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. 

Comparative approaches to study the evolution of nucleotide diversity

Study of diversity at the nucleotide sequence level across the whole genome have provided a useful understanding of numerous processes. However, until recently these studies have been largely focussed within a species but using different populations. This is set to change with the explosion of datasets that are being generated in many species across the globe. We have made our tiny bit of contribution to the use of such an approach with a recent pre-print on bioRxiv "Genome-wide signatures of genetic variation within and between populations - a comparative perspective". 

Many other studies (Singhal et al., Van Doren et al., Ludo et al.) have shown this pattern of correlated landscapes of diversity and divergence. Some have even addressed other questions related to speciation rateshabitat preference as well as their impact on the diversity and divergence landscape. We are also seeing studies in other species groups such as primates and trees. Theoretically oriented groups have also started getting into the nitty gritty of things by trying to understand the patterns better and get into the processes driving them.

The figure-1 (b) from the bioRxiv paper is very interesting as I managed to sneak in the flags of both Germany and Sweden :). We had to cut it in our paper now published with a different title "Genome-wide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa". 

Sunday, April 23, 2017

Abundance of elements on planet earth correlates with year of discovery

We hypothesized that chemical elements that are more abundant and easier to purify in elemental form would be discovered earlier. Obvious evidence for our hypothesis is that heavier elements such as Tennessine have been synthetically created and have been first described as late as the past decade. A better way to evaluate our hypothesis would be to look at all chemical elements discovered till now.

Using the timeline of chemical element discoveries from wikipedia and comparing to the abundance of these elements shows a significant negative correlation (r=-0.27; p-value: 0.0002421). Below figure show the golden age of discovery of chemical elements stretching from 1600 to 2000. Although many of the commonly used metals were well known to the "ancients", a large majority of the elements were discovered within the span of the last 400 years. The negative correlation suggests that less abundant materials were discovered later than the more abundant materials. Rapid discovery of chemical elements overlaps with the timing of the great divergence.

Chemical element abundance vs Year of discovery

Since the abundance of elements on earth is negatively correlated (r=-0.45; p-value: 8.336e-10) with the atomic numbers of the elements, we see a positive correlation (0.53; p-value < 2.2e-16) between the atomic number of elements and when they were discovered. Instead of just using the abundance of elements, a better measure would be the weight of both abundance and ease of extraction.

It would be interesting to see if such correlations would exist on other planets. Would the class of the planet determine the correlation?

The star trek Voyager episode "Emanations" set in the year 2371 (stardate 48623.5), says that 246 elements are known to federation science. This is almost double the number known now. This suggests another age of discovery in the near future. The BBC has an interesting article on what new wonders await us in the outer reaches of the periodic table. However, as yet it is not clear how far the extended periodic table can be extended synthetically and how many of these elements will be found naturally. 

Tuesday, March 7, 2017

Ann Arbor to Chicago union station - a train journey via Amtrack

A train journey from Ann Arbor to Chicago is an easy way to travel. Amtrak runs multiple trains throughout the day on this route which actually starts from Pontiac. The journey of approximately 4 hours can frequently be delayed by upto 30 minutes. Apart from experiencing this first hand, I also overheard a very upset American complaining that this delay had resulted in him reaching 30 minutes late to his job interview. Hopefully, he will still get the job as the interviewer seemed sympathetic to his cause. 

Ann Arbor, Amtrak station, Front entrance in March 2017

The train route meanders down from Ann Arbor through Jackson, Battle creek, Kalamazoo, Niles, and New Buffalo before entering the state of Illinois. After stopping over at Michigan city, it heads into Chicago to stop at the union station.

Kalamazoo is approximately the mid-point (for travelers from Detroit) located 142 miles from Detroit and 138 miles from Chicago. The phrase Timbuktu to Kalamazoo (both real places) commonly used by English speakers to refers to journeys between exotic places. The word is thought to originate from native American's of the Hopewell culture. The journey ends at the historic Union station of Chicago.

Wednesday, January 25, 2017

The sun rises in the east

What you see here is the sun rising. It most definitely is rising in the east.

Let's hope it's not a sunset :) If it was not clear before, let me make myself clear (as if it matters), all views expressed on this blog are my own personal views and don't reflect the views of my employers.

Monday, December 26, 2016

Why god hates ring species?

If god has an inordinate fondness for beetles, then he must surely hate ring species. As eminent evolutionary biologist, prominent god denier and all round good guy retired Professor Jerry Coyne notes in his blog, there are no ring species. Atleast no ring species that meet the textbook definition. He describes how genetic evidence has shown that even the most well regarded ring species have been shown to have some levels of allopatry. 

Being a long time follower of his blog, why evolution is true as well as his numerous papers and books that have established the field of Speciation, i was over joyed to write a digest for journal Evolution around this topic. The other great name in Speciation, Trevor Price has worked on Ring Species making this one of those cool things that has captivated the imagination of very smart people. Barriers to gene flow and ring species formation is a recent article that uses agent based model simulations to show how ring species formation requires narrow corridors. These narrow corridors are highly susceptible to disruption due to local changes. Such disruption can result in allopatry. 

"Tiny" amounts of allopatry can lead to a ring species not meeting the textbook definition. So obviously, god hates ring species :) and that is why he "designed" such a characteristic feature. On a more serious note, this paper does highlight the importance of using simulations in the field of Evolution. Hopefully, we will see increasing use of such approaches in the future.

Thursday, November 17, 2016

Stable polypoidy in yeast identified through experimental evolution

The paper we discussed today in the journal club is a topic that has always been very fascinating. Polyploidy, especially speciation driven by polyploidy is thought to be very common among plants. Janaki Ammal, "attributes the higher rate of plant speciation in the northeast Himalayas compared to the northwest to polyploidy" in her paper : The effect of the Himalayan uplift on the genetic composition of the flora of Asia. Infact, a lot of work done by her revolves around polyploidy. Some of this work is fascinating and seems relevant even today. One could continue her research program today and still be very current.

Coming back to the paper, it is yeast not plants. It makes it easier to study due to the ease of manipulation. Title of the paper is "Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast". After constructing the strains, experimental evolution was conducted for 1000 generations to evolve the required strains. All that is needed for figure 1 and 7 is flow cytometry. Figure 3 and 5 are both relative fitness assay's and seem doable but need a lot of work. However, figure 2 and 4 need a array platform and might be out of reach.

The fact that they are able to pin down the the Sch9 gene and the TORC pathway takes the paper to the next level. Although it is not clear what the mechanism is or how general and widespread this pathway can be in stabilizing polyploidy. It would of course be interesting to see if the natural polyplod isolates from the evolution canyon show changes in this very pathway.