Kruttika’s work testing the impact of butterfly caterpillar microbiomes on growth and survival is published! This was a major collaborative effort with Krushnamegh Kunte, and very new kind of work for our lab. The results were puzzling because unlike patterns from other insects, butterflies seem to be just fine without their bacteria. But in conjunction with Rittik and Ashwin’s recent results with dragonflies, it seems that we’ve uncovered one end of the spectrum of host-microbe interactions. The end that spells “meh!” rather than “I need you”. Here’s a cartoon summary of the work by Kruttika and Shreya. Also read a lay summary here; or read the paper for more details!
Mrudula and Joshua’s paper measuring the incidence and fitness effects of antagonistically pleiotropic mutations is now out in Evolution!
As they improve at performing one function, organisms often get worse at another function. Such a negative relationship between two functions (or traits) is called a tradeoff, and is a central idea in evolutionary biology. Tradeoffs may constrain adaptation, and underlie many important evolutionary processes such as the evolution of organisms’ life history strategies, diversification and speciation. One way in which tradeoffs can arise is via mutations that are antagonistically pleiotropic. These mutations increase fitness in one environment, while simultaneously decreasing fitness in another. Antagonistic pleiotropy (AP) could therefore explain tradeoffs if such mutations were frequent and had large fitness effects. However, the frequency and fitness effects of these mutations remains poorly studied.
We measured the frequency and fitness effects of AP mutations across 11 different carbon sources in a large set of random single mutations in Escherichia coli. Our results suggest that overall AP is very rare, and that AP-mediated tradeoffs are unlikely to constrain adaptation very often. Thus, while there is no denying that tradeoffs are abundant in nature, it is unlikely that they are caused by single antagonistically pleiotropic mutations. Rather, accumulation of multiple mutations in genes that are not under very strong selection may degrade other functions, presenting as a tradeoff.
For more details, browse the paper or the associated NCBS news article.
A cool infographic about our recent paper on the induction of food preferences in Tribolium larvae. Graphic by Ipsa Jain.
Vrinda and Swastika’s paper on larval food choice behaviour in response to prior experience with new foods is out in Ecological Entomology!
Several decades ago, it was observed that the juvenile (or larval) stages of several insects change their feeding preference in response to prior experience (“induction of preference”). We explored this trait in the ecological context of a generalist insect. Using behavioural experiments and larval fitness measurements, we characterized the induction of preference in the generalist red flour beetle, Tribolium castaneum, whose natural habitat (stored grain warehouses) presents high heterogeneity in resource availability. We explored how the induction of preference in the larval stage affects feeding behaviour in temporally or spatially heterogenenous habitats.
As observed in previous studies, we found that the feeding preference of beetle larvae is highly plastic. We also found such plasticity under spatial and temporal resource heterogeneity, even when these resources were suboptimal. Interestingly, induction does not occur for a resource that decreases larval survival, but does occur for resources that decrease fitness in a less severe manner, by slowing down development rate. We think that such food preference induction may facilitate the expansion of this species’ dietary niche in unfamiliar habitats. If this is true, and if feeding preference is under selection in heterogeneous habitats, then this implies that generalists may often pay a cost of slow development in a novel resource, because the benefits of using the new resource outweigh the costs of specialization on only a few familiar resources.
For more details, read the paper.
Gaurav’s large-scale phylogenetic analysis of bacterial tRNA modification systems is now published in MBE!
An important property of tRNA molecules is the ability for wobble base pairing. Apart from the widely known GU wobble pairing, chemically modified bases in a tRNA extend wobble base pairing rules. Such tRNA modifications therefore expand the pool of tRNA in the cell and allow a handful of tRNAs to recognize all 61 codons. tRNA modifications also reduce translational errors, increase bacterial growth, and improve virulence, and should therefore face strong positive selection. However, the evolutionary history of bacterial tRNA modifications and their impact on tRNA gene content has remained unclear.
In this paper, we mapped the occurrence of five known tRNA modifications across 1093 bacteria. We found that while most modifications were ancient, some were repeatedly lost in several major lineages. Interestingly, most losses of modifications were associated with the retention or secondary gain of unmodified tRNAs, which would complete the full tRNA set. And, subsequent gain or retention of unmodified tRNA was phylogenetically correlated with the genome GC content of bacteria. Thus, our paper highlights the complex interplay between GC content, tRNA genes and tRNA modifications, and traces their evolutionary history. We hope you enjoy reading the paper as much as we enjoyed working on this project!
