Pictured from left to right: Atahualpa Castillo Morales, Laura Landweber, Marc Tollis, Alejandra Rodriguez- Verdugo, W. Ford Doolittle, Mia Levine, Sudhir Kumar, Isabela Jeronimo Bezerra Marcos, James Fleming and Joseph Palmer 

Congratulations to the recipients of the SMBE 2017 annual awards! As announced at the SMBE 2017 Annual Meeting: 

Mia Levine, University of Pennsylvania, Allan Wilson Junior Award for Independent Research

Dr. Mia Levine is an Assistant Professor in the Department of Biology and the Epigenetics Institute at the University of Pennsylvania. The Levine Lab investigates how intra-genomic conflict shapes the evolution of DNA packaging proteins. Together with her trainees, Mia combines evolutionary genetics with transgenics, genomics, and cell biology to identify selfish genetic elements that drive host protein adaptation and to uncover the functional consequences for chromosome integrity and transmission. Mia graduated magna cum laude with a BA in Biology from the University of Pennsylvania, where she is now faculty. She earned an MSc in Ecology from the University of Illinois, Urbana-Champaign under Dr. Ken Paige and an NSF GRFP-supported PhD in population genetics from the Center of Population Biology at the University of California, Davis under Dr. David Begun. Mia joined the Fred Hutchinson Cancer Research Center to work with Dr. Harmit Malik as a postdoctoral fellow supported by an NIH NIGMS Ruth L. Kirschstein NRSA and an NIH NIGMS K99 Pathway to Independence Award. Mia is currently a Forbeck Foundation Scholar and recipient of an NIH NIGMS R35 Maximizing Investigators’ Research Award.

W. Ford Doolittle, Dalhousie University, Motoo Kimura Lifetime Contribution Award

W. Ford Doolittle was born in Urbana, Illinois in 1942. He attended Harvard College (BA in Biochemical Sciences) and Stanford University (PhD in Biological Sciences, with Charles Yanofsky). After postdoctoral work with Sol Spiegelman and Norman Pace, he took up a position at Dalhousie University, in Halifax, Nova Scotia, where he has been ever since. For twenty years he directed the Evolutionary Biology Program of the Canadian Institute for Advanced Research. His 300+ papers include experimental proof of the endosymbiont hypothesis, early molecular studies of cyanobacteria, the first shuttle vector and mapping systems for Archaea, and the metagenomic discovery of actinorhodopsin. Of a more theoretical nature are his developments of the "introns-early" hypothesis, the notion of "selfish DNA", Constructive Neutral Evolution as an alternative to selection, and a reconsideration of the Tree of Life in the light of lateral gene transfer. He is currently more concerned with philosophical issues, such as the meaning of "function" and the possibility of "Darwinizing Gaia". He is a Fellow of the Royal Society of Canada and a member of the US National Academy of Sciences, and the winner of the 2013 Gerhard Herzberg Gold Medal and the 2017 Killam Prize in Natural Sciences, Canada's highest awards.

Toni Gabaldón, CRG, Margaret Dayhoff Mid-Career Award

Toni Gabaldón has a degree in Biochemistry and Molecular Biology from the University of Valencia (Spain), and obtained his PhD (under the supervision of Martijn Huynen) in 2005 at he Nijmegen Center for Molecular Life Sciences. Nijmegen (The Netherlands). Since September 2008, he leads the Comparative Genomics group of the Centre for Genomic Regulation (CRG) in Barcelona (Spain), and is associate professor at the University Pompeu Fabra. Gabaldón has been working in the fields of comparative and evolutionary genomics where he has made significant contributions to the understanding of how genomes and phenotypes evolve across species. Major contributions from his research include providing fundamental insights into the origin an evolution of eukaryotes and their organelles; evolution of function across gene families and the implications of orthology and paralogy; and the study of genome evolution in eukaryotes, including non-vertical processes such as horizontal gene transfer and hybridization. He has authored over 140 publications and has been awarded the prestigieous ERC Starting and Consolidator grants, and the ICREA Professorship.

Sudhir Kumar, Temple University, recipient of the SMBE Community Service Award

Sudhir Kumar, Temple University, SMBE Community Service Award

Sudhir Kumar has been an early leader in exploring the theoretical and empirical intersection of evolutionary biology with computational biology, and forging accessible tools that allow researchers from diverse backgrounds to harness the analytical power of modern computational biology. With a background in Biological Sciences and Electrical & Electronics Engineering from Birla Institute of Technology and Sciences, he completed a Ph.D. and postdoctoral work in Genetics at Pennsylvania State University, mentored by Dr. Masatoshi Nei. During this period, he worked to develop the first version of Molecular Evolutionary Genetics Analysis (MEGA), a freely-accessible software package that has been maintained and improved over more than 20 years since its release. The enduring popularity of MEGA results from Kumar’s responsiveness to community needs and dedication to accessibility and scientific rigor. He has made numerous contributions to the mathematical theory of phylogenetics through advances in estimating evolutionary distances, inference of divergence times, and algorithms for constructing phylogenetic trees. Kumar and his laboratory continue to work actively on improving phylogenetic theory and applications to the growing field of phylomedicine, which explores disease via phylogenetic methods and makes predictions informed by evolutionary biology. Sudhir Kumar is currently the Laura H. Carnell Professor and the Director of the Institute for Genomics and Evolutionary Medicine at Temple University. He has served the SMBE community as elected Secretary, webmaster, President, chair of the organizing committee of the SMBE annual meeting in 2006 in Tempe, Arizona, and is currently serving as Editor-in-Chief of the society journal Molecular Biology and Evolution.

Alejandra Rodríguez-Verdugo, Uppsala University, MBE Best Student Paper Award (https://www.ncbi.nlm.nih.gov/pubmed/26500250)

Anouk Willemsen, MIVEGEC - Centre IRD de Montpellier,  GBE Best Student Paper Award (https://www.ncbi.nlm.nih.gov/pubmed/27604880)

Walter M. Fitch Award for Best Student Presentation:

Anna Vickrey, University of Utah

Best Poster Awards for Postdoctoral Researchers:

Marc Tollis
Elizabeth Atkinson
Atahualpa Castillo Morales

Best Poster Awards for PhD Students:

James Fleming
Pinglin Cao
Magdalena Kubiak

Best Poster Awards for Undergraduate Researchers:

Isabela Jeronimo Bezerra Marcos
Joseph Palmer
Dan Werndly

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MBE | Most Read

Molecular Biology and Evolution

Wed, 22 Nov 2017 00:00:00 GMT

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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

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Species Tree Root Inference from Gene Duplication Events

Tue, 26 Sep 2017 00:00:00 GMT

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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

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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

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GBE | Most Read

Genome Biology & Evolution

Emergence and Spread of Epidemic Multidrug-Resistant Pseudomonas aeruginosa

Wed, 29 Nov 2017 00:00:00 GMT

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

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

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

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

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.