Rosa Rubicondior: Refuting Creationism - Confirmnation of A Denisovan Skull

Figure 1 The geographic locations and proteomic profiles for the Pleistocene hominin individuals with palaeoproteomic data.

The Middle Pleistocene cranium recovered in Harbin, Heilongjiang Province, northeastern China.

Key Evidence Links Harbin Individual's Nearly Complete Skull to a Denisovan--Institute of Vertebrate Paleontology and Paleoanthropology.

One of the enduring problems with the Denisovans has been the lack of substantial physical evidence. Although their existence was first confirmed through DNA analysis of a finger bone discovered in the Denisova Cave in Siberia, and genetic traces of interbreeding with Homo sapiens are widespread throughout Southeast Asia and Melanesia—suggesting a remarkably adaptable and far-ranging hominin—fossil evidence has remained frustratingly scant. Beyond the Siberian finger bone, we have only a few bone fragments from a cave on the Tibetan Plateau and a jawbone dredged up by fishermen off the coast of Taiwan. These scattered remnants were insufficient to assign a clear taxonomic identity, so the group remained simply ‘the Denisovans’.

That gap in the fossil record now appears to have been dramatically narrowed. A near-complete skull, dubbed the 'Harbin skull'—also known as 'Dragon Man' or Homo longi—has now been identified as belonging to a Denisovan. This remarkable specimen, found in northeastern China, may finally give the Denisovans a face and, by the conventions of biological nomenclature, the name Homo longi. Since it is the most complete and morphologically distinct fossil now associated with the group, Homo longi may become the formal species name, superseding the informal label ‘Denisovan’.

Of course, Denisovans pose an even greater challenge to creationist dogma than they ever did to palaeoanthropology. Their existence is fundamentally at odds with the belief that all humans descend from a single ancestral couple who committed the so-called Original Sin, for which redemption is supposedly possible only through accepting the mythologised sacrifice of Jesus. The evidence now shows not only that there was no original couple, but that there wasn’t even a single founding species. Modern non-African humans are the product of complex interbreeding events between at least three archaic human lineages—thousands of years before the Earth was allegedly created, according to young-Earth creationist timelines.

The identification of the Harbin skull as Denisovan has just been published by researchers from the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, China. Their findings appear in papers in Cell and Science, and in a news release from the Chinese Academy of Sciences Institute of Vertebrate Paleontology and Paleoanthropology.

The age and geographical distribution of the main known species within the genus Homo, including Homo longi:

Homo habilis

Age: ~2.4 to 1.5 million years ago (Ma)
Location: Eastern and Southern Africa (e.g., Olduvai Gorge, Tanzania; Koobi Fora, Kenya)
Notes: Often regarded as the earliest member of the genus Homo, with a mix of primitive and derived traits.

Homo rudolfensis (debated species)

Age: ~2.4 to 1.8 Ma
Location: East Africa (notably Kenya)
Notes: Known primarily from a single skull (KNM-ER 1470); sometimes considered a variant of H. habilis.

Homo erectus

Age: ~1.9 Ma to as recently as 100,000 years ago
Location: Africa, Asia (Indonesia, China), Europe (Georgia)
Notes: One of the most successful and widespread early humans; evidence from Java (H. erectus soloensis), China (Zhoukoudian), and Dmanisi in Georgia.

Homo ergaster (sometimes considered African H. erectus)

Age: ~1.9 to 1.4 Ma
Location: Africa
Notes: Considered by many to be the direct ancestor of later Homo species, including H. erectus and H. sapiens.

Homo heidelbergensis

Age: ~700,000 to 200,000 years ago
Location: Europe, Africa, possibly western Asia
Notes: Likely ancestor of both Homo neanderthalensis and Homo sapiens; known from sites in Germany, Spain, and Africa.

Homo neanderthalensis (Neanderthals)

Age: ~400,000 to 40,000 years ago
Location: Europe and western Asia
Notes: Adapted to cold climates; interbred with H. sapiens.

Homo sapiens (Modern humans)

Age: ~300,000 years ago to present
Location: Originated in Africa, now global
Notes: Evolved in Africa, spread worldwide in multiple waves beginning ~60,000 years ago.

Homo floresiensis

Age: ~100,000 to 50,000 years ago
Location: Flores Island, Indonesia
Notes: Small-bodied species, possibly a descendant of an early Homo erectus population; the so-called "Hobbit."

Homo luzonensis

Age: ~67,000 years ago
Location: Luzon Island, Philippines
Notes: Known from teeth and bones; small-bodied like H. floresiensis, but distinct.

