Ant transmutations

 Ever since I read about Indian jumping ants in the Atlantic, I've been wondering how this works (epic-)genetically speaking.

When the queen of an Indian jumping ant colony dies:

Within hours of their queen’s death, female workers will begin to joust, fencing with their antennae, and nipping at each other’s heads. These dominance tournaments can last for more than a month, until, at long last, a dozen or so champions triumph. While the losers slink away to resume their workerly duties, the victors cast aside their former peasant status and become a new class of pseudo-royals called gamergates (no, not that kind). The queen phase of the colony ends, and the gamergate phase begins: Monarchy transforms into oligarchy, and new gamergates step up as each generation dies. The consequences of these tiny tussles range from the sociopolitical to the molecular. In earning the title of gamergate (pronounced gamm-ər-gayt), a female ant gains nearly exclusive rights to her colony’s reproductive responsibilities; she is among the very few of her sisters that can fertilize their eggs with the sperm of their brothers, the only available males. The transition rewires worker ants, altering their behavior and physiology until they become docile, nursery-bound “egg-laying machines,” Penick said. Gamergates stop leaving the nest. They lose their food-foraging chops and the will to hunt, relegating themselves instead to the darkness of their underground chambers, where they churn out eggs. They feast exclusively on the paralyzed prey served to them by workers. Normally these ants leap at assailants when disturbed—the classic “jumping” behavior that earned the species its name—but when confronted by intruders, gamergates cower and hide. Even their bodies reprioritize. The ants’ life span extends from six or seven months to three years or more. Their venom glands recede, and their ovaries swell to about five times their original size; the ants become, in a sense, perpetually pregnant. In perhaps the most astounding change of all, the ants’ brain shrinks by about 20 to 25 percent in volume when they become gamergates. (For humans, that’d be the rough equivalent of losing a hunk of brain the size of two tennis balls.) The downsizing isn’t uniform: The insects appear to selectively jettison bits of their brain devoted to hunting, foraging, spatial mapping, and the anty equivalent of critical thinking—a move that likely reroutes precious bodily resources to the ovaries. Jumping-ant brains are already quite small, about a tenth of a cubic millimeter in volume. But brain tissue is “very energetically costly,” Floria Mora-Kepfer Uy, an entomologist at the University of Rochester, told me. And when the future of the colony is at stake, every calorie counts. “There’s a trade-off between reproduction and cognition,” Uy said. It is a heavy crown to wear atop a newly lightened head.

But what is even stranger is that the changes are reversible:

In a new paper published today in Proceedings of the Royal Society B, Penick, Liebig, and their colleagues report that the gamergate transformation is entirely reversible, down to the mind-boggling changes the ants’ brain tissue undergoes. When the researchers isolated gamergates from their colonies, depriving them of the social signals needed to maintain their über-fertile status, then reintroduced them to their peers, the ants rapidly regressed into workers. Their ovaries shriveled, leaving room for their venom glands to grow; their brains ballooned out. They reacquired their aggressive fighting acumen, and would once again jump when provoked. Functionally sterilized and juiced back up with intellect, they became once again indistinguishable from their commoner kin.

It must be that various genes are turned off and on. How much (or little) of this epigenetic flexibility is retained in homo sapiens?

The Epigenetics of Poverty

 A preliminary, from Wiki: "DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts to repress gene transcription. In mammals, DNA methylation is essential for normal development and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging, and carcinogenesis."

Someone drew my attention to this: Poverty leaves a mark on our genes.  This is from 2019.

A new Northwestern University study challenges prevailing understandings of genes as immutable features of biology that are fixed at conception.

Previous research has shown that socioeconomic status (SES) is a powerful determinant of human health and disease, and social inequality is a ubiquitous stressor for human populations globally. Lower educational attainment and/or income predict increased risk for heart disease, diabetes, many cancers and infectious diseases, for example. Furthermore, lower SES is associated with physiological processes that contribute to the development of disease, including chronic inflammation, insulin resistance and cortisol dysregulation.

In this study, researchers found evidence that poverty can become embedded across wide swaths of the genome. They discovered that lower socioeconomic status is associated with levels of DNA methylation (DNAm) -- a key epigenetic mark that has the potential to shape gene expression -- at more than 2,500 sites, across more than 1,500 genes.

In other words, poverty leaves a mark on nearly 10 percent of the genes in the genome.

Lead author Thomas McDade said this is significant for two reasons.

