Saccharum hybrids and E. K. JANAKI AMMAL

It is almost the end of November; it is the month in which JA was born. JA was the granddaughter of John Child Hannyngton and Kunhi Kurumbi Kuruvai. So, it is possible to say that JA was 1/4th British. In recent years, we have seen more articles written about JA and her work from Indian and British authors. After her return to India following the invitation by the then PM, JA worked at various places in India. During this period, the paper titled "Further studies in Saccharum-zea hybrid I. Mitotic studies" was published by JA in Heredity volume 28, pages 141–142 (1972). It has been five decades since this article was published. In this entire time, the article is cited ~5 times. A genomic view of this work would be interesting and will probably happen at some point. 

The sacred Peafowl on Mount K2

Being second at anything generally means you have lost the race. However, if you are the second-highest mountain on Earth, it is still a pretty astounding place to be. Mount K2, also popular as Savage Mountain, excels at killing people and is probably one of the most deadly mountains to climb. At a height of over 8600 meters, K2 has very little flora and fauna. Peafowl are most definitely not part of K2 native fauna. So why does the blog post have a title claiming the sacred peafowl has made its way to Mount K2?

If you have seen the first episode of Season 4 of the TV series Madam Secretary (which follows the fictional life of a woman US secretary of state), you will know it is called the "News Cycle". The TV show features a fictional US secretary of state but is based on various current affairs spanning the TV series's time frame (2014-2019). In this episode, the secretary meets the Assistant Vice-Minister of  Foreign Affairs for Timor-Leste (located in Southeast Asia) to make a political point. Unfortunately, the minister suddenly and inexplicably dies during the meeting. Before the secretary and her team figure out what is happening, a blogger (much more popular than the current one) suggests the secretary killed the Assistant Vice-Minister. The blog/website is a fringe website called "Champion of Facts". Soon, the story starts trending on social media (erstwhile Twitter). The secretary appears on a pre-scheduled news show to discuss serious policy issues, only to be sidetracked by the anchor to address these rumours bolstered by the secretary's political opponents. The secretary responds with "...this is obvious crackpot theorizing, which quite possibly is the work of a disinformation campaign by a foreign power. What Senator Morejon is doing by legitimizing this baseless story, it's not just immoral and unethical. It undermines the stability of democratic government."

She continues:

"Reliable information is the bedrock of any institution, be it science, government or private enterprise. If citizens can't tell the difference between fact and fiction, then the entire project of civilisation turns to dust."

Soon, a crowd gathers outside the TV studio, chanting, "Murderer!! Murderer!!". "Lock her up!" Deja Vu?

The words of Supreme Court Justice Louis Brandeis from over a century ago: “Sunlight is said to be the best of disinfectants.” are echoed by Nadine, the secretary's chief of staff. Following this, the secretary and her team race to reveal the truth behind the murder of the Assistant Vice-Minister of Foreign Affairs. The episode ends with the USA and China cooperating with each other to bring down the actual murderers. However, the citizens still have a tough time believing the secretary is not a murderer.

Now, coming back to peafowl, the most consequential population genomic research regarding green peafowl was published two years ago by the journal Proceedings of the Royal Society B. In this article titled "Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl (Pavo muticus)" the authors demonstrate the effect human forces have had in the endangerment of the green peafowl. As with other journals of the Royal Society, the reviewer's comments are made public upon publication of the article. 

The first reviewer makes several comments with the following really crucial points:

Line 120: There is good north-south sampling, but the western populations were not sampled, so parts of the range were not included.

Line 238: The term iconic is used in several places, and while the Indian peafowl might be considered iconic (well-recognized worldwide), the green peafowl is much less known in many parts of the world, so it may not really be iconic. 

However, neither of the reviewers had any concerns regarding the analysis of population structure, mostly about limited sampling across the range. The second main result is "(b) Lack of population structure". Using 790 898 putatively unlinked and neutral loci from the total 22 unrelated modern samples of the green peafowl, the authors found no signals of stratification among the sampled individuals, with the lowest CV error at K = 1. This analysis is done to justify pooling the samples into one single run of the demography inference software SMC++. The statement is, "Therefore, we pooled these samples in the subsequent demographic inference."

The discussion section has a sub-section titled "(c) Conservation implications". One of the take-home messages is, "Fortunately, this study predicted that extensive climatically suitable habitats remain in both continental Southeast Asia and Java Island for this endangered bird." 

The study suggests the possibility of population recovery through active conservation intervention by:

• restrictions on hunting
• habitat conservation
• re-introductions

Although the article's main message is to suggest the role of human forces in the decline of the peafowl populations, it has various unsaid/underappreciated implications. First, the identification of a K of 1 for the widespread sampling, including "11 from southwest China, seven from Thailand, one from Cambodia and the remaining 12 seized by Chinese customs with a probable origin of Vietnam. We also resequenced six museum specimens stored in Kunming Natural History Museum of Zoology and collected from southwest China during 1956–1976, a period with relatively abundant green peafowls." This suggests a lack of sub-structure within the species.

