SMBE Bylaws

(Updated June 2013)

ARTICLE 1. Name.

The name of the organization shall be the Society for Molecular Biology and Evolution, hereafter called “the Society.” The Society shall be an international organization.

ARTICLE 2. Purpose.

The purposes of the Society are to provide facilities for association and conference among molecular evolutionists and to further the goals of molecular evolutionary biology and its practitioners, including the publication of the two journals, Molecular Biology and Evolution (MBE), and Genome Biology and Evolution (GBE).

ARTICLE 3. Membership.

All individuals actively interested in any field of molecular evolutionary biology shall be eligible for active membership. One becomes an active member when the dues are accepted or when they accept an invitation by the Society.

ARTICLE 4. Officers and Council.

a. Composition. The officers of the organization shall be the Immediate Past President, the President, the President-elect, the Secretary, and the Treasurer. A full council will also have six elected councilors. The officers and the councilors shall constitute the Council. The Chief Editors of MBE and GBE will also serve on the Council as ex officio non-voting members.

b. Nominations. The President shall appoint a Nominating Committee by the end of December each year to propose candidates for the following year’s election of Council members who will begin their duties January 1 of the year after the election. The Nominating Committee shall consist of three to five active Society members who are not members of the Council. The Secretary shall be an ex officio non-voting member of the Committee. The Committee shall be chaired by a senior Society member. Once the Nominating Committee is formed, the Secretary shall inform the entire Society membership of its composition and invite suggestions for nominees. Two candidates shall be put forward for each office to be filled. The candidates for Councilors shall be presented in a single list in alphabetical order.
Upon recommendation by the Council, a single name may be put forward for the offices of Treasurer and/or Secretary. The Nominating Committee may or may not accept this recommendation. Candidates for all offices must be Society members at the time of the election.

c. Election of Officers shall be by a simple majority of those voting.  Election of Councilors shall be by plurality of those voting, where members are permitted to vote for any number of candidates up to and including the number of Councilor positions being filled.  Ties are to be resolved by the Council.
Elections shall be held by mail ballot. Here and elsewhere in these Bylaws, the term “mail” shall be interpreted as standard postal mail, electronic mail, or other types of clear announcement to the Society membership.

d. Terms of Officers, Councilors, and Chief Editors. The terms of the officers shall be three years. A person elected for Presidency shall serve as President-elect, President, and Past-President for the first, second, and third year, respectively. Councilors will each serve 3-year staggered terms so that two new councilors are elected annually. The Chief Editors of MBE and of GBE shall be appointed by the Council. The terms of the Chief Editors shall be five years but may be extended or terminated by the Council after consultation with members of their respective Editorial Boards. The terms of the Secretary and the Treasurer shall be staggered. Terms shall begin on January 1, except for the Chief Editors, who shall assume their duties so as to be responsible for the next volumes of their respective journals. An overlap period between out-going and in-coming Chief Editors, Secretary, and Treasurer may be negotiated with terms mutually agreed upon and approved by Council. During any overlap period, final decisions on matters concerning each position will be determined by the individual actually serving at that time (defined by the start dates indicated above).

e. Vacancies. Vacancies on the Council shall be filled by appointment by the Council, except: in the event of a vacancy in the Office of President, the President-elect shall become the President for the remainder of the unexpired term as well as for the subsequent term. In the event of vacancy of any other office, the Council shall appoint an active member to serve for the remainder of the year, and the office shall be filled at the next annual election.

f. Duties.
i) President. The President shall preside at the meetings of the Society and the Council. With the advice of the Council, the President shall appoint such committees and representatives as may be needed. With the exception of the Nominating Committee, Committees shall consist of a maximum of one Council member and at least two Society members not on Council. Individuals not members of the Society may be asked to join committees and may be offered a one one-year gratis membership.

ii) President-elect. The President-elect shall preside in the absence of the President. The President-elect shall direct the planning of annual meetings in accordance with rules established by the Council.

iii) Past-president. The Past President shall Chair the Fitch Committee to choose participants in the Fitch Symposium. This committee or another appointed by the Past-president shall also take responsibility for awarding travel grants and promoting participation at annual meetings of younger scientists and under-represented groups.

iv) Secretary. The Secretary shall: (1) keep the records of the Society; (2) send to all members the date and place of the annual meeting, a call for contributions to be presented at that meeting, and a call for suggestions for nomination for all offices to be filled by election; (3) At least six weeks before the annual meeting, send all members a ballot bearing the names of nominees for office; (4) prepare minutes of the annual meeting and present an annual report to the members concerning actions of the Council and activities of the Society and its Committees and representatives; (5) deposit those records of the Society no longer needed on an electronic archive accessible through the Society web site; in addition to Society records such as all formal reports, minutes of Council and Society meetings, and materials relating to the annual meetings, other material deemed of historical value may be deposited in the archive only with approval of Council; and (6) be responsible for maintaining the Society web site; for this purpose, the Council may designate a webmaster.

v) Treasurer. The Treasurer shall: (1) have charge of all funds of the Society and be responsible for their investment; (2) be bonded in an appropriate amount fixed by the Council; and (3) prepare an annual statement to the members of the financial status of the Society. This annual statement shall be reviewed by two auditors appointed by the President before the annual meeting of the Society.

vi) Councilors. Elected councilors shall participate in all matters of the Council and attend annual meetings of the Society.

vii) Chief Editors. Each Chief Editor shall carry out policy decisions of the Council, report directly to the Council, and be authorized to act for his/her respective Editorial Boards in arriving at Editorial decisions and conducting routine business. Editorial Board meetings may be held by electronic means. Each of the Editors shall submit an annual report to the Society regarding the operation of their respective journals. Chief Editors shall also serve as non-voting ex officio members of the Council.

