The Walter M. Fitch Award

The Fitch Award honors the best presentation at the Walter M. Fitch symposium, which provides a forum for young investigators to showcase their exemplary research at the annual meeting of the Society for Molecular Biology and Evolution (SMBE).


As the name suggests, this symposium and the associated prize honors Dr. Walter M. Fitch, who was a pioneer in many areas of molecular evolution, in particular the methodology of phylogenetic reconstruction, the estimation of genetic distances, the study of rate constancy in proteins and DNA sequences, the evolution of codon usage, and retroviral evolution. He also made significant contributions to virology, the origin of life, taxonomy, genetics, and molecular biology. For his work, he was elected to the National Academy of Sciences, the American Philosophical Society, the American Academy of Arts and Sciences, and the Linnean Society. With Masatoshi Nei, he co-founded the journal Molecular Biology and Evolution, and served as editor-in-chief for its first 10 years. He also co-founded the Society for Molecular Biology and Evolution and served as its first president.


Walter Monroe Fitch was born in San Diego, California, on May 21, 1929. He attended the University of California, Berkeley, where he received a bachelor’s degree in chemistry in 1953 and a Ph.D. in comparative biochemistry in 1958. He was a post-doctoral scholar at both Stanford and University College (London), and held full professorships at the University of Wisconsin and the University of Southern California. He came to University of California, Irvine in 1989 as a Distinguished Professor and later became the Chair of the Department of Ecology and Evolutionary Biology. Walter M. Fitch died on March 11, 2011, at the age of 81.

Past Recipients

Year Name Title
 2017 Anna Vickrey, University of Utah, USA  Domestic pigeon’s checkered past: wing color pattern variation is associated with one gene, two mechanisms, and interspecific introgression
 2016 Katya Kosheleva, Harvard University, USA Weakly selected standing variants dominate adaptation for 1000 generations in sexual, laboratory evolved yeast populations 
 2015 Aline Muyle, Université Lyon 1, Lyon, France. Evolution of dosage compensation in the dioecious plant Silene latifolia
 2014 Alex Cagan, Max Planck Institute, Leipzig, Germany  Genetic variants underlying tameness and agression.
2013 Karen Wong Miller, UC Berkeley, USA Genome-Wide Scans Reveal a Young Candidate Speciation Gene in Drosophila athabasca.
2012 Elizabeth Perry, University Of Oregon, USA Repeatability in evolution varies with scale, organism, and the nature of selection.
2011 Kerry Geiler-Samerotte, Harvard University, USA The selective cost of misfolded protein toxicity and a concomitant evolutionary adaptation.
2010 Takashi Tsuchimatsu, University of Zurich, Switzerland Evolution of self-compatibility in Arabidopsis thaliana by a mutation in the male specificity gene.
2009 Joshua Bayes, Fred Hutchinson Cancer Research Center, USA The molecular basis of hybrid sterility caused by the hybrid sterility gene Odysseus.
2008 Jean-François Gout, Centre National de la Recherche Scientifique, France Translational control of intron splicing in eukaryotes.
2007 David Des Marais, Duke University, USA Gene duplication allows substrate specialization in a biosynthetic enzyme.
2006 Jennifer Cork, North Carolina State University, USA Characterizing three candidate balanced polymorphisms in Arabidopsis thaliana: a reverse genetics approach.
Joanna Kelley, University of Washington, USA Positive selection in primate tooth enamelin and evidence for human population specific adaptation.
2005 Leslie Collins, Massey University, New Zealand Cutting it in the RNA World: the spliceosome and splicing in ancestral eukaryotes.
2004 Barbara Engelhardt, University of California at Berkeley, USA Protein function prediction using a Bayesian model of molecular function evolution.
2003 Yoav Gilad, Max Planck Institute for Evolutionary Anthropology, Germany Loss of olfactory receptor genes is coupled to the acquisition of full trichromatic color vision.
2002 Ying Chen, University of Munich, Germany Functional analysis of phylogenetically conserved sequence elements in intron 1 of the Drosophila melanogaster Adh gene.
2001 Jeffrey Townsend, Harvard University, USA Global gene expression variation in natural isolates of Saccharomyces cerevisiae.
2000 Eric A. Gaucher, University of Florida, USA Functional analysis of proteins using covarion-based evolutionary approaches: elongation factors.
1999 Dennis Lavrov, University of Michigan, USA Arthropod phylogeny based on gene arrangement and other characters from mitochondrial DNA.
1998 Mark Siegal, Harvard University, USA Functional evolutionary analysis of genes coplaced into the Drosophila genome.
1997 Christiane Biermann, State University of New York at Stony Brook, USA Sequence variation in the sea urchin sperm protein BINDIN is generated by recombination and length mutations.
Paul Taylor, University of Leicester, UK Diversity and mutational analyses of the Y-specific mini-satellite, MSY1.
1996 Dmitri A. Petrov, Harvard University, USA Birth and death of processed pseudogenes in Drosophila: Molecular evolution of a non-LTR retrotransposable element.
1995 Hiroki Oota, University of Tokyo, Japan Phylogenetic analysis of 2,000 year old human remains of Japan (Yayoi period) based on mitochondrial DNA sequences.
1994 Alan Cooper, Smithsonian Institution, USA Avian evolution in New Zealand as revealed by mitochondrial DNA.
Janet Kornegay, University of California at Berkeley, USA Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin.
1993 Youn-Ho Lee, University of California at San Diego, USA The divergence of species-specific abalone sperm lysin is promoted by positive Darwinian selection: implications regarding speciation.