"First, we have known for a long time that SES is a powerful determinant of health, but the underlying mechanisms through which our bodies 'remember' the experiences of poverty are not known," said McDade, professor of anthropology in the Weinberg College of Arts and Sciences at Northwestern and director of the Laboratory for Human Biology Research.

"Our findings suggest that DNA methylation may play an important role, and the wide scope of the associations between SES and DNAm is consistent with the wide range of biological systems and health outcomes we know to be shaped by SES."

Secondly, said McDade, also a faculty fellow at Northwestern's Institute for Policy Research, experiences over the course of development become embodied in the genome, to literally shape its structure and function.

"There is no nature vs. nurture," he adds.

McDade said he was surprised to find so many associations between socioeconomic status and DNA methylation, across such a large number of genes.

"This pattern highlights a potential mechanism through which poverty can have a lasting impact on a wide range of physiological systems and processes," he said.

The original paper is here.

A criticism of the field is here: Social epigenomics: Are we at an impasse?

Peak Gene

Interesting article.

We have reached peak gene, and passed it.

Ken Richardson in "It's The End Of The Gene As We Know It" 

In scientific, as well as popular descriptions today, genes “act,” “behave,” “direct,” “control,” “design,” “influence,” have “effects,” are “responsible for,” are “selfish,” and so on, as if minds of their own with designs and intentions.

But at the same time, a counter-narrative is building, not from the media but from inside science itself.... Scientists now understand that the information in the DNA code can only serve as a template for a protein. It cannot possibly serve as instructions for the more complex task of putting the proteins together into a fully functioning being, no more than the characters on a typewriter can produce a story.

...

First, laboratory experiments have shown how living forms probably flourished as “molecular soups” long before genes existed. They self-organized, synthesized polymers (like RNA and DNA), adapted, and reproduced through interactions among hundreds of components. That means they followed “instructions” arising from relations between components, according to current conditions, with no overall controller: compositional information, as the geneticist Doron Lancet calls it.
In this perspective, the genes evolved later, as products of prior systems, not as the original designers and controllers of them. More likely as templates for components as and when needed: a kind of facility for “just in time” supply of parts needed on a recurring basis.

...

We have traditionally thought of cell contents as servants to the DNA instructions. But, as the British biologist Denis Noble insists in an interview with the writer Suzan Mazur, “The modern synthesis has got causality in biology wrong … DNA on its own does absolutely nothing until activated by the rest of the system … DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.”

PS: the proposed definition of "gene" by Portin and Wilkins:

A gene is a DNA sequence (whose component segments do not necessarily need to be physically contiguous) that specifies one or more sequence-related RNAs/proteins that are both evoked by Genetic Regulatory Networks and participate as elements in Genetic Regulatory Networks, often with indirect effects, or as outputs of Genetic Regulatory Networks, the latter yielding more direct phenotypic effects.

Wiki tells us: A genetic regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expressionlevels of mRNA and proteins.  

Some.Rakhigarhi news from April 2016

An Amar Ujala photo-story from April 14, 2016 says that a total of 18 skeletons have been recovered from Rakhigarhi.

The Tribune of Chandigarh reported that 15 skeletons were recovered in the recent round of excavation.

The sources said excavators had opened 20 graves and skeletons had been found in 15 of them. They said DNA samples were being sent to the laboratories for bio-molecular scientific analysis.

The archeologists said the DNA samples would be analysed at the Centre for Cellular and Molecular Biology (CCMB), Hyderabad; Howard University, USA; and the Seoul National University, South Korea.

This I had missed.  I had thought that they were still trying to get aDNA from the skeletons excavated in 2014, and apparently, so did Tony Joseph, in his article in the Hindu.

Metspalu v Laziridis: trying to understand

Am trying to square Metspalu, et. al.'s 2011 paper and Laziridis et. al.'s 2016 paper.

Here's what's bugging me.  The diagram below is a crop from a diagram in the Metspalu paper, a graphical representation of the genetic make-up of various populations.

You can see South Asia is mainly k5 and k6.  k6 is mostly confined to South Asia, while k5 extends into Central Asia, the Caucasus, the Middle East and into Western Europe.

They write:

We found no regional diversity differences associated with k5 at K = 8. Thus, regardless of where this component was from (the Caucasus, Near East, Indus Valley, or Central Asia), its spread to other regions must have occurred well before our detection limits at 12,500 years. Accordingly, the introduction of k5 to South Asia cannot be explained by recent gene flow, such as the hypothetical Indo-Aryan migration. The admixture of the k5 and k6 components within India, however, could have happened more recently—our haplotype diversity estimates are not informative about the timing of local admixture.

