Creationism in Crisis - How Modern Papuans' Immune System Was Shaped By Denisovans.

A paper published in PLOS Genetics will make grim reading for Creationists. It reports that a population of humans has an immune system at least partly inherited from an archaic species of Hominin - the Denisovans.

Papuan children. Denisovan immune system?

The problem with a superstition that says all humans are descended from a single couple who were magicked into existence just a few thousand years ago, is that this would mean every human alive should have pretty much identical physiology, even allowing for the warp-speed evolution in the few thousand years since a supposed flood exterminated everyone save eight related individuals who survive on a wooden boat for about a year.

Some credulous Creationists have been fooled into believing that, to account for all the extant species and so little room on the wooden boat.

Seriously! I'm not making this up! There really are grown adults who believe that really happened, and that the Bronze Age myth that tells the tale is real history, even though it entails believing in a rate of evolution far in excess of anything proposed by science, or even considered feasible, with multiple new species evolving sometimes in a single generation.

Sadly for these deluded individuals, real-world facts keep on refuting their superstition, needing greater and greater mental gymnastics to cope with the cognitive dissonance stemming from reality and their preferred view of reality being so divergent.

One of those pieces of evidence is that that the people of Papua New-Guinea have remnants of the DNA of archaic humans who lived several hundred thousand years before Creationists believe humans were created, and who were extinct by the time this creation supposedly happened, so there is no way they could have interbred with Denisovans, if the Creationist origin myth had even a modicum of truth about it, and yet the evidence is that they did.

Real world evidence shows us that when modern Homo sapiens expanded their range out of Africa, they met up with and interbred with the descendants of an earlier migration out of Africa, probably by H. erectus or one of its descendants such as H. heidelbergensis. Two of these descendant species were the Neanderthals of Western Eurasia and their sister species, the Denisovans of Eastern and South-eastern Eurasia. So, all modern non-African humans have some Neanderthal and/or some Denisovan DNA. In other words, modern non-African humans not only don't have a founding couple, as per Creationist mythology; they don't even have a founding species, being hybrids of at least three different Homo species
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According to information provided by PLoS:

Sequences of Denisovan DNA are located near immune-related genes and regulate their activity
Modern Papuans’ immune system likely evolved with a little help from the Denisovans, a mysterious human ancestor who interbred with ancient humans, according to a new study led by Irene Gallego Romero of the University of Melbourne, Australia, published on December 8, 2022 in the open access journal PLOS Genetics.

Papuans, the indigenous peoples of New Guinea Island, owe up to 5% of their genome to Denisovans, an extinct group closely related to Neanderthals who are known only by their DNA and sparse remains in Siberia and Tibet. To better understand the significance of this genetic contribution, researchers searched the genomes of 56 Papuan individuals to see if they carried Denisovan or Neanderthal DNA sequences, and then predicted how those sequences might affect the functioning of different types of cells.

We show that not only Neanderthal, but also Denisovan DNA is very likely to contribute to gene expression in human populations. Further validations will reveal whether these effects are mostly cell type specific or consistent across cells.

Dr. Davide Vespasiani, first author
Melbourne Integrative Genomics
School of Biosciences
University of Melbourne, Parkville, Australia

Based on the location of the non-human sequences, the team found that in Papuans, Denisovan DNA – but not Neanderthal DNA – appears to strongly and consistently affect immune cells and functions. Further testing in cell cultures confirmed that Denisovan DNA sequences successfully regulated nearby genes, turning their expression up or down in ways that could affect how people respond to infections.

Some of the Denisovan DNA that has persisted in Papuan individuals until today plays a role in regulating genes involved in the immune system. Our study is the first to comprehensively shed light on the functional legacy of Denisovan DNA in the genomes of present-day humans.

Dr. Irene Gallego Romero, senior author
Melbourne Integrative Genomics
School of Biosciences
University of Melbourne, Parkville, Australia
And Center for Genomics, Evolution and Medicine
University of Tartu, Tartu, Estonia

The new study suggests that Denisovan DNA sequences altered the immune response in early modern humans living in New Guinea and nearby islands, potentially helping them adapt to their local environment. The researchers conclude that further exploring how DNA from extinct human ancestors affects gene expression may be the key to understanding the consequences of interbreeding between ancient humans and other groups. The results also support the idea that archaic DNA has had a broad impact in shaping the genetic diversity and evolution of modern humans, and has likely affected multiple characteristics in people who inherited Denisovan and Neanderthal DNA.

It is not hard to understand that inheriting an immune system that had been evolving for hundreds of millions of years in the local environment, with its complement of pathogens, gave the newly-arrived H. sapiens a considerable advantage over those with no such inheritance, so these new genes would have spread quickly through the population.

In the abstract and authors' summary to their open access paper in PLOS Genetics the authors say:

Abstract

Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.

Author summary

Humans of Papuan ancestry owe roughly 5% of their genome to Denisovans, a poorly characterised archaic hominin. While introgressed DNA segments can be readily identified, understanding their biological consequences remains challenging. By examining the distribution of introgressed DNA against existing functional genomics datasets, it is possible to predict the phenotypes they impact. In Papuans, Denisovan DNA, but not Neanderthal, strongly and consistently affects immune cells and immune-related processes of potential evolutionary relevance. In vitro testing of introgressed variants confirms these predictions, suggesting Denisovan variants can impact gene regulation in vivo. Variation in gene expression might be key to understanding the consequences of admixture between modern humans and archaic hominins, as has been observed with Neanderthal DNA in other human populations.

Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, Kinipi C, et al. (2022)
Denisovan introgression has shaped the immune system of present-day Papuans.
PLoS Genet 18(12): e1010470. https://doi.org/10.1371/journal.pgen.1010470

Copyright: © 2022 The authors.
Published by PLoS. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Yet another casual and unintentional refutation of Creationism and especially the ludicrous Creationist claim that the TOE is about to be replaced by their childish Bronze Age mythology, complete with magic and an imaginary supernatural creator.

Weirdly, Creationists purport to find it hard to believe that modern human genes are the remnants of the evolved genes of archaic hominins yet have no problem believing the remnants of the evolved cultures and origin myths of archaic H. sapiens.

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