Interestingly, another study re-sequenced 14+1 (used for de novo assembly) additional green peafowl and generated a "Chromosome-Level Genome Assembly of the Green Peafowl (Pavo muticus) ". This adds up to a dataset of 38+15=53 green peafowl genomes. All 15 re-sequenced samples from this second study are from individuals in captivity. These high-quality published datasets provide a fairly reasonable dataset for further analysis and inference. The pre-print by Patil et al., 2023 does just that. By investigating the genetic structure among the samples using PCA, structure analysis, phylogenetic tree building, coalescent split time estimation and demographic history reconstruction, it is claimed that at least three distinct populations can be identified among the green peafowl sampled by these two studies. This would somewhat contradict the earlier paper's result "(b) Lack of population structure". However, the whole sample set analysed by Patil et al., 2023 is much larger than those available in the initial study. It would appear that increasing sample size helped identify the population structure within the green peafowl. Identifying this population structure is not the only major result of the manuscript of Patil et al., 2023. Another notable result is the identification of a putative inter-species hybrid peafowl individual with genetic ancestry of both the blue and green peafowl species. The paper claims the presence of such hybrids may have implications for maintaining captive populations. 

Genomics is no rocket science but has many of the same jingoistic stereotypes. The sequencing and assembly of the giant panda genome by scientists from BGI has political symbolism, as this species has appeared on the Gold Panda coins issued by the People's Republic of China. The video below about Zambia's space program, led by Edward Makuka Nkoloso, also paints a picture of the surprising links between nationalism and scientific progress. If nothing else, the term Afronaut and its widespread use in literary work would not have happened without Nkoloso. It would not be an exaggeration to say that Makuka Nkoloso inspires many.

Given the strong emotions surrounding the space program, the moon landing by Americans in July 1969 was claimed to have been faked. A crazy conspiracy theory to support this claim began circulating soon after the moon mission. Using "evidence" such as the flag is flapping, the shadows not parallel to each other, the Van Allen belt would have killed the astronauts, etc., the conspiracy theorists try to ground their claims in some sort of logic. Another less well-known conspiracy theory associated with the moon landing is the claim of ancient ruins of a once glorious civilisation that thrived on the moon. Many other conspiracy theories have been spawned over the decades since the initial moon landing. A 60-minute Australia episode explores these two conspiracy theories and has real scientists debunk each of the "logical arguments" made by the conspiracy nuts. This documentary also features an interview with a NASA scientist who says that these claims have largely been ignored as responding to them would give more credence to conspiracies.

Mittal et al., 2019 claimed that the results in Figure 3C of a paper published in 2017 in the highly reputed journal Science Advances were not supported by data (see Supplementary Figure S3 in the Mittal paper). However, the repute of the SA paper has garnered over 100 citations post-2019 and continues to grow. In contrast, the SR paper claiming the results are not supported has less than 20 citations, most of which are potential self-citations. Now, are these claims as crazy as the moon landing conspiracy theories? Opinions of people tend to have a greater influence on how human society acts rather than facts. After all, Derek Lowe, the popular blogger and chemist, goes on to call Scientific Reports (in not so many words) a fake research publishing predatory machine in his blog "In the pipeline".

Interestingly, Derek Lowe's blog is published on the same website, www.science.org, as the journal Science Advances. Based on this, it is logical for any sane person to form an opinion that the article published by a predatory machine cannot be trusted when it is criticising the actual incarnation of integrity. Hence, it is unsurprising that "Predatory-journal papers have little scientific impact". By extension, authors who publish in predatory journals are gullible entities whose results can never be trusted. Why do we believe things that aren't true? Philip Fernbach has a TEDx talk that answers this question. He argues, "Understanding is contagious". This contagious understanding, paired with ignorance, can lead to us believing in things that aren't true. 

After constructive and quality-improving reviews of the Patil et al., 2023 pre-print, the manuscript is finally published in a real, honest-to-God, non-predatory journal (Conservation Genetics). The title still remains "Conservation implications of diverse demographic histories: the case study of green peafowl (Pavo muticus, Linnaeus 1766)". Interestingly, this is the first paper on any peafowl to be published by this journal. Will this suffer the same fate of ignorance, or will it stimulate more work on the diversity within green peafowl is something that only time will tell.

Cilia are made up of gene products too

We have discussed gene loss in the host and its relationship with viral pathogens earlier concerning C9 and the TCP. Despite its fame and obvious importance to chicken health, the loss of C9 seems to have had zero impact in the almost one-year period in which the "Birth and Death in the Terminal Complement Pathway" article has been live on the internet, PubMed and the well-read journal Molecular Immunology. The complicated lives of the rich and powerful are hard to comprehend. So looking at less well-known and hard-to-study genes seems a better bet, given the multi-citation success of PLGRKT. 

Hopefully, the pandemic of the century (Covid-19) is done and dusted. Let's pray to the Supreme Lord Krishna to ensure it was indeed the PoTC (Pandemic of the Century) and move ahead with our lives. However, that would mean another PoTC is due in the next century, and if covid has taught us anything, you can never be too prepared to deal with it. So it is natural for us to continue working on increasing our knowledge to deal with the next PoTC. While most of us were hiding, scared in our homes, the brave few were working round the clock on a war footing to stop covid. One such covid warrior is Lisa A. Chakrabarti from the Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France. 