___________
PS: thanks to guest's comment below, I know clarification is needed: Metspalu et. al. run  ADMIXTURE, which estimates how much a modern sample of unrelated individuals derives their ancestry from a set of postulated ancestral populations.

 The typical dataset consists of genotypes at a large number J of single nucleotide poly- morphisms (SNPs) from a large number I of unrelated individuals. These individuals are drawn from an admixed population with contributions from K postulated ancestral populations. Population k contributes a fraction qik of individual i’s genome.

You try various Ks and ADMIXTURE also estimates the standard errors on the results.  Reich 2009 used a Principal Components Analysis (PCA) to come up with ANI/ASI.  ADMIXTURE was created in 2009 apparently. 

We are told:

Choice of an appropriate value for K is a notoriously difficult statistical problem. It seems to us that this choice should be guided by knowledge of a population’s history. Be- cause experimentation with different values of K is advisable, admixture prints values of the familiar AIC (Akaike Information Criterion) and BIC (Bayesian Information Criterion) statistics, widely applied in model selection. 

_______________ 

 Strictly speaking, their detection limit is 500 generations, and they use 25 years per generation. The point is that k5 in South Asia dates to more than 500 generations or 12,500 years ago.

The next is a little leap of mine - is it justified? In the Ancestral North Indian/Ancestral South Indian (ANI/ASI) model,  ANI corresponds to k5 and ASI corresponds to k6.  That this is so is not entirely clear to me.

We now come to Laziridis et. al.  They do an ancient DNA (aDNA) analysis of Near Eastern samples (Near Eastern with respect to Europe)  dating from 12000 to 1400 years ago, and they refer to aDNA analyses of Steppe inhabitants; as far as I know, the Steppe aDNA does not go back before 12000 years.  Now, the Laziridis paper says:

We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe...

 But if ANI == k5, and k5 spread before 12500 years ago (strictly speaking, 500 generations, while the aDNA dates are presumably radiocarbon dates) why would one expect to explain ANI in terms of contemporary peoples or peoples younger than ANI?

Perhaps one can say that Near Eastern aDNA,  Steppe aDNA and ANI (k5) all arose from the mixture of two ancestral populations X and Y (ancestors of the 12000-year-ago-people) and the Near Eastern aDNA and the Steppe aDNA represent relatively unmixed descendants of X and Y respectively, while ANI is a descendant mixture of X and Y.   I don't think this is what the Laziridis paper does.

My guess is Laziridis et. al. instead of sticking to just to genetics, also buy into the predominant theory of the spread of Indo-European languages, and hence attempt to explain ANI in this illogical way, or else Laziridis thinks the Metspalu paper is wrong and ANI(k5) is younger than 12500 years; or else I have misunderstood Laziridis or else ANI != k5.

PS: the most probable of the above alternatives is that I misunderstand Lazirides, the second most probable is that Laziridis et. al. don't think Metspalu is correct, and ANI is (much) younger than 12500 years.

_____
PS: Jan 6: This larger excerpt of a diagram in Metspalu shows ADMIXTURE with K=8 and K=12 (K is the number of hypothetical ancestral populations) and you can see that it does not really change the story that most of Indian ancestry traces to two components.  One would hope that one can come up with an objective definition of k5, k6 that is the same when computed with different but adequate samples.

Rakhigarhi news

Tony Joseph in the Hindu writes: (highlights added)
(PS: for a take on the non-news content of Tony Joseph's article, see this.)

The site was excavated and the skeletons were recovered in the beginning of 2014 by a team of archaeologists led by Vasant Shinde, Vice Chancellor of Deccan College, Pune. For the 61-year-old Shinde, this project is the culmination of a long and distinguished career in archaeology that has seen him lead excavations at important Harappan and other sites across the country. But Rakhigarhi is a project with a difference.

In the three-and-a-half years since its excavation, Professor Shinde has brought together scientists from Indian and international institutions like the Centre for Cellular and Molecular Biology, Hyderabad (CCMB), Harvard Medical School, Seoul National University, and the University of Cambridge to work on different parts of the project, including extracting and analysing DNA from these ancient people, reconstructing their faces, and studying the remains of their habitation to understand their daily habits and ways of life.

Soccer and Genetics

I'm keenly waiting to hear the genetics explanation for why the US doesn't do well in world soccer tournaments for men.  Till then, there is stuff like this.