Award Information

Eligibility: Current graduate students and postdoctoral researchers who received their primary doctoral-level degree no earlier than one year prior to the start of the annual meeting of the society. A candidate for the award must become member of the Society at least a month before the first day of the annual meeting.


Application Requirements

  • An abstract (250 word max) for the proposed presentation.
  • A one page expanded summary of the research, including an explanation of the broad significance or importance of the work.
  • A Curriculum Vitae.
Application: Via the abstract submission system for the annual meeting for which the award applies.

Contest: A committee convened by the SMBE Council will choose eight finalists from among the applications. Each selected finalist will present a 15-minute talk in the Walter M. Fitch Symposium at the annual meeting. Based on these presentations, a winner will be chosen by an anonymous expert panel and awarded the Walter M. Fitch Prize (US $2000). All finalists will receive a one-year, online student/postdoc MBE subscription and travel support for attending the meeting (at same rates as other travel awards, see here). 

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Molecular Biology and Evolution

Wed, 14 Feb 2018 00:00:00 GMT

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Study Determines New Geographic Origins of Brown Rats

Thu, 11 Jan 2018 00:00:00 GMT

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A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

Tue, 02 Jan 2018 00:00:00 GMT

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Sources of Robustness and Constrained Evolvability during Coevolution

Tue, 19 Dec 2017 00:00:00 GMT

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Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity

Thu, 23 Nov 2017 00:00:00 GMT

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Genome Biology & Evolution

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee

Mon, 05 Mar 2018 00:00:00 GMT

Humans experience higher rates of age-associated diseases than our closest living evolutionary relatives, chimpanzees. Environmental factors can explain many of these increases in disease risk, but species-specific genetic changes can also play a role. Alleles that confer increased disease susceptibility later in life can persist in a population in the absence of selective pressure if those changes confer positive adaptation early in life. One age-associated disease that disproportionately affects humans compared with chimpanzees is epithelial cancer. Here, we explored genetic differences between humans and chimpanzees in a well-defined experimental assay that mimics gene expression changes that happen during cancer progression: A fibroblast serum challenge. We used this assay with fibroblasts isolated from humans and chimpanzees to explore species-specific differences in gene expression and chromatin state with RNA-Seq and DNase-Seq. Our data reveal that human fibroblasts increase expression of genes associated with wound healing and cancer pathways; in contrast, chimpanzee gene expression changes are not concentrated around particular functional categories. Chromatin accessibility dramatically increases in human fibroblasts, yet decreases in chimpanzee cells during the serum response. Many regions of opening and closing chromatin are in close proximity to genes encoding transcription factors or genes involved in wound healing processes, further supporting the link between changes in activity of regulatory elements and changes in gene expression. Together, these expression and open chromatin data show that humans and chimpanzees have dramatically different responses to the same physiological stressor, and how a core physiological process can evolve quickly over relatively short evolutionary time scales.