Update: Also see an NCBS news piece about this work here.
Kruttika’s work on the bacterial communities of butterflies is now out in the journal Royal Society Open Science! This was our first large butterfly project, and it was a lot of fun. We collaborated with Krushnamegh Kunte for this project. We chased butterflies, learned to identify different species, and combed through different host plants to find camouflaged larvae and pupae. Then we got back to the lab, and brainstormed our way through molecular work and microbiome analysis.
Butterflies start their life as a tiny egg, giving rise to a hungry caterpillar that ravenously feeds on plant leaves (solid food). The caterpillar morphs through a non-feeding pupal stage to emerge as an adult butterfly that feeds only on nectar and other fluids. We predicted that this dramatic dietary and developmental transformation should result in very different bacterial communities across life stages of each butterfly species. Surprisingly, we found this pattern in only a few butterfly species. This suggested that though all butterflies undergo dramatic dietary and developmental transition, the associated bacterial communities do not change in the same manner across different hosts. Across different butterfly species, dietary variation was strongly associated with distinct bacterial communities. Surprisingly, larvae (which are relatively specialized on single host plants) showed relatively similar microbiomes, whereas more generalist adults (which feed on nectar from many flowers) harboured distinct bacterial communities. Thus, adult butterflies seem to impose a stronger filter on their gut communities. Overall, our results suggest that butterflies have not evolved strong associations with their gut microbes, despite large dietary and developmental variation.
For more about butterflies and their bacteria, read the paper!
Krushnamegh Kunte and I edited a special virtual issue of the journal MBE (Molecular Biology and Evolution), featuring a few papers arising from the 2016 Genetics of Adaptation meeting we organized – and more. It’s on the MBE website now – check it out!
I’m so happy that our work on the fitness effects of sex ratio in flour beetles is finally out in the American Naturalist! I say “finally” because this work represents multiple years of hard work by a large-ish team, including people from Radhika Venkatesan’s lab at NCBS. In fact, apart from me, all other lab members who are authors on this paper have long left the lab for other pursuits. Altogether, this project has been a fine example of the typical scientific process: you observe something strange; you formulate some hypotheses to explain the observation given prior work in the area; you test these hypotheses and find that none of them explain the pattern; you mope around frustrated for a while; eventually you come up with new hypotheses, perhaps after expanding your “related prior work” universe; and finally you get somewhere and learn something new!
In this case, we found that flour beetle females have higher fitness in male-biased groups, contradicting prior results in various animals that female fitness is lower in male-biased groups. Typically, most explanations of female fitness given biased sex ratio have revolved around sexual conflict. After testing many hypotheses that might explain this pattern, we found that female fitness is inversely proportional to the number of females in the group, with almost no role for males. We could also reject potential mechanisms that relied on direct interactions between individuals – including sexual competition, a crowd favourite – because we saw that flour that had been used by many females elicited the same response as the females themselves. Radhika’s lab helped us pinpoint female-secreted benzoquinones as the primary chemicals responsible for this indirect, flour-mediated effect. Quinones are toxic compounds secreted by flour beetles; females produce more quinones than males, and increase production in the presence of other females or high quinone concentration. Apart from governing female fitness effects in the context of sex ratio, the positive feedback in quinone production may thus allow it to broadly regulate population density. We are very excited about this possibility, and in the coming years we hope to figure out the physiological effects, and broader evolutionary impacts, of quinones .
You can a news story about this work here, or read the paper here.
We have a new paper this month, in Genome Biology and Evolution. This paper follows from the lab’s long standing interest in codon usage bias, and describes Saurabh’s analysis to understand how codon use and tRNA gene numbers vary with bacterial growth rate. Typically, highly expressed genes use specific synonymous codons more often, compared to other genes in the genome. Across bacterial species, this “codon usage bias” (CUB) increases with growth rate. However, most previous studies focused on average CUB (of genes or genomes). We explored the possibility that selection could act differently on codons of different amino acids, depending on how often each amino acid is used to make proteins. The link between growth rate and CUB is thought to involve tRNA gene copies, which also increases with growth rate, and should co-evolve with codon use. Interestingly, there are detailed theoretical predictions about how CUB, tRNA gene copies, and amino acid usage should be related to each other. We tested these predictions, but found that the patterns don’t match the predictions. (What more can a theory ask for!) Specifically, we found that CUB of specific amino acids does not increase with usage of the amino acids as expected. This suggests that we are missing some pieces of the puzzle, and we have some new suggestions about the next steps to find them. For more, read the paper!