In their paper titled "SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance" published in Nature Communications, Robinot and Hubert et al. use "a reconstructed human bronchial epithelium model" to study the structural and functional consequences of SARS-CoV-2 infection. They find "rapid loss of the ciliary layer" using their robust assay procedure. Several other prominent studies have found that the cilia are affected by viral infections such as the one caused by SARS-CoV-2. Interestingly, these changes to the epithelium have also been identified using golden Syrian hamsters as a model. The study titled "Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters" by Bryche et al. finds "massive damage of the olfactory epithelium as early as 2 days post nasal instillation of SARS-CoV-2, resulting in a major loss of cilia necessary for odour detection". Based on these studies, it has been suggested that the loss of odour detection experienced by many of the covid infected individuals is due to the loss of the cilia. The tiny cilia lining the epithelia seem to have a prominent role when it comes to mighty viral pathogens. 

When Buddhabhushan et al. found that genes that code for parts of the ciliary apparatus are lost in chicken and a few other bird species, it was an interesting find from the perspective of how they may differ in their susceptibility to pathogens. It would also be possible that the change in the cilia could alter the ability to smell things. The prevalence of olfactory receptor genes has been linked to differences in the sense of smell among birds. Hence, a follow-up to the study titled "Avian olfactory receptor gene repertoires: evidence for a well-developed sense of smell in birds?" could focus on unorthodox genes such as those identified by  Buddhabhushan et al. Very little research has been conducted to date on the functions of the genes WDR93 and CFAP46. While it is known that they are part of the central apparatus projection D (C1d), the role of these genes in host-pathogen interaction is unclear. Two or three papers briefly suggest a role for WDR93 in dealing with pathogens. Further experimental work will need to decode the relevance using extensive experimental approaches.

Experimental studies of the cilia and their functionality have been challenging due to the lack of high throughput assays and the difficulties involved in the study of cilia. The recent pandemic has helped refocus efforts on studying cilia for its motility using cell culture approaches. A recent paper published in the journal Royal Society Open Science provides a very useful software resource to perform automated measurements of ciliary motility. The paper titled "Assessing motile cilia coverage and beat frequency in mammalian in vitro cell culture tissues" presents "a novel and open-source method" to "fully characterize cilia beating frequency and motile cilia coverage in an automated fashion without user intervention". The technical advancements involved in this manuscript involve the use of several image analysis methods and results in a GUI-based tool called Canvas. All publications in the journal Royal Society Open Science publish the peer review report online and is available on the Web of Science with citable doi's. So it is possible to see how many reviewers were involved and what comments were raised by them.

In the genetics section of the journal, the most recent article is about the evolution of the gene ADH7 and its link with diet. 

1. The dataset spanning seven orders consists of 59 mammalian species: 27 bat, nine treeshrew, 11 rodent, four opossum and eight additional small to mid-sized mammal species in Central and South America, the Caribbean, as well as Southeast Asia.
2. The sequences were obtained using target capture plus massive parallel sequencing, or Sanger sequencing following PCR amplification of exon 7.
3. The authors find high concordance in the sequences generated by these two methods. The only differences between the two sequencing methods seem to be a result of SNP's and inter-individual variation.
4. The HybPiper pipeline is also used to recover the gene sequences and assemble them into full-length gene sequences.
5. Interestingly, the authors find the presence of multiple copies of the ADH7 gene and note: "The presence of a second ADH7 gene in bats was not known at the time we designed the baits for our target capture sequencing, complicating our assembly pipeline. As expected with short-read sequencing data, attempts to fully assemble these paralogues separately from our reads were not successful; however, variation in bat ADH7 sequences at site 294 could be determined by visually inspecting the mapped shorts reads in IGV"
6. The full dataset consisting of the following was compiled:
1. 59 mammalian species new data
2. 85 ADH7 sequences curated in a previous study (Genetic evidence of widespread variation in ethanol metabolism among mammals: revisiting the ‘myth' of natural intoxication)
3. 30 sequences newly mined from NCBI
7. After the dataset was compiled, model testing was done with a phylogenetic correction to test "if a frugivorous and/or nectarivorous diet correlates with"
1. retention/pseudogenization; n = 166
2. presence of a substitution at site 294 (yes/no) as a binary dependent variable (n = 133)
8. For testing the hypothesis, the following Phylogenetic generalized linear models (PGLM) were used:
1. The maximum penalized likelihood estimation (MPLE) and 
2. The IG10 method

The two main results from tests done on these data are:

1. Diet and putative functional variation at site 294
2. Diet and putative gene functionality

Finally, the authors discuss the interpretation of the two predictions made by them:

1. Primarily frugivorous and/or nectarivorous species will have substitutions at site 294 to valine or to other amino acids with similar physical and chemical properties, i.e. hydrophobic nature and a large side chain
2. The ADH7 genes of highly insectivorous, carnivorous/sanguinivorous or herbivorous species will be pseudogenized due to relaxed selection, as they are less likely to be exposed to dietary ethanol

Both this ADH7 paper and the previous one published in Biology Letters share several authors, such as Amanda D. Melin from the University of Calgary, Canada. The Biology Letters paper has seen a great deal of popularity in the media due to its links with animal intoxication. In terms of methodology, both papers are rather similar. However, the authors do spend a considerable amount of time and effort to estimate gene loss timing using the Meredith et al. method in the first paper. Given the sensitivity of the Meredith method to the set of species used in estimating the gene loss timing, its use is not as widespread as it might have been if the estimates were robust. Moreover, some of the assumptions used to estimate the time of gene loss are not true in most cases. All of these articles are published by journals of the Royal Society and are part of Open Science. What is Open Science?

The benefits of Open Science are described in this short video from the Royal Society. 