Denisovans (now likely Homo longi)

Age: ~300,000 to 50,000 years ago (estimated from DNA and fossil dating)
Location: Siberia (Denisova Cave), Tibet, possibly SE Asia
Notes: Genetic evidence shows interbreeding with H. sapiens. Now associated with the Harbin skull from China (~146,000 years old), recently assigned as Homo longi.

Homo naledi

Age: ~335,000 to 236,000 years ago
Location: South Africa (Rising Star cave system)
Notes: Small brain but complex behaviour; debated position within the Homo genus.

Key Evidence Links Harbin Individual's Nearly Complete Skull to a Denisovan
“What Denisovans looked like, despite their genetic contributions to present-day East Asians and Oceanians? ” This is one of the most important questions that has arisen since the discovery of the Denisovans 15 years ago.
Now, recent research by a team led by FU Qiaomiei from the Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, and JI Qiangof Hebei GEO University has helped answer this question by confirming that a nearly complete hominin skull discovered near Harbin belongs to the Denisovan lineage. It dates back to at least 146,000 years ago.

The team developed a method for automatic identification of human populations based on ancient proteins, revealing the most informative ancient human proteome to date. They also optimized extraction techniques and developed bioinformatic algorithms to trace the evolution of ancient human DNA from Pleistocene dental calculus, successfully retrieving host mitochondrial DNA from the dental calculus of the Harbin cranium.

These evidences suggest that the Harbin cranium is indeed Denisovan and is linked to the early Denisovan lineage from Siberia. These findings were recently published online in the journals Science and Cell, respectively.

The Harbin cranium, dating back at least 146,000 years, provides crucial insights into the wide distribution of Denisovans in Asia. Prior to this discovery, Denisovan fossils were limited and fragmentary, complicating our understanding of their morphology and evolutionary history. The Harbin fossil, identified as a new species, Homo longi, shares significant morphological similarities with Denisovan remains found at other locations.

The research team conducted independent palaeoproteomic analyses and innovative ancient DNA experiments on the Harbin cranium and its dental calculus. For the first time, their findings conclusively linked the nearly complete skull to the Denisovan population, resolving a question that has persisted since Denisovans were first identified through ancient DNA in 2010.

Using a newly established palaeoproteomic system, the team analyzed mass spectrometric data from the Harbin cranium, identifying over 308,000 peptide-spectrum, more than 20,000peptides, and confirming 95 endogenous proteins. This extensive dataset surpasses previous results from contemporaneous fossils.

The team also discovered 122 single amino acid polymorphisms (SAPs) unique to Hominidae species, confirming the Harbin individual’s classification within the Homo genus.

Notably, they identified three positions unique to Denisovans, establishing a phylogenetic link between the Harbin individual and Denisova 3.

Despite the challenges of ancient DNA research, the team successfully retrieved mitochondrial DNA from dental calculus samples with a lot of effort. They optimized extraction methods and constructed multiple libraries, ultimately identifying Denisovan-specific mutations for further analysis.

The results confirmed that the Harbin individual belongs to an early mtDNA lineage of Denisovans, suggesting a wide distribution from Siberia to Northeast China during the late Middle Pleistocene. This study highlights the potential of dental calculus for preserving ancient human DNA, opening a new window into the genetic research of Middle Pleistocene hominins.

The two studies not only resolve the classification controversy surrounding the Harbin cranium and reveal the relatively complete skull morphology of Denisovans, but also provide important references for identifying other ancient human fossils in East Asia that may belong to the Denisovan lineage, such as those from Dali and Jinniushan.

Publications:
Fu, Qiaomei; Bai, Fan; Rao, Huiyun; Chen, Shaokun; Ji, Yannan; Liu, Aoran; Bennett, E. Andrew; Liu, Feng; Ji, Qiang.
The proteome of the late Middle Pleistocene Harbin individual. Science 0, eadu9677; DOI:10.1126/science.adu9677

Fu, Qiaomei; Cao, Peng; Dai, Qingyan; Bennett, E. Andrew; Feng, Xiaotian; Yang, Melinda A.; Ping, Wanjing; Pääbo, Svante; Ji, Qiang
Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium
Cell> (2025); DOI: 10.1016/j.cell.2025.05.040

Abstract
Denisovans are a hominin group primarily known through genomes or proteins, but the precise morphological features of Denisovans remain elusive due to the fragmentary nature of discovered fossils. Here we report ninety-five endogenous proteins retrieved from a nearly complete cranium from Harbin, China, dating to at least 146,000 years ago and previous assigned to a new species, Homo longi. This individual has three Denisovan derived amino acid variants and clusters with Denisova 3, suggesting the Harbin individual belongs to a Denisovan population. This study fills the gap between morphological and molecular evidence, enhancing our understanding of Denisovans’ spatiotemporal dispersal and evolutionary history.

