Homo Erectus DNA Makes Up 1-3% of the Denisovan Genome

Homo erectus reached the Indonesian island of Java some 300,000 years later than many researchers have assumed, a new study finds.

Analyzing volcanic material from sediment that had yielded H. erectus fossils at Java’s Sangiran site shows that the extinct, humanlike hominids likely arrived on the island around 1.3 million years ago, scientists report in the Jan. 10 Science.



More than 100 H. erectus fossils have been found at Sangiran since 1936, many by local residents. For around the last 20 years, many researchers have accepted Sangiran sediment dates — based on analyses of the rate of decay of radioactive argon in volcanic rocks — that put H. erectus on the island from about 1.7 million until 1 million years ago. Others have disputed that timeline, saying the best evidence points to an H. erectus presence at Sangiran from between 1.3 million and 1.1 million years ago until roughly 600,000 years ago.

The new study supports that younger timeline. Researchers, led by paleoanthropologist Shuji Matsu’ura of the National Museum of Nature and Science in Tsukuba City, Japan, analyzed volcanic mineral grains, or zircons, from above, below and within sediment layers where H. erectus fossils had been found. One approach gauged the time since zircons had crystallized, and the other estimated the time since a volcanic eruption deposited zircons at Sangiran.

The World Heritage archaeological site of Sangiran in Central Java is widely regarded as one of the most important sites in understanding the evolution of our early ancestors and their slow march across the globe.

It has produced a steady stream of Homo erectus finds since 1936, now totaling over 100 specimens.

However, despite decades of research, the chronology of the Sangiran site remains uncertain and controversial, particularly the timing of Homo erectus’ first appearance in the region.



To solve this long-standing chronological controversy, Dr. Shuji Matsu’ura from Japan’s National Museum of Nature and Science and colleagues used a combination of fission-track and Uranium/Lead (U/Pb) dating to determine the age of zircon grains found above, below and within the hominin-bearing layers of the Sangiran fossil deposit.

They found that the first appearance date for the Sangiran hominins is most likely 1.3 million years ago and less than 1.5 million years ago.

“Concerning the first appearance date of Homo erectus in the Sangiran area, our results provide a probable date of 1.3 million years ago and a maximum possible date of 1.45 million years ago,” the researchers said.

“Another hominin specimen that has been contended to be the earliest Javanese Homo erectus is the Mojokerto skull from the Perning site in East Java,” they added.

“This skull is now concluded to be less than 1.49 million years old.”

“Thus, the hominin dispersal into Java is resolved to be less than 1.5 million years ago.”

Dating the arrival of the first hominins in Java
The World Heritage archaeological site at Sangiran on the island of Java in Indonesia has major importance for the understanding of human arrival and evolution in Asia. However, the timing of the first appearance of Homo erectus at the site has been controversial. Using a combination of dating techniques for hominin-bearing sediments, Matsu'ura et al. resolved the arrival of H. erectus at ∼1.3 million years ago (see the Perspective by Brasseur). This dating suggests that the earliest hominins in Sangiran are at least 200,000 years younger than has been thought and may represent an important step to the resolution of the controversy.



Abstract
The chronology of the World Heritage Site of Sangiran in Indonesia is crucial for the understanding of human dispersals and settlement in Asia in the Early Pleistocene (before 780,000 years ago). It has been controversial, however, especially regarding the timing of the earliest hominin migration into the Sangiran region. We use a method of combining fission-track and uranium-lead dating and present key ages to calibrate the lower (older) Sangiran hominin-bearing horizons. We conclude that the first appearance datum for the Sangiran hominins is most likely ~1.3 million years ago and less than 1.5 million years ago, which is markedly later than the dates that have been widely accepted for the past two decades.

