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.