Geographic distribution of the substitution identified in the SLC30A9 gene in current human populations and possible scenarios of Denisovan introgression. Ancestral SLC30A9 corresponds to the version of the gene prior to interbreeding between Denisovans and sapiens. SLC30A9 variant, refers to the version shared with Denisovans.
Credit: Jorge Garcia and Elena Bosch.
Licensed under Creative Commons 4.0. Created with mapchart
Licensed under Creative Commons 4.0. Created with mapchart
A team of researchers led by the Institute of Evolutionary Biology (IBE), a joint center of the Superior Council of Scientific Research (CSIC) and Pompeu Fabra University (UPF) , and by the Department of Medicine and Life Sciences (MELIS) of the UPF, has identified one of the most widespread traces of the genetic inheritance of the extinct Denisovans in modern humans.
These genes probably played an important role in helping early Homo sapiens adapt quickly to a cold climate, but, because they are involved in the regulation of zinc and play a part in cellular metabolism could also be a contributory factor in predisposition to mental health disorders such as depression and schizophrenia.
It's tempting to assume that they may also have contributed to a growth in religion since many 'prophets' seem to have had schizophrenic disorders in which they heard voices. However, that's not the main worry for creationists in this research. What they need to cope with is the fact that all this happened in that vast expanse of time before 'Creation week' when creationists believe the universe was magicked up from nothing, just 10,000 years ago.
There is also the matter of Homo sapiens not having a single founding couple who were created without ancestors, and don't even come from a single species, but are a hybrid between several related species.
So, just who were these Denisovans?
Tell me about the Denisovans and the genes extra-African humans inherited from them. Denisovans are an extinct hominin group that is known from genetic and archaeological evidence. They are a sister group to the Neanderthals and are thought to have lived in Eurasia during the Pleistocene epoch, roughly from 300,000 to 50,000 years ago. The Denisovan lineage was first identified through the analysis of a finger bone fragment and a tooth found in the Denisova Cave in Siberia, Russia. These remains were dated to be at least 50,000 years old.The team of researchers found that the genetic variant, which is found throughout all non-African populations, but which is rare in African populations, is in a region of our genome that is closely similar to a region of the Denisovan genome but is absent in Neanderthals. The team conclude that it must have been due to an ingression of Denisovan genes as Homo sapiens spread out of Africa into Eurasia and co-existed with Denisovans. Because the variant in the SLC30A9 gene was strongly beneficial in the Eurasian climate, it spread quickly through the non-African population.
One of the most significant discoveries related to Denisovans is their genetic legacy in modern humans. Genetic studies have shown that, to some extent, Denisovans interbred with both Neanderthals and modern humans. As a result, people of non-African descent (i.e., individuals whose ancestors did not originate in Africa) carry a small but significant amount of Denisovan DNA in their genomes.
The extent of Denisovan gene flow into the modern human population varies by region. For instance, Melanesians, indigenous people of Papua New Guinea and nearby islands, have the highest proportion of Denisovan DNA, with around 4-6% of their genetic heritage originating from Denisovans. East Asian and Southeast Asian populations also have some Denisovan genetic contributions, but to a lesser extent, typically around 1-2%.
The interbreeding between Denisovans and early modern humans likely occurred as these groups encountered each other in Asia. The Denisovan DNA that has been passed down to modern humans is thought to have conferred certain advantages, as genes acquired from interbreeding often do. Researchers have identified specific genes associated with immune function, altitude adaptation, and metabolism that appear to have come from Denisovans.
While we have this fascinating genetic evidence of Denisovan interbreeding, the physical appearance and culture of Denisovans are still largely a mystery because we have very few fossils and artifacts from this ancient group. Nonetheless, the discovery of Denisovans has significantly expanded our understanding of human evolution and our complex interactions with other hominin species in the past.
Do Denisovans have a Latin name? If not, why not?
Denisovans do not have a formal Latin or scientific name in the same way that many species do. This is primarily because the designation "Denisovans" is an informal, colloquial term that was coined after the Denisova Cave in Siberia, Russia, where the first evidence of this ancient hominin group was discovered.
Scientific names, or binomial nomenclature, are typically used to classify and name species based on a formal taxonomic system established by the scientific community. These names are usually derived from Latin or Greek and are assigned after careful taxonomic analysis and peer-reviewed research.
