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.

@OfficialSMBE Feed

MBE | Most Read

Molecular Biology and Evolution

Wed, 14 Feb 2018 00:00:00 GMT

Thu, 11 Jan 2018 00:00:00 GMT

Study Determines New Geographic Origins of Brown Rats

Thu, 11 Jan 2018 00:00:00 GMT

Tue, 09 Jan 2018 00:00:00 GMT

A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

Tue, 02 Jan 2018 00:00:00 GMT

Tue, 26 Dec 2017 00:00:00 GMT

Thu, 21 Dec 2017 00:00:00 GMT

Sources of Robustness and Constrained Evolvability during Coevolution

Tue, 19 Dec 2017 00:00:00 GMT

Tue, 19 Dec 2017 00:00:00 GMT

Tue, 19 Dec 2017 00:00:00 GMT

Mon, 11 Dec 2017 00:00:00 GMT

Fri, 08 Dec 2017 00:00:00 GMT

Fri, 08 Dec 2017 00:00:00 GMT

Wed, 06 Dec 2017 00:00:00 GMT

Wed, 06 Dec 2017 00:00:00 GMT

Wed, 06 Dec 2017 00:00:00 GMT

Wed, 06 Dec 2017 00:00:00 GMT

Wed, 06 Dec 2017 00:00:00 GMT

Tue, 05 Dec 2017 00:00:00 GMT

Tue, 05 Dec 2017 00:00:00 GMT

Tue, 05 Dec 2017 00:00:00 GMT

Fri, 01 Dec 2017 00:00:00 GMT

Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity

Thu, 23 Nov 2017 00:00:00 GMT

Thu, 09 Nov 2017 00:00:00 GMT

Tue, 05 Sep 2017 00:00:00 GMT

GBE | Most Read

Genome Biology & Evolution

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee

Mon, 05 Mar 2018 00:00:00 GMT

Humans experience higher rates of age-associated diseases than our closest living evolutionary relatives, chimpanzees. Environmental factors can explain many of these increases in disease risk, but species-specific genetic changes can also play a role. Alleles that confer increased disease susceptibility later in life can persist in a population in the absence of selective pressure if those changes confer positive adaptation early in life. One age-associated disease that disproportionately affects humans compared with chimpanzees is epithelial cancer. Here, we explored genetic differences between humans and chimpanzees in a well-defined experimental assay that mimics gene expression changes that happen during cancer progression: A fibroblast serum challenge. We used this assay with fibroblasts isolated from humans and chimpanzees to explore species-specific differences in gene expression and chromatin state with RNA-Seq and DNase-Seq. Our data reveal that human fibroblasts increase expression of genes associated with wound healing and cancer pathways; in contrast, chimpanzee gene expression changes are not concentrated around particular functional categories. Chromatin accessibility dramatically increases in human fibroblasts, yet decreases in chimpanzee cells during the serum response. Many regions of opening and closing chromatin are in close proximity to genes encoding transcription factors or genes involved in wound healing processes, further supporting the link between changes in activity of regulatory elements and changes in gene expression. Together, these expression and open chromatin data show that humans and chimpanzees have dramatically different responses to the same physiological stressor, and how a core physiological process can evolve quickly over relatively short evolutionary time scales.

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

Thu, 01 Mar 2018 00:00:00 GMT

Amino acid usage in a proteome depends mostly on its taxonomy, as it does the codon usage in transcriptomes. Here, we explore the level of variation in the codon usage of a specific amino acid, glutamine, in relation to the number of consecutive glutamine residues. We show that CAG triplets are consistently more abundant in short glutamine homorepeats (polyQ, four to eight residues) than in shorter glutamine stretches (one to three residues), leading to the evolutionary growth of the repeat region in a CAG-dependent manner. The length of orthologous polyQ regions is mostly stable in primates, particularly the short ones. Interestingly, given a short polyQ the CAG usage is higher in unstable-in-length orthologous polyQ regions. This indicates that CAG triplets produce the necessary instability for a glutamine stretch to grow. Proteins related to polyQ-associated diseases behave in a more extreme way, with longer glutamine stretches in human and evolutionarily closer nonhuman primates, and an overall higher CAG usage. In the light of our results, we suggest an evolutionary model to explain the glutamine codon usage in polyQ regions.

Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation

Thu, 22 Feb 2018 00:00:00 GMT

Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1–5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.

Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure

Wed, 21 Feb 2018 00:00:00 GMT

The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = πN/πS) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (Ne) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus—two mouse subspecies with different Ne. Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small Ne (M. m. musculus) was three times higher than that observed for that with large Ne (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population.

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention

Wed, 21 Feb 2018 00:00:00 GMT

Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21–22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions. Here, we define a deterministic model that represents the propagation of active TEs, aspects of the host response and the accumulation of silenced TEs. We describe general properties of the model and also fit it to biological data in order to explore two questions. The first is why two overlapping pathways are maintained, given that both are likely energetically expensive. Under our model, RdDM silenced TEs effectively even when the initiation of silencing was weak. This relationship implies that only a small amount of RNAi is needed to initiate TE silencing, but reinforcement by RdDM is necessary to efficiently counter TE propagation. Second, we investigated the reliance of the host response on rates of TE deletion. The model predicted that low levels of deletion lead to few active TEs, suggesting that silencing is most efficient when methylated TEs are retained in the genome, thereby providing one explanation for the large size of plant genomes.

Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

Wed, 21 Feb 2018 00:00:00 GMT

There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.

Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism

Wed, 14 Feb 2018 00:00:00 GMT

Human infection with the gastrointestinal pathogen Campylobacter jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analyzed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multihost (ecological generalist) ST-21 and ST-45 clonal complexes (CCs). Combined nucleotide and amino acid sequence analysis identified 12 human-only amino acid KPAX clusters among polyphyletic lineages within the common disease causing CC21 group isolates, with no such clusters among CC45 isolates. Isolate sequence types within human-only CC21 group KPAX clusters have been sampled from other hosts, including poultry, so rather than representing unsampled reservoir hosts, the increase in relative frequency in human infection potentially reflects a genetic bottleneck at the point of human infection. Consistent with this, sequence enrichment analysis identified nucleotide variation in genes with putative functions related to human colonization and pathogenesis, in human-only clusters. Furthermore, the tight clustering and polyphyly of human-only lineage clusters within a single CC suggest the repeated evolution of human association through acquisition of genetic elements within this complex. Taken together, combined nucleotide and amino acid analysis of large isolate collections may provide clues about human niche tropism and the nature of the forces that promote the emergence of clinically important C. jejuni lineages.

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

Wed, 14 Feb 2018 00:00:00 GMT

Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small. Here, we took advantage of methods for culturing H. defensa outside of aphids to generate complete genomes and transcriptome data for four strains of H. defensa from the pea aphid Acyrthosiphon pisum. Chosen strains also spanned the breadth of the H. defensa phylogeny and differed in strength of protection conferred against parasitoids. Results indicated that strains shared most genes with roles in nutrient acquisition, metabolism, and essential housekeeping functions. In contrast, the inventory of mobile genetic elements varied substantially, which generated strain specific differences in gene content and genome architecture. In some cases, specific traits correlated with differences in protection against parasitoids, but in others high variation between strains obscured identification of traits with likely roles in defense. Transcriptome data generated continuous distributions to genome assemblies with some genes that were highly expressed and others that were not. Single molecule real-time sequencing further identified differences in DNA methylation patterns and restriction modification systems that provide defense against phage infection.

Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome

Thu, 08 Feb 2018 00:00:00 GMT

Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth’s cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was >90%. Three genomic islands were identified in the E. antarcticum B7 genome. These islands contained genes involved in flagella biosynthesis and chemotaxis, as well as enzymes for carotenoid biosynthesis. Clustering of cold shock proteins by Ka/Ks ratio suggests the occurrence of a positive selection over these genes. Neighbor-joining clustering of complete genomes showed that the E. sibiricum was the most closely related to E. antarcticum. A total of 92 genes were shared between Exiguobacterium and Psychrobacter. A reduction in the genomic content of E. antarcticum B7 was observed. It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. In our study, eight genomes of Exiguobacterium and Psychrobacter were compared and analysed. Psychrobacter showed higher genomic plasticity and E. antarcticum B7 presented a large decrease in genomic content without changing its ability to grow in cold environments.

The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity

Tue, 06 Feb 2018 00:00:00 GMT

Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Mon, 05 Feb 2018 00:00:00 GMT

Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.

An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae

Sat, 03 Feb 2018 00:00:00 GMT

Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.