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Shuji Matsu’ura et al. 2020. Age control of the first appearance datum for Javanese Homo erectus in the Sangiran area. Science 367 (6474): 210-214; doi: 10.1126/science.aau8556

RESULTS
DAN5 and BSN12 sites at Gona: Stratigraphy and archaeology
Abundant stone artifacts, fossil fauna, and a hominin partial calvarium (BSN12/P1) were found at BSN12 (Figs. 3 and 4) in direct association with the Boolihinan Tuff (BHT) (4). Mode 1 artifacts were recovered in situ from the BHT, and glass shards of tephra that geochemically match the BHT were found cemented onto the BSN12/P1 parietal and on both Mode 1 and Mode 2 artifacts (Figs. 3 and 4, fig. S1, sections S1 to S4, and auxiliary data file 1A). Twenty-eight meters of reversely magnetized sediments overlie the BHT, capped by an additional 18+ m of normally magnetized sediments that we assign to the upper Matuyama and Brunhes Chrons, respectively (Fig. 2 and auxiliary data file 1B). Normally magnetized sediments occur 6 m below the BHT, which we interpret to represent the Olduvai Subchron (1.95 to 1.78 Ma ago) (4). The BHT shows strong geochemical affinities with a tuff from Melka Kunture, Ethiopia, dated to 1.262 ± 0.034 Ma ago (1σ uncertainty on ages reported here and elsewhere in text) (5) (auxiliary data file 1, A and B, and sections S1 to S3), consistent with its stratigraphic position in the middle of the Matuyama Chron.


Fig. 3 Hominin crania.
(A) DAN5/P1 neurocranium—four views: lateral, frontal, superior, and posterior. (B) BSN12/P1 frontal—three views: superior (original fossil and cast), lateral, and frontal. (C) BSN12/P1 vault—conjoined parietal and frontal viewed along midline anterior—is to the right. Scale bars, 40 mm (DAN5/P1) and 20 mm (BSN12/P1). For additional views, see the Supplementary Materials. Photo Credit: Scott W. Simpson, Case Western Reserve University.



Fig. 4 Diagnostic stone artifacts.
Two opposing views of Acheulian (Mode 2) and Oldowan (Mode 1) stone tools from (A) BSN12 and (B) DAN5. For each site, the Mode 1 cores are on the bottom row. Photo Credit: Michael J. Rogers, Southern Connecticut State University.

At the DAN5 locality, ~5.7 km northeast of BSN12 (figs. S2 to S5), a well-preserved hominin cranium DAN5/P1 (Fig. 3) and both Mode 1 and Mode 2 artifacts associated with cutmarked bones (sections S4 and S5) were found eroding in weakly developed paleosols that were later buried and overprinted by a well-developed vertic paleosol (Fig. 2, fig. S4, sections S6 and S7, and auxiliary data file 1, C to E, for paleosol descriptions of both the DAN5 and BSN12 sites). Although much of the cranium was found on the surface, the occipital and left maxilla were found in situ, along with six manuports and one Oldowan core (figs. S2 to S5). Freshly eroded Mode 1 and Mode 2 artifacts and fauna were also collected at the DAN5 hominin site, DAN5-South (~140 m south-southwest), and DAN5-West (~50 m west-northwest), all within the same general stratigraphic context, and subsequent site visits yielded additional freshly eroded artifacts and fauna bearing evidence of stone tool cutmarks. All the DAN5 area artifacts and fossils were found in close proximity and from the same stratigraphic interval within a fining upward sequence (Fig. 2 and figs. S2 to S5). The DAN5 artifacts and fossils come from a siltstone unit in reversed magnetized sediments 6.5 m above the top of the Olduvai Subchron and 10.5 m below the base of the Jaramillo Subchron (4), with a well-developed, 8- to 9-m-thick, cumulic paleosol separating the artifacts and cranium from the normally magnetized stratigraphic interval above (Fig. 2). The DAN5 artifacts and cranium are constrained between 1.78 and 1.07 Ma. Using average local sedimentation rates (auxiliary data file 1B), the age estimate of DAN5 can be interpolated and narrowed to ~1.6 to 1.5 Ma (4). This estimate is reasonable, given the thick paleosol and gravel that separate DAN5 from the base of the Jaramillo Subchron above and the stratigraphic proximity to the underlying Olduvai Subchron (Fig. 2 and sections S1 to S3).

