SMBE Everywhere


SMBEeverywhere 2022-23 Program

SMBE Everywhere is a series of ten virtual, 1-day Global Symposia which will occur in time zones across the globe starting in July 2022 and running through April 2023. Each GS will consist of plenary talks, contributed talks, and a poster session that span 6 to 7 hrs total (with a break in the middle). Talks will be delivered live with the option to record, and recorded talks and posters will be available in the Gathertown space until June 2023. The Gathertown platform will also allow for real-time interactions during and between each GS throughout the year.

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GS1: SMBE Everywhere Launch: Presidential Plenary, SMBE Award Talks, Graduate Student Excellence Symposia, and Panel Discussion on Parachute Science
Anyone wishing to submit an abstract for a poster presentation that does not fit into one of the specific themes of the GS series is welcome to submit an abstract to GS1.

Date: July 11, 2022               
Time: 14:00 - 22:00 UTC
Abstract submission deadline: CLOSED      
Geo region/Timezone: All
Speakers:
SMBE Presidential Address: 
James McInerney (Univ of Nottingham)
Faculty Research Award Winner Talks
Molly Schumer, (Stanford Univ), SMBE Early Career Research Excellence Award
Philipp Messer, (Cornell Univ), SMBE Mid-Career Research Excellence Award
Charles Aquadro (Cornell Univ), SMBE Lifetime Contribution Award
Graduate Student Excellence Symposium
Steven Fiddaman, University of Oxford
Jacob Steenwyk, University of California, Berkeley
Diana Cruz Dávalos, University of Lausanne
Jessica Warren, Arizona State University
Chris Kyriazis, UCLA
Robert Driver, East Carolina University
Caroline Weisman, Princeton University
Wendy Valencia-Montoya, Harvard University
Agneesh Barua, Okinawa Institute of Science and Technology Graduate University (OIST)

Parachute Science Panel Discussion: See HERE for more information!
Moderators:
Harmit Malik (Fred Hutchinson Cancer Research Center), María Avila (UNAM)
Organizers: Stephen Wright (Univ of Toronto, Canada) and Sarah Schaack (Reed College, USA)


GS2: Sustainability, Equity, and Efficiency in Computational Biology
Date: July 12, 2022               
Time: 16:00 - 20:00 UTC
Abstract submission deadline: CLOSED    
Geo region/Timezone: NA/SA
Invited Speakers: Jason Grealey (Children's Medical Research Institute, Australia), Sudhir Kumar (Temple Univ)  
Organizers: Beatriz Mello (Universidade Federal do Rio de Janeiro, Brazil), Alessandra Lamarca (Laboratório Nacional de Computação Científica, Brazil), and Sudhir Kumar (Temple Univ, USA)


GS3: Mutational Biases and Adaptation
Date: August 2, 2022           
Time: 12:00 - 20:00 UTC
Abstract submission deadline: CLOSED
Geo region/Timezone: NA/SA…Europe/Africa
Invited Speakers: Deepa Agashe (National Centre for Biological Sciences/Tata Institute of Fundamental Research), Alejandro Couce (Polytechnic Univ of Madrid)
Organizers: James Horton (Univ of Bath, UK) and David McCandlish (Cold Spring Harbor Laboratory, USA)


GS4: Using Ancestral Recombination Graphs (ARGs) to Infer Evolutionary Processes
Date: September 30, 2022    
Time: 14:00-21:00 UTC
Abstract submission deadline: CLOSED
Geo region/Timezone: NA/SA
Invited Speakers: Wilder Wohns (Broad Institute)  
Organizers: Christian Huber (Pennsylvania State, USA), Débora Brandt (UC Berkeley, USA), Diego Ortega-Del Vecchyo (National Autonomous Univ of Mexico, MX), Charleston Chiang (Univ of Southern California, USA)


GS5: Evolutionary Genomics of Host-Pathogen Interactions and Antimicrobial Drug Resistance
Date: October 20, 2022         
Time: 14:00 - 22:00 UTC
Abstract submission deadline: CLOSED        
Geo region/Timezone: Oceania....NA/SA…Europe
Invited Speakers: Kayla King (Univ of Oxford, Oxford, UK), Jacques Fellay (École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland), Vaughn Cooper (Univ of Pittsburgh, Pittsburgh, United States), Amy Cain (Macquarie Univ, Sydney, Australia)
Organizers: Santiago Castillo-Ramírez (Universidad Nacional Autónoma de México, MX), Ellen Leffler (Univ of Utah, USA), Azim Ansari (Univ of Oxford, UK)


