SMBE Council

Laura Landweber, President

Departments of Biochemistry & Molecular Biophysics and Biological Sciences

Columbia University, New York, NY 10032

Laura.Landweber@columbia.edu

 

Bill Martin, President-Elect (& Editor-in-chief, Genome Biology and Evolution)

Institut for Molecular Evolution

Heinrich-Heine-Universität, Universitätsstr.1, 40225 Düsseldorf, Germany

bill@hhu.de

 

George Zhang, Past-President

Department of Ecology and Evolutionary Biology

University of Michigan, Natural Science Bldg, 830 N University, Ann Arbor, MI 48109

jianzhi@umich.edu

 

David Pollock, Secretary

Department of Biochemistry and Molecular Genetics

University of Colorado Anschutz Medical Campus, Building 500, 13001 E. 17th Place, Campus Box C290, Aurora, CO 80045

secretary.smbe@gmail.com

 

Juliette de Meaux, Treasurer

Institute of Botany

University of Cologne, Zulpicher str. 47b, D-50674 Cologne, Germany

treasurer.smbe@gmail.com

 

Kateryna Makova, Councillor (2015-2017)

Department of Biology

Director, Center for Medical Genomics, Pennsylvania State University

310 Wartik Lab, University Park, PA 16802

kmakova@bx.psu.edu

 

Emma Teeling, Councillor (2015-2017)

School Of Biology & Environment Science

Science Centre – West, Belfield, Dublin 4, Ireland

emma.teeling@ucd.ie

 

Maud Tenaillon, Councillor (2016–2018)

Quantitative Genetics and Evolution - Le Moulon INRA

University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay F-91190, Gif-sur-Yvette, France

tenaillon@moulon.inra.fr

 

Adam Eyre-Walker, Councillor (2016–2018)

School of Life Sciences

University of Sussex, Brighton, BN1 9QG, United Kingdom

a.c.eyre-walker@sussex.ac.uk

 

Joanna Masel, Councillor (2017-2019)

Department of Ecology & Evolutionary Biology

University of Arizona, Tucson, AZ 85721

masel@u.arizona.edu

 

Jay Storz, Councillor (2017-2019)

School of Biological Sciences

University of Nebraska, Lincoln, NE 68588

jstorz2@unl.edu

 

Sudhir Kumar, ex officio (Editor-in-chief, Molecular Biology and Evolution)

Intitute for Genomics & Evolutionary Medicine (iGEM)

Department of Biology, Temple Univeristy, 1925 N. 12th St, Philadelphia, PA 19122

s.kumar@asu.edu


SMBE Past Councils

Year President President-Elect Past-President Secretary Treasurer Councillors Ex Officio Councillors 
 2016 George Zhang Laura Landweber Joe Felsenstein
James McInerney
Juliette de Meaux
  • Maud Tenaillon
  • Adam Eyre-Walker
  • Sandra Baldauf
  • David Liberles
  • Emma Teeling
  • Kateryna Makova

  • Sudhir Kumar
  • Bill Martin

2015 Joe Felsenstein George Zhang Brandon Gaut James McInerney  Juliette de Meaux  

  • Marta Wayne
  • Harmit Malik
  • Sandra Baldauf
  • David Liberles
  • Emma Teeling
  • Kateryna Makova


Marta Wayne
Harmit Malik
Sandra Baldauf
David Liberles
Emma Teeling 
Katerina Makova
Marta Wayne
Harmit Malik
Sandra Baldauf
David Liberles
Emma Teeling 
Katerina Makova

  • Sudhir Kumar
  • Bill Martin


2014 Brandon Gaut Joe Felsenstein Sudhir Kumar James McInerney Aoife McLysaght
  • Laurent Duret
  • Yoko Satta
  • Marta Wayne
  • Harmit Malik
  • Sandra Baldauf
  • David Liberles
 
2013 Sudhir Kumar Brandon Gaut Charles Aquadro James McInerney Aoife McLysaght
  • Soojin Yi
  • Laurent Duret
  • Yoko Satta
  • Marta Wayne
  • Harmit Malik
 
2012 Charles Aquadro Sudhir Kumar Ken Wolfe Manyuan Long Aoife McLysaght
  • Robin Bush
  • Soojin Yi
  • Laurent Duret
  • Yoko Satta
 