Many open-access journals are actually predatory and are known to entrap unsuspecting scientists, especially from low- and middle-income countries (LMICs). So how to know if a journal is predatory? Some brilliant folk have come up with useful criteria to identify predatory journals. However, as they note in their article, it can be very tricky to distinguish between predatory and legitimate journals. Royal Society Open Science has various read and publish agreements with major universities worldwide to cover the article processing charges. So in some cases, the authors from these universities are assured by the university that this is not deemed a predatory journal by them. Based on this reasoning, it would appear Royal Society Open Science is not a predatory journal, and the publication of the article titled "Concurrent loss of ciliary genes WDR93 and CFAP46 in phylogenetically distant birds" by Buddhabhushan et al. may not be an example of entrapment of unsuspecting entities. 

Black to the bone: A story of chicken dispersal across Asia

Located in the heart of India, Madhya Pradesh (MP) is a melting-pot state that shares its borders with Uttar Pradesh (UP) and Rajasthan in the north, with Maharashtra and Chattisgarh in the south. Gujarat, on the west coast of India, also shares a border with MP, although along only two districts (Alirajpur and Jhabua). Our story beings in these districts where more than 90% of the people spoke the Bhili language, according to the 2011 survey. This region represents what remains of the mighty Bhil kingdom that potentially spanned across central India in the distant past. Shiv Kumar Tiwari, in his book "Tribal Roots of Hinduism," suggests the Bhil history can be traced back to the epics of Mahabharat and Ramayan. Tiwari goes on to discuss the complex history shared by Bhils and Rajputs in the subsequent period. However, much of this knowledge is hard to verify and is primarily based on legend (see Pages 268 to 272).

The "Imperial Gazetteer of India, v. 8, p. 145." notes that the Bhopawar Agency (a sub-agency of Central India Agency) either included or was located north of the "mountainous forest-clad region, in which the Ali-Rajpur, Barwani, and Jobat States lie, known as Bhilwara or the 'Bhil country,' a wild and sparsely inhabited tract.". The Bhil are mentioned in British times for their rebellions. In his book "Law Enforcement in Tribal Areas," Srikanta Gosh mentions important Bhil rebellions in 1846, 1857–58, and 1868. Our story is focused on Kadaknath, an extremely unique and fascinating breed of chicken, primarily cultivated by the Bhil. Kadaknath is popular for its "grey-black" meat which has a distinctive texture and taste. The past few years (2019-2023) have seen a revival of interest in this breed of chicken. However, historical records of this breed are hard to find. Given that the history of the Bhil before the arrival of the British in India is patchy, it's not surprising that the earliest historical records of Kadaknath that we can find date to the British era.

A. E. SLATER of the Mission Poultry Farm, Etah, United Provinces, India, wrote a journal article about "THE POULTRY INDUSTRY IN INDIA" in 1945 (World's Poultry Science Journal (Volume 1, 1945 - Issue 2)). This article is the oldest written mention of Kadaknath that we could find after searching the internet repositories. Talking about various "Indigenous Indian Breeds", Kadaknath finds mention in the fourth place. However, Kadaknath is spelt as Karaknath or even Karnatak by Slater. We can be certain he is talking about Kadaknath as he clearly says, "The Karnatak, also called the Karaknath, a breed of fowls noted for its black skin.". Despite calling it an Indigenous Indian breed, Slater does not mention anything about the native range of this breed in India. It is possible that Slater was listing out Kadaknath after having come across this in earlier literature. For instance, the book Cock fighting all over the world. by Finsterbusch, C. A (published in 1929) also finds mention of “Karnatak” or “ Karaknath. A copy of the book is available online from Duke University libraries. Interestingly, Finsterbusch quotes an older book the “Murgh Nama,” from the “Sayd-gah-i-Shawkati,” written by the Nawab (Nabob) Yar Muhammad Khan of the State of Rabpur (potentially Rampur) and written in the year 1883. The text referring to Kadaknath is as follows:

Third, the “Karnatak” or “ Karaknath a breed in which the skin, bones, tongue, eyes and blood are all black ; this breed is useless for fighting. These fowls are probably from the Karnatak, Deccan, just as “sabzwar” is the name of a breed of fowls from Sabzwar in Persia. The test of this breed is the colour of the tongue, which should be black.

Apart from this mention of Kadaknath on page 420, an earlier mention is made while talking about the Silkie chicken. The paragraph mentions the introduction of Sumatra and the Black Javanese game into India by the "Mohammedans". The actual text is as follows:

The Black game fowl of Java, may be related to the Black Sumatra, though not identical. We shall learn further on, how, both, Sumatra and Black Javanese game came into India introduced by the Mohammedans, scattered there and eventually lost, but how part of this blood came to give their share towards producing the world’s most astounding and perfect game fowl, the Rajah Murghi or Asil of Lucknow. That a black fowl existed, there is not the slightest doubt. The Persian knew it as well as the Hindu of the Deccan. It has been described in 1882 by the Nawab Yar Muhammad Khan in his Urdu-book “Sayd-gah-i Shawkati” as a bird in which the skin, bones, tongue, eyes and blood are all black. The Hindustani name for the breed is “Karnatac.” In Persia a similar breed is known as “Sabzwar,” probably the name having been derived from a place of the same name in Persia ; the test of this breed is the colour of the tongue, which must be completely black. 