GS6: Genetics of Adaptation
Date: November 21 & 22, 2022     
Time: 03:30 AM-11:30 AM UTC
Abstract submission deadline: CLOSED
Geo region/Timezone: Asia/Oceania
Invited Speakers: Jun-Yi Leu (Institute of Molecular Biology, Academia Sinica), Jun Kitano, NIG, Japan;
Organizers: Krushnamegh Kunte and Deepa Agashe (National Centre for Biological Sciences/Tata Institute of Fundamental Research, India)


GS7: Beyond the SNP: Structural Variants and Repetitive DNA in Genomics and Evolution
Date: February 15, 2023       
Time: 7pm - 1am UTC
Abstract submission deadline: CLOSED
Registration Deadline:
February 6, 2023
Geo region/Timezone: Oceania...NA/SA
Invited Speakers: Rachel O’Neill (Univ of Connecticut, USA), Tim Connallon (Monash Univ, Australia) 
Organizers: Julie Blommaert, Nicolas Altemose, Valentina Peona, Maren Wellenreuther, Jana Wold


GS8: Genomics in a Changing World: Conservation, Invasive Species, and Climate Change
Date: 22nd February (23 February NZT)
Time: 9pm - 4am UTC (4pm-11pm EST on 22nd Feb and 10am-5pm 23 Feb in New Zealand) 
Abstract submission deadline: CLOSED
Geo region/Timezone: Oceania....NA/SA
Invited Speakers: Carol Eunmi Lee (Univ of Wisconsin, USA), Kara Layton (Univ of Aberdeen, UK), Maui Hudson (Univ of Waikato, NZ), Alana Alexander (Univ of Otago, NZ)         
Organizers: Ang McGaughran (Univ of Waikato), Manpreet Dhami (Manaaki Whenua Landcare Research), Priscilla Salloum (Univ of Otago), Michael Knapp (Univ of Otago), Pascale Lubbe (Univ of Otago)


GS9: Epigenomics in Evolution
Date: Mar 1st (NZ/Australia)/Feb 28th (Europe/US)          
Time: 16:00-22:00 UTC
Abstract submission deadline: CLOSED
Geo region/Timezone: Oceania....NA/SA
Invited Speakers: 
Eva Jablonka (Tel Aviv University), Christina Richards (University of South Florida, University of Tübingen)
Organizers: Dafni Anastasiadi (Plant and Food Research, NZ), Sheri Johnson (Univ of Otago, NZ), Clare Venney (Université Laval, Canada), Maren Wellenreuther (Plant and Food Research and the Univ of Auckland, NZ)


GS10: Genetics and Evolution of Sex Differences
Date: April 26 - April 27, 2023 (Americas/Europe/Africa) and April 27 - April 28, 2023 (Oceania)       
Time: 8pm-11pm UTC
Abstract submission deadline: CLOSED   
Geo region/Timezone: Oceania....NA/SA
Invited Speakers: David Page (Whitehead Institute and MIT) and Mark Kirkpatrick (Univ of Texas at Austin)           
Organizers: Ludovic Dutoit (Univ of Otago, NZ), Sarah Flanagan (Univ of Canterbury, NZ), Arbel Harpak (UT Austin, USA), Filip Ruzicka (Monash Univ, Australia), Ziyue Gao (Univ of Pennsylvania, USA)

Organising Committee

SMBE Council Liaisons:

Sarah Schaack
Reed College, Department of Biology
Portland, OR, USA

Stephen Isaac Wright
Department of Ecology & Evolutionary Biology
Toronto, ON, Canada

@OfficialSMBE Feed

MBE | Most Read

Molecular Biology and Evolution

Correction: Sex Differences in 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism in Bicyclus anynana Wing Patterns

Tue, 06 Jun 2023 00:00:00 GMT

This is a correction to: Shivam Bhardwaj and others, Sex Differences in 20-Hydroxyecdysone Hormone Levels Control Sexual Dimorphism in Bicyclus anynana Wing Patterns, Molecular Biology and Evolution, Volume 35, Issue 2, February 2018, Pages 465–472, https://doi.org/10.1093/molbev/msx301