Our new paper describing Imroze and Arun’s massive experiment with thousands of infected beetles was recently published online. Within about 10 generations of exposure to Bacillus thuringiensis, flour beetles evolved divergent immune responses: either improved but generalized immune resistance, or specific immune priming (memory). We think that the divergent response is driven by the frequency of exposure to the pathogen. However, for replicate populations within a given exposure treatment, we found a very high degree of parallelism. This is the first report of evolved immune memory in insects, and we are very excited to now figure out the underlying mechanisms. Read the NCBS news article about this work here, or read the paper.
Update, 24 June 2018: The Hindu covered our work in an article; check it out!
While collecting ants for his MSc thesis project on ant communities in the Andaman Islands, Gaurav Agavekar found two species of ants from the genus Tetramorium that turned out to be new to science. Along with Evan Economo’s lab at OIST Japan, he recently described these species in a paper in PeerJ. The new species – T. krishnani and T. jarawa – are named in honor of the late Prof KS Krishnan (NCBS), and the indigenous Jarawa people of the Andaman Islands. Read more about the work here.
Update, Feb 2018: Gaurav’s work is covered in an article on Mongabay India.
All organisms age. One prominent hypothesis suggests that infections experienced early in life accelerate ageing. In collaboration with Jens Rolff, Imroze tested this idea in mealworm beetles (Tenebrio molitor). He found that young beetles injected with bacterial cell components mounted an immune response that damaged their vital organs – Malpighian tubules, equivalent to kidneys – and resulted in faster ageing. Experimental down-regulation of phenoloxidase (a key component of the immune response) via RNAi allowed beetles to live longer. Similarly, older beetles infected with a live pathogen also lived longer if their immune response was suppressed. Thus, inflammation induced by immune responses may generally accelerate ageing in various contexts. These results suggest that natural selection is nearly blind to immune self-harm because its effects are felt later in life, after peak reproduction. Similar mechanisms may operate in other organisms, as ageing is a feature of most multi-cellular organisms including humans.
Read the early online version of the paper here.
Update: Here is a really nice graphic that Kruttika and Gaurav made, that captures some of the fun results from this work.
Our work showing rapid, parallel adaptation in Methylobacterium extorquens is now out online on the MBE website. The work represents a huge team effort from members of my former postdoctoral lab and my current lab at NCBS- Mrudula, Kruttika, Gaurav and Alefiyah. We are very excited about this paper, partly because of the surprisingly large adaptive benefits of synonymous mutations, and also because we show that no single mechanism underlies these fitness effects. Our understanding of the evolution of codon bias just got murkier, but also that much more interesting- we need new hypotheses!
You can access the paper here, and read a news article about it on the NCBS webpage.
Imroze and Arun’s paper describing immunosenescence in flour beetles will be out in the January 2016 issue of the Journal of Animal Ecology! You can find the paper here.
Here’s a brief summary of the work described in the paper. In many animals, immune function decreases with age so that older animals are more likely to die from infections. We found that this pattern is also true for flour beetles (Tribolium castaneum): older beetles are more susceptible to infection by Bacillus thuringiensis. Oddly though, individual components of innate immune function (such as phenoloxidase activity) did not decrease with age. This mismatch could arise due to tradeoffs with other fitness components (e.g. fecundity or external antibacterial secretions). If young beetles invested in other aspects of fitness, they may not be able to invest more in immune function, and hence the levels of innate immune components may be lower than optimal. However, we did not find evidence for such a tradeoff. Another possibility is other factors affecting immune function end up muddying the expected relationship between immune components and age. Indeed, we found that a beetle’s sex and mating status also affect its immune function, and complex interactions between these factors determine immune function. The molecular mechanisms mediating these effects remain unclear and it is likely that we are missing other important factors that alter immune function. However, our work shows that a deeper understanding of life history, tradeoffs and fitness is necessary to understand how and why animals become more susceptible to infections as they age.