Best Graduate Student Paper

These awards provide recognition for outstanding student papers in both SMBE journals. 

All articles published in the two SMBE journals, Molecular Biology & Evolution and Genome Biology & Evolution, in the calendar year prior to the meeting are eligible for nomination. The best student paper of the year in each journal will receive the prize. 


Award recipients in 2017


For MBE: Alejandra Rodríguez-Verdugo, Uppsala University

First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes


For GBE: Anouk Willemsen, MIVEGEC - Centre IRD de Montpellier

Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus



Award recipients in 2016 for papers published in 2015

For MBE: Emily Clare Baker,  

The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. Mol Biol Evol 32:2818-31.

For GBE: award shared by Daniel Tamarit and Kirsten Ellegaard, 
Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees. Genome Biol Evol 7:1455-73


 How to Enter:

Please send the name of the nominee, a scan of the signed advisor letter, and the name of the paper for which the award is to be considered as a SINGLE PDF to smbe@allenpress.com with the subject of "Best Graduate Student Paper Prize". If possible, please denote if the paper was published in MBE or GBE.

Award Information

Eligibility & Nomination:


  •       All articles published in the two SMBE journals, Molecular Biology & Evolution and Genome Biology & Evolution (one prize for each journal), in the calendar year 2015 are automatically eligible if the final publication date of the nominated paper is not more than two years later than the date of the nominee's PhD
  •      The nominated early-stage researcher must be the first author or joint first-author of the nominated paper.
  •      An article and its first author can be nominated by anyone, including the first author.
  •      A signed letter from the PhD advisor, MSc advisor, or equivalent, confirming that the paper was part of the nominee’s thesis or graduate work is required.


The nomination must provide:

  • A one-page justification for the nomination, including the broader impact of the work and any scientific metrics, news activities or other tangible aspects that make the article stand out from its peers.  Shared first-authorship is also subject to nomination; if both first-authors are students and the article wins, the award will go to both authors.
  • A signed letter from the PhD advisor, MSc advisor, or equivalent, confirming that the paper was part of the nominee’s thesis or graduate work

Process: The editor-in-chief of each journal will convene separate selection committees, which will choose one awardee each.

The Prize: The best student paper winners will be given a certificate, a prize of $2,000 and a travel award to the next annual meeting. 


@OfficialSMBE Feed

MBE | Most Read

Molecular Biology and Evolution

Wed, 22 Nov 2017 00:00:00 GMT

Wed, 22 Nov 2017 00:00:00 GMT

Wed, 22 Nov 2017 00:00:00 GMT

Exploring the Adaptation Extremes of Human High Altitude Sickness and Fitness

Wed, 22 Nov 2017 00:00:00 GMT

Tibetans, Ethiopians, and Peruvians.

Wed, 22 Nov 2017 00:00:00 GMT

Thu, 16 Nov 2017 00:00:00 GMT

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Thu, 28 Sep 2017 00:00:00 GMT

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Tue, 26 Sep 2017 00:00:00 GMT

Species Tree Root Inference from Gene Duplication Events

Tue, 26 Sep 2017 00:00:00 GMT

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Mon, 25 Sep 2017 00:00:00 GMT

Tue, 19 Sep 2017 00:00:00 GMT

DNA Sequence Polymorphism Analysis of Large Data Sets

Mon, 18 Sep 2017 00:00:00 GMT

1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.">http://www.ub.edu/dnasp">http://www.ub.edu/dnasp.

Thu, 14 Sep 2017 00:00:00 GMT

Thu, 14 Sep 2017 00:00:00 GMT

Tue, 12 Sep 2017 00:00:00 GMT

Mon, 11 Sep 2017 00:00:00 GMT

selective sweeps wherein large shifts in the allele frequencies occur at a few loci and evolution via small changes in the allele frequencies at many loci. Although the first process has been thoroughly investigated within the framework of population genetics, the latter is based on quantitative genetics and is much less understood. Here we summarize results from our recent theoretical studies of a quantitative genetic model of polygenic adaptation that makes explicit reference to population genetics to bridge the gap between the two frameworks. Our key results are that polygenic adaptation may be a rapid process and can proceed via subtle or dramatic changes in the allele frequency depending on the sizes of the phenotypic effects relative to a threshold value. We also discuss how the signals of polygenic selection may be detected in the genome. Although powerful methods are available to identify signatures of selective sweeps at loci controlling quantitative traits, the development of statistical tests for detecting small shifts of allele frequencies at quantitative trait loci is still in its infancy.

