Sunday, May 6, 2018

So long and thanks for all the fish : Does the bottlenose dolphin demographic history have a message?

Bottlenose dolphins have enthralled human beings by their amazing performances in dolphinariums and have been part of popular culture becoming the most popular of all dolphin species, while also stimulating public concern over the welfare of display animals. The song "So Long, and Thanks for All the Fish" has established a cult following for this species. 

The genome of the common bottlenose dolphin Tursiops truncatus was sequenced during the boom days of the genomics era when assembling a genome was still considered cool. This initial effort was part of the 29 mammals project. However, we have long since passed that point. So, by the time Yim et al., sequenced the genome of the Minke whale, it was standard practice to look at aquatic adaptation in numerous related species. In addition to looking at coding level changes, they cleverly "Estimated whale population size history". Existing cetacean genomes were also roped into this analysis of effective population size history.

Of the four genomes analyzed in the Yim et al., paper the most surprising result was seen for the bottlenose dolphin that showed an increase in Ne that started at the beginning of the ice age. If this pattern were true it could have interesting implications for understanding the effect of climate change on the demographic history of species. In our preprint titled "Population genomic analysis reveals contrasting demographic changes of two closely related dolphin species in the last glacial", we delve into bottlenose demographic history. 

Few key highlights of our manuscript:

  1. In addition to analyzing the genomes of four common bottlenose dolphin individuals from the public sequencing repository (SRA), we also sequenced four genomes of Indian bottlenose dolphin individuals. The comparison of these 8 genomes shows contrasting demographic changes in the two sister species. 
  2. We use 3 different programs (PSMC, MSMC & SMC++) to reconstruct the demographic history of both dolphin species.
  3. After reconstructing the changes in effective population size, we use the pseudo-diploid analysis of all pairs of these 8 genomes to analyze 28 pseudo-diploid genomes. Based on this we estimate the split times between species as well as between populations within species.
  4. For all our analysis we perform quality control to ensure robustness of our results. Repeat regions are identified using repeat masker program and masked out. Coverage of each individual genome is considered to rule out the possibility of coverage dependent biases in results. Although mutation rate and generation times are fairly well-known for cetaceans, we looked at the combinations of 4 mutation rate estimates and 4 generation time estimates. We find that the main conclusions remain unaltered even after varying all these parameters.
  5. Considerable effort is spent on optimizing the settings of the PSMC program. First, the bootstrap analysis is done with 100 bootstraps for each individual to look at within genome heterogeneity. Next various setting for the -p parameter was tried out to have sufficient resolution in the PSMC results while also having a sufficient number of recombination events after 20 iterations of the program.
It is worth noting that the field of population size history estimation has matured well. New methods that are able to estimate Ne in more recent times have helped answer many questions that were not possible to answer with older methods. For example, the recent analysis of the Tibetan frog (Nanorana parkeri) genome using both G-PhoCS and PSMC brings traditional demographic analysis together with PSMC which had made its way into genomic papers all by itself.

A truly new direction to use of effective population size histories is presented in a preprint posted on biorxiv titled  "Comparative demography elucidates the longevity of parasitic and symbiotic relationships.". Despite the immense potential in using comparative demography to answer questions in studying parasitic and symbiotic relationships, it will be interesting to see how robust these inferences are and whether they can be supported by independent sources of evidence. Our study on dolphins also explores this aspect of the contribution of predator and prey abundance on population size. 

Friday, March 30, 2018

Anandi Gopal Joshi - Google Doodle - This year will probably see one for Janaki Ammal

It has been a while since I have written about JA. A lot has happened in that time. The most significant new thing is the Janaki Ammal Scholarships instituted by the John Innes Centre. I am very curious to know if students have joined a Ph.D. position availing this fellowship.  

Closer to home, today is the 153rd birthday of Anandi Gopal Joshi (one of the earliest Indian female physician). Google in its infinite wisdom decided to honor her with a doodle (see below). She has a degree certificate in one hand and appears to be wearing a stethoscope.  The image behind her is also split into two halves, one half is what could be her native country which had a scarcity of multi-storied houses during her time and the other half seems to be a townhouse in rural US of A. The trees also change accordingly.

For JA, they would need to have 3 continents, some sugar cane, brinjal and most definitely have karyotypes with various ploidy levels.

Anandi Gopal JoshiĆ¢€™s 153rd birthday

Now all I can hope for is that the folks at Google put two and two together and make a doodle for Janaki Ammal this year. Her birthday is on 4th of November and it will be 121 years. But then again it might take 32 more years. 

Wednesday, October 18, 2017

Getting creative with molecular biology

Creating something new using concepts you have learned leads to a better understanding of the subject.  Instead of simply remembering the ideas of somebody else, one can actually remember how one used those ideas to create something new. Yet, it is not easy to convince educators about the utility of using visual arts to teach science. A recent review titled "The Role of the Visual Arts in Enhancing the Learning Process" tries to make a case for visual arts in enhancing the learning process.

The class on "Flow of genetic information" that i am currently teaching got a chance to get creative this week. They were given 3 activities to do in the class.

Task 1: Compare DNA replication, Transcription & Translation and create an easy to understand diagram/table.

Task 2: Compare different information flow processes considering as many examples as you can think of

Task 3: Show the hierarchical organization of DNA

  • Use color chalk if needed.
  • Pay special attention to differences between prokaryotes & eukaryotes
Here are the end results:
Task 1

Task 2

Task 3

Thursday, August 24, 2017

Does the central dogma paper have hidden Masonic iconography?

A lot has been written about Freemasonry in recent times. One of the most prominent features of the iconography associated with free masons is the Eye of Providence. The traditional depiction of this involves a triangle or pyramid shape.

If you have read the paper Central Dogma of Molecular Biology by Francis Crick, you might have noticed that the paper is filled with figures that look like above screen grab. It is a triangle and has some circles. This would actually be a very smart way to sneak in Masonic iconography. Was Francis Crick a free mason? It is actually possible, as it has been argued that some of the most powerful and intellectually gifted people have been part of free masonry.

Monday, June 26, 2017

A beetle to be proud of

June is almost over. It has already started raining here in Bhopal. The weather is now at that pleasant optima when it's neither too hot nor too rainy. Wish it could stay like this forever. Humidity is another thing altogether. It is really a pleasure to go out walking in the campus.

You have the frogs making their calls in one place and the beetles roaming in another. See below picture of a beetle we managed to capture.

Wednesday, May 31, 2017

Nautapa - nine hottest days of the season

The end of May is generally the time for Nautapa, the nine hottest days of the season. The term originates from the Hindu astronomical calendar. Here is the sun early in the morning on the 5th day of Nautapa.

Wednesday, May 17, 2017

The Ponds at Georgetown - ducks

The Ponds at Georgetown or simply the ponds is a very pleasant place to live. Here is a picture of few ducks in the pond that is just beside the bus stop (bus #5).

If you zoom-in, at the far end of the pond you can see ducklings swimming. I counted 6 of them in total. While waiting for the bus, I could see a rodent (not sure if it was just a fat rat or some other) trying to swim into the flock and catch one of the ducklings. Probably that was breakfast.

One could imagine this is an advertisement for the place. With great public transportation proximity to the city as well as ypsilanti it is well situated.