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, recipient of the 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, recipient of the 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, won the Margaret Dayhoff Mid-Career Award

Toni Gabaldón has a degree in Biochemistry and Molecular Biology from the University of Valencia, with a special mention. After assisting in teaching tasks and working during 4 years on yeast gene expression regulation at the Biochemistry department of that university, he moved in 2001 to Nijmegen University (The Netherlands) where he worked in comparative genomics and evolution at the bioinformatics department of the NIjmegen Center for Molecular Life Sciences. In 2005 he obtained his PhD from the Nijmegen University, which obtained the NCMLS award for the best thesis of the year. He was awarded and EMBO postdoctoral fellowship to move to the bioinformatics department at CIPF (Valencia, Spain) where he worked during three years in comparative genomics. In September 2008, he was appointed group leader at the Centre for Genomic Regulation, where he is leading the Comparative Genomics group. He also is ICREA research professor since 2013.
Overall, he has authored over 130 publications. 73 of them are published between 2012 and 2017 (27 of which as corresponding author). He teaches bioinformatics and comparative genomics in several Master courses and he is an associate professor at the Pompeu Fabra University (Barcelona, Spain).


Sudhir Kumar, Temple University, won the 2017 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, won the MBE Best Student Paper Award (https://www.ncbi.nlm.nih.gov/pubmed/26500250)
Anouk Willemsen, 
MIVEGEC - Centre IRD de Montpellier, won the GBE best student paper award (https://www.ncbi.nlm.nih.gov/pubmed/27604880)
Anna Vickrey, University of Utah, won the Walter M. Fitch Award for Best Student Presentation.

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

2017-08-03

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2017-08-03

Did Medieval Religious Rules Drive Domestic Chicken Evolution?

2017-08-03

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TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.

2017-04-29

2017-04-29

BLAST and InterProScan. Orthology filters applied to BLAST results reduced the rate of false positive assignments by 11%, and increased the ratio of experimentally validated terms recovered over all terms assigned per protein by 15%. Compared with InterProScan, eggNOG-mapper achieved similar proteome coverage and precision while predicting, on average, 41 more terms per protein and increasing the rate of experimentally validated terms recovered over total term assignments per protein by 35%. EggNOG-mapper predictions scored within the top-5 methods in the three GO categories using the CAFA2 NK-partial benchmark. Finally, we evaluated eggNOG-mapper for functional annotation of metagenomics data, yielding better performance than interProScan. eggNOG-mapper runs ∼15× faster than BLAST and at least 2.5× faster than InterProScan. The tool is available standalone and as an online service at http://eggnog-mapper.embl.de.">http://eggnog-mapper.embl.de">http://eggnog-mapper.embl.de.

2017-04-28

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the frequency of the derived allele, rs117799927 G, was extremely low among worldwide populations (0.005) but exceptionally high in Mongolians (0.247). Approximate Bayesian computation-based age estimation showed that the rs117799927 G allele emerged or positive selection began to operate 50 generations before the present, near the age of the climate anomaly named Late Antique Little Ice Age. Furthermore, rs117799927 showed significant associations with multiple adiposity-related traits in Mongolians and allelic difference in enhancer activity in cells of adipocyte lineage, suggesting that positive selection at 3p12.1 might be related to adaptation in the energy metabolism system. These findings provide novel evidence for a very recent positive-selection event in Homo sapiens and offer insights into the roles of genes in 3p12.1 in the adaptive evolution of our species.

2017-04-21

Could Mitochondria “Bend” Nuclear Regulation?

2017-04-21

2017-04-19

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2017-04-08

site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.

2017-04-08

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GBE | Most Read

Genome Biology & Evolution

Whole-Genome Sequence of the Anaerobic Isosaccharinic Acid Degrading Isolate, Macellibacteroides fermentans Strain HH-ZS

2017-08-16

Abstract
The ability of micro-organisms to degrade isosaccharinic acids (ISAs) while tolerating hyperalkaline conditions is pivotal to our understanding of the biogeochemistry associated within these environs, but also in scenarios pertaining to the cementitious disposal of radioactive wastes. An alkalitolerant, ISA degrading micro-organism was isolated from the hyperalkaline soils resulting from lime depositions. Here, we report the first whole-genome sequence, ISA degradation profile and carbohydrate preoteome of a Macellibacteroides fermentans strain HH-ZS, 4.08 Mb in size, coding 3,241 proteins, 64 tRNA, and 1 rRNA.

Ultraconserved Sequences Associated with HoxD Cluster Have Strong Repression Activity

2017-08-14

Abstract
Increase in the complexity of organisms during evolution strongly correlates with the increase in the noncoding DNA content of their genomes. Although a gradual increase in the proportion of repetitive DNA elements along with increasing complexity is known, most of the noncoding components of the genome remain uncharacterized. A nonrepetitive but highly conserved noncoding component of the genome in vertebrates, called ultraconserved DNA sequences, constitutes up to 5% of the human genome. The function of most of the ultraconserved DNA elements is not well known. One such ultraconserved stretch of DNA has been identified upstream of the HoxD cluster in vertebrates. We analyzed the function of these elements in different cell lines and zebrafish. Our results suggest that these ultraconserved sequences work as repressor elements. This is the first report which reveals the repressor function of ultraconserved sequences and implicates their role in the regulation of developmental genes.

Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences

2017-08-02

Abstract
The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota). We found that the intron data contained stronger and more congruent phylogenetic signals than the CDS data. In agreement with this observation, concatenation and species-tree analyses of the intron data set yielded well-resolved and identical phylogenies, whereas the CDS data set produced weakly supported and incongruent results. Further analyses showed that the phylogeny inferred from the intron data is highly robust to data subsampling and change in outgroup, but the CDS data produced unstable results under the same conditions. Interestingly, gene tree statistical results showed that the most frequently observed gene tree topologies for the CDS and intron data are identical, suggesting that the major phylogenetic signal within the CDS data is actually congruent with that within the intron data. Our final result of Laurasiatheria phylogeny is (Eulipotyphla,((Chiroptera, Perissodactyla),(Carnivora, Cetartiodactyla))), favoring a close relationship between Chiroptera and Perissodactyla. Our study 1) provides a well-supported phylogenetic framework for Laurasiatheria, representing a step towards ending the long-standing “hard” polytomy and 2) argues that intron within genome data is a promising data resource for resolving rapid radiation events across the tree of life.

The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees

2017-08-02

Abstract
Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects.

Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture

2017-07-11

Abstract
Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the “First Sundaland People.” To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

2017-06-19

Abstract
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes.

Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum

2017-05-25

Abstract
Trypanosomes cause a variety of diseases in man and domestic animals in Africa, Latin America, and Asia. In the Trypanozoon subgenus, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis, whereas Trypanosoma brucei brucei, Trypanosoma evansi, and Trypanosoma equiperdum are responsible for nagana, surra, and dourine in domestic animals, respectively. The genetic relationships between T. evansi and T. equiperdum and other Trypanozoon species remain unclear because the majority of phylogenetic analyses has been based on only a few genes. In this study, we have conducted a phylogenetic analysis based on genome-wide SNP analysis comprising 56 genomes from the Trypanozoon subgenus. Our data reveal that T. equiperdum has emerged at least once in Eastern Africa and T. evansi at two independent occasions in Western Africa. The genomes within the T. equiperdum and T. evansi monophyletic clusters show extremely little variation, probably due to the clonal spread linked to the independence from tsetse flies for their transmission.