Adaptation Lab

Welcome to Deepa Agashe’s lab at the National Centre for Biological Sciences (NCBS), Bangalore!

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New paper: Females drive sex ratio effects

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!

BeetleQuinoneSketchIn 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.

New paper: Amino acid specific codon usage and translational selection

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!

Wellcome Trust/DBT India Alliance Fellowship

I am very happy to say that for the next 5 years (beginning January 2018), a large part of our work will be generously funded by a Wellcome Trust/DBT India Alliance Intermediate Fellowship Award.

As part of the grant, I have an open postdoctoral position for a microbiologist or an entomologist who is interested in host-microbial interactions and would like to work at the interface of experimental and computational analyses. To apply, please write to me with your CV, a brief statement of your research interests, a summary of any one of the published papers from our lab, and a note about how you see yourself fitting within our group.

New paper: Experimental evolution of insect immune memory

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.

Winter conference season

This winter is packed with exciting meetings! Here’s the menu:

Pratibha and I just returned from a fantastic SMBE satellite meeting in Kaziranga, Assam. Congratulations to Pratibha for getting a travel grant to present her work! The meeting brought together a bunch of people working on microbial evolution in natural and experimental populations. There was lively discussion on a wide range of topics in microbial evolution, good food, and of course, Rhinos. Big thanks to the key organizers, Siddartha Sankar Satapathy and Edward Feil!

Vrinda and I are now off to IISER Pune for a Conference on Evolutionary and Integrative Biology. The speaker lineup includes many seasoned and new evolutionary biologists across India, so we are looking forward to an exciting meeting.

Soon after this, the whole lab (and our campus) will participate in the 2018 NCBS Annual Talks. Mrudula, Rittik, Laasya, and Gaurav Agavekar will each present posters about their work; and Gaurav Diwan will present a short talk.

Finally, to conclude this conference season I will speak at an Indo-French workshop on Evolutionary Developmental and Cell biology (EVODECE) at the Observatoire Oceanologique de Banyuls sur Mer in France. The meeting is funded by CEFIPRA and DST, and features a very diverse collection of evolutionary and cell biologists from India and France.

Do come talk to us if you spot us at any of these events!

Gaurav describes new ant species

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.

Aparna wins award at SPEEC-Up 2017

SPEEC-Up 2017 was the first iteration of what we hope will be an annual 3-minute talk competition for students of ecology, evolution and conservation in Bangalore. The event was a lot of fun, and a great way to get introduced to a wide range of work from our neighbours. I am truly happy to have had a chance to listen to so many cool talks.

We had three competitors from the lab- Kruttika, Aparna and Rittik all gave great talks about their respective work with insect gut microbes. We’re very happy that Aparna won a runner-up prize for her talk on beetle gut microbes! Here she is, accepting her award (with joint winner Vignesh).

Aparna_SpeecUp

Open postdoctoral position

I am recruiting a postdoctoral fellow to analyze bacterial communities associated with flour beetles. The postdoctoral fellow will work with a team of researchers towards the following goals:

  • Quantify the repeatability of ecological and evolutionary changes in the gut microbiome of an insect adapting to a new diet
  • Determine the metabolic and genetic basis of the microbiome changes
  • Test the importance of inter-species associations in driving microbiome changes

The position is fully funded through a grant from the Wellcome Trust-DBT India Alliance, and will begin from January 2018 for a maximum of 5 years.

  • A background in evolutionary biology, ecology, or microbiology is essential
  • Experience with handling anaerobic microbes would be beneficial
  • Experience with coding or mathematical modeling would be beneficial
  • The ability and motivation to think and work independently is important

To apply, please write to me with the following details:

  • Your CV
  • A short paragraph (~300 words) summarizing your research interests and career goals
  • Contact information for 2 people who can write a letter of recommendation for you
  • A 1-page summary of any paper from our lab. Include your criticisms and any questions that arise from the work