SMBE Bylaws

(Updated October 2019)

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 Editors in Chief (EiCs) of MBE and GBE will also serve on the Council as ex officio non-voting members.

b. Eligibility. All members of the society shall be eligible to be officers or council members, with the following provisos.

i) EiCs are ex officio members of council, and are not eligible to be officers or councilors while serving as EiCs.

ii) A voting council member whose third and final year on Council ended in the past calendar year is not eligible to be reelected to the Council during the current calendar year.

iii) An individual may not be elected to the same Council position more than once.

c. Nominations. The President shall appoint a Nominating Committee and its chair 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. 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. The Committee shall do their best to ensure that the list of candidates reflects the diversity of SMBE members. The Nominating Committee may put forward a single name for the offices of Treasurer and/or Secretary, in which case, this action must be approved by the Council. Candidates for all offices must be Society members at the time of the election.

d. 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 electronic ballot.

e. Terms of Officers, Councilors, and Editors in Chief (EiCs). 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 terms of the Secretary and the Treasurer shall be staggered. Terms shall begin on January 1, except for the EiCs, 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 EiCs, 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). The EiCs of MBE and of GBE shall be appointed by the Council. The terms of the EiCs shall be up to five years, may be staggered in time, and may be terminated by the Council after consultation with members of their respective Editorial Boards. Limiting EiCs to one term is encouraged, and EiCs shall not serve more than two terms on any SMBE journals.

f. 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.

g. 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 establish committees and appoint representatives as 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 publish 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; 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 and social media.

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) Editors in Chief. Each EiC 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. EiCs 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, electronic meetings should occur over reasonable periods of time to allow full participation, and all Council members shall be made aware of the meeting in a timely fashion.


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 EiC 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 of members within a reasonable time period set by the President.

ARTICLE 7. Voting.

Actions of the Council at a duly constituted Council meeting require a majority of those present to approve. A Council 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 polling of the membership on any issue. Actions taken by a majority of the voting members in a polling are binding on the Council except for contradictions of or 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 the society’s journals, although Society membership without a subscription shall be 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 are past due shall not be considered active, voting members and shall not receive any benefits of membership until their dues are paid.

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 Editors in Chief from a list of candidates submitted to the Council by each EiC and approved by the Council. Editorial Board members shall serve three-year terms which may be renewed by the EiC. EiCs 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. EiCs 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. Codes of Conduct.

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

The society shall have a publicly available standing policy against bullying and harassment, including a process for dealing with violations. This policy shall apply to all society related business.

All meetings of the society shall have a well-publicized code of conduct, to which members must agree prior to registering for meetings.

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 an online ballot. 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 iteration of the 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.

The bylaws were amended on October 26, 2019 by the vote of the members of SMBE. The amendments were passed by a vote of 368 to 12.

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MBE | Most Read

Molecular Biology and Evolution

Correction to: Population Genetic Considerations Regarding Evidence for Biased Mutation Rates in Arabidopsis thaliana

Fri, 24 Mar 2023 00:00:00 GMT

This is a correction to: Brian Charlesworth, Jeffrey D Jensen, Population Genetic Considerations Regarding Evidence for Biased Mutation Rates in Arabidopsis thaliana, Molecular Biology and Evolution, Volume 40, Issue 2, February 2023, msac275, https://doi.org/10.1093/molbev/msac275

New Insights into the Evolution and Gene Structure of the Mitochondrial Carrier Family Unveiled by Analyzing the Frequent and Conserved Intron Positions

Tue, 14 Mar 2023 00:00:00 GMT

Abstract
Mitochondrial carriers (MCs) belong to a eukaryotic protein family of transporters that in higher organisms is called the solute carrier family 25 (SLC25). All MCs have characteristic triplicated sequence repeats forming a 3-fold symmetrical structure of a six-transmembrane α-helix bundle with a centrally located substrate-binding site. Biochemical characterization has shown that MCs altogether transport a wide variety of substrates but can be divided into subfamilies, each transporting a few specific substrates. We have investigated the intron positions in the human MC genes and their orthologs of highly diversified organisms. The results demonstrate that several intron positions are present in numerous MC sequences at the same specific points, of which some are 3-fold symmetry related. Many of these frequent intron positions are also conserved in subfamilies or in groups of subfamilies transporting similar substrates. The analyses of the frequent and conserved intron positions in MCs suggest phylogenetic relationships not only between close but also distant homologs as well as a possible involvement of the intron positions in the evolution of the substrate specificity diversification of the MC family members.