An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation

Tue, 23 May 2023 00:00:00 GMT

Abstract
Since the pioneering work of Dobzhansky in the 1930s and 1940s, many chromosomal inversions have been identified, but how they contribute to adaptation remains poorly understood. In Drosophila melanogaster, the widespread inversion polymorphism In(3R)Payne underpins latitudinal clines in fitness traits on multiple continents. Here, we use single-individual whole-genome sequencing, transcriptomics, and published sequencing data to study the population genomics of this inversion on four continents: in its ancestral African range and in derived populations in Europe, North America, and Australia. Our results confirm that this inversion originated in sub-Saharan Africa and subsequently became cosmopolitan; we observe marked monophyletic divergence of inverted and noninverted karyotypes, with some substructure among inverted chromosomes between continents. Despite divergent evolution of this inversion since its out-of-Africa migration, derived non-African populations exhibit similar patterns of long-range linkage disequilibrium between the inversion breakpoints and major peaks of divergence in its center, consistent with balancing selection and suggesting that the inversion harbors alleles that are maintained by selection on several continents. Using RNA-sequencing, we identify overlap between inversion-linked single-nucleotide polymorphisms and loci that are differentially expressed between inverted and noninverted chromosomes. Expression levels are higher for inverted chromosomes at low temperature, suggesting loss of buffering or compensatory plasticity and consistent with higher inversion frequency in warm climates. Our results suggest that this ancestrally tropical balanced polymorphism spread around the world and became latitudinally assorted along similar but independent climatic gradients, always being frequent in subtropical/tropical areas but rare or absent in temperate climates.

A Caenorhabditis elegans Male Pheromone Feminizes Germline Gene Expression in Hermaphrodites and Imposes Life-History Costs

Sat, 20 May 2023 00:00:00 GMT

Abstract
Sex pheromones not only improve the reproductive success of the recipients, but also impose costs, such as a reduced life span. The underlying mechanisms largely remain to be elucidated. Here, we show that even a brief exposure to physiological amounts of the dominant Caenorhabditis elegans male pheromone, ascr#10, alters the expression of thousands of genes in hermaphrodites. The most dramatic effect on the transcriptome is the upregulation of genes expressed during oogenesis and the downregulation of genes associated with male gametogenesis. This result reveals a way in which social signals help to resolve the inherent conflict between spermatogenesis and oogenesis in a simultaneous hermaphrodite, presumably to optimally align reproductive function with the presence of potential mating partners. We also found that exposure to ascr#10 increased the risk of persistent intestinal infections in hermaphrodites due to pathological pharyngeal hypertrophy. Thus, our study reveals ways in which the male pheromone can not only have beneficial effects on the recipients’ reproduction, but also cause harmful consequences that reduce life span.

GBE | Most Read

Genome Biology & Evolution

Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter, a Model for Speciation in the Sea

Wed, 07 Jun 2023 00:00:00 GMT

Abstract
Echinometra lucunter, the rock-boring sea urchin, is a widely distributed echinoid and a model for ecological studies of reproduction, responses to climate change, and speciation. We present a near chromosome-level genome assembly of E. lucunter, including 21 scaffolds larger than 10 Mb predicted to represent each of the chromosomes of the species. The 760.4 Mb assembly includes a scaffold N50 of 30.0 Mb and BUSCO (benchmarking universal single-copy orthologue) single copy and a duplicated score of 95.8% and 1.4%, respectively. Ab-initio gene model prediction and annotation with transcriptomic data constructed 33,989 gene models composing 50.4% of the assembly, including 37,036 transcripts. Repetitive elements make up approximately 39.6% of the assembly, and unresolved gap sequences are estimated to be 0.65%. Whole genome alignment with Echinometra sp. EZ revealed high synteny and conservation between the two species, further bolstering Echinometra as an emerging genus for comparative genomics studies. This genome assembly represents a high-quality genomic resource for future evolutionary and developmental studies of this species and more broadly of echinoderms.