2011 Ken Wolfe Charles Aquadro Jody Hey Manyuan Long John Archibald
  • Dan Graur
  • Robin Bush
  • Soojin Yi
 
2010 Jody Hey Ken Wolfe Michael Lynch Manyuan Long John Archibald
  • Ziheng Yang
  • Dan Graur
  • Robin Bush
 
2009 Michael Lynch Jody Hey Paul Sharp George Zhang John Archibald
  • Laura Landweber
  • Ziheng Yang
  • Dan Graur
 
2008 Paul Sharp Michael Lynch Deborah Charlesworth George Zhang Marta L. Wayne
  • Charles Aquadro
  • Laura Landweber
  • Ziheng Yang
 
2007 Deborah Charlesworth Paul Sharp Montserrat Aguade George Zhang Marta L. Wayne
  • Michael Lynch
  • Charles Aquadro
  • Laura Landweber
 
2006 Montserrat Aguade Deborah Charlesworth Jeffrey R. Powell Sudhir Kumar Marta L. Wayne
  • Laura Katz
  • Michael Lynch
  • Charles Aquadro
 
2005 Jeffrey R. Powell Montserrat Aguade John C. Avise Sudhir Kumar Marta L. Wayne
  • Jody Hey
  • Laura Katz
  • Michael Lynch
 
2004 John C. Avise Jeffrey R. Powell Naoyuki Takahata Sudhir Kumar Marta L. Wayne
  • Brian Golding
  • Jody Hey
  • Laura Katz
 
2003 Naoyuki Takahata John C. Avise Michael T. Clegg Marcy K. Uyenoyama Marta L. Wayne
  • Howard Ochman
  • Brian Golding
  • Jody Hey
 
2002 Michael T. Clegg Naoyuki Takahata Daniel L. Hartl Marcy K. Uyenoyama Richard C. Hudson
  • Montserrat Aguade
  • Howard Ochman
  • Brian Golding
 
2001 Daniel L. Hartl Michael T. Clegg Wen-Hsiung Li Marcy K. Uyenoyama Richard C. Hudson
  • Tomoko Ohta
  • Montserrat Aguade
  • Howard Ochman
 
2000 Wen-Hsiung Li Daniel L. Hartl Andrew G. Clark Marcy K. Uyenoyama Richard C. Hudson
  • Pekka Pamilo
  • Tomoko Ohta
  • Montserrat Aguade
 
1999 Andrew G. Clark Wen-Hsiung Li Richard C. Lewontin Marcy K. Uyenoyama Richard C. Hudson
  • Wilfred W. de Jong
  • Pekka Pamilo
  • Tomoko Ohta
 
1998 Richard C. Lewontin Andrew G. Clark David Penny Linda D. Strausbaugh Richard C. Hudson
  • W. Ford Doolittle
  • Wilfred W. de Jong
  • Pekka Pamilo
 
1997 David Penny Richard C. Lewontin Margaret G. Kidwell Linda D. Strausbaugh Richard C. Hudson
  • Maryellen Ruvolo
  • W. Ford Doolittle
  • Wilfred W. de Jong
 
1996 Margaret G. Kidwell David Penny Wesley M. Brown Linda D. Strausbaugh Richard C. Hudson
  • Ross A. Crozier
  • Maryellen Ruvolo
  • W. Ford Doolittle
 
1995 Wesley M. Brown Margaret G. Kidwell Masatoshi Nei Linda Maxson Richard C. Hudson
  • Ross A. Crozier
  • Maryellen Ruvolo
 
1994 Masatoshi Nei Wesley M. Brown Walter M. Fitch Linda Maxson Linda Maxson Ross A. Crozier  
1993 Walter M. Fitch Masatoshi Nei Linda Maxson Linda Maxson Caro-Beth Stewart  

@OfficialSMBE Feed

MBE | Most Read

Molecular Biology and Evolution

2017-08-03

2017-08-03

2017-08-03

Did Medieval Religious Rules Drive Domestic Chicken Evolution?

2017-08-03

2017-08-03

2017-05-19

2017-05-15

2017-05-08

2017-05-04

2017-05-02

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

2017-04-28

2017-04-27

2017-04-27

2017-04-21

2017-04-21

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

2017-04-18

2017-04-18

2017-04-14

2017-04-14

2017-04-12

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

2017-04-04

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.