Massive Somatic and Germline Chromosomal Integrations of Polydnaviruses in Lepidopterans

Tue, 07 Mar 2023 00:00:00 GMT

Abstract
Increasing numbers of horizontal transfer (HT) of genes and transposable elements are reported in insects. Yet the mechanisms underlying these transfers remain unknown. Here we first quantify and characterize the patterns of chromosomal integration of the polydnavirus (PDV) encoded by the Campopleginae Hyposoter didymator parasitoid wasp (HdIV) in somatic cells of parasitized fall armyworm (Spodoptera frugiperda). PDVs are domesticated viruses injected by wasps together with their eggs into their hosts in order to facilitate the development of wasp larvae. We found that six HdIV DNA circles integrate into the genome of host somatic cells. Each host haploid genome suffers between 23 and 40 integration events (IEs) on average 72 h post-parasitism. Almost all IEs are mediated by DNA double-strand breaks occurring in the host integration motif (HIM) of HdIV circles. We show that despite their independent evolutionary origins, PDV from both Campopleginae and Braconidae wasps use remarkably similar mechanisms for chromosomal integration. Next, our similarity search performed on 775 genomes reveals that PDVs of both Campopleginae and Braconidae wasps have recurrently colonized the germline of dozens of lepidopteran species through the same mechanisms they use to integrate into somatic host chromosomes during parasitism. We found evidence of HIM-mediated HT of PDV DNA circles in no less than 124 species belonging to 15 lepidopteran families. Thus, this mechanism underlies a major route of HT of genetic material from wasps to lepidopterans with likely important consequences on lepidopterans.

GBE | Most Read

Genome Biology & Evolution

Inside the Shark Nursery: The Evolution of Live Birth in Cartilaginous Fish

Wed, 15 Mar 2023 00:00:00 GMT

A new study in Genome Biology and Evolution reveals that egg yolk proteins may have been co-opted to provide maternal nutrition in live-bearing sharks and their relatives.

Chromosome-scale Genome Assembly of the Yellow Nutsedge (Cyperus esculentus)

Tue, 21 Feb 2023 00:00:00 GMT

Abstract
The yellow nutsedge (Cyperus esculentus L. 1753) is an unconventional oil plant with oil-rich tubers, and a potential alternative for traditional oil crops. Here, we reported the first high-quality and chromosome-level genome assembly of the yellow nutsedge generated by combining PacBio HiFi long reads, Novaseq short reads, and Hi-C data. The final genome size is 225.6 Mb with an N50 of 4.3 Mb. More than 222.9 Mb scaffolds were anchored to 54 pseudochromosomes with a BUSCO score of 96.0%. We identified 76.5 Mb (33.9%) repetitive sequences across the genome. A total of 23,613 protein-coding genes were predicted in this genome, of which 22,847 (96.8%) were functionally annotated. A whole-genome duplication event was found after the divergence of Carex littledalei and Rhynchospora breviuscula, indicating the rich genetic resources of this species for adaptive evolution. Several significantly enriched GO terms were related to invasiveness of the yellow nutsedge, which may explain its plastic adaptability. In addition, several enriched Kyoto Encyclopedia of Genes and Genomes pathways and expanded gene families were closely related with substances in tubers, partially explaining the genomic basis of characteristics of this oil-rich tuber.

Evolutionary History of the Poecilia picta Sex Chromosomes

Tue, 21 Feb 2023 00:00:00 GMT

Abstract
The degree of divergence between the sex chromosomes is not always proportional to their age. In poeciliids, four closely related species all exhibit a male heterogametic sex chromosome system on the same linkage group, yet show a remarkable diversity in X and Y divergence. In Poecilia reticulata and P. wingei, the sex chromosomes remain homomorphic, yet P. picta and P. parae have a highly degraded Y chromosome. To test alternative theories about the origin of their sex chromosomes, we used a combination of pedigrees and RNA-seq data from P. picta families in conjunction with DNA-seq data collected from P. reticulata, P. wingei, P. parae, and P. picta. Phylogenetic clustering analysis of X and Y orthologs, identified through segregation patterns, and their orthologous sequences in closely related species demonstrates a similar time of origin for both the P. picta and P. reticulata sex chromosomes. We next used k-mer analysis to identify shared ancestral Y sequence across all four species, suggesting a single origin to the sex chromosome system in this group. Together, our results provide key insights into the origin and evolution of the poeciliid Y chromosome and illustrate that the rate of sex chromosome divergence is often highly heterogenous, even over relatively short evolutionary time frames.

Egg Yolk Protein Homologs Identified in Live-Bearing Sharks: Co-Opted in the Lecithotrophy-to-Matrotrophy Shift?

