Archaic Admixture

Living people carry Neanderthal DNA in every population studied, and Melanesians carry 4 to 6 percent Denisovan DNA, so the archaic humans had fertile children with modern humans. The archaic ancestry is depleted on the X chromosome and in testis genes, a sign of partial hybrid sterility that no creationist has answered.

By AI (Claude Opus 5.5, thinking level unavailable; split from an earlier draft) Draft:  October 2026

"This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years." — Sriram Sankararaman and colleagues, 20161

Summary

Neanderthals and Denisovans had children with the ancestors of living people, and those children were fertile.  That is the strongest evidence that the archaic populations were human, and the creationist reading gains most here.  The same data carry a pattern that cuts the other way, and no creationist has answered it.

What the genomes show.

  1. They interbred with modern humans, and the children were fertile. Green and colleagues found in 2010 that 1 to 4 percent of the genome of people outside Africa came from Neanderthals.2 Prüfer refined that to 1.8 to 2.6 percent in 2017.3 Reich found 4 to 6 percent Denisovan ancestry in Melanesians.4 Chen found 17 megabases of Neanderthal sequence in the average African, and concluded that Neanderthal DNA survives "in every modern human population studied to date."5 Descendants alive today are the biological test of a fertile cross, and it is passed.
  2. They passed the test a creationist set. Marvin Lubenow, writing about the Tasmanians, called interfertility "the one and only valid test proving that they were fully human—the test of interfertility with other humans."6 Neanderthals and Denisovans pass it.
  3. The fused chromosome 2 is shared. Denisovans carried it, and Meyer's team said a karyotype difference would likely have reduced hybrid fertility.7 Denisovans sets out the reads.
  4. The archaic populations also mixed with each other. Denisova 11 had a Neanderthal mother and a Denisovan father; Denisovans sets out the case.

The signal that cuts the other way.

  1. The mixing left the marks of partial hybrid sterility. Neanderthal ancestry is depleted in genes expressed in the testis and about five-fold on the X chromosome,8 and Denisovan ancestry shows the same pattern.1 No creationist author has supplied a living species that shows the same depletion between two of its populations, which is what an answer needs.

Verdict.  Interbreeding shows the Neanderthals and Denisovans were people, and their descendants are alive in every population studied.  The X-chromosome and testis-gene depletion is the sharpest thing in the mainstream's hand, and it stays unanswered until a comparative case is found.

Part 1: How much Neanderthal DNA living people carry

The 1 to 4 percent, and what it rests on.  Green's 2010 team found that Neanderthals share more derived alleles with Europeans and Asians than with Africans.  Fitting a population model to that excess gave the famous figure:  "between 1 and 4% of the genomes of people in Eurasia are derived from Neandertals."2  The number is a model fit and it assumes the mixing happened 50,000 to 80,000 years ago.  With a second high-coverage genome closer to the population that actually did the mixing, Prüfer raised it:  "non-African populations outside Oceania carry between 1.8-2.6% Neandertal DNA", with East Asians at 2.3 to 2.6 and western Eurasians at 1.8 to 2.4.3  Sankararaman's 2014 map of where in the genome that ancestry sits gave a mean of 1.38 percent in East Asians and 1.15 percent in Europeans, against 0.08 percent in the Luhya of Kenya.8

Africa was not left out.  The early methods found almost no Neanderthal DNA in Africans because they used African genomes as the unmixed reference.  Chen and Akey's 2020 method needs no such reference.  Applied to 2,504 genomes, it found "on average 17 Mb of Neanderthal sequence per individual in the African samples", where earlier work had found under a megabase.5  Their conclusion is the one a creationist article wants and should quote exactly:  "remnants of Neanderthal genomes survive in every modern human population studied to date."5  Two causes are proposed:  migration back into Africa from the ancestors of Europeans, and gene flow from an early modern human group into Neanderthals.  It is also a caution:  a published figure moved by a factor of about twenty when the method changed.

Part 2: Denisovan ancestry

Denisovan ancestry.  Reich's 2010 paper found the Denisovan population "contributed 4–6% of its genetic material to the genomes of present-day Melanesians" and suggested "it may have been widespread in Asia".4  Meyer's 2012 refinement gives 6.0 ± 0.9 percent in Papuans by one method and 3.0 ± 0.8 by a method that also models Neanderthal admixture;  the two are not the same quantity and an article should say which it is using.  Sankararaman's 2016 study separated Neanderthal from Denisovan segments in 257 genomes and found more Denisovan ancestry in South Asia than existing models predicted.1

Adaptive introgression.  Some archaic variants rose in frequency because they helped the people who carried them.  The best-known case, the Denisovan EPAS1 variant carried by Tibetans, has its own article, EPAS1 and the Tibetan Highlands.  Other cases have not been researched for this article yet.

Denisova 11.  The archaic populations also met each other.  Slon's 2018 genome of a girl from Denisova Cave, with a Neanderthal mother and a Denisovan father, is set out in Denisovans.

Part 3: Partial incompatibility

The signal that cuts the other way.  Interbreeding happened, and the pattern it left is not what two fully interchangeable populations would leave.  Sankararaman's 2014 map found Neanderthal ancestry depleted near genes, depleted in genes expressed in the testis, and depleted about five-fold on the X chromosome, "which is known to harbor a disproportionate fraction of male hybrid sterility genes".8  In 2016 the same group found the same X-chromosome and testis-gene depletion for Denisovan ancestry, and wrote:  "This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years."1  Mendez's 2016 Neanderthal Y chromosome adds a mechanism.  It carries missense changes in three genes that produce male-specific H-Y antigens, and "It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups."9  X-linked and testis-gene depletion are the classic markers of hybrid male sterility in mice and fruit flies.

What a creationist can say about that, and what it needs.  Not that the result is wrong.  That the effect is partial:  Neanderthal ancestry on the X is depleted, not absent, and Sankararaman's own phrase is "mixtures of human populations", not mixtures of species.  Partial incompatibility between populations of one species is a matter of degree.  But that answer needs a comparative case, a living species in which two populations show the same X-linked and testis-gene depletion of introgressed ancestry and are still one species by every other test.  No creationist author has supplied one.  Nothing in Lubenow, Cuozzo, Carter, Line or Jordan mentions the X-chromosome result at all.

Objections and responses

"Interbreeding does not make them the same species.  Lions and tigers interbreed."  Ligers are usually sterile in one sex.  Neanderthal and Denisovan ancestry is carried by people alive today, across every population tested,5 which requires fertile hybrids in both sexes over many generations.  Carter's complaint about Reasons to Believe, which accepts the interbreeding and then rejects the biological species concept to keep Neanderthals out, is fair.10  The objection would need to explain the fusion junction reads in Meyer's Denisovan too.

"The X-chromosome depletion shows they were a separate species."  It shows partial incompatibility, which is documented within species and is a matter of degree.  Sankararaman's own phrase is "mixtures of human populations".1  But this objection deserves more than that.  No creationist has produced the comparative case it needs, and until one does, the objection stands as the sharpest thing in the mainstream's hand.

Issues and unanswered questions

  1. A comparative case for partial incompatibility. A living species with X-linked and testis-gene depletion of introgressed ancestry between two of its populations. Without it the creationist answer to Sankararaman is words.
  2. A post-Babel fit to the same data. Green's 1 to 4 percent is a model fit that assumes the mixing happened 50,000 to 80,000 years ago. A young-earth model needs its own fit to the same allele counts, and none has been published.

Where the creationist side is weakest.  On the X chromosome.  No creationist treatment engages it.

Where the mainstream side is weakest.  The admixture percentage in Africans moved by a factor of twenty when the method changed.

Verdict

The archaic populations had fertile children with modern humans, and their DNA is in every living population studied.  That is the evidence that they were people, and it is strong.  The creationist reading of Neanderthals and Denisovans as post-Babel human populations is on its firmest ground here.

The pattern of the mixing has not been answered.  Depletion on the X chromosome and in testis genes is what partial hybrid male sterility leaves behind.  It does not make them separate species, since Sankararaman himself calls them "mixtures of human populations",1 but a creationist answer needs a living comparative case, and none has been offered.

Companion pages

Sources

  1. 1.

    Sankararaman, Sriram et al.  “The combined landscape of Denisovan and Neanderthal ancestry in present-day humans.”  Current Biology 26(9):1241–1247.  May 9, 2016.  A genome study that separated Denisovan DNA from Neanderthal DNA in 257 genomes from 120 populations, 20 of them Oceanian.  It found more Denisovan DNA in South Asia than existing models of history predicted, and it found that Denisovan DNA, like Neanderthal DNA, was depleted near genes.  The article cites it for the South Asian finding and for the claim that reduced male fertility shows in both kinds of archaic DNA.

    1. 1a.

      Section Summary:  “This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.” ↩ ↩ ↩ ↩ ↩

    2. 1b.

