Contrasting Tick Species Behaviors: A Course-based Undergraduate Research Experience (CURE)

Tick-borne diseases are on the rise throughout the world, and there is a need to better understand tick behavior in order to identify potential new interventions. Ticks have a complex life history and can survive months off-host. There is a lack of large-scale data on off-host tick behavior, which leaves a gap in understanding of tick biology outside of tick-host interactions. Introducing undergraduate students to authentic research early in their studies can help prepare them for independent inquiry in upper-level classes. To address the student needs and fill gaps in tick research, students in introductory biology courses recorded observations of ticks in sealed terraria each week for one semester. Students recorded 11,905 observations of two species of nymphal ticks over 10 weeks. The results showed that Amblyomma americanum nymphs were observed more frequently and quested higher than Ixodes scapularis nymphs

Gain-of-Function Experiments With Bacteriophage Lambda Uncover Residues Under Diversifying Selection in Nature

Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here, we demonstrate that two residues of λ’s J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses

Gain-of-Function Experiments With Bacteriophage Lambda Uncover Residues Under Diversifying Selection in Nature

Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here, we demonstrate that two residues of λ’s J protein are required for the new function. In natural λ variants, these amino acid sites are highly diverse and evolve at high rates. Insertions and deletions at these locations are associated with phylogenetic patterns indicative of ecological diversification. Our results show that viral evolution in the laboratory mirrors that in nature and that laboratory experiments can be coupled with protein sequence analyses to identify the causes of viral evolution in the real world. Furthermore, our results provide evidence for widespread host-shift evolution in lambdoid viruses

Gene level selection is a conceptually complete theory of evolution

<p>Recent workers have argued that evolutionary theory is<br>incomplete, due to several unsolved problems in the<br>field. These problems include the evolution of sex, the<br>evolution of complexity, and speciation. Theoretical<br>ideas such as modularity, robustness, and evolvability<br>have been proposed as part of an “Extended Synthesis,” necessary to solve these problems (Pigliucci 2009).</p> <p>Further, recent empirical work in microbes has<br>challenged key ideas of the Modern Synthesis. In<br>particular, workers have argued that the mutation rate<br>might be an adaptive trait in microbes (Martincorena<br>2012, Paul 2013). Other workers have questioned the<br>role of natural selection in the evolution of complex<br>genomes and organisms (Lynch 2007). Here, I argue<br>that the Modern Synthesis is conceptually complete<br>(Williams 1966, Dawkins 1976, Lynch 2007). Considering evolution as an adaptive process working on genes, with organisms as higher-level, but temporary coalitions made of genes, is sufficient to turn these theoretical problems into mere “puzzles.” Higher levels of selection might largely serve to change the genetic, somatic, and ecological environments to which genes adapt (Williams 1966). I propose some hypotheses for future exploration in microbial and digital evolution experiments.</p> <p> </p

Data from: Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

Few experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors’ origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage

DRYAD-STLE-analysis

Data files and scripts for all analyses and figures in Maddamsetti and Lenski (2018)

Genome structure of odd-numbered clones from recombinant populations after 1000 generations of the STLE.

<p>The REL606 genomic coordinates are shown on the x-axis, centered on the <i>oriC</i> origin of replication, and the source populations are shown on the y-axis. Genetic markers are shown as vertical lines, with the color indicating the origin of each marker. Markers specific to K-12 donors are yellow; markers specific to recipient clones are blue; markers in deleted regions are light purple; new mutations that arose during the STLE are black; and LTEE-derived mutations that were replaced by donor DNA during the STLE are red. In addition, symbols indicate mutations in genes under positive selection in the LTEE (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007199#pgen.1007199.t001" target="_blank">Table 1</a>). Open circles indicate nonsynonymous point mutations; open squares are synonymous mutations; open triangles are indels; and x-marks are IS-element insertions. Replaced and new mutations in the genes in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007199#pgen.1007199.t001" target="_blank">Table 1</a> are labeled by their gene names.</p

Loci containing nonsynonymous mutations in odd-numbered recipient clones from non-mutator populations that were replaced by donor alleles.

<p>Loci containing nonsynonymous mutations in odd-numbered recipient clones from non-mutator populations that were replaced by donor alleles.</p