ARTICLE 5. Meetings.

Meetings of the Council may be called by the president or any three other members of the Council. Meetings of the Council may be by electronic means or teleconference. The time and place of the Annual Meeting of the Society shall be determined by the Council at the recommendation of the President-Elect. The registration fee shall be set by the organizing Committee in consultation with the Council to allow a lower fee for members than for non- members.
A Society Business Meeting shall coincide with the annual meeting. At the business meeting, the President shall present an annual report of the Society, including the financial status and the next annual meeting. Each Chief Editor shall present a report concerning the publications of the Society journals. At the business meeting, the President shall also solicit recommendations concerning any Society activities to be considered by the Council.

ARTICLE 6. Quorum.

Two thirds of the Council shall constitute a quorum for Council meetings; in the case of electronic meetings, two-thirds of Council must respond within a reasonable time period set by the President in order to be considered a quorum. A quorum of the membership shall be those attending a duly called meeting or responding to a polling by mail within a reasonable time period set by the President.

ARTICLE 7. Voting.

Actions of the Council at a duly constituted meeting require a majority of those present to approve. A meeting is duly constituted if properly called and a quorum is present. Actions of the membership at the annual meeting also require a majority, but are not binding on the Council excepting demands for a mail polling of the membership on any issue. Actions taken by a majority of the active membership in a mail polling are binding on the Council except amendments to these by-laws (see article 11).

ARTICLE 8. Finances.

a. Budget. The Council shall be responsible for determining the budget. Expenditures in accord with the budget are to be jointly authorized by the President and Treasurer.
b. Dues. Annual dues shall be determined by the Council and will normally include a subscription to MBE, although Society membership without a subscription is an option. Graduate students who provide evidence of their status are entitled to active membership at reduced cost. Postdoctoral Fellows are also entitled to active membership at a reduced cost. Payment shall be due January 1. New members shall be billed for dues from the previous January 1, and shall receive MBE for the entire year. Members who have not paid their dues by January 1 shall be dropped from the rolls. GBE shall be an open access journal, and is therefore freely available to members as well as nonmembers.

ARTICLE 9. Publications.

a. Journals. The Society shall publish 1) Molecular Biology and Evolution [MBE] and 2) Genome Biology and Evolution [GBE] as its official journals. Publication in the journals shall be open to members and non-members alike. Acceptance shall be decided after Editorial review solely on merit and suitability. Other publications may be issued as the Council shall authorize.

b. Editorial Boards. The Editorial Boards of society journals will consist of Senior Editors and/or Associate Editors. They shall be appointed by the respective Chief Editors from a list of candidates submitted to the Council by each Chief Editor and approved by the Council. Editorial Board members shall serve three-year terms which may be renewed by the Chief Editor. Chief Editors may also appoint Guest Editors to the Editorial Board for special journal issues and manuscripts. Guest Editor appointments must be restricted to handing one or a few manuscripts. Chief Editors may retire any member of the Editorial Board prior to the completion of their three-year term in order to improve editorial efficiency and to make room for appointment of editors who will enhance the scientific excellence and breadth.

ARTICLE 10. Procedural Problems.

Procedural problems will be resolved according to Robert’s Rules of Order.

ARTICLE 11. Amending By-Laws.

Amendments to the Bylaws may be proposed by Council or by petition of Society members, whose proposal must be approved by Council. The Bylaws may be changed by a two-thirds vote of the members voting in a mail ballot. Mail voting ceases 45 days and online voting ceases 15 days after initial announcement. Proposed Bylaws changes must be accompanied by an explication and rationale for the proposed changes.

Adopted June 12, 1992 by unanimous vote of those attending meeting and amended by mail ballot October 8, 1993, March 1, 1995, March 30, 2007, November 7, 2008 and January 19, 2011.

This bylaws was passed on January 13, 2011, by the election of the SMBE members with 98% approval. Among the 239 ballots returned, 235 voted for the Bylaws amendments proposed by the council, which led to this Bylaws, and 4 voted to keep the previous Bylaws.

The bylaws were amended on July 10, 2013 by the vote of the members of SMBE. The amendments were passed by a vote of 248 to 26.

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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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Arctic Inuit, Native American Adaptations to Cold and Body Fat Distribution May Originate from Extinct Ancient Hominid Interbreeding


New Study Provides Research Framework for Tracing Human Migration Events After ‘Out of Africa’ Origins


<span class="paragraphSection">As more DNA sequencing data continues to become available, including extinct hominids, a new human origins study has been performed that augments a trio of influential papers published in 2016 in the journal Nature.</span>

Shell Game: Understanding Gene Patterns Behind Mollusk Diversity


<span class="paragraphSection">From kids walking on the beach to major museums, the amazing diversity of conch shells have captivated the eyes of collectors.</span>

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


<span class="paragraphSection">With an alarming growth in antibiotic resistance and doctors increasingly having to resort to last-chance antibiotics to save patients, is there a better way for hospitals to manage antibiotic treatment regimens?</span>

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>

GBE | Most Read

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>