New paper: Antagonistic pleiotropy is rare!

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.

Runners_tradeoffs

 

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.

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2019 Preparatory school on Population Genetics and Evolution

popgen2019-poster_smallKavita Jain (JNCASR) and I have organized a series of ICTS Schools on Population Genetics and Evolution since 2014. To help participants get better prepared for the next school (scheduled in 2020), we are now introducing a preparatory school in Feb 2019. The intensive 1-week school will introduce biologists to key mathematical tools, and non-biologists to key biological concepts.

Applications open on 15 Oct, and will be accepted until 15 Nov 2018. Find more information here.

New paper: Prior experience changes food choice behaviour in beetle larvae

graphical abstract finalVrinda 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.

New paper: Wobble-based insights into the bacterial genetic code

Trna IMAGEGaurav’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.

Summer conferences, 2018 edition

We have another fun summer conference season lined up this year; as usual, most lab members have received travel awards. Come hear about our work if you happen to be at these meetings!

Mrudula, Kruttika, Laasya, Saurabh, Joshua and I will be at the SMBE meeting in Yokohama, Japan, starting 8 July. We’re all super excited that Mrudula was chosen as a Fitch award finalist this year, with the added perk that SMBE will cover her trip. Kruttika also has a registration award from SMBE, and an Infosys travel award from NCBS. This should be an especially fun meeting as we celebrate 50 years of the Neutral Theory of molecular evolution.

Around July end, Pratibha will attend her first international meeting abroad: the Gordon Research Conference and seminar on C1 metabolism in Maine, USA. She will be supported by a travel award from the Dept of Science and Technology (DST, India).

Finally, at the end of August, Mrudula and Vrinda will join me at the 2nd Joint Evolution meeting in Montpellier, France. They both have travel grants from the SSE. This promises to be a crazy gathering of evolutionary biologists and we’re looking forward to it!

Kruttika wins award for talk

Kruttika_BoB_awardCongratulations to Kruttika for winning the runner-up prize for best student talk at the Biology of Butterflies meeting! She spoke about finding a new example of Wolbachia bacteria distorting the sex ratio of a butterfly.

Picture: Kruttika receiving her award from Naomi Pierce.

Coming up: Science Cafe talk

ScienceCafe_DeepaOur campus has a new outreach program under the Science and the City initiative: the BLiSc Science Cafe (BLiSc = Bangalore Life Science Cluster). I will kick off this program with a talk at MyBoTree in Kormangala, Bangalore, this coming Sunday (11 am, June 24). Come hear about the exciting world of microbes that live with and within us, and how they have shaped life on earth!

The Science Cafe is a series of monthly science talks across cafes, bookstores, social, public and performative spaces in Bangalore. The idea is to bring down barriers between science and the public, take advantage of informal environments to discuss our science, and share what we do in a space that is less academic but more relaxed. Events are open to all, so drop by!

Update: This was a really fun event, and I really enjoyed interacting with the fantastic audience. I didn’t know when the scheduled hour passed; the crowd was very curious and wanted to know more! You can view a recording of the talk here.

New paper: Butterflies and their bacteria

Eurema_blandaKruttika’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!