An example of evolution if progress this week comes from a team of researchers from the universities of Tartu (Estonia), Toulouse (France), and Papua New Guinea. They have carried out an extensive analysis on blood samples from two populations in Papua New-Guinea who have remained isolated for the 50,000 years since Homo sapiens arrived on the Island.
One group occupies the highlands and the other group lives in the lowlands, making this a living laboratory to measure the effects of the different environments on the genomes of the two populations.
Different environments provide different drivers of evolutionary adaptation; for instance, the highlanders have adapted to a low oxygen partial pressure and comparatively few pathogens and an absence of mosquitoes; while the lowlands have both mosquitoes and a higher level of endemic pathogens. How each group has adapted to these different environments provides a text-book example of how the environment drives evolution and how isolation results in divergence.
The team's work is published, open access, in Nature Communications and is explained in a press release from Tartu University, Estonia:
Genetic adaptations have impacted the blood compositions of two populations from Papua New GuineaTechnical details and background to the research are given in the team's open access paper:
Papua New Guinea (PNG) has a wide range of environments, each presenting unique challenges to human survival. Highlanders and lowlanders of PNG are striking examples of populations facing distinct environmental stress. Whereas the highlanders encounter low oxygen availability due to altitude, the lowlanders are exposed to specific pathogens that are absent in the highlands, such as malaria. Despite these strong environmental pressures, the specific adaptations of these populations have remained overlooked. A new study published in Nature Communications on Tuesday, 30 April 2024 sheds light on the genetic adaptations of Papua New Guineans in response to their unique environmental pressures.
The new findings presented rely on new whole-genome sequences from highlanders and lowlanders from Papua New Guinea. The data was collected by the Papuan Past project, which brings together researchers from the universities of Tartu (Estonia), Toulouse (France), and Papua New Guinea.
We explored the signatures of selection in newly sequenced whole genomes of 54 PNG highlanders from Mt Wilhelm (Chimbu Province) and 74 PNG lowlanders from Daru Island (Western Province). We hypothesised that the genomes of both populations have been shaped differently to mitigate the detrimental effects of their respective environments.
Dr François-Xavier Ricaut, co-corresponding author
Centre de Recherche sur la Biodiversité et l’Environnement (CRBE)
Université de Toulouse, Toulouse, France.Boats in Daru Island (left) and view of the highlands of Papua New Guinea (right)François-Xavier Ricaut.One of these genetic variants under selection in Papua New Guinean highlanders might impact the red blood cell count. A higher red blood count helps the highlander adapt to the lower oxygen availability in the highlands. On the contrary, the selected variant in the lowlanders is associated with the percentage of white blood cells.The genetic variants under selection identified in our study show associations with blood-related phenotypes.
Dr Mathilde André, lead author
Centre for Genomics, Evolution & Medicine
Institute of Genomics
University of Tartu, Tartu, Estonia
This supports the idea that hypoxia might have been the main driving force of selection that has acted on Papua New Guinean highlanders. However, specific pathogens might have shaped the genome of lowlanders through selection.
Dr Mathilde André.Interestingly, both the variants also affect the heart rate of individuals with those mutations. This multiplicity highlights the complexity of interpreting the role of genetic mutations. One mutation can affect multiple phenotypes altogether.
Dr Nicolas Brucato, co-author
Centre de Recherche sur la Biodiversité et l’Environnement (CRBE)
Université de Toulouse, Toulouse, France.Denisova is one of the archaic hominin populations living in Asia before modern humans settled in Papua New Guinea around 50 thousand years ago. Although Denisova quickly went extinct around that time, they have interbred with Papua New Guinean ancestors and left their legacy in the genome of modern Papua New Guineans. This study suggests that a genetic mutation in Denisova that impacts a specific protein structure has been directly passed to Papua New Guinean genomes.Interestingly, one of the top candidates for selection in lowlanders has a non-human origin [Denisova]. It looks like the altered protein is beneficial for the lowlanders to survive in their environment. Although we do not know the exact cause of this selection, this mutation might help the lowlanders overcome malaria.
Dr Mayukh Mondal, co-lead author
Centre for Genomics, Evolution & Medicine
Institute of Genomics University of Tartu, Tartu, Estonia.
This new insight into how local adaptation has shaped the genomes and phenotypes of Papua New Guinean highlanders and lowlanders differently points out the necessity of investigating populations with diverse backgrounds to shed light on the key aspects of human biology.
AbstractIn just 50,000 years, these populations have diversified in ways that only make sense as the result of environmental selectors acting over time, and such is one of these environmental selectors, namely the presence of the malaria parasite, that the lowland population, where mosquito vectors are present, appear to have retained a variant that may have helped Denisovan's resist malaria!
Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count – both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.
