Adaptation Lab

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

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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!

Announcing the 2018 SPEEC-UP competition

Speecup poster 2018 finalI’m happy to announce that the 2nd edition of the SPEEC-UP 2018 meeting is open for abstracts. The meeting features student presentations (including research project staff and postdocs) on Ecology, Evolution, Environmental Sciences and Conservation. The meeting is organised by a bunch of folks from ATREE, IISc, NCBS, Dakshin, NCF, and WCS. 

This year, SPEEC-UP will be held at CES, IISc on 31st August 2018. Here is the link for abstract submission (deadline: 25th June).
http://speecup-blr.weebly.com/
 
This is a Bangalore centric student event to provide a platform for students and faculty to get together. There are prizes worth Rs 40k to be won, so do consider competing!

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.