Patagonian monsters: May 2019

Saturday, May 18, 2019

An earlier Human - Neanderthal split? (400,000 years earlier!)

Aida Gómez-Robles published a paper in Science Advances three days ago (May 15, 2019 - Dental evolutionary rates and its implications for the Neanderthal–modern human divergence, Vol. 5, no. 5, eaaw1268 DOI: 10.1126/sciadv.aaw1268) in which she finds evidence that "support[s] a pre–800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals".

This is really remarkable, as it pushes the conventionally accepted date of divergence back in time from 400 to 800 thousand years ago.

This far older age was worked out by studying ancient Neanderthal teeth from the Sima de los Huesos site in Spain.

Gomez-Robles compared fossilised teeth from archaic hominins such as Australopithecus afarensis, Australopithecus africanus, Paranthropus robustus, Paranthropus boisei, and ancient ones such as Homo habilis, Asian specimens of H. erectus, a Sima de los Huesos H. neanderthalensis and of course, us: Homo sapiens, Other Neanderthal teeth from different sites in Europe were deliberatel left out of the comparative study.

The idea behind the comparison was to see how the shape of teeth in hominins changed over time. Gomez-Robles found that they evolve, and do so at a steady pace. This let estimate when each of these species split from each other.

The conclusion: "The simplest explanation of the results presented in this study is that Neanderthals and modern humans diverged before 0.8 Ma ago", our Last Common Ancestor (LCA) with Neanderthals dates back to 800,000 years ago.

Gomez-Robles goes on to spell out the implications of this more ancient split:

" If the phenotypic LCA of Neanderthals and modern humans was older than 800 ka, this would imply that all fossil hominins younger than this age are no longer valid candidates to occupy this ancestral position. Some fossils younger than this age, however, are frequently considered to be part of the last common ancestral species to Neanderthals and modern humans. These fossils, usually ascribed to Homo heidelbergensis, include European and African specimens, such as Mauer, Arago, Petralona, Bodo, Kabwe, etc., and maybe even some Asian specimens. If Neanderthals and modern humans diverged earlier than 800 ka ago, then all these fossils have to be related either to Neanderthals or to modern humans, or they can be part of a sister lineage to both of them. These fossils, however, cannot be ancestral to Neanderthals and modern humans because they would postdate their evolutionary divergence. An evolutionary relationship between these fossils and both Neanderthals and modern humans would be possible only if they were part of an older ancestral species that persisted in time as a relic species after the actual split of both lineages. Effectively, this scenario would mean that the H. heidelbergensis fossils are part of a sister group to Neanderthals and modern humans but that the evolutionary change from their putative ancestral populations did not involve speciation."

Of course, there are confounding factors that can explain the structural differences in teeth without requiring such an older age, for instance: the teeth evolved quicker in a small population of Neanderthals, isolated from other human groups, making them seem older while they are actually only 400 Ky old.

Tuesday, May 7, 2019

Oldest human footprint in the Americas, in Chile 16 Kya

A paper published in PLOS (Moreno K, Bostelmann JE, Macías C, Navarro-Harris X, De Pol-Holz R, Pino M (2019) A late Pleistocene human footprint from the Pilauco archaeological site, northern Patagonia, Chile. PLoS ONE 14(4): e0213572. https://doi.org/10.1371/journal.pone.0213572) reports finding the "oldest human footprint" in America, North or South.

Pilauco, is close to Osorno, in Chile's Patagonian Lake District. This site is very close (60 miles away) to the Monte Verde site, where ancient remains (Pre-Clovis) were found, but their age was questioned.

The team's dating places this footprint at 15,600 years ago. And this is indeed older than any other human footprint in America.

The interesting part is that its age challenges theories about the peopling of America, which had suggested that modern humans entered America some 13,000 years ago.

Here we have a footprint far older than that date, and far, far away from Beringia!

Why should we assume that they were new arrivals? Couldn't these people have reached Chile 20, 25 or even 100 Kya?

See this video on the footprint:

More findings will clarify our doubts.

Thursday, May 2, 2019

Homo erectus lived in Java with two other ape species: Meganthropus and the ancestors of orangutans

An articl Published: 08 April 2019 in Nature Ecology & Evolution,(Evidence for increased hominid diversity in the Early to Middle Pleistocene of Indonesia by Clément Zanolli et al., reports that at least two species of great apes coexisted with Homo erectus in Indonesia over 1 M years ago.

We already knew that Homo erectus lived with the ancestors of modern orangutans, but now a third ape has been reported, and all three species lived together on the island of Java.

The scientists analyzed teeth discovered in 1941 by Gustav von Koenigswald (which he assigned to a new species, the Meganthropus) and found that they didn't belong to either Homo erectus or the ancestral orangutans.

They apparently belong to another ape, the Meganthropus. The thickness of the teeths' enamel and the positioning of the cusps set them apart from the other two species. Furthermore their wear pattern is similar to that of modern and ancient organgutans, meaning that they ate a similar diet of fruits.

The article is behind a paywall, but the abstract is accessible:

Since the first discovery of Pithecanthropus (Homo) erectus by E. Dubois at Trinil in 1891, over 200 hominid dentognathic remains have been collected from the Early to Middle Pleistocene deposits of Java, Indonesia, forming the largest palaeoanthropological collection in South East Asia. Most of these fossils are currently attributed to H. erectus.
However, because of the substantial morphological and metric variation in the Indonesian assemblage, some robust specimens, such as the partial mandibles Sangiran 5 and Sangiran 6a, were formerly variably allocated to other taxa (Meganthropus palaeojavanicus, Pithecanthropus dubius, Pongo sp.).
To resolve the taxonomic uncertainty surrounding these and other contentious Indonesian hominid specimens, we used occlusal fingerprint analysis (OFA) to reconstruct their chewing kinematics; we also used various morphometric approaches based on microtomography to examine the internal dental structures.
Our results confirm the presence of Meganthropus as a Pleistocene Indonesian hominid distinct from Pongo, Gigantopithecus and Homo, and further reveal that Dubois’s H. erectus paratype molars from 1891 are not hominin (human lineage), but instead are more likely to belong to Meganthropus.

Meganthropus

The hominin which Gustav von Koenigswald discovered and named Meganthropus was big. He estimated its size as being two-thirds of that of the Chinese Gigantopithecus, which in turn was twice the size of modern gorