Motoo Kimura Lifetime Contribution Award

This award is intended for outstanding senior members of the SMBE community.  The primary criterion is a record of truly outstanding research that has contributed broadly to the field of Molecular Biology and Evolution.  The prize includes recognition at the annual SMBE banquet, a cash prize of $2000 and a travel award to attend the annual meeting.  This award will be made annually and initiated by the SMBE council.


This award is intended for outstanding senior members of the SMBE community.  The primary criterion is a record of truly outstanding research that has contributed broadly to the field of Molecular Biology and Evolution.  The prize includes recognition at the annual SMBE banquet, a cash prize of $2000 and a travel award to attend the annual meeting.  This award will be made annually and initiated by the SMBE council.


This award is intended for outstanding senior members of the SMBE community.  The primary criterion is a record of truly outstanding research that has contributed broadly to the field of Molecular Biology and Evolution.  The prize includes recognition at the annual SMBE banquet, a cash prize of $2000 and a travel award to attend the annual meeting.  This award will be made annually and initiated by the SMBE council.



W. Ford Doolittle, Dalhousie University, won 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.


2016 SMBE Motoo Kimura Lifetime Contribution Award Winner: Nancy Moran

Nancy Moran's long-term interests are in the evolution of biological complexity, such as that apparent in complex life histories, in intimate interactions among species and in species-diversity of clades and communities. Her research has focused extensively on symbiosis, particularly between multicellular hosts and microbes.  In her storied career, she has demonstrated ancient coevolution between aphids and their plant hosts, and has characterized mutualistic symbiotic interactions between aphids and Buchnera bacteria and between other insect and symbiont clades. She found that these mutualisms are ancient, dating to the origins of major insect clades, and that the long term vertical transmission of the bacterial symbionts has caused extreme genome degradation and shrinkage. Her ongoing projects include phylogenetic and genomic studies of previously unstudied insect symbioses, experiments on gene expression of symbionts within hosts, computational reconstruction of the content and arrangement of genes in bacterial ancestors, and experimental investigations of coevolved gut communities within social bees. She has previously been awarded a MacArthur Fellowship and the International Prize for Biology, and has been a member of that National Academy of the Sciences since 2004. She is currently the Leslie Surginer Endowed Professor in the Department of Integrative Biology at the University of Texas, Austin.

Award Information

Eligibility: Awardees are likely to be at least 25 years past their doctoral degrees. Members of the SMBE Council are not eligible for any awards during their years on council or in the year immediately following their service.

Nomination:  Nomination will be an open process that begins with a call to SMBE members, typically early in the calendar year.

All nominations will include:

  • A nomination letter that includes a recommendation for the candidate.

  • A one-page statement summarizing the candidate’s work and its fit to the award. 
  • A CV of the candidate.  
  • A second recommendation letter

Process:  The President will convene an awards committee that will choose among those nominated.  It may also choose not to award the prize if no suitable candidates are nominated.

 

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MBE | Most Read

Molecular Biology and Evolution

Study Finds Large Chromosomal Swaps Key to Banana Domestication

2017-08-24

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A Fast and Accurate Supertree Algorithm

2017-07-05

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2017-06-08

swarming in the bacterium Pseudomonas aeruginosa. Using genetic engineering, we excised a locus encoding a key metabolic regulator and disrupted P. aeruginosa’s metabolic prudence, the regulatory mechanism that controls expression of swarming public goods and protects this social behavior from exploitation by cheaters. Then, using experimental evolution, we followed the joint evolution of the genome, the metabolome and the social behavior as swarming re-evolved. New variants emerged spontaneously with mutations that reorganized the metabolome and compensated in distinct ways for the disrupted metabolic prudence. These experiments with a unicellular organism provide a detailed view of how metabolism—currency of all physiological processes—can determine the costs and benefits of a social behavior and ultimately influence how an organism behaves towards other organisms of the same species.

2017-05-31

2017-05-30

2017-05-30

(Nei Lecture, SMBE 2016, Gold Coast)

2017-05-29

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The Deep Evolution of Amoebae

2017-05-15

2017-05-15

Smart Model Selection in PhyML

2017-05-11

command-line (to be integrated in pipelines) and a web server (http://www.atgc-montpellier.fr/phyml-sms/).">http://www.atgc-montpellier.fr/phyml-sms/">http://www.atgc-montpellier.fr/phyml-sms/).

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GBE | Most Read

Genome Biology & Evolution

Distribution, Diversity, and Long-Term Retention of Grass Short Interspersed Nuclear Elements (SINEs)

2017-08-17

Abstract
Instances of highly conserved plant short interspersed nuclear element (SINE) families and their enrichment near genes have been well documented, but little is known about the general patterns of such conservation and enrichment and underlying mechanisms. Here, we perform a comprehensive investigation of the structure, distribution, and evolution of SINEs in the grass family by analyzing 14 grass and 5 other flowering plant genomes using comparative genomics methods. We identify 61 SINE families composed of 29,572 copies, in which 46 families are first described. We find that comparing with other grass TEs, grass SINEs show much higher level of conservation in terms of genomic retention: The origin of at least 26% families can be traced to early grass diversification and these families are among most abundant SINE families in 86% species. We find that these families show much higher level of enrichment near protein coding genes than families of relatively recent origin (51%:28%), and that 40% of all grass SINEs are near gene and the percentage is higher than other types of grass TEs. The pattern of enrichment suggests that differential removal of SINE copies in gene-poor regions plays an important role in shaping the genomic distribution of these elements. We also identify a sequence motif located at 3′ SINE end which is shared in 17 families. In short, this study provides insights into structure and evolution of SINEs in the grass family.

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.

Comparative Genomics Reveals Two Major Bouts of Gene Retroposition Coinciding with Crucial Periods of Symbiodinium Evolution

2017-08-07

Abstract
Gene retroposition is an important mechanism of genome evolution but the role it plays in dinoflagellates, a critical player in marine ecosystems, is not known. Until recently, when the genomes of two coral-symbiotic dinoflagellate genomes, Symbiodinium kawagutii and S. minutum, were released, it has not been possible to systematically study these retrogenes. Here we examine the abundant retrogenes (∼23% of the total genes) in these species. The hallmark of retrogenes in the genome is the presence of DCCGTAGCCATTTTGGCTCAAG, a spliced leader (DinoSL) constitutively trans-spliced to the 5′-end of all nucleus-encoded mRNAs. Although the retrogenes have often lost part of the 22-nt DinoSL, the putative promoter motif from the DinoSL, TTT(T/G), is consistently retained in the upstream region of these genes, providing an explanation for the high survival rate of retrogenes in dinoflagellates. Our analysis of DinoSL sequence divergence revealed two major bursts of retroposition in the evolutionary history of Symbiodinium, occurring at ∼60 and ∼6 Ma. Reconstruction of the evolutionary trajectory of the Symbiodinium genomes mapped these 2 times to the origin and rapid radiation of this dinoflagellate lineage, respectively. GO analysis revealed differential functional enrichment of the retrogenes between the two episodes, with a broad impact on transport in the first bout and more localized influence on symbiosis-related processes such as cell adhesion in the second bout. This study provides the first evidence of large-scale retroposition as a major mechanism of genome evolution for any organism and sheds light on evolution of coral symbiosis.

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.