Subsequent to the pre-Independence article by Slater, the next mentions of Kadaknath we can trace in the literature date to the 1980s. The following two articles from the 1980s probably coincide with the establishment of a government poultry farm in Jhabua and denote a period of renewed interest.

• RAO, G.V. (1980) Sexual dichromatism with respect to shank colour in Karakanath New Hampshire and White-Leghorn cross-breeds. Indian Poultry Gazette, 64: 45–47.
• RAO, G.V. & THOMAS, P.C. (1984) The breed characteristics of Kadaknath breed of indigenous (Desi) chicken. Avian Research, 68: 55–57.

Unfortunately, we could not locate the full text or abstract of these two articles. Several articles related to Kadknath appear in the literature after these two articles. The link between Kadaknath and Jhabua first appears in the following article: Parmar, S. N. S. 2003. “Characterization of Kadaknath Breed of Poultry (Famous Black Bird of Jhabua).” Jawaharlal Nehru Krishi Vidyalaya, Jabalpur (M. P.) Technical Bulletin DRS/2003/01, 1–21. Once again, this article could not be found online. It is possible these initial articles contain some information about how Kadakanth, a black-bone chicken, ended up in Jhabua, Madhya Pradesh. Discussions with people knowledgeable about Kadaknath did not turn up any clear and verifiable claims. It is generally assumed that Kadaknath "originated from the Kathiwar Alirajapur jungles" and Kadaknath "has been raised for centuries by the Bhil and Bhilala tribes". A search of libraries and other resource persons may shed some light on this matter.

The gap in literature from 1945 to 1980 might be due to the literature from this period being largely offline. The exact reason for the increased interest in Kadaknath in the 80's is hard to understand. Nonetheless, in the "Proof of Origin (Historical records)" listed when the GI Tag was issued for Kadaknath, the oldest record cited is a document titled "Reviving the Indigenous Poultry Breed-Kadaknath (Good Practice Code: INGP04)". In this document, it is mentioned that a breeding farm was established in 1982:

In 1982, the Animal Husbandry Department of Madhya Pradesh established a breeding farm and hatchery in Jhabua district, with the objective of conserving and propagating Kadaknath in and around the district.

If not for the article by Slater and the book by Finsterbusch, it would have been hard to fathom the "true history" of Kadaknath. Unless we can find older literary or ancient DNA evidence for the existence of Kadaknath or black-bone chicken, the earliest date we can be certain of is in the 1900's. By this time in history, the silkie breed was known well enough for Bateson and Punnet to publish the findings of their six-year-long project ending in 1911. They also say that silky fowl is well defined in earlier text.

As a description of the Silky Fowl may be found in any of the standard works on poultry it is unnecessary for us to dwell upon the characters of the breed except in so far as they enter into this particular series of experiments.

Another article on the silkie fowl from 1927 is authored by Dunn and Jull of U.S. Department of Agriculture. These articles strongly suggest the spread of silkie fowl in the 1800’s. The silkie chicken breed itself was probably the result of early chicken breeders combining exotic traits found in various breeds together. Hence, it is conceivable that the black-bone phenotype pre-dates the Silkie breed.

The "Tamil Bell" effect

The Tamil Bell refers to a broken bronze bell discovered in ~1836 by a Cornish Christian missionary, William Colenso, near Whangarei in the Northland Region of New Zealand. Colenso, a fellow of the Royal Society, found the bell being used to boil potatoes by Māori women. Interestingly, the rim of the bell has an inscription in the Tamil language that can be roughly translated as "Mohoyiden Buks ship’s bell". How exactly this bell ended up with the Māori has remained an enduring mystery. The "Tamil Bell" effect refers to this paradox of finding an artefact out of its place in space and time. A more common name for such artefacts is OOPArt or out-of-place artefact. 

Wikipedia's definition for an artefact is "a general term for an item made or given shape by humans, such as a tool or a work of art, especially an object of archaeological interest". While Kadaknath is not really a tool or a work of art per se, it has been given shape by humans making it a popular breed of domesticated chicken. So it could be considered an OOPArt. It would be out of place in Jhabua as chicken domestication initially happened in Southeast Asia and then spread across the world. If we accept that Kadaknath is OOPArt, the question then becomes one of interpretation.

OOPArt has generally been found to fall under one of the following sub-headings.

1. Questionable interpretations: Kadaknath has been studied by various research groups in India to examine the black meat phenotype using different approaches. Physical descriptions of the meat, crossing experiments, as well as characterisation of the contents using high-throughput approaches, have consistently found support for Fibromelanosis. Hence, it does not appear that Kadaknath or its black-bone phenotype is being interpreted incorrectly.
2. Alternative interpretations: A simple alternative explanation for Kadaknath ending up in Jhabua is that it travelled from a different location (potentially China) potentially through a marine route.
3. Natural objects mistaken for artefacts: Kadaknath is definitely derived from a natural object. However, the changes that made it into the breed we see today are what make it Kadaknath and not just any other chicken. As long as the distinction between Kadaknath and natural chicken is clear, we can rule out this sub-heading of mistaken identity.
4. Erroneously dated objects: Based on the writing of Slater, we can date the Kadaknath prior to Indian Independence. However, the claims of this breed being raised by the Bhils for centuries is hard to verify. If the Kadaknath breed reached Jhabua during the British period, the provenance would probably have been known to Slater. However, record-keeping and communication between distant places were not as easy as it is today. So it is easily possible that Kadaknath reached Jhabua during the British occupation of India.
5. Modern-day creations, forgeries and hoaxes: The good thing about Slater mentioning Kadaknath is that we can be certain that this breed is not a modern-day creation or forgery perpetrated post-independence. However, we cannot rule out the possibility of such a hoax being conceived during the British period. Even if it were a hoax, why Kadaknath would be associated with the Bhils, whom the British had classified as "criminals", is hard to explain.