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

Thu, 01 Mar 2018 00:00:00 GMT

Amino acid usage in a proteome depends mostly on its taxonomy, as it does the codon usage in transcriptomes. Here, we explore the level of variation in the codon usage of a specific amino acid, glutamine, in relation to the number of consecutive glutamine residues. We show that CAG triplets are consistently more abundant in short glutamine homorepeats (polyQ, four to eight residues) than in shorter glutamine stretches (one to three residues), leading to the evolutionary growth of the repeat region in a CAG-dependent manner. The length of orthologous polyQ regions is mostly stable in primates, particularly the short ones. Interestingly, given a short polyQ the CAG usage is higher in unstable-in-length orthologous polyQ regions. This indicates that CAG triplets produce the necessary instability for a glutamine stretch to grow. Proteins related to polyQ-associated diseases behave in a more extreme way, with longer glutamine stretches in human and evolutionarily closer nonhuman primates, and an overall higher CAG usage. In the light of our results, we suggest an evolutionary model to explain the glutamine codon usage in polyQ regions.

Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation

Thu, 22 Feb 2018 00:00:00 GMT

Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1–5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.

Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure

Wed, 21 Feb 2018 00:00:00 GMT

The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = πN/πS) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (Ne) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus—two mouse subspecies with different Ne. Our results revealed a positive relationship between the magnitude of selection intensity and the ω estimated for genes. For genes under high selective constraints, the ω estimated for the subspecies with small Ne (M. m. musculus) was three times higher than that observed for that with large Ne (M. m. castaneus). However, this difference was only 18% for genes under relaxed selective constraints. We showed that the observed relationship is qualitatively similar to the theoretical predictions. We also showed that, for highly expressed genes, the ω of M. m. musculus was 2.1 times higher than that of M.m. castaneus and this difference was only 27% for genes with low expression levels. These results suggest that the effect of effective population size is more pronounced in genes under high purifying selection. Hence the choice of genes is important when ω is used to infer the effective size of a population.

Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention

Wed, 21 Feb 2018 00:00:00 GMT

Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21–22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions. Here, we define a deterministic model that represents the propagation of active TEs, aspects of the host response and the accumulation of silenced TEs. We describe general properties of the model and also fit it to biological data in order to explore two questions. The first is why two overlapping pathways are maintained, given that both are likely energetically expensive. Under our model, RdDM silenced TEs effectively even when the initiation of silencing was weak. This relationship implies that only a small amount of RNAi is needed to initiate TE silencing, but reinforcement by RdDM is necessary to efficiently counter TE propagation. Second, we investigated the reliance of the host response on rates of TE deletion. The model predicted that low levels of deletion lead to few active TEs, suggesting that silencing is most efficient when methylated TEs are retained in the genome, thereby providing one explanation for the large size of plant genomes.

Divergent Evolutionary Trajectories of Two Young, Homomorphic, and Closely Related Sex Chromosome Systems

Wed, 21 Feb 2018 00:00:00 GMT

There exists extraordinary variation among species in the degree and nature of sex chromosome divergence. However, much of our knowledge about sex chromosomes is based on comparisons between deeply diverged species with different ancestral sex chromosomes, making it difficult to establish how fast and why sex chromosomes acquire variable levels of divergence. To address this problem, we studied sex chromosome evolution in two species of African clawed frog (Xenopus), both of whom acquired novel systems for sex determination from a recent common ancestor, and both of whom have female (ZW/ZZ) heterogamy. Derived sex chromosomes of one species, X. laevis, have a small region of suppressed recombination that surrounds the sex determining locus, and have remained this way for millions of years. In the other species, X. borealis, a younger sex chromosome system exists on a different pair of chromosomes, but the region of suppressed recombination surrounding an unidentified sex determining gene is vast, spanning almost half of the sex chromosomes. Differences between these sex chromosome systems are also apparent in the extent of nucleotide divergence between the sex chromosomes carried by females. Our analyses also indicate that in autosomes of both of these species, recombination during oogenesis occurs more frequently and in different genomic locations than during spermatogenesis. These results demonstrate that new sex chromosomes can assume radically different evolutionary trajectories, with far-reaching genomic consequences. They also suggest that in some instances the origin of new triggers for sex determination may be coupled with rapid evolution sex chromosomes, including recombination suppression of large genomic regions.

Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism

Wed, 14 Feb 2018 00:00:00 GMT

Human infection with the gastrointestinal pathogen Campylobacter jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analyzed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multihost (ecological generalist) ST-21 and ST-45 clonal complexes (CCs). Combined nucleotide and amino acid sequence analysis identified 12 human-only amino acid KPAX clusters among polyphyletic lineages within the common disease causing CC21 group isolates, with no such clusters among CC45 isolates. Isolate sequence types within human-only CC21 group KPAX clusters have been sampled from other hosts, including poultry, so rather than representing unsampled reservoir hosts, the increase in relative frequency in human infection potentially reflects a genetic bottleneck at the point of human infection. Consistent with this, sequence enrichment analysis identified nucleotide variation in genes with putative functions related to human colonization and pathogenesis, in human-only clusters. Furthermore, the tight clustering and polyphyly of human-only lineage clusters within a single CC suggest the repeated evolution of human association through acquisition of genetic elements within this complex. Taken together, combined nucleotide and amino acid analysis of large isolate collections may provide clues about human niche tropism and the nature of the forces that promote the emergence of clinically important C. jejuni lineages.

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

Wed, 14 Feb 2018 00:00:00 GMT

Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small. Here, we took advantage of methods for culturing H. defensa outside of aphids to generate complete genomes and transcriptome data for four strains of H. defensa from the pea aphid Acyrthosiphon pisum. Chosen strains also spanned the breadth of the H. defensa phylogeny and differed in strength of protection conferred against parasitoids. Results indicated that strains shared most genes with roles in nutrient acquisition, metabolism, and essential housekeeping functions. In contrast, the inventory of mobile genetic elements varied substantially, which generated strain specific differences in gene content and genome architecture. In some cases, specific traits correlated with differences in protection against parasitoids, but in others high variation between strains obscured identification of traits with likely roles in defense. Transcriptome data generated continuous distributions to genome assemblies with some genes that were highly expressed and others that were not. Single molecule real-time sequencing further identified differences in DNA methylation patterns and restriction modification systems that provide defense against phage infection.

Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome

Thu, 08 Feb 2018 00:00:00 GMT

Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth’s cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was >90%. Three genomic islands were identified in the E. antarcticum B7 genome. These islands contained genes involved in flagella biosynthesis and chemotaxis, as well as enzymes for carotenoid biosynthesis. Clustering of cold shock proteins by Ka/Ks ratio suggests the occurrence of a positive selection over these genes. Neighbor-joining clustering of complete genomes showed that the E. sibiricum was the most closely related to E. antarcticum. A total of 92 genes were shared between Exiguobacterium and Psychrobacter. A reduction in the genomic content of E. antarcticum B7 was observed. It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. In our study, eight genomes of Exiguobacterium and Psychrobacter were compared and analysed. Psychrobacter showed higher genomic plasticity and E. antarcticum B7 presented a large decrease in genomic content without changing its ability to grow in cold environments.

The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity

Tue, 06 Feb 2018 00:00:00 GMT

Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological and evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates. Using whole genome bisulfite sequencing, we compared genome-wide DNA methylation patterns between threespine stickleback males and females and between stickleback reared at different environmental salinities. Apparent hypermethylation of the younger evolutionary stratum of the stickleback X chromosome in females relative to males suggests a potential role of DNA methylation in the evolution of heteromorphic sex chromosomes. We also demonstrate that rearing salinity has genome-wide effects on DNA methylation levels, which has the potential to lead to the accumulation of epigenetic variation between natural populations in different environments.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Mon, 05 Feb 2018 00:00:00 GMT

Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.

An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae

Sat, 03 Feb 2018 00:00:00 GMT

Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion–deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10−9 per site per generation and indel rate of 1.55 × 10−10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.