Sat, 09 Sep 2017 00:00:00 GMT

Tue, 05 Sep 2017 00:00:00 GMT

Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds

Tue, 05 Sep 2017 00:00:00 GMT

A Package for Phylogenetic Networks

Mon, 04 Sep 2017 00:00:00 GMT

Wed, 30 Aug 2017 00:00:00 GMT

Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation

Wed, 30 Aug 2017 00:00:00 GMT

Thu, 24 Aug 2017 00:00:00 GMT

Wed, 05 Jul 2017 00:00:00 GMT

GBE | Most Read

Genome Biology & Evolution

Emergence and Spread of Epidemic Multidrug-Resistant Pseudomonas aeruginosa

Wed, 29 Nov 2017 00:00:00 GMT

Abstract
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized whole genome sequence (WGS) analyses to define the population structure of 185 P. aeruginosa clinical isolates from several countries. Of these 185 isolates, 136 were categorized into sequence type (ST) 235, one of the most common types worldwide. Phylogenetic analysis showed that these isolates fell within seven subclades. Each subclade harbors characteristic drug resistance genes and a characteristic genetic background confined to a geographic location, suggesting that clonal expansion following antibiotic exposure is the driving force in generating the population structure of MDR P. aeruginosa. WGS analyses also showed that the substitution rate was markedly higher in ST235 MDR P. aeruginosa than in other strains. Notably, almost all ST235 isolates harbor the specific type IV secretion system and very few or none harbor the CRISPR/CAS system. These findings may help explain the mechanism underlying the emergence and spread of ST235 P. aeruginosa as the predominant MDR lineage.

Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma

Tue, 21 Nov 2017 00:00:00 GMT

Abstract
Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, although the commensal Spiroplasma diminutum lacks identifiable pathogenicity factors, the pathogenic Spiroplasma taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer. However, it is unclear if these acquired genes have been integrated into the regulatory network. In this study, we inferred the gene content evolution in these bacteria, as well as examined their transcriptomes in response to glucose availability. The results indicated that both species have many more gene acquisitions from the Mycoides-Entomoplasmataceae clade, which contains several important pathogens of ruminants, than previously thought. Moreover, several acquired genes have higher expression levels than the vertically inherited homologs, indicating possible functional replacement. Finally, the virulence factor and its functionally linked genes in S. taiwanense were up-regulated in response to glucose starvation, suggesting that these acquired genes are under expression regulation and the pathogenicity may be a stress response. In summary, although differential gene losses are a major process for symbiont divergence, gene gains are critical in counteracting genome degradation and driving diversification among facultative symbionts.

The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine

Mon, 20 Nov 2017 00:00:00 GMT

Abstract
The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)—an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM’s autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.

Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System

Tue, 14 Nov 2017 00:00:00 GMT

Abstract
Many bivalve species have two types of mitochondrial DNA passed independently through the female line (F genome) and male line (M genome). Here we study the cytochrome oxidase I protein in such bivalve species and provide evidence for differences between the F and M proteins in amino acid property values, particularly relating to hydrophobicity and helicity. The magnitude of these differences varies between different regions of the protein and the change from the ancestor is most marked in the M protein. The observed changes occur in parallel and in the same direction in the different species studied. Two possible causes are considered, first relaxation of purifying selection with drift and second positive selection. These may operate in different ways in different regions of the protein. Many different amino acid substitutions contribute in a small way to the observed variation, but substitutions involving alanine and serine have a quantitatively large effect. Some of these substitutions are potential targets for phosphorylation and some are close to residues of functional importance in the catalytic mechanism. We propose that the observed changes in the F and M proteins might contribute to functional differences between them relating to ATP production and mitochondrial membrane potential with implications for sperm function.

The Novel Evolution of the Sperm Whale Genome

Wed, 13 Sep 2017 00:00:00 GMT

Abstract
The sperm whale, made famous by Moby Dick, is one of the most fascinating of all ocean-dwelling species given their unique life history, novel physiological adaptations to hunting squid at extreme ocean depths, and their position as one of the earliest branching toothed whales (Odontoceti). We assembled the sperm whale (Physeter macrocephalus) genome and resequenced individuals from multiple ocean basins to identify new candidate genes for adaptation to an aquatic environment and infer demographic history. Genes crucial for skin integrity appeared to be particularly important in both the sperm whale and other cetaceans. We also find sperm whales experienced a steep population decline during the early Pleistocene epoch. These genomic data add new comparative insight into the evolution of whales.