Mon, 20 Feb 2023 00:00:00 GMT

Abstract
Reproductive modes of vertebrates are classified into two major embryonic nutritional types: yolk deposits (i.e., lecithotrophy) and maternal investment (i.e., matrotrophy). Vitellogenin (VTG), a major egg yolk protein synthesized in the female liver, is one of the molecules relevant to the lecithotrophy-to-matrotrophy shift in bony vertebrates. In mammals, all VTG genes are lost following the lecithotrophy-to-matrotrophy shift, and it remains to be elucidated whether the lecithotrophy-to-matrotrophy shift in nonmammalians is also associated with VTG repertoire modification. In this study, we focused on chondrichthyans (cartilaginous fishes)—a vertebrate clade that underwent multiple lecithotrophy-to-matrotrophy shifts. For an exhaustive search of homologs, we performed tissue-by-tissue transcriptome sequencing for two viviparous chondrichthyans, the frilled shark Chlamydoselachus anguineus and the spotless smooth-hound Mustelus griseus, and inferred the molecular phylogeny of VTG and its receptor very low-density lipoprotein receptor (VLDLR), across diverse vertebrates. As a result, we identified either three or four VTG orthologs in chondrichthyans including viviparous species. We also showed that chondrichthyans had two additional VLDLR orthologs previously unrecognized in their unique lineage (designated as VLDLRc2 and VLDLRc3). Notably, VTG gene expression patterns differed in the species studied depending on their reproductive mode; VTGs are broadly expressed in multiple tissues, including the uterus, in the two viviparous sharks, and in addition to the liver. This finding suggests that the chondrichthyans VTGs do not only function as the yolk nutrient but also as the matrotrophic factor. Altogether, our study indicates that the lecithotrophy-to-matrotrophy shift in chondrichthyans was achieved through a distinct evolutionary process from mammals.

A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly

Sat, 18 Feb 2023 00:00:00 GMT

Abstract
We present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, and separated from the most closely related Odonata with a reference genome 150 million years ago. Using PacBio HiFi reads and Hi-C data for scaffolding we produce one of the most high-quality Odonata genomes to date. A scaffold N50 of 206.6 Mb and a single copy BUSCO score of 96.2% indicate high contiguity and completeness.

Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data

Fri, 17 Feb 2023 00:00:00 GMT

Abstract
There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have been found to occupy distinct habitats and display remarkable characteristics, which are attracting an increased amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 Ma, which supports the speciation hypothesis that links A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analyses highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybee species, which was useful for giant honeybee conservation.

OrthoPhy: A Program to Construct Ortholog Data Sets Using Taxonomic Information

Fri, 17 Feb 2023 00:00:00 GMT

Abstract
Species phylogenetic trees represent the evolutionary processes of organisms, and they are fundamental in evolutionary research. Therefore, new methods have been developed to obtain more reliable species phylogenetic trees. A highly reliable method is the construction of an ortholog data set based on sequence information of genes, which is then used to infer the species phylogenetic tree. However, although methods for constructing an ortholog data set for species phylogenetic analysis have been developed, they cannot remove some paralogs, which is necessary for reliable species phylogenetic inference. To address the limitations of current methods, we developed OrthoPhy, a program that excludes paralogs and constructs highly accurate ortholog data sets using taxonomic information dividing analyzed species into monophyletic groups. OrthoPhy can remove paralogs, detecting inconsistencies between taxonomic information and phylogenetic trees of candidate ortholog groups clustered by sequence similarity. Performance tests using evolutionary simulated sequences and real sequences of 40 bacteria revealed that the precision of ortholog inference by OrthoPhy is higher than that of existing programs. Additionally, the phylogenetic analysis of species was more accurate when performed using ortholog data sets constructed by OrthoPhy than that performed using data sets constructed by existing programs. Furthermore, we performed a benchmark test of the Quest for Orthologs using real sequence data and found that the concordance rate between the phylogenetic trees of orthologs inferred by OrthoPhy and those of species was higher than the rates obtained by other ortholog inference programs. Therefore, ortholog data sets constructed using OrthoPhy enabled a more accurate phylogenetic analysis of species than those constructed using the existing programs, and OrthoPhy can be used for the phylogenetic analysis of species even for distantly related species that have experienced many evolutionary events.