A High Frequency of Chromosomal Duplications in Unicellular Algae Is Compensated by Translational Regulation

Tue, 23 May 2023 00:00:00 GMT

Abstract
Although duplications have long been recognized as a fundamental process driving major evolutionary innovations, direct estimates of spontaneous chromosome duplication rates, leading to aneuploid karyotypes, are scarce. Here, from mutation accumulation (MA) experiments, we provide the first estimates of spontaneous chromosome duplication rates in six unicellular eukaryotic species, which range from 1 × 10−4 to 1 × 10−3 per genome per generation. Although this is ∼5 to ∼60 times less frequent than spontaneous point mutations per genome, chromosome duplication events can affect 1–7% of the total genome size. In duplicated chromosomes, mRNA levels reflected gene copy numbers, but the level of translation estimated by polysome profiling revealed that dosage compensation must be occurring. In particular, one duplicated chromosome showed a 2.1-fold increase of mRNA but translation rates were decreased to 0.7-fold. Altogether, our results support previous observations of chromosome-dependent dosage compensation effects, providing evidence that compensation occurs during translation. We hypothesize that an unknown posttranscriptional mechanism modulates the translation of hundreds of transcripts from genes located on duplicated regions in eukaryotes.

T Residues Preceded by Runs of G Are Hotspots of T→G Mutation in Bacteria

Mon, 22 May 2023 00:00:00 GMT

Abstract
The rate of mutation varies among positions in a genome. Local sequence context can affect the rate and has different effects on different types of mutation. Here, I report an effect of local context that operates to some extent in all bacteria examined: the rate of T→G mutation is greatly increased by preceding runs of three or more G residues. The strength of the effect increases with the length of the run. In Salmonella, in which the effect is strongest, a G run of length three 3 increases the rate by a factor of ∼26, a run of length 4 increases it by almost a factor of 100, and runs of length 5 or more increase it by a factor of more than 400 on average. The effect is much stronger when the T is on the leading rather than the lagging strand of DNA replication. Several observations eliminate the possibility that this effect is an artifact of sequencing error.

Genome-Wide Discovery of Structural Variants Reveals Distinct Variant Dynamics for Two Closely Related Monilinia Species

Mon, 22 May 2023 00:00:00 GMT

Abstract
Structural variants (SVs) are variants with sizes bigger than 50 bp and capable of changing the size, copy number, location, orientation, and sequence content of genomic DNA. Although these variants have been proven to be extensive and involved in many evolutionary processes along the tree of life, there is still insufficient information on many fungal plant pathogens. In this study, the extent of SVs, as well as single-nucleotide polymorphisms (SNPs), has been determined for two prominent species of the Monilinia genus (the causal agents of brown rot disease in pome and stone fruits): Monilinia fructicola and Monilinia laxa for the first time. The genomes of M. fructicola were found to be more variant-rich in contrast to M. laxa based on the reference-based variant calling (with a total number of 266.618 and 190.599 SNPs and 1,540 and 918 SVs, respectively). The extent, as well as distribution of SVs, presented high conservation within the species and high diversity between the species. Investigation of potential functional effects of characterized variants revealed high potential relevance of SVs. Moreover, the detailed characterization of copy number variations (CNVs) for each isolate revealed that around 0.67% of M. fructicola genomes and 2.06% of M. laxa genomes are copy number variables. The variant catalog as well as distinct variant dynamics within and between the species presented in this study opens doors for many further research questions.

The First Genome of the Cold-Water Octocoral, the Pink Sea Fan, Eunicella verrucosa

Sat, 20 May 2023 00:00:00 GMT

Abstract
Cold-water corals form an important part of temperate benthic ecosystems by increasing three-dimensionality and providing an important ecological substrate for other benthic fauna. However, the fragile three-dimensional structure and life-history characteristics of cold-water corals can leave populations vulnerable to anthropogenic disturbance. Meanwhile, the ability of temperate octocorals, particularly shallow-water species, to respond to adjustments in their environment linked to climate change has not been studied. This study reports the first genome assembly of the pink sea fan (Eunicella verrucosa), a temperate shallow-water octocoral species. We produced an assembly of 467 Mb, comprising 4,277 contigs and an N50 of 250,417 bp. In total, 213 Mb (45.96% of the genome) comprised repetitive sequences. Annotation of the genome using RNA-seq data derived from polyp tissue and gorgonin skeleton resulted in 36,099 protein-coding genes after 90% similarity clustering, capturing 92.2% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) ortholog benchmark genes. Functional annotation of the proteome using orthology inference identified 25,419 annotated genes. This genome adds to the very few genomic resources currently available in the octocoral community and represents a key step in allowing scientists to investigate the genomic and transcriptomic responses of octocorals to climate change.