      Section Deserts of archaic ancestry:  “Some of the most striking features of the introgression maps are the archaic ancestry deserts: windows longer than 10Mb at which the archaic ancestry proportion is <1/1000 ( Figure 3A ; Supplemental Experimental Procedures, section S5 ).  We identified 18 Neanderthal ancestry deserts”. ↩

  2. 2.

    Green, Richard E. et al.  “A draft sequence of the Neandertal genome.”  Science 328(5979):710–722.  May 7, 2010.  A genome paper that sequenced a draft Neanderthal genome of more than 4 billion nucleotides from three bones from Vindija Cave in Croatia.  Its model fit gave the estimate of 1 to 4 percent Neanderthal DNA in people outside Africa, and it counted 78 changes to protein-coding genes that became fixed in modern humans but not in Neanderthals.  The article cites it for those two findings and for the draft genome itself.

    1. 2a.

      Section Implications for modern human origins:  “The data suggest that between 1 and 4% of the genomes of people in Eurasia are derived from Neandertals.”  The estimate assumes gene flow 50,000 to 80,000 years ago. ↩ ↩

  3. 3.

    Prüfer, Kay et al.  “A high-coverage Neandertal genome from Vindija Cave in Croatia.”  Science 358(6363):655–658.  Nov 3, 2017.  A genome paper that sequenced the genome of a female Neanderthal who lived about 50 thousand years ago at Vindija Cave in Croatia, to about 30-fold coverage.  Her two copies of the genome differed less than those of present-day humans do, which the authors read as a sign that Neanderthal populations were small, and she was more closely related to the Neanderthals who mixed with the ancestors of people outside sub-Saharan Africa than the Siberian Neanderthal was.  The article cites it for her heterozygosity, for the 1.8 to 2.6 percent Neanderthal share in non-Africans and for the absence of long homozygous runs.

    1. 3a.

      “We find that non-African populations outside Oceania carry between 1.8-2.6% Neandertal DNA ( Fig. 4A ), higher than previous estimates of 1.5-2.1% ( 2 ).  As described ( 25 ), East Asians carry somewhat more Neandertal DNA (2.3-2.6%) than people in Western Eurasia (1.8-2.4%).” ↩ ↩

  4. 4.

    Reich, David et al.  “Genetic history of an archaic hominin group from Denisova Cave in Siberia.”  Nature 468(7327):1053–1060.  Dec 23, 2010.  A genome paper that sequenced DNA from a finger bone found in Denisova Cave in Siberia to 1.9-fold coverage, meaning each position in the genome was read about 1.9 times on average.  It named the group Denisovans, found that they were not part of the Neanderthal gene flow into Eurasians, and estimated that they contributed 4 to 6 percent of the genome of present-day Melanesians.  The article cites it for that 4 to 6 percent figure, for the mitochondrial DNA of the Denisovans, and for the nuclear genome placing them as a sister group of Neanderthals.

    1. 4a.

      Section Abstract:  “This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians.  We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch.” ↩ ↩

  5. 5.

    Chen, Lu et al.  “Identifying and interpreting apparent Neanderthal ancestry in African individuals.”  Cell 180(4):677–687.e16.  Feb 20, 2020.  A genome study that introduced IBDmix, a new probabilistic method that finds Neanderthal DNA in living people without using a modern reference population.  The authors applied it to 2,504 individuals from geographically diverse populations and found a stronger Neanderthal signal in Africans than earlier work had seen.  The article uses it for the finding that remnants of Neanderthal genomes survive in every modern human population studied to date.

    1. 5a.

      Section Results:  “Surprisingly, we identified on average 17 Mb of Neanderthal sequence per individual in the African samples analyzed, and this value was similar across the mostly northern African subpopulations represented in the dataset (ranging from 16.4 Mb/individual in ESN to 18.0 Mb/individual in LWK; Figure 2A ; Table S4 ).” ↩

    2. 5b.

      Section Summary:  “Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.” ↩ ↩ ↩

  6. 6.

    Lubenow, Marvin L.  Bones of Contention: A Creationist Assessment of Human Fossils.  Baker Books, Grand Rapids.  Revised edition.  2004.  A creationist book that assesses human fossils.  The article uses it as the standard creationist book on human fossils, and takes its test of interbreeding, which the admixture studies later passed, as the test that matters.

    1. 6a.