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies

Thu, 16 Feb 2023 00:00:00 GMT

Abstract
Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences

Wed, 15 Feb 2023 00:00:00 GMT

Abstract
Taxonomically restricted genes (TRGs) are unique for a defined group of organisms and may act as potential genetic determinants of lineage-specific, biological properties. Here, we explore the TRGs of highly diverse and economically important Bacillus bacteria by examining commonly used TRG identification parameters and data sources. We show the significant effects of sequence similarity thresholds, composition, and the size of the reference database in the identification process. Subsequently, we applied stringent TRG search parameters and expanded the identification procedure by incorporating an analysis of noncoding and non-syntenic regions of non-Bacillus genomes. A multiplex annotation procedure minimized the number of false-positive TRG predictions and showed nearly one-third of the alleged TRGs could be mapped to genes missed in genome annotations. We traced the putative origin of TRGs by identifying homologous, noncoding genomic regions in non-Bacillus species and detected sequence changes that could transform these regions into protein-coding genes. In addition, our analysis indicated that Bacillus TRGs represent a specific group of genes mostly showing intermediate sequence properties between genes that are conserved across multiple taxa and nonannotated peptides encoded by open reading frames.

The Impact of Sample Size and Population History on Observed Mutational Spectra: A Case Study in Human and Chimpanzee Populations

Wed, 15 Feb 2023 00:00:00 GMT

Abstract
Recent studies have highlighted variation in the mutational spectra among human populations as well as closely related hominoids—yet little remains known about the genetic and nongenetic factors driving these rate changes across the genome. Pinpointing the root causes of these differences is an important endeavor that requires careful comparative analyses of population-specific mutational landscapes at both broad and fine genomic scales. However, several factors can confound such analyses. Although previous studies have shown that technical artifacts, such as sequencing errors and batch effects, can contribute to observed mutational shifts, other potentially confounding parameters have received less attention thus far. Using population genetic simulations of human and chimpanzee populations as an illustrative example, we here show that the sample size required for robust inference of mutational spectra depends on the population-specific demographic history. As a consequence, the power to detect rate changes is high in certain hominoid populations while, for others, currently available sample sizes preclude analyses at fine genomic scales.

Increased Sampling and Intracomplex Homologies Favor Vertical Over Horizontal Inheritance of the Dam1 Complex

Wed, 15 Feb 2023 00:00:00 GMT

Abstract
Kinetochores connect chromosomes to spindle microtubules to ensure their correct segregation during cell division. Kinetochores of human and yeasts are largely homologous, their ability to track depolymerizing microtubules, however, is carried out by the nonhomologous complexes Ska1-C and Dam1-C, respectively. We previously reported the unique anti-correlating phylogenetic profiles of Dam1-C and Ska-C found among a wide variety of eukaryotes. Based on these profiles and the limited presence of Dam1-C, we speculated that horizontal gene transfer could have played a role in the evolutionary history of Dam1-C. Here, we present an expanded analysis of Dam1-C evolution, using additional genome as well as transcriptome sequences and recently published 3D structures. This analysis revealed a wider and more complete presence of Dam1-C in Cryptista, Rhizaria, Ichthyosporea, CRuMs, and Colponemidia. The fungal Dam1-C cryo-EM structure supports earlier hypothesized intracomplex homologies, which enables the reconstruction of rooted and unrooted phylogenies. The rooted tree of concatenated Dam1-C subunits is statistically consistent with the species tree of eukaryotes, suggesting that Dam1-C is ancient, and that the present-day phylogenetic distribution is best explained by multiple, independent losses and no horizontal gene transfer was involved. Furthermore, we investigated the ancient origin of Dam1-C via profile-versus-profile searches. Homology among 8 out of the 10 Dam1-C subunits suggests that the complex largely evolved from a single multimerizing subunit that diversified into a hetero-octameric core via stepwise subunit duplication and subfunctionalization of the subunits before the origin of the last eukaryotic common ancestor.

Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi

Wed, 15 Feb 2023 00:00:00 GMT

Abstract
Genome assemblies are growing at an exponential rate and have proved indispensable for studying evolution but the effort has been biased toward vertebrates and arthropods with a particular focus on insects. Onychophora or velvet worms are an ancient group of cryptic, soil dwelling worms noted for their unique mode of prey capture, biogeographic patterns, and diversity of reproductive strategies. They constitute a poorly understood phylum of exclusively terrestrial animals that is sister group to arthropods. Due to this phylogenetic position, they are crucial in understanding the origin of the largest phylum of animals. Despite their significance, there is a paucity of genomic resources for the phylum with only one highly fragmented and incomplete genome publicly available. Initial attempts at sequencing an onychophoran genome proved difficult due to its large genome size and high repeat content. However, leveraging recent advances in long-read sequencing technology, we present here the first annotated draft genome for the phylum. With a total size of 5.6Gb, the gigantism of the Epiperipatus broadwayi genome arises from having high repeat content, intron size inflation, and extensive gene family expansion. Additionally, we report a previously unknown diversity of onychophoran hemocyanins that suggests the diversification of copper-mediated oxygen carriers occurred independently in Onychophora after its split from Arthropoda, parallel to the independent diversification of hemocyanins in each of the main arthropod lineages.