If Kadaknath travelled to Jhabua from some other location through a ship, an important question to consider is whether it was possible to transport live animals across long distances in the past. One well-known example of long-distance transport of an animal from India to Lisbon is that of a rhino. The story is that Afonso de Albuquerque (Governor of Portuguese India) wanted to build a fort in Diu (a city in the kingdom of Cambay). However, at the time (in 1514), Cambay was governed by Sultan Muzafar. With the authorisation of King D. Manuel I, an envoy was sent to the Sultan to request his permission to build the fort. While Muzafar did not agree to this request, he was grateful for the gifts and gave Albuquerque a rhinoceros. The description of the journey undertaken by this rhino is reproduced below:

Chained fast on board and living only on dried straw, hay and cooked rice for the duration of the 4 month journey, the rhino and his Indian handler, finally disembarked where Torre de Belem was being built in May 1515.

The animal's arrival in Lisbon caused great commotion and curiosity, not only in Portugal but in the whole of Europe. Its physical form, weighing more than two metric tonnes, and thick, wrinkled skin that formed three large folds giving the strange appearance of armor.

Based on written descriptions sent back to Nuremberg and other parts of Europe by merchants in Lisbon, Albrecht Dürer created his own depiction of the rhino. Although inaccurate, Dürer’s striking depiction piece of art and became the standard throughout Europe of what rhinos looked like, inspiring dozens of other paintings and artists.

Remembering Ancient Roman stories about the deadly rivalry between elephants and rhinoceroses, King D. Manuel I decided to see if this was true.

He organised a bout between the two animals to which he also invited the Queen and her ladies-in-waiting, as well as other important guests. When the two beasts were placed opposite each other the elephant panicked and ran away the moment the rhinoceros began to approach it.

The rhinoceros, sporting a green velvet collar decorated with golden roses and carnations, was one of the gifts. The ship left Lisbon in December 1515 but sailed into a violent storm off the coast of Genoa and sunk, killing the whole crew. Although rhinos can swim, because it was tied up the animal also died.

In Portugal the rhinoceros was immortalised and a representation of it decorates one of the bartizans in the Tower of Belém.

It can also be can be found in Alcobaça Monastery, where there is a naturalistic full-body representation of the animal in the form of a gargoyle in the Cloister of Silence.

The example story of the rhino provides many interesting hints about how exotic animals were prized possessions and served as artefacts exchanged among royalty. Therefore, it is conceivable that black-bone chicken dispersed across Asia due to its exotic meat colour. Sea trade and movement of animals and exotica in prehistoric times may be difficult to imagine, let alone be reconstructed using scientific tools. The article "Across the Indian Ocean: the prehistoric movement of plants and animals" by Fuller. et al., 2010 does a good job of delving into this challenging topic. Written in 2010, the article goes on to say 

Like bananas, chickens are a staple food source of traditional African villages, but nevertheless, have their origins in the red junglefowl (Gallus gallus), which is native from sub-Himalayan northern India through southern China and Southeast Asia. Across this area, chickens were probably brought into domestication more than once, as suggested by genetic data, although good zooarchaeological data remains scarce (see Fuller 2007: 400–401; Kanginakudru et al. 2008; Berthouly-Salazar et al. 2010).

Recent publications based on nuclear genomic data contradict these early mitochondrial marker-based studies in claiming a single domestication event for all domestic chickens.

Going glocal

The word glocal means "reflecting or characterized by both local and global considerations". The Kadaknath story is the epitome of glocality in being very popular in Madhya Pradesh and having a global connection with other black-bone chicken breeds. Comparing the Indian black-bone chicken breed to global breeds may have been inconceivable a few years earlier due to data scarcity. However, the last 3 years have seen a deluge of studies on black-bone chicken from China and Korea. 

1. Comparative genomics and selection analysis of Yeonsan Ogye black chicken with whole-genome sequencing: 120 newly sequenced and shared by the Animal Genetic Resources Station, National Institute of Animal Science, Rural Development Administration (South Korea) and the remaining 68 public whole-genome chicken samples were collected from Sequence Read Archive (120+68=188).
2. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye: Illumina (several insert sizes) + PacBio total: 482.8 Gbp.

Even before genetic studies, the causative changes for the fibromelanosis seen in Kadaknath was attributed to the Fm locus described in Silkie chicken based on crossing experiments by Arora et al., 2011. The 2011 study (Received 26 Aug 2010) follows in the footsteps of papers on black-bone chicken from Sweden (Dorshorst Received August 26, 2009, and July 5, 2011) and Japan (August 25, 2011). The junctions of the Fm locus are reported in these early papers. Hence, a PCR-based assay can easily verify the junctions at the Fm locus in Kadakanth. 