      Page 151:  “In spite of one hundred years of being considered 'animals' and 'missing links,' the Tasmanians continually passed the one and only valid test proving that they were fully human—the test of interfertility with other humans.”  The passage is about the Tasmanians.  The article applies the same test to Neanderthals. ↩

  7. 7.

    Meyer, Matthias et al.  “A high-coverage genome sequence from an archaic Denisovan individual.”  Science 338(6104):222–226.  Oct 12, 2012.  A genome paper that sequenced the finger bone of a Denisovan to about 31-fold coverage, using a new way of preparing the DNA that recovered at least 6-fold and 22-fold more DNA molecules than the two earlier preparations from the same bone.  It estimated how much Denisovan DNA is in present-day people and listed the genetic changes that set modern humans apart.  The article cites it for the fused chromosome 2 and for the count of 260 human-specific protein changes.

    1. 7a.

      Page 225, section Denisovan genomic features:  “The great apes have 24 pairs of chromosomes whereas humans have 23.  This difference is caused by a fusion of two acrocentric chromosomes that formed the metacentric human chromosome 2 (25) and resulted in the unique head-to-head joining of the telomeric hexameric repeat GGGGTT.  A difference in karyotype would likely have reduced the fertility of any offspring of Denisovans and modern humans.  We searched all DNA fragments sequenced from the Denisovan individual and identified 12 fragments containing joined repeats.  By contrast, reads from several chimpanzees and bonobos failed to yield any such fragments (8).  We conclude that Denisovans and modern humans (and presumably Neandertals) shared the fused chromosome 2.” ↩

  8. 8.

    Sankararaman, Sriram et al.  “The genomic landscape of Neanderthal ancestry in present-day humans.”  Nature 507(7492):354–357.  Mar 20, 2014.  A genome study that mapped the Neanderthal DNA in 1,004 present-day people by inferring which stretches of their genomes came from Neanderthals.  It found large regions with almost no Neanderthal DNA, and Neanderthal DNA was depleted near genes, in genes active in the testis and on the X chromosome.  The article cites it for the Neanderthal shares of the European and East Asian populations and for the depletion on the X chromosome.

    1. 8a.

      Section Abstract:  “Neandertal ancestry is significantly reduced in genes specifically expressed in testis, and there is an approximately 5-fold reduction of Neandertal ancestry on chromosome X, which is known to harbor a disproportionate fraction of male hybrid sterility genes 20 – 22 .  These results suggest that part of the reduction in Neandertal ancestry near genes is due to Neandertal alleles that reduced fertility in males when moved to a modern human genetic background.” ↩ ↩

    2. 8b.

      Section Results:  “the proportion of confidently inferred Neandertal ancestry has a mean of 1.38% in East Asians and 1.15%”.  The 1.15 percent is for Europeans.  The preceding sentence gives the Luhya figure of 0.08 percent. ↩

  9. 9.

    Mendez, Fernando L. et al.  “The divergence of Neandertal and modern human Y chromosomes.”  American Journal of Human Genetics 98(4):728–734.  Apr 7, 2016.  A genome study that recovered about 120 kilobases of Y-chromosome DNA from one Neanderthal from El Sidrón in Spain and compared it with chimpanzee and modern human sequences.  It put the split between Neanderthal and modern human Y chromosomes at about 588 thousand years, about 2.1 times longer than the common ancestor of A00, the deepest living Y lineage, and the other living lineages, and that date is superseded by Petr and colleagues' 2020 estimate of about 370,000 years.  The article cites it for the 588 thousand year figure that creationist writing still quotes, quotes its wording, and draws on its H-Y antigen changes.

    1. 9a.

      Section Abstract:  “We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y , TMSB4Y , USP9Y, and KDM5D .  Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens.  Antigens derived from KDM5D , for example, are thought to elicit a maternal immune response during gestation.  It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.” ↩

  10. 10.

    Carter, Robert W.  “Neanderthal genome like ours.”  Creation Ministries International.  May 19, 2010.  A 2010 web article by Robert Carter, who writes about genetics for Creation Ministries International, updated 1 June 2010.  It says the draft Neanderthal genome, which covers about 60 percent of the genome, strengthens the creationist case that Neanderthals were fully human, and it offers three possible scenarios for who they were.  The article uses it for those three scenarios and for Carter's admission that realistic modeling has yet to be performed.

    1. 10a.

      On Reasons to Believe, an old-earth organization.  “they conclude that this is clear evidence of interbreeding, but then they reject the biological species concept (one of the fundamental theorems of biology) and claim that evidence of interbreeding does not mean two organisms belong to the same species!” ↩