The DAN5 and BSN12 stone tool assemblages include Mode 2 handaxes and picks (“large cutting tools” or LCTs) and Mode 1 artifacts (unshaped cores and débitage) (Fig. 4, Table 1, and section S4). The two Gona sites highlighted here were close to riverine sources of raw materials containing trachyte, rhyolite, and basalt cobbles from which most of the artifacts were made. The DAN5 LCTs share broad similarities with those from other early Acheulian sites, such as Konso (Ethiopia) (6) and Kokiselei (Kenya) (7), but differ in some details (table S1). About half of the DAN5 and BSN12 handaxes were made on cobbles, whereas a majority of the handaxes at the 1.75-Ma and younger Konso sites were flake-based (6). A majority of the DAN5 handaxes (87%) were bifacially worked, with better representation of unifacial flaking at Konso. The early Konso handaxes also appear to be longer on average and slightly thinner than those of DAN5. The differences between the Gona and Konso assemblages probably relate to raw material characteristics (flakes from large boulders used at Konso versus smaller cobbles used more often at Gona).

Table 1 Composition of the BSN12 and DAN5 artifact assemblages.
Surface artifacts are likely from the same stratigraphic context as the hominin fossils, although confidence in this assessment is low. “In context” artifacts are confidently considered to be from the same stratigraphic context as the hominin fossil site because they (i) were excavated in situ [5 artifacts from BSN12A and 11 from DAN5 (Main [M] and West [W])], (ii) were found encased in the BHT (at BSN12), or (iii) were recovered after refreshing from previously surface-scraped areas after subsequent biennial site revisits, such as at DAN5-South (S), DAN5-M, and DAN5-W.

DAN5 and BSN12 hominin crania
The larger BSN12/P1 (Fig. 3, fig. S6, sections S8 and S9, and table S2) adult calvarium includes portions of the right orbital margin, frontal squama, and left parietal. The BSN12/P1’s robust supraorbital torus is less arched and thickens laterally where it is joined by the temporalis lines. There is slight sagittal keeling of the vault with some thickening at bregma and parasagittal flattening of the parietal. Endocranial volume is estimated to be between 800 and 900 ml. The robusticity of the supraorbital torus suggests that the individual was a male.

The more complete DAN5/P1 cranium includes much of the vault and maxillae with right P4-M1 and left P3-M3 (Fig. 3, fig. S7, sections S8 and S9, and tables S2 and S3). The vault is globular with an arching supraorbital torus that thins laterally and projects anteriorly forming a well-defined post-toral sulcus. The small endocranial volume (~598 ml) makes it the smallest adult erectin known from Africa (fig. S7). The vault lacks evidence of sagittal keeling although there is a midline parietal swelling above lambda. The vault is thickened at asterion, and lambda and angular tori are present. The anterior margin of the zygomatic root is transversely oriented, and the absence of anterior inflation of the maxillary sinus produces a deep canine fossa. Although the canine is missing, its alveolus is short and ends below the nasal floor indicating a small root. The combination of a gracile neurocranium and face along with a small canine alveolus suggests that this individual was female.

The smaller more gracile DAN5/P1 and the larger more robust BSN12/P1 crania share derived anatomical features diagnostic for H. erectus, yet they differ in several ways (e.g., overall size, details of supraorbital torus robusticity and morphology, sagittal and coronal contours of the vault, degree of midline keeling, and course of the temporalis lines) that require further comment (see sections S8 and S9). The DAN5/P1 cranium bears similarity to the 1.85- to 1.76-Ma Dmanisi crania (8, 9), the 1.6- to 1.5-Ma juvenile KNM-ER 42700 (10), and the small 0.95-Ma Olorgesailie [KNM-OL 45500 (11)] H. erectus crania, and it differs from the typical Asian H. erectus crania by having a smaller endocranial volume, a weakly flexed occipital, and lack of continuous mound-like occipital torus—characters that may correlate with overall size (10, 12). The BSN12/P1 fossil is similar to the more robust African specimens such as Olduvai Hominid 9, the ca. 1-Ma specimens from Middle Awash, Ethiopia [BOU-VP-2/66 (13)] and Buia, Eritrea [UA-31 (14)], and those from Indonesia and eastern Asia by having a longer and lower vault with a thickened supraorbital torus. This anatomical variation in the Gona specimens can be interpreted in several ways. First, the older DAN5/P1 individual may retain more primitive anatomy (e.g., smaller size, gracile vault, and thin supraorbital tori) than the younger BSN12/P1 fossil, and this variation is due to secular anagenetic evolutionary trends within African H. erectus. Alternatively, the size and anatomical variation observed in the Gona specimens is primarily a consequence of sexual dimorphism within a single species. Last, these fossils might reflect a degree of taxonomic diversity previously unrecognized in the Afar for the genus Homo (15).