Fu, Qiaomei; Bai, Fan; Rao, Huiyun; Chen, Shaokun; Ji, Yannan; Liu, Aoran; Bennett, E. Andrew; Liu, Feng; Ji, Qiang.
The proteome of the late Middle Pleistocene Harbin individual. Science 0, eadu9677; DOI:10.1126/science.adu9677

© 2025 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Highlights

Host DNA was retrieved from the dental calculus of a Middle Pleistocene hominin
The Harbin mtDNA (>146 ka) is linked to early Denisovan mtDNAs
Denisovan mtDNA is directly connected to a nearly complete hominin cranium

Summary
Denisovans have yet to be directly associated with a hominin cranium, limiting our understanding of their morphology and geographical distribution. We have attempted to retrieve DNA from a nearly complete Middle Pleistocene cranium from Harbin (>146 ka), northeastern China. Although no DNA could be retrieved from a tooth or the petrous bone, mitochondrial DNA (mtDNA) could be isolated from dental calculus. The mtDNA falls within Denisovan mtDNA variation and is related to an mtDNA branch carried by early Denisovan individuals in southern Siberia, previously observed in Denisova Cave. This suggests that Denisovans inhabited a large geographical range in Asia in the Middle Pleistocene. The association of Denisovan mtDNA with the Harbin cranium allows a better understanding of the morphological relationships between Denisovans and other East Asian Middle Pleistocene fossils. Furthermore, the retrieval of host DNA from dental calculus opens new possibilities for genetic research on Middle Pleistocene hominins.
Graphical abstract

Introduction
More than 20 Middle Pleistocene (78–300 thousand years [ka] ago) sites have been identified in China.^1,2,3,4,5,6 With improvements in dating and morphological studies of fossils at these sites, our understanding of ancient populations in East and Southeast Asia during this period is greatly enhanced. Hominin populations from Middle Pleistocene East Asia show a high degree of morphological diversity after 300 ka.⁷ However, in spite of this, no genetic contribution from archaic hominins other than Denisovans or Neanderthals has been identified in Paleolithic or present-day Asian populations. Sampling of ancient DNA from Middle Pleistocene sites in North Asia and Europe^{8,9,10,11,12,13} has shown the power of genetic evidence to clarify the relationships of Middle Pleistocene humans to present-day populations. One discovery made possible by the retrieval of ancient DNA was the identification of an archaic human population from Denisova Cave in Siberia, referred to as Denisovans, that was distinct from Neanderthals.^8,9 However, the morphology of Denisovans remains largely unknown because Denisovan DNA recovered to date derives from fragmented bones and teeth that possess little morphological information.¹⁴ Further, no direct DNA evidence linked to morphology has been found in present-day China, a region that Denisovan populations are likely to have inhabited.^8,9,10,14

Denisovans coexisted with modern humans and are a sister group to Neanderthals,^8,9,10 with whom they shared ancestors around 400,000 years ago.¹⁵ Studies of Denisovan DNA from fossils and indirectly from introgressed fragments in modern human genomes show that at least two Denisovan lineages have introgressed into modern humans.^{9,10,15,16,17,18,19,20} Of these, one is more closely related to individuals from Denisova Cave than the other.²⁰ Although Denisovans are speculated to have once had a large geographical range throughout Asia, to date, the only molecular evidence of Denisovans in Asia is from teeth, fragmentary bones, and cave sediments from Denisova Cave in Siberia^{8,9,10,11,12,13,21} ; a mandible, rib, and cave sediments from Baishiya Cave on the Tibetan Plateau^4,22,23 ; and a mandible from the Penghu Channel in Taiwan.²⁴ Furthermore, samples from a cave in Laos (Tam Ngu Hao 2) have been suggested to be Denisovan based on morphological analysis.²⁵

Throughout this study, we refer to “Denisovans” as the 7 previously described individuals from Denisova Cave (Denisova 2, Denisova 3, Denisova 4, Denisova 8, Denisova 19, Denisova 20, and Denisova 21),^{8,9,10,11,12,13} excluding other individuals and their genetic data due to a more distant genetic relationship (Sima de los Huesos),26,27 ambiguous relationships to individuals from Denisova Cave (Tam Ngu Hao 2), or a lack of associated skeletal fragments (Baishiya Cave sediment).

