</span>



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Mathematical Modeling Study Shows Why Present Clinical Antibiotic Management Strategies Do Little to Curb Resistance


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Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest <span style="font-style:italic;">Drosophila suzukii</span> using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling locations). To do this, we use approximate Bayesian computation (ABC), which has improved the reconstruction of invasion routes, but can be computationally expensive. We use our study to illustrate the use of a new, more efficient, ABC method, ABC random forest (ABC-RF) and compare it to a standard ABC method (ABC-LDA). We find that Japan emerges as the most probable source of the earliest recorded invasion into Hawaii. Southeast China and Hawaii together are the most probable sources of populations in western North America, which then in turn served as sources for those in eastern North America. European populations are genetically more homogeneous than North American populations, and their most probable source is northeast China, with evidence of limited gene flow from the eastern US as well. All introduced populations passed through bottlenecks, and analyses reveal five distinct admixture events. These findings can inform hypotheses concerning how this species evolved between different and independent source and invasive populations. Methodological comparisons indicate that ABC-RF and ABC-LDA show concordant results if ABC-LDA is based on a large number of simulated datasets but that ABC-RF out-performs ABC-LDA when using a comparable and more manageable number of simulated datasets, especially when analyzing complex introduction scenarios.</span>

Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication


<span class="paragraphSection"><span style="font-style:italic;">Yezi Xiang, Chien-Hsun Huang, Yi Hu, Jun Wen, Shisheng Li, Tingshuang Yi, Hongyi Chen, Jun Xiang, and Hong Ma</span></span>

Evolution of DNA Methylation across Insects


<span class="paragraphSection">Adam J. Bewick, Kevin J. Vogel, Allen J. Moore, and Robert J. Schmitz</span>

Corrigendum Correction to “Novel hydrogenosomes in the microaerophilic jakobid Stygiella incarcerata ”


<span class="paragraphSection">Mol. Biol. Evol. 33(9):2318–2336. doi: <strong><a href="article.aspx?volume=&page=">10.1093/molbev/msw103<span></span></a></strong></span>

Antibiotic Cycling and Antibiotic Mixing: Which One Best Mitigates Antibiotic Resistance?


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Can we exploit our burgeoning understanding of molecular evolution to slow the progress of drug resistance? One role of an infection clinician is exactly that: to foresee trajectories to resistance during antibiotic treatment and to hinder that evolutionary course. But can this be done at a hospital-wide scale? Clinicians and theoreticians tried to when they proposed two conflicting behavioral strategies that are expected to curb resistance evolution in the clinic, these are known as “antibiotic cycling” and “antibiotic mixing.” However, the accumulated data from clinical trials, now approaching 4 million patient days of treatment, is too variable for cycling or mixing to be deemed successful. The former implements the restriction and prioritization of different antibiotics at different times in hospitals in a manner said to “cycle” between them. In antibiotic mixing, appropriate antibiotics are allocated to patients but randomly. Mixing results in no correlation, in time or across patients, in the drugs used for treatment which is why theorists saw this as an optimal behavioral strategy. So while cycling and mixing were proposed as ways of controlling evolution, we show there is good reason why clinical datasets cannot choose between them: by re-examining the theoretical literature we show prior support for the theoretical optimality of mixing was misplaced. Our analysis is consistent with a pattern emerging in data: neither cycling or mixing is a priori better than the other at mitigating selection for antibiotic resistance in the clinic.<strong><span style="font-style:italic;">Key words</span></strong>: antibiotic cycling, antibiotic mixing, optimal control, stochastic models.</span>

A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa


<span class="paragraphSection"><div class="boxTitle">Abstract</div>A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.</span>

Oncogenes without a Neighboring Tumor-Suppressor Gene Are More Prone to Amplification


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Focal copy number gains or losses are important genomic hallmarks of cancer. The genomic distribution of oncogenes and tumor-suppressor genes (TSG) in relation to focal copy number aberrations is unclear. Our analysis revealed that the mean distance of TSGs from oncogenes was significantly shorter than that of noncancer genes, suggesting that oncogenes and TSGs tend to be in close physical proximity in the human genome. Such relationship was conserved in mouse and drosophila. Pan-cancer analysis using data from The Cancer Genome Atlas indicated that oncogenes without a nearby TSG are more prone to amplification. In conclusion, our study provides evidence for the nonrandom distribution of oncogenes and TSGs across different species. Our data also support that the existence of a neighboring TSG can suppress amplification of an oncogene, shedding new light on a previously unappreciated protective mechanism of TSGs.</span>

