Update for my Oct. 5, 2025 post, Lake Mungo man revisited: maybe the Aboriginal people were not the first to reach Australia. A study published on Nov. 28, 2025 has uncovered interesting information on the date that humans reached Australia, and their interactions with archaic humans in Southeast Asia.
The paper is Francesca Gandini et al., (2025) Genomic evidence supports the “long chronology” for the peopling of Sahul. Sci. Adv. 11, eady9493 (2025).DOI:10.1126/sciadv.ady9493
The paper explores when modern numans settled in Sahul, a landmass that spanned Australia, Tasmania, Papua New Guinea, and smaller islands on the now submerged continental shelf (under the sea since ice melted at the end of the last Ice Age). It aimed at validating the "long chronology" with an arrival around 60 to 65,000 years ago, against the "short chronology" which proposed an arrival 47 to 51,000 years ago.
The authors analyzed DNA and used a genetic clock to time the arrival, which they place around 60,000 years ago. They also found that people arrived using two entry routes.
I have expressed my doubts about the accuracy of genetic clocks in several posts (See the useless genetic clocks), but let's look into this paper and its findings.
Near Oceania was peopled early
The authors found that " We also draw Oceania together with Sahul, finding that Near Oceania was first settled at around the same time as Sahul, followed by intense ongoing exchange." This is interesting as we find that people who used watercraft were already living in Near Oceania (New Guinea, Bismarck Archipelago, and the main Solomon Islands), 60,000 years ago. And would have had plenty of time to cross the Pacific Ocean and reach America!
The molecular clock
The time is set by the exit from Africa which this paper sets by defining the age of mtDNA haplogroup L3 "the African ancestor of all non-African mitogenomes" at 73 to 89,000 years old. This date "robustly precludes any contribution to the modern non-African mitochondrial pool from earlier dispersals before 90 ka, as proposed by some researchers." Which is a limitation. The ages could actually be older, humans left Africa in different waves over the past 200 ky.
The date for Y-chromosome haplogroups is similar; the paper states that "non-African lineages diverg[ed] from ~71 (63 to 81) ka."
The paper used ADMIXTURE tools to analyze genome-wide data (see my comment on this type of tool).
The authors admit the bias and the need to "define" initial parameters by hand: "The Bayesian approach has some problems that have received little attention. In practice, it gives extremely variable outputs, such that any given rate is hard to replicate. The outcome depends on precisely which samples are included in the calibration; even with similar sets of samples, the estimated rate can be very different, and biases appear toward the ages of the predominant samples used in the calibration. Moreover, in the cases of ages in the range 40 to 80 ka, there are few calibration points... In addition to age bias, there is also a profound geographical and phylogenetic bias: Only 2 out of 12 samples used were non-European, and only Tianyuan belongs to haplogroup N. Moreover, one sample (the Iceman) was inadvertently uncalibrated, reducing its age by >12%. Although subsequent calibration attempts have been made with more samples, these have exacerbated the biases."
In the "Materials and Methods" section the phylogenetic analyses and molecular clock dating assumptions and adjustments are explained, like: "We converted mutational distances (both ML and ρ) into years using the substitution rate of about one mutation every 3624 years for the entire mitogenome and correcting for purifying selection using the calculator provided by Soares et al."
The paper suggests a "Northern Route": from Borneo to Sulawesi (Celebes), Banda Archipelago and into Western Papua, and reaching Australia via the Cape York Peninsula in Queensland. The "Southern Route" went from Java, to Sumatra, Sunda, Flores, and Timor, reaching Australia through Arnhem Land and northern Western Australia.
It also mentions archaic admixtures: "The connection of Sahul populations to Aboriginal Philippine groups is reinforced by the presence of distinctively high levels of Denisovan-related archaic-related introgression in both, possibly relating to interbreeding with Homo luzonensis, in the Philippines, and Homo floresiensis, in Wallacea, or even within Sahul itself."
I always like to focus on the oddities, the things that authors point out as "remarkable"or, in this case, "notably", it is the following:
"We also included in this analysis our Iron Age sample from Sulawesi, which carries the Papuan mitochondrial Q1l lineage, alongside 17 further genomes from ancient Wallacea, including a pre-Neolithic sample from Sulawesi (41, 42) (fig. S8). Notably, despite its clear Papuan mtDNA ancestry, the Iron Age sample was the only archaeological sample from Wallacea to carry no discernible Oceanian autosomal ancestry. This result is confirmed by PCA (fig. S9). This indicates both that ancestry from New Guinea, while ancient (41), was not ubiquitous in prehistoric Wallacea, but possibly (at least, since the spread of the Neolithic) restricted to coastal regions, and that sufficient time had elapsed for the ancestry represented by the maternal lineage to have been “washed out” of the autosomal genome in this individual."
This means that the original, Papuan mtDNA was found in an Iron Age (1700 BP) person in Sulawesi, yet it lacked the autosomal (all the other chromosomes) that would mark it as an Oceanian, it carried the input of other non-Oceanian people that diluted its ancestral autosomal DNA. This seems quite obvious since the ancestors of modern Polynesians made their way across this region in recent times, on their way to the Pacific Islands.
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