Confirming the presence of Denisovans can be challenging for several reasons. For example, it is unclear whether the specimen from Laos falls within Denisovan variation, as the proteomic analysis has not yielded genetic markers specific to Denisovans. Moreover, our understanding of Denisovan morphology is limited. Even when genetic material is available, identifying a specimen as a Denisovan is not straightforward. For example, the mitochondrial DNA (mtDNA) from 400,000-year-old individuals found at Sima de los Huesos falls outside the known Denisovan mitochondrial diversity yet is more similar to Denisovan mtDNA than to that of Neanderthals, whereas their nuclear DNA is more closely related to Neanderthals.^26,27

A notable late Middle Pleistocene cranium has been recovered in Harbin, Heilongjiang Province, northeastern China and dated to a minimum age of 146 ka2 (Figure 1A). This cranium has been classified as a new species, named Homo longi, based on its morphology.² However, its morphology has been suggested to be related to the Xiahe mandible,1 which has been associated with Denisovans through proteomic analysis.4 No genetic information has been retrieved from the Harbin specimen, presumably due to its age. In fact, human DNA has only been sequenced from skeletal remains from four sites that are older than 100 ka: individuals dating to ∼400 ka from Sima de los Huesos2^6,27 ; two Neanderthals dating to ∼120 ka from Hohlenstein-Stadel Cave in southwestern Germany²⁸ and Scladina Cave in Belgium²⁹ ; bone fragments from Denisova Cave dating to 187–217,¹³ 190,³⁰ and 123–194 ka³¹ (Figure 1B).

Figure 1 The Harbin cranium and geographic location of hominin specimens older than 100 ka where human DNA has been retrieved

(A) The Middle Pleistocene cranium recovered in Harbin, Heilongjiang Province, northeastern China. (B) Map of geographic locations and dates for some sites where human DNA from individuals older than 100 ka has been retrieved. Harbin ∼146 ka (sampled in this study), Baishiya Karst Cave ∼100 ka (sedimentary DNA), Denisova Cave 123–217 ka (bones from layers 14 and 15 of the East Chamber and layer 22.1 of the Main Chamber), Scladina Cave ∼120 ka, and Hohlenstein-Stadel Cave ∼124 ka. Circles indicate Denisovan mtDNA or Denisovan-like mtDNA; squares indicate Neanderthal mtDNA.

Fu, Qiaomei; Cao, Peng; Dai, Qingyan; Bennett, E. Andrew; Feng, Xiaotian; Yang, Melinda A.; Ping, Wanjing; Pääbo, Svante; Ji, Qiang
Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium
Cell> (2025); DOI: 10.1016/j.cell.2025.05.040

Copyright: © 2025 The authors.
Published by Elsevier Inc. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The identification of the Harbin skull as belonging to the Denisovan lineage — now likely formalised as Homo longi — poses yet another major challenge to creationist claims about human origins. Central to most forms of creationism, especially the young-Earth variety, is the belief that all humans are descended from a single ancestral couple, specially created without evolutionary history. This couple—usually equated with the biblical Adam and Eve—are believed to have existed mere thousands of years ago, and to have passed on a genetic legacy common to all people today. From this myth stems the theological concept of Original Sin, inherited by all humans and said to require divine redemption.

But the emerging picture from palaeoanthropology and genomics utterly refutes this notion. The existence of the Denisovans, now embodied in the remarkably complete Harbin skull, reveals that our species is not the result of a single, discrete act of creation, but rather the product of a long and complex evolutionary process—one in which multiple hominin lineages coexisted, interacted, and interbred. Modern non-African humans carry traces of Denisovan and Neanderthal DNA, evidence of extensive admixture between *Homo sapiens* and these archaic relatives. There was not a single founding couple, nor even a single founding species.

Moreover, Homo longi appears to have been a fully distinct lineage, adapted to its own ecological niche in Ice Age Asia, yet genetically close enough to interbreed with modern humans. This undermines the idea that Homo sapiens are uniquely and separately created, as opposed to being part of a diverse and branching evolutionary tree. The sheer temporal and geographical depth of hominin diversity—stretching back hundreds of thousands, even millions, of years—renders the idea of a recent, isolated origin for humans not just improbable, but demonstrably false.

In short, discoveries like *Homo longi* don't just fill gaps in the fossil record—they expose the theological and scientific bankruptcy of creationist models. They demonstrate that human origins cannot be reduced to simplistic narratives rooted in ancient mythology but must instead be understood through the lens of evolutionary biology, population genetics, and deep time.

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