Tag Archives: Genetics

Ancient Link Between India and Australia

The study of the human genome continues to yield new insights about our history. A new study on the variation seen across human populations has revealed an ancient migration from India to Australia 141 generations ago, one that hadn’t been on record.

It is accepted that human populations migrated out of Africa and subsequently colonized the world. Some previous studies have shown that a wave of migration (called the ‘southern route’ of migration) to the Australian landmass occurred around 45000 years ago, following which this population remained isolated until colonization by Europeans in the 18th Century. This study upends this conclusion.

How Does Such Genetic Analysis Work?

Before the era of airplanes and global migration, populations across the world were relatively isolated, mainly because of geographical barriers, and often because of cultural and social barriers. Thus, members of each population would only breed with other members of the same population. Over time, this lack of interbreeding, or genetic mixing between different populations, led to distinct patterns that could be seen in each population. It is by looking at similarities and differences in these that we can compare genetic data.

A Study of Global Populations

The distribution of samples used in the study. [Image Source: PNAS: doi: 10.1073/pnas.1211927110]

Researchers at the Max Planck Institute for Evolutionary Anthropology collected ‘genotype data’—genetic data only at commonly varying locations in the genome—from different populations across the world (see figure above), and looked for patterns of similarities across these populations in terms of their genetic data. Using this genetic data and known rates of genetic change, they found a genetic link between populations from Australia, New Guinea and Mamanwa (an ancient group from the Philippines). This is consistent with the ‘southern route’ theory. What was novel was a significant similarity between Indian populations and Australian populations. This indicates a pattern of gene flow from India to Australia approximately 4230 years ago, a period called the Holocene.

Genetic Link Matches Archaeological Record—Coincidence?

This is fascinating because of an archaeological factoid of this period. This represents the period when changes in tool technology, food processing and a dog native to Australia called the dingo emerged on the Australian subcontinent. Could this emergence be related to the migration occurring in the same period?

It is plausible that this wave of migration was not direct, i.e., it could have been through the region of S.E. Asia, which shares long cultural links with Australia. However, the patterns of similarity seen between the Indian and Australian populations are not seen in the South-East Asian populations which were also included in this study. This means that there was a direct migration between India and Australia.

The study of our past is a fascinating one. Genetic data is an invaluable tool in this pursuit, and provides a tangible way for mankind to trace its evolutionary past.

You can read about this research here.

Could Your Genes Tell You Why You Hate Cilantro?

The next time you make a face at the cilantro (coriander in certain parts of the world) on your plate, you can blame your genes. A genetic component for the intense dislike of cilantro has been found.

Before you get outraged by the thought of studies performed on culinary preferences, responses to cilantro has been thought of as interesting for quite a while. There are polarizing reactions to it, with some people comparing its taste to soap. On the other hand, it continues to be used generously in South Asian and Latin American cuisines. This even prompted the New York Times to publish an article called ‘Cilantro Haters, It’s Not Your Fault’.

The distinct flavor of cilantro is because it contains a class of molecules called aldehydes. It was thus hypothesized that differences in proteins that can detect these molecules—called receptors—could be responsible for the strong variation in response to the herb. Now, researchers at the sequencing company 23andMe have used genome sequences of 14000 Europeans to hunt out a genetic cause.

Cilantro (also called coriander) is commonly used in many cuisines across the world. Different populations, however, often have sharply contrasting perceptions of its taste.

‘Crowdsourcing’ Data

This research was part of a larger group of projects under 23andMe, which could be called crowdsourcing. In this process, the company sequences people’s genomes and provides genetic analysis. Clients willing to participate in 23andMe’s research are then asked to fill up a questionnaire about various traits that might be genetic, for instance, whether they think cilantro has a ‘soapy’ taste (another example could be eye color). The company then uses this data for their analysis. In this experiment, they found that one varying position in the genome—called a single nucleotide polymorphism (SNP)—was found to be associated with the way people think cilantro tastes. To put it another way, people who detest cilantro were much more likely to have one version of this SNP as opposed to people who like it, who are more likely to have another version.

Having found this SNP, they realized that it lies within a cluster of 8 olfactory receptor genes, genes involved in the perception of smells. This could thus be a strong candidate gene responsible for the divisive response to cilantro.

However, this SNP only explains a very low percentage of the variance in the trait. What does this mean? Ideally, we would expect to be able to predict a person’s response to cilantro based on the SNP she has. However, that is not the case, only 1.5% of the variance in the trait can be explained. This could be because there are multiple genes that act together in determining cilantro response (and they have only managed to capture one of them), or that only a small amount of cilantro response is actually genetic. Thus, in the latter case, even a significant SNP cannot significantly affect cilantro detection. This study was only performed on a European population, studies capturing a greater diversity could yield further answers.

You can read about this research here.

Of Mice that Sing

A movie called ‘Ratatouille’ showed us a cartoon mouse that could cook up wonders. The real world matches this with mice that don’t just squeak, but sing too.

Singing for the Women

Scotinomys teguina are mice from the mountains of Costa Rica which communicate by singing. Before you start preparing to teach your next non-avian pet the latest from Adele, the singing capacity of these marvelous creatures is restricted to trilling—a rapid alternation between two adjacent notes. In several species of birds, males with greater trill production are seen to be greater threats by rivals, and seen as more attractive by females. Likewise, the male singing mouse emits a series of rapid high-pitched chirps to attract mates and fend off rivals.