A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea)

Wed, 15 Feb 2023 00:00:00 GMT

Abstract
Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron–sulfur cluster (ISC) pathway-mediated Fe–S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.

The Ancestral Mitotic State: Closed Orthomitosis With Intranuclear Spindles in the Syncytial Last Eukaryotic Common Ancestor

Wed, 08 Feb 2023 00:00:00 GMT

Abstract
All eukaryotes have linear chromosomes that are distributed to daughter nuclei during mitotic division, but the ancestral state of nuclear division in the last eukaryotic common ancestor (LECA) is so far unresolved. To address this issue, we have employed ancestral state reconstructions for mitotic states that can be found across the eukaryotic tree concerning the intactness of the nuclear envelope during mitosis (open or closed), the position of spindles (intranuclear or extranuclear), and the symmetry of spindles being either axial (orthomitosis) or bilateral (pleuromitosis). The data indicate that the LECA possessed closed orthomitosis with intranuclear spindles. Our reconstruction is compatible with recent findings indicating a syncytial state of the LECA, because it decouples three main processes: chromosome division, chromosome partitioning, and cell division (cytokinesis). The possession of closed mitosis using intranuclear spindles adds to the number of cellular traits that can now be attributed to LECA, providing insights into the lifestyle of this otherwise elusive biological entity at the origin of eukaryotic cells. Closed mitosis in a syncytial eukaryotic common ancestor would buffer mutations arising at the origin of mitotic division by allowing nuclei with viable chromosome sets to complement defective nuclei via mRNA in the cytosol.

Genome Evolution in Plants: Complex Thalloid Liverworts (Marchantiopsida)

Thu, 02 Feb 2023 00:00:00 GMT

Abstract
Why do some genomes stay small and simple, while others become huge, and why are some genomes more stable? In contrast to angiosperms and gymnosperms, liverworts are characterized by small genomes with low variation in size and conserved chromosome numbers. We quantified genome evolution among five Marchantiophyta (liverworts), measuring gene characteristics, transposable element (TE) landscape, collinearity, and sex chromosome evolution that might explain the small size and limited variability of liverwort genomes. No genome duplications were identified among examined liverworts and levels of duplicated genes are low. Among the liverwort species, Lunularia cruciata stands out with a genome size almost twice that of the other liverwort species investigated here, and most of this increased size is due to bursts of Ty3/Gypsy retrotransposons. Intrachromosomal rearrangements between examined liverworts are abundant but occur at a slower rate compared with angiosperms. Most genes on L. cruciata scaffolds have their orthologs on homologous Marchantia polymorpha chromosomes, indicating a low degree of rearrangements between chromosomes. Still, translocation of a fragment of the female U chromosome to an autosome was predicted from our data, which might explain the uniquely small U chromosome in L. cruciata. Low levels of gene duplication, TE activity, and chromosomal rearrangements might contribute to the apparent slow rate of morphological evolution in liverworts.

Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians

Sat, 21 Jan 2023 00:00:00 GMT

Abstract
Ion channels are highly diverse in the cnidarian model organism Nematostella vectensis (Anthozoa), but little is known about the evolutionary origins of this channel diversity and its conservation across Cnidaria. Here, we examined the evolution of voltage-gated K+ channels in Cnidaria by comparing genomes and transcriptomes of diverse cnidarian species from Anthozoa and Medusozoa. We found an average of over 40 voltage-gated K+ channel genes per species, and a phylogenetic reconstruction of the Kv, KCNQ, and Ether-a-go-go (EAG) gene families identified 28 voltage-gated K+ channels present in the last common ancestor of Anthozoa and Medusozoa (23 Kv, 1 KCNQ, and 4 EAG). Thus, much of the diversification of these channels took place in the stem cnidarian lineage prior to the emergence of modern cnidarian classes. In contrast, the stem bilaterian lineage, from which humans evolved, contained no more than nine voltage-gated K+ channels. These results hint at a complexity to electrical signaling in all cnidarians that contrasts with the perceived anatomical simplicity of their neuromuscular systems. These data provide a foundation from which the function of these cnidarian channels can be investigated, which will undoubtedly provide important insights into cnidarian physiology.

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Fri, 12 Aug 2022 00:00:00 GMT

Abstract
Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.