Deleterious Variants in Asian Rice and the Potential Cost of Domestication


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a “cost of domestication”. Here, we investigated the numbers and frequencies of deleterious variants in Asian rice (<span style="font-style:italic;">Oryza sativa</span>), focusing on two varieties (<span style="font-style:italic;">japonica</span> and <span style="font-style:italic;">indica</span>) and their wild relative (<span style="font-style:italic;">O. rufipogon</span>). We investigated three signals of a potential cost of domestication in Asian rice relative to <span style="font-style:italic;">O. rufipogon</span>: an increase in the frequency of deleterious SNPs (dSNPs), an enrichment of dSNPs compared with synonymous SNPs (sSNPs), and an increased number of deleterious variants. We found evidence for all three signals, and domesticated individuals contained ∼3–4% more deleterious alleles than wild individuals. Deleterious variants were enriched within low recombination regions of the genome and experienced frequency increases similar to sSNPs within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating system from outcrossing to predominantly selfing. Forward simulations suggest that this shift in mating system may have been the dominant factor in shaping both deleterious and neutral diversity in rice.</span>

Seed Plant-Specific Gene Lineages Involved in Carpel Development


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot <span style="font-style:italic;">Arabidopsis thaliana</span>. To unravel the evolution of the carpel GRN and to discriminate between “early” and “late” steps in carpel evolution, we calculated thorough phylogeny reconstructions based on sequenced genomes. The <span style="font-style:italic;">A. thaliana</span> carpel GRN members <span style="font-style:italic;">ALCATRAZ</span> (<span style="font-style:italic;">ALC</span>), <span style="font-style:italic;">CRABS CLAW</span> (CRC), <span style="font-style:italic;">HALF FILLED</span> (<span style="font-style:italic;">HAF</span>), <span style="font-style:italic;">HECATE</span> (<span style="font-style:italic;">HEC</span>), <span style="font-style:italic;">INDEHISCENT</span> (<span style="font-style:italic;">IND</span>), <span style="font-style:italic;">NGATHA</span> (<span style="font-style:italic;">NGA</span>), and <span style="font-style:italic;">SPATULA</span> (<span style="font-style:italic;">SPT</span>) were analyzed in their phylogenetic context. We find that the carpel GRN components are of various ages, but interestingly, we identify especially high retention rates for carpel development genes in Brassicaceae. Our data suggest that genes whose <span style="font-style:italic;">A. thaliana</span> homologs are involved in processes already present in the most recent common ancestor of seed plants, such as reproductive meristem termination or adaxial/abaxial polarity specification, are not retained in duplicates after whole genome duplications (WGD). In contrast, genes involved in processes associated with derived carpel characters in <span style="font-style:italic;">Arabidopsis</span>, such as the transmitting tract or style development show a higher gene retention rate after WGD. This work provides a starting point for analyses of carpel genes in early diverging angiosperms which would be very informative for evolutionary studies.</span>

The Origin of Mitochondrial Cristae from Alphaproteobacteria


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Mitochondria are the respiratory organelles of eukaryotes and their evolutionary history is deeply intertwined with that of eukaryotes. The compartmentalization of respiration in mitochondria occurs within cristae, whose evolutionary origin has remained unclear. Recent discoveries, however, have revived the old notion that mitochondrial cristae could have had a pre-endosymbiotic origin. Mitochondrial cristae are likely homologous to the intracytoplasmic membranes (ICMs) used by diverse alphaproteobacteria for harnessing energy. Because the Mitochondrial Contact site and Cristae Organizing System (MICOS) that controls the development of cristae evolved from a simplified version that is phylogenetically restricted to Alphaproteobacteria (alphaMICOS), ICMs most probably transformed into cristae during the endosymbiotic origin of mitochondria. This inference is supported by the sequence and structural similarities between MICOS and alphaMICOS, and the expression pattern and cellular localization of alphaMICOS. Given that cristae and ICMs develop similarly, alphaMICOS likely functions analogously to mitochondrial MICOS by culminating ICM development with the creation of tubular connections and membrane contact sites at the alphaproteobacterial envelope. Mitochondria thus inherited a pre-existing ultrastructure adapted to efficient energy transduction from their alphaproteobacterial ancestors. The widespread nature of purple bacteria among alphaproteobacteria raises the possibility that cristae evolved from photosynthetic ICMs.</span>

Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual—a <span style="font-style:italic;">bona fide</span> speciation event. The extent to which this happens is not known. Here, we consider the origin of <span style="font-style:italic;">Arabidopsis suecica</span>, a selfing allopolyploid between <span style="font-style:italic;">Arabidopsis thaliana</span> and <span style="font-style:italic;">Arabidopsis arenosa</span>, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural <span style="font-style:italic;">A. suecica</span> accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in <span style="font-style:italic;">A. suecica</span> revealed that both loci carry non-functional alleles. The locus inherited from the selfing <span style="font-style:italic;">A. thaliana</span> is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing <span style="font-style:italic;">A. arenosa</span> is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from <span style="font-style:italic;">A. thaliana</span> is predicted to transcriptionally silence the allele inherited from <span style="font-style:italic;">A. arenosa</span>, suggesting that loss of self-incompatibility may have been instantaneous. </span>

The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice


<span class="paragraphSection"><div class="boxTitle">Abstract</div>The origin of domesticated Asian rice (<span style="font-style:italic;">Oryza sativa</span>) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (<span style="font-style:italic;">japonica</span>, <span style="font-style:italic;">indica</span>, and <span style="font-style:italic;">aus</span>) arose separately from progenitor <span style="font-style:italic;">O. rufipogon</span> and/or <span style="font-style:italic;">O. nivara</span>. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from <span style="font-style:italic;">O. rufipogon</span> was <span style="font-style:italic;">O. sativa</span> ssp. <span style="font-style:italic;">japonica</span>, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of <span style="font-style:italic;">O. rufipogon</span> populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from <span style="font-style:italic;">japonica</span> to both <span style="font-style:italic;">indica</span> (∼17%) and <span style="font-style:italic;">aus</span> (∼15%), which led to the transfer of domestication alleles from early-domesticated <span style="font-style:italic;">japonica</span> to proto-<span style="font-style:italic;">indica</span> and proto-<span style="font-style:italic;">aus</span> populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in <span style="font-style:italic;">O. sativa</span> ssp. <span style="font-style:italic;">japonica</span>, and introgressive hybridization from early <span style="font-style:italic;">japonica</span> to proto-<span style="font-style:italic;">indica</span> and proto-<span style="font-style:italic;">aus</span> led to domesticated <span style="font-style:italic;">indica</span> and <span style="font-style:italic;">aus</span> rice.</span>

Co-Option and De Novo Gene Evolution Underlie Molluscan Shell Diversity


<span class="paragraphSection"><div class="boxTitle">Abstract</div>Molluscs fabricate shells of incredible diversity and complexity by localized secretions from the dorsal epithelium of the mantle. Although distantly related molluscs express remarkably different secreted gene products, it remains unclear if the evolution of shell structure and pattern is underpinned by the differential co-option of conserved genes or the integration of lineage-specific genes into the mantle regulatory program. To address this, we compare the mantle transcriptomes of 11 bivalves and gastropods of varying relatedness. We find that each species, including four <span style="font-style:italic;">Pinctada</span> (pearl oyster) species that diverged within the last 20 Ma, expresses a unique mantle secretome. Lineage- or species-specific genes comprise a large proportion of each species’ mantle secretome. A majority of these secreted proteins have unique domain architectures that include repetitive, low complexity domains (RLCDs), which evolve rapidly, and have a proclivity to expand, contract and rearrange in the genome. There are also a large number of secretome genes expressed in the mantle that arose before the origin of gastropods and bivalves. Each species expresses a unique set of these more ancient genes consistent with their independent co-option into these mantle gene regulatory networks. From this analysis, we infer lineage-specific secretomes underlie shell diversity, and include both rapidly evolving RLCD-containing proteins, and the continual recruitment and loss of both ancient and recently evolved genes into the periphery of the regulatory network controlling gene expression in the mantle epithelium.</span>

