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

2017-10-30

Fat-Rich Diets and Adaptation Among Indigenous Siberian Populations

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Mate Selection Found to Evolve from Response to Flower Odors

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2017-07-17

Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

2017-07-16

2017-07-16

two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.

2017-07-11

2017-06-28

GBE | Most Read

Genome Biology & Evolution

RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel ( Anguilla rostrata )

2017-11-10

Abstract
The American Eel (Anguilla rostrata) has an exceptional life cycle characterized by panmictic reproduction at the species scale, random dispersal, and selection in a highly heterogeneous habitat extending from subtropical to subarctic latitudes. The genetic consequences of spatially-varying selection in this species have been investigated for decades, revealing subtle clines in allele frequency at a few loci that contrast with complete panmixia on the vast majority of the genome. Because reproduction homogenizes allele frequencies every generation, sampling size, and genomic coverage are critical to reach sufficient power to detect selected loci in this context. Here, we used a total of 710 individuals from 12 sites and 12,098 high-quality single nucleotide polymorphisms to re-evaluate the extent to which local selection affects the spatial distribution of genetic diversity in this species. We used environmental association methods to identify markers under spatially-varying selection, which indicated that selection affects ∼1.5% of the genome. We then evaluated the extent to which candidate markers collectively vary with environmental factors using additive polygenic scores. We found significant correlations between polygenic scores and latitude, longitude and temperature which are consistent with polygenic selection acting against maladapted genotypes in different habitats occupied by eels throughout their range of distribution. Gene functions associated with outlier markers were significantly enriched for the insulin signaling pathway, indicating that the trade-offs inherent to occupying such a large distribution range involve the regulation of metabolism. Overall, this study highlights the potential of the additive polygenic scores approach in detecting selective effects in a complex environment.

Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing

2017-10-31

Abstract
Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa.

Legionella Becoming a Mutualist: Adaptive Processes Shaping the Genome of Symbiont in the Louse Polyplax serrata

2017-10-23

Abstract
Legionellaceae are intracellular bacteria known as important human pathogens. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to the gammaproteobacterial family Enterobacteriaceae, which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been reported from lice of the genus Polyplax. Here, we sequenced the complete genome of this symbiont and compared its main characteristics to other Legionella species and insect symbionts. Based on rigorous multigene phylogenetic analyses, we confirm this bacterium as a member of the genus Legionella and propose the name Candidatus Legionella polyplacis, sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive degeneration, including considerable size reduction (529.746 bp, 484 protein coding genes) and a severe decrease in GC content (23%). We identify several possible constraints underlying the evolution of this bacterium. On one hand, Ca. Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced convergent evolution, perhaps due to adaptation to similar hosts. On the other hand, some metabolic differences are likely to reflect different phylogenetic positions of the symbionts and hence availability of particular metabolic function in the ancestor. This is exemplified by different arrangements of thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal gene transfer is shown to play a significant role in the adaptive and diversification process. Particularly, we show that Ca. L. polyplacis horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted this bacterium when becoming an obligate mutualist.

The Diversification of Zika Virus: Are There Two Distinct Lineages?

2017-10-23

Zika virus (ZIKV) has caused explosive epidemics in the Pacific and the Americas, posing a serious threat to public health. Conventional opinion advocates that ZIKV evolved into two distinct lineages, namely, African and Asian. Descendants of this latter lineage dispersed globally causing major epidemics. However, based on shared amino acid replacements and phylogenetic analyses, it was recently contentiously proposed that the Asian lineage was a direct descendant of the African lineage. To address this contentious issue, we reconstructed a phylogenetic tree of ZIKV using the method based on shared amino acid replacements and found that ZIKV evolved into two distinct lineages. This supports the conventional phylogenetic divergence pattern of ZIKV. Evidence of recombination and sequencing errors was identified among the large collection of ZIKV. As such problematic sequences could confound the phylogenetic analyses, they were removed. Bayesian phylogenetic analyses using the improved sequence data enabled estimates for the divergence time in the past of the African and Asian lineages of ∼180 years ago. Moreover, we found that the Asian lineage viruses did not evolve at an elevated rate. Our findings provide additional support for the conventional opinion that the Asian lineage of ZIKV diverged from the African lineage.