Researchers at the University of Texas are now studying these mice to try and understand the genes that lead to this singing behavior—genes which could in turn regulate language in humans. It is known that music and language are processed by the same brain systems in humans in a part of the brain called the temporal lobes.

Looking for a ‘Singing Gene’

It is one gene in particular that is being studied, a gene called FOXP2 (Forkhead Box Protein P2). This gene is highly conserved across humans, singing mice and lab mice. In humans, mutations of this gene has been found to lead to speech and language disorders. In birds, removing this gene leads to inaccurate song imitation. The research team is sequencing this entire gene in the singing mice and looking for segments of DNA that are present only in the singing mouse as opposed to the lab mouse; from this set of changes, the team then filters out those that are likely to have occurred by chance and have no biological significance. The remaining gene changes are those that could be responsible for the ability of the singing mice to trill.

Another way to study this single gene is to look at its function. This protein regulates the expression and activities of a host of other proteins—what are they? “We found that when an animal hears a song from the same species, these neurons that carry FOXP2 become activated. So we think that FOXP2 may play a role in integrating that information,” said Lauren O’Connell, a researcher in Steven Phelps’s lab, where this research is being conducted. They are now making the mice listen to songs, and record all the genes that are activated, to see which ones could be activated by FOXP2. This information will help us form the complete link between the gene and the biological property of singing or language in humans.

You can learn more about this research here.

The Woolly Mammoth To Return From The Dead, Guarantee Korean and Russian Scientists

The magnificent beasts shall once more roam this planet. This may be an overstatement, but South Korean and Russian scientists intend to research a proper cloning technique to recreate the wooly mammoth by trying and gestating the fertilized egg in the womb of an Indian elephant mother. The fertilization, after the required genetic modification, will be done in the lab.

Coming back from the dead?

Several very neatly preserved remains of mammoths, from more than 10,000 years ago, were found under the Siberian permafrost. The first step is to extract the DNA. With the DNA, the scientists are trying to recreate blood protein. If all goes well, the next step will be to create the nuclei of mammoth cells, which will contain the required genetic material. This will then be implanted in the cell of an Indian elephant. Since the two species are genetically very similar, this is the best bet! The gestation period will be 22 months. Research for this entire process should be complete by the next 5 years.


Cloning has been a long-time obsession for many geneticists. It’s a great way to showcase the giant leaps in genetics that have happened in the last 50 or so years. After the sheep Dolly, the world’s first cloned mammal and Snuppy, the first cloned dog, followed by numerous other clones like a cat and a coyote, this is the natural big leap! Even Chinese scientists are interested in this project.

There have always been raised eyebrows and pessimistic  opinions about being able to ‘tinker with the very essence of life itself’. Brushing all those silly opinions aside, let us just marvel at the very prospect of a giant mammoth being resurrected.

Google To Store DNA Data Online, Make It Free For Researchers

The price to pay for a service getting cheaper is the increased demand, and consequently the larger amounts of data generated due to that. When the National Institute of Health (NIH) announced that it might have to consider dropping funding to Sequence Read Archive (SRA), Google stepped in aiming to protect the huge bank of genetic data amassed from several individuals over the years. Google began talks with DNAnexus, a Mountain View, California firm, aiming to keep funding the genetic database, put it online and then make it free for researchers from across the globe. The problem? The data is huge!

A More Virulent Moore’s Law

Recently NIH backtracked and said that they’ll support SRA in the near future. DNAnexus went ahead and said that they wanted a Plan B, keeping a mirrorof the information available at SRA. DNAnexus CEO Andreas Sundquist said that they intend to build up a better public repository, one that is easy to search and access information from.

If you thought the solid state industry has grown phenomenally, hear Andreas Sandquist on the growth of the genetic industry:

DNA sequencing becomes 10 times cheaper every 18 months, thanks to hardware improvements. It’s sort of like Moore’s law on steroids!

Just to give you as estimated figure, the cost of gene sequencing for an entire person was around $30,000 in the US a year ago. Now, it is down to $4000! Considering that each genome is 3 billion letters (that’s 3,000,000,000 letters) long, it takes 3 terabits of data for every person’s genome. The space crunch is inevitable. Now, with the gene sequencing techniques getting cheaper, we expect sequencing to enter mainstream medical lab testing at reasonable rates. This is going to create an even bigger space crunch. There is another worry about the information being made accessible to people who need it. SRA is a great database, but very disorganized. This is where Google and its data-crunching capabilities come into play something that has made Google a household name.

Everyone’s Online!

In the near future, predicts Sandquist, everyone’s genetic information will be available online. What’s the big deal about that, you ask? With information about mutations present online, it will be easier to figure out how pathogens evolve and work out a way to find a cure for many diseases. It will significantly reduce the time required to test new drugs.

This isn’t Google’s first foray into genomics. Sergey Brin and his wife has constantly funded 23andme, a Mountain View organization, which was co-founded by Brin’s wife and helps people understand the genetic cause of their diseases.

Guess in the future you can even Google up someone’s genetic make-up. Isn’t that cool?