The local importance of Kadaknath in India and, more importantly, in Madhya Pradesh can be attributed to the various medicinal properties attributed to the meat and eggs of this chicken breed. Testimonials suggest people have definitely been eating Kadaknath post-Independence. The recent popularity of Kadaknath can be attributed to/evidenced by some of the following events:

1. The popular cricket captain M S Dhoni ordered 2000 Kadaknath chickens for breeding at his farm in Ranchi
2. The movie Kadakanth written and directed by V S Shivan released in April 2022

The out-of-China hypothesis

The most popular idea in currently available literature is that Black-bone chicken has an origin in Southern China. China's own record of animal genetic resources lists 20 black-bone chicken breeds compared to just one black-bone breed in India. The black-bone chicken breed found in China seems to have its origin in Chinese BBC. Hence, the out-of-china hypothesis could explain the spread of not only the black-bone chicken breeds but all domesticated chickens. Other out-of-China events are documented for other species and verified using exceeding-large genomic datasets.

GI Tag and Indigenousness of the Kadaknath Chicken Breed

The geographical indications tag was issued for "Jhabua Kadaknath Black Chicken Meat" for - GI Application No. 378 and is recorded in the GEOGRAPHICAL INDICATIONS JOURNAL NO. 104 (MARCH 28, 2018). The evidence for the native origin of Kadaknath in Jhabua starts from the 1980s in these records. Indigenous origin is an emotive topic in every corner of the world. The lack of records prior to the 1980s will hopefully be resolved with more concerted efforts on this front.

Shinde et al., 2023 investigate several questions related to Kadaknath and other BBC using whole-genome sequencing data from several chicken breeds. The article is published in Frontiers in Genetics, an open-access publisher. Despite all the concerns and challenges associated with OA publishers, Frontiers has one feature that is interesting and unique. The names of the reviewers who reviewed the article and "endorsed" the manuscript are listed along with the handling editor. Matching the multi-country dataset analysed, the reviewers are from China, Korea and USA (India). The reviewer comments and responses are unfortunately not made public upon acceptance. The data generated as part of this study is the first whole-genomic dataset of Kadaknath chicken from India. Hopefully, more  Kadaknath data will get generated in the following years to understand how prevalent the signatures of selection are across the country.

Some of the main results from this paper are as follows:

1. Kadaknath is a distinct breed of black-bone fowl
2. *Fm_2 is the correct arrangement of duplicated regions at the Fm locus
3. All black-bone chicken breeds share the same rearrangement junctions at the Fm locus
4. Isolation by distance pattern suggests dispersal between India and China
5. Genome-wide signatures of selection in Kadaknath chicken

Based on these results, we can argue that the GI Tag is clearly justified. Even though Shinde et al., show a common origin for all BBC, it is yet to be established whether BBC originated in China or at some other location. If the currently popular out-of-China hypothesis were to be supported by future studies, the selection signatures seen in Kadaknath are still unique to this breed.  All life has a common origin. Yet we define species derived from this common origin as Endemic to a certain region. Similarly, the nativeness or indigenousness of a breed can be defined following changes that occurred at a certain point in time. Hence, the study by Shinde et al. improves our understanding of the history of this breed and also provides molecular markers that establish its unique identity.

One important finding from the Shinde et al., study is the identification of amino-acid-altering changes unique to Kadaknath that are found in a region with clear selective sweep signatures. Future efforts to understand the functional consequences would be essential to know what these changes mean and how they affect the fitness of Kadaknath compared to other breeds.

Rāja Vidyā Yog: Yog through the King of Sciences

Chapter 9: With 34 verses or shlokas, the ninth chapter is of intermediate length and is completely a monologue by Lord Bhagavan Sri Krishna.

Krishna, the Supreme Personality of Godhead (Shloka 1-34): 34 Shlokas

Brief Summary: In this chapter, the lord imparts the most confidential wisdom to relieve one of the miseries of material existence. The knowledge and corresponding methods provided by the lord shall help in liberating from inauspiciousness. 

• Bound by the cycle of birth and death until god realization.
• All of creation and its creatures are within Krishna, but he is beyond all of them.
• Just as the wind rests in the sky, all human beings rest in Krishna.
• All things are manifested from Krishna at the time of creation but go back to him during annihilation. This process of creation and annihilation is cyclic at the will of the lord.
• Lord Krishna is unbiased/neutral, transcendental, and unaffected by his actions.
• Demonic=atheistic=never attains Krishna.
• Evolved sense of self (i.e., found in great devotees who always chant my glory, worship me with devotion, and bow down before me)--> under the protection of divine nature.
• Knowledge will also lead to unity with the lord.
• Krishna= ritual=scarifice=offering to ancestors=healing herb=transcendental chant=fuel of the offering (butter and fire).
• Krishna=syllabal Om= three Vedas= father=mother=sustainer=proteector of the universe.
• Krishna=master=sustainer=witness=abode=friend=eternal seed
• Krishna=Heat & Rain=spirit matter.
• Birth in higher celestial planets for those with knowledge of the three Vedas. However, when the results of their pious activities are exhausted, they fall back into the realm of mortals. 
• Those devotees attain liberation who worship with exclusive devotion and meditate on the transcendental form of Krishna.
• Those who worship demigods are also trying to attain me but are using the wrong approach.
• Worship of demigods--> attain demigods
• Worship of ancestors--> attain ancestors
• Worship of ghost & spirit --> Will take birth among such beings
• Worship the Lord --> Live with the Lord
• Krishna will accept it if one offers a leaf, flower, fruit, or water with love and devotion.
• Offer everything that you do, eat, and perform to Krishna. This will free you from bondage from the results of the action.
• I envy nobody; I am impartial and equal to all.
• Even if somebody has bad tendencies but is a devoted Krishna follower, that person is on the correct path and considered virtuous. Such a person will quickly return to the path of dharma and long-lasting peace.
• Everyone can attain Krishna irrespective of their birth, birth caste, gender, and tendencies when they take refuge in Krishna.