miRNAs in Ancient Tissue Specimens of the Tyrolean Iceman


<span class="paragraphSection"><div class="boxTitle">Abstract</div>The analysis of nucleic acids in ancient samples is largely limited to DNA. Small noncoding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ancient samples, we profiled microRNAs in cryoconserved mummies. First, we established the approach on a World War One warrior, the “Kaiserjäger”, which has been preserved for almost one century. Then, we profiled seven ancient tissue specimens including skeletal muscle, stomach mucosa, stomach content and two corpus organ tissues of the 5,300-year-old copper age mummy Iceman and compared these profiles to the presence of organ-specific miRNAs in modern tissues. Our analyses suggest the presence of specific miRNAs in the different Iceman’s tissues. Of 1,066 analyzed human miRNAs, 31 were discovered across all biopsies and 87 miRNAs were detected only in a single sample. To check for potential microbiological contaminations, all miRNAs detected in Iceman samples and not present in ancient samples were mapped to 14,582 bacterial and viral genomes. We detected few hits (3.9% of miRNAs compared with 3.6% of miRNAs). Interestingly, the miRNAs with higher abundance across all ancient tissues were significantly enriched for Guanine (<span style="font-style:italic;">P</span> value of 10–13) and Cytosine (<span style="font-style:italic;">P</span> value of 10–7). The same pattern was observed for modern tissues. Comparing miRNAs measured from ancient organs to modern tissue patterns highlighted significant similarities, e.g., for miRNAs present in the muscle. Our first comprehensive analysis of microRNAs in ancient human tissues indicates that these stable molecules can be detected in tissue specimens after 5,300 years.</span>

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Genome Biology & Evolution

Genomic and Transcriptomic Analysis Reveals Spliced Leader Trans-Splicing in Cryptomonads


<span class="paragraphSection">Spliced leader trans-splicing (SLTS) is a poorly understood mechanism that is found in a diversity of eukaryotic lineages. In SLTS, a short RNA sequence is added near the 5′ ends of the transcripts of protein-coding genes by a modified spliceosomal reaction. Available data suggest that SLTS has evolved many times, and might be more likely to evolve in animals. That SLTS might be more likely to evolve in the context of the generally complex transcriptomes characteristic of animals suggests the possibility that SLTS functions in gene regulation or transcriptome diversification, however no general novel function for SLTS is known. Here, I report SLTS in a lineage of cellularly complex unicellular eukaryotes. Cryptomonads are a group of eukaryotic algae that acquired photosynthetic capacity by secondary endosymbiosis of a red alga, and that retain a reduced copy of the nucleus of the engulfed alga. I estimate that at least one-fifth of genes in the model cryptomonad <span style="font-style:italic;">Guillardia theta</span> and its relative <span style="font-style:italic;">Hanusia phi</span> undergo SLTS. I show that hundreds of genes in <span style="font-style:italic;">G. theta</span> generate alternative transcripts by SLTS at alternative sites, however I find little evidence for alternative protein production by alternative SLTS splicing. Interestingly, I find no evidence for substantial operon structure in the <span style="font-style:italic;">G. theta</span> genome, in contrast to previous findings in other lineages with SLTS. These results extend SLTS to another major group of eukaryotes, and heighten the mystery of the evolution of SLTS and its association with cellular and transcriptomic complexity.</span>

Evolutionary Thrift: Mycobacteria Repurpose Plasmid Diversity during Adaptation of Type VII Secretion Systems


<span class="paragraphSection">Mycobacteria have a distinct secretion system, termed type VII (T7SS), which is encoded by paralogous chromosomal loci (ESX) and associated with pathogenesis, conjugation, and metal homeostasis. Evolution of paralogous gene families is of interest because duplication is an important mechanism by which novel genes evolve, but there are potential conflicts between adaptive forces that stabilize duplications and those that enable evolution of new functions. Our objective was to delineate the adaptive forces underlying diversification of T7SS. Plasmid-borne ESX were described recently, and we found evidence that the initial duplication and divergence of ESX systems occurred on plasmids and was driven by selection for advantageous mutations. Plasmid conjugation has been linked to T7SS and type IV secretion systems (T4SS) in mycobacteria, and we discovered that T7SS and T4SS genes evolved in concert on the plasmids. We hypothesize that differentiation of plasmid ESX helps to prevent conjugation among cells harboring incompatible plasmids. Plasmid ESX appear to have been repurposed following migration to the chromosome, and there is evidence of positive selection driving further differentiation of chromosomal ESX. We hypothesize that ESX loci were initially stabilized on the chromosome by mediating their own transfer. These results emphasize the diverse adaptive paths underlying evolution of novelty, which in this case involved plasmid duplications, selection for advantageous mutations in the mobile and core genomes, migration of the loci between plasmids and chromosomes, and lateral transfer among chromosomes. We discuss further implications for the choice of model organism to study ESX functions in <span style="font-style:italic;">Mycobacterium tuberculosis</span>.</span>