Introduction
After the first arrival of modern humans in New Guinea around 50 thousand years ago (kya)1, they rapidly spread across the different environmental niches of the island2,3. Since the Holocene (around 11 kya), the population of Papua New Guinea (PNG) has been unevenly distributed, with most of the population living at altitudes between 1600 and 2400 m above sea level (a.s.l.)4,5. This population distribution pattern is remarkable considering the challenges PNG highlanders face at this altitude, like the lower oxygen availability to the body6. Indeed, various detrimental conditions, such as reduced birth weight7 and shorter life span8, have been observed at altitudes as low as 1500 m a.s.l. Studies investigating the hypoxic response of the human body in high-altitude populations (living above 2500 m a.s.l.) revealed that selection acted on genes involved in the Hypoxia-Inducible Factor (HIF) pathway9, which is the principal response mechanism to low oxygen at the cellular level. This pathway regulates angiogenesis, erythropoiesis, and glycolysis10. Some high-altitude populations show a limited increase in haemoglobin concentration11 in response to the lower oxygen levels. Indeed, an increase in haemoglobin concentration – as observed in native lowlanders ascending to altitude – boosts oxygen transport but also results in higher blood viscosity12. In the long term, that process may cause Chronic Mountain Sickness (CMS) and cardiovascular complications12. Interestingly, Tibetan highlanders show selection that is associated with a more restrained increase of haemoglobin concentration at altitude due to increased plasma volume13. This suggests that hypoxia might lead to the selection of a complex haematological response that overcomes the increase in blood viscosity when enhancing oxygen transport. Signatures of selection have also been observed in populations living at intermediate altitudes (above 1500 m a.s.l.)14,15. For example, the Andean Calchaquíes carry genomic signatures of selection for pathways associated with the nitric oxide metabolism and with the neurotransmitter GABA16. In addition, signatures of positive selection to altitude have also been found among Ethiopians currently living at 1800 m a.s.l.15 and in the Caucasus population living at intermediate altitudes of 2000 m a.s.l.14. These studies suggest that the genomic signature of selection can occur even at intermediate altitudes in response to more moderate selection pressure.
However, the role of selection in response to the environmental challenges by altitude on the genomes of PNG highlanders, who inhabited this environment for the last 20,000 years3, remains mostly unknown. PNG highlanders significantly differ from PNG lowlanders in height, chest depth, haemoglobin concentration, and pulmonary capacities17. Similar differences have been observed between Andean, Tibetan and Ethiopian highlanders and their corresponding lowland populations18. However, various factors, like phenotypic plasticity19, diet or physical activities, could explain these phenotype differences. In this paper, we explored whether these phenotypes can also be linked to adaptive processes acting on the genome of the PNG highlanders.
Another strong environmental pressure in PNG is infectious diseases (e.g., malaria, dysentery, pneumonia, tuberculosis, etc) that are the leading cause of death in PNG20. In this pathogenic environment, malaria stands out among others because it might affect highlanders and lowlanders differently. The incidence of malaria varies enormously between the lowlands and the highlands. While PNG accounted for nearly 86% of the malaria cases in the Western Pacific Region in 202021, malaria is practically absent in PNG highlands, possibly because of a limited dispersal of Anopheles, the main vector of malaria, at high altitude4. It has been suggested that malaria might explain the unbalanced population distribution between PNG highlands and lowlands22 and thus induces a selection pressure specific to lowlanders. Nonetheless, the period when this specific pathogenic pressure started to impact Papuans remains unclear22.
Besides facing these environmental pressures, PNG populations also stand out by their high levels of Denisovan introgression23. Denisovan introgressed variant might contribute to Tibetans’ adaptation to altitude15 and affect the immune system of the PNG population24. Moreover, because some archaic variants show signals of selection among the overall Papuan population25,26,27, it is conceivable that archaic introgression has contributed to beneficial alleles in PNG populations. However, to date, it remains elusive to which extent archaic introgression contribution to local adaptation varies between PNG populations.
In this study, we identified the genomic regions that show signatures of selection in 54 newly sequenced PNG highlanders and 74 lowlanders. We then screened for the SNP that most likely drives the selection signal in each genomic region under selection. We also explored phenotype associations with candidate SNPs. Finally, we scanned regions under selection for the presence of introgressed archaic haplotypes and assessed the role of introgressed alleles on adaptive processes. Our research provides new insights into local adaptation in PNG populations and its implications on health.
Fig. 5: Median-joining haplotype networks for the windows 5kbp down- and upstream rs368120563, the candidate SNP for the genomic region chr1:88800562-89326878 under selection in PNG lowlanders.This variant is in high-LD (r² = 0.94) with an introgressed ambiguous haplotype.
Of particular embarrassment for creationists is the fact that most of this period of selection happened 40,000 years before they think the universe existed and has continued unbroken before, during and after when they believe there was a genocidal flood that would have killed all the inhabitants of Papua New Guinea, when any carriers of Denisova DNA would have perished, obliterating any Denisova DNA, and the present diversity would have occurred in the couple of thousand years since the descendants of the small handful of Middle-Eastern survivors got there.
The idea is, of course, too preposterous for words, but not as preposterous as the thought that there are grown adults who believe it.
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New Guinea is fascinating but ultra dangerous. At sea level there's an abundance of malaria, venomous animals and at high altitudes there's less oxygen and the temperature gets colder.
ReplyDeleteIt's well known that Michael Rockefeller disappeared in Papua New Guinea in 1961. It's speculated that he either drowned, was eaten by Sharks or crocodiles, or lost his life in the jungle either by contracting malaria, or being bitten by a venomous snake, or starvation or dehydration, or he was killed by one of the tribes he was studying. Water abounds in rainforests and jungles but all of it is unsafe and unfit for humans to drink. Wild fruits are unevenly distributed in the jungle with some locations having abundant fruit and other places having none. Most fruits are seasonal and there might not be any fruits for many miles. One has to know where to look and one has to be physically able to travel to get from one fruit source to another. It's no Garden of Eden anywhere in the world.
New Guinea is also home to Cryptids or unknown animals. One of them is the Ropen which is similar to a Pterosaur and the Row which is a four legged Reptilian creature which was sighted by author Charles Miller.Volcanoes abound in New Guinea as well making it even more dangerous and more scary. It would be nice to visit but it's way too dangerous. A malevolent being made this dangerous world.