In the case of Denisovans, since our knowledge about them is primarily based on genetic evidence and a limited number of ancient DNA fragments, there hasn't been enough information to formally classify them as a separate species or subspecies according to established taxonomic rules. Consequently, researchers have not assigned a formal scientific name to Denisovans. Instead, the term "Denisovans" is used as a convenient way to refer to this hominin group in popular and scientific literature.
As more discoveries are made and more information becomes available, it's possible that in the future, Denisovans may be formally classified and receive a scientific name based on established taxonomic procedures.
The result is a different amino acid in a zinc transporter protein between populations in Asia and Africa today. According to the press release from the Universitat Pompeau Fabra, Barcelona, Catalunya, Spain:
Zinc, an essential trace element for human health, is an important messenger that transfers as much information from the outside into the cells as it does between different cellular compartments. Its lack causes growth, neurological and immune alterations, although "its regulation is still poorly studied due to the lack of molecular tools to follow the flow of zinc".The team's findings are published, open access in PLOS Genetics:
[Rubén] Vicente's laboratory identified that the observed variant causes a new zinc balance within the cell, promoting a change in metabolism. By altering the endoplasmic reticulum and mitochondria of cells, this variation results in a potential metabolic advantage for coping with a hostile climate. "The observed phenotype makes us think of a possible adaptation to the cold," says Vicente .
Denisovan genetic inheritance could affect the mental health of European and Asian populations
Zinc transport is also involved in the excitability of the nervous system, and plays a role in people's balance and mental health.
The team points to the fact that the variant found in this zinc transporter, which is expressed in all tissues of the body, is associated with a greater predisposition to suffer from some psychiatric diseases. These include anorexia nervosa, attention deficit hyperactivity disorder, autism spectrum disorder, bipolar disorder, depression, obsessive compulsive disorder (OCD), and schizophrenia.
[…]
The team points out that this is probably the most geographically widespread Denisovan genetic adaptation discovered so far. "For example, a variant in the EPAS1 gene inherited from Denisovans allows adaptation to life at altitude, but is found only in the Tibetan population. However, in our case the impact extends to all populations outside of Africa", concludes Bosch .
AbstractIn addition to the problem of all this interbreeding with an archaic hominid occurring thousands of years before 'Creation Week' and the evidence that a founder couple magically appearing without ancestors, is just a fairy story invented by primitive people who knew no better, there is an additional problem for intelligent [sic] design proponents in the evidence that a large number of us have a genetic variant that predisposes us to mental health issues in return for being better adapted to a Eurasian climate than our African ancestry had prepared us for.
SLC30A9 encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans. Author summary
Contrasting continental signatures of positive natural selection have been previously found in the human SLC30A9 gene encoding the protein ZnT9, which transports zinc across cell membranes. Here we investigate the genetic variants that have been targeted by natural selection in the surrounding region of this gene and which molecular and whole-body changes may have brought about. We found that two major SLC30A9 variant combinations (haplotypes) that are extremely frequent in Africa and East Asia, respectively, are expressed differentially. These two haplotypes also differ at one site that creates an amino acid difference at ZnT9; the version most often found outside Africa avoiding zinc overload in the endoplasmic reticulum and mitochondria and directly influencing mitochondrial activity. Moreover, we found that this substitution, which is known to be associated with greater susceptibility to several neuropsychiatric disorders, is present in the Denisova and displays accompanying patterns of variation that could be suggestive of adaptive introgression. Since mitochondria play an important role in skeletal muscle energy metabolism, we speculate that adaptation to cold may have driven this selection event outside Africa, while also impacting predisposition to neuropsychiatric disorders in modern humans.
Roca-Umbert A, Garcia-Calleja J, Vogel-González M, Fierro-Villegas A, Ill-Raga G, Herrera-Fernández V, et al. (2023)
Human genetic adaptation related to cellular zinc homeostasis. PLoS Genet 19(9): e1010950. https://doi.org/10.1371/journal.pgen.1010950
Copyright: © 2023 The authors.
Published by PLOS. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Surely, an intelligent, omnipotent designer could have given us this adaptation without the mental health problems.
But then evolution by natural selection gives us a perfectly rational explanation for these sorts of evolutionary compromises between a strongly beneficial trait and a weakly deleterious trait associated with it, without the need to invoke a supernatural magician and make excuses for its evident incompetence.
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