Anityam asukam lokam (i.e., the world is temporary and full of misery) for all. Therefore strive to attain Lord Krishna.

Favorite Shlokas:

Shloka 6:

yathākāśha-sthito nityaṁ vāyuḥ sarvatra-go mahān

tathā sarvāṇi bhūtāni mat-sthānītyupadhāraya

Shloka 17:

ahaṁ kratur ahaṁ yajñaḥ svadhāham aham auṣhadham

mantro ’ham aham evājyam aham agnir ahaṁ hutam

pitāham asya jagato mātā dhātā pitāmahaḥ

vedyaṁ pavitram oṁkāra ṛik sāma yajur eva cha

Why do we need to find and quantify distinctive features of a lineage?

Lineage-specific genes, or LSG's have received a great deal of attention in genomic studies of evolution. However, the challenge involved in assembling and annotating genomes has meant that getting accurate numbers and definitive lists has proved difficult. Nonetheless, it has been shown that "Many, but not all, lineage-specific genes can be explained by homology detection failure." Several well-known examples of lineage-specific genes have been the focus of detailed study. For instance, the loss of several functionally related genes in the yeast baker's yeast Saccharomyces cerevisiae has been linked to the loss of corresponding phenotypes. Conclusively establishing the reasons for lineage-specific genes is also troublesome. LSG's can be inferred due to loss, rapid sequence divergence, duplication of genes, or other evolutionary events. Ruling out various possibilities and disentangling the cause and effect is not always possible.

Apart from LSG's, other lineage-specific changes have been noted in cis-regulatory elements, changes in interaction partners, etc. What is the contribution of these different lineage-specific changes? Which changes have had a large role in phenotypic evolution? Are these changes correlated, and if so, in what ways? These kinds of questions regarding the relevance and implications of lineage-specific changes (LSCs) can be answered when the changes can be quantified with confidence by ruling out various bioinformatics artifacts. Once we have answers to these questions, we may begin to understand the evolution of genetic changes from a different perspective. 

Lineage-specific accumulation of repeats in genomes has also been studied, although mostly in non-genic regions. For instance, in a comparison of plant genomes, Patil et al. identified large differences in the repeat content of closely related species. Do similar changes occur in protein repeats? How rampant are such changes genome-wide? These are intriguing questions, especially when it is known that some genes have rapid changes in protein repeat content. Among the various genes that are worthy of study (GWoS), immune genes occupy the prime place. Hence, it is no wonder that Teekas et al. do a comprehensive study of protein repeat evolution in immune genes. In their article titled "Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes," they screen the annotated genomes of vertebrates for orthologs that contain protein repeats. Having identified orthologous repeats in orthologous genes, they quantify the expansion or contraction of repeats. Since these sorts of changes in repeat length seem to have a phylogenetic signal, they use PIC (Phylogenetically Independent Contrasts) to identify changes that are most distinctive in specific lineages. What if any of these changes have functional consequences will have to be seen. This approach developed by Teekas et al. opens the door for large scales identification of candidate proteins that may have "tuning knobs" of evolution. On the other hand, if these changes in repeat length have no consequence whatsoever, they reveal the regions of immune genes that are plastic to such changes.

Kantara, Dhanta Kathe: the legend of the forest

It is very rare that a Kannada movie that does not fit into a traditional genre becomes a huge hit, not just in Karnataka but across India. This is even more remarkable when the movie is not a high-budget star-studded enterprise. A folk story about the legend of the enchanted forest does have great appeal when combined with great visuals of the forest and the traditional "Bhoota Kola" dance. Although never actually stated, the movie is about the Western Ghats of India. If any forest in the world is enchanted, the Western Ghats would be the first place one would think of. As a biodiversity hotspot, the forests of the Western Ghats hold many marvelous treasures that remain hidden from humankind. 

We sequenced the genome of the Mesua Ferrea tree last year to investigate the demographic history of several forest trees. This year, we follow that up with the genome of the Wild Jack (Ayani) or Artocarpus hirsutus. Generating the genomes of forest plants by itself will not bring out the magic and lore hidden in their base pairs. Rather, interesting insights that could help us understand the adaptation of these trees to their unique habitat and how this has been achieved through changes in the genome would be of great value not only for commercial exploitation but also to sustain the forests and their diversity. In the pre-print, Patil et al. present the newly generated genome of the Wild Jack and compare its genome with that of two other species of the genus Artocarpus. By doing such comparative genomic analysis, various changes to gene sequences, as well as the complement of genes, are identified. Interestingly, it is found that the repeat content has changed drastically in the closely related commonly cultivated species Artocarpus heterophyllus (Jackfruit). Subsequently, the effect of these repeats on demographic inference is also investigated and builds upon previous work on Populus and human genomes. Nonetheless, the role of habitat is found to be more pronounced than that of repeats or the region of the genome used for the analysis. What other secrets does the enchanted forest hold? Will we ever be able to explore this forest further and what impact this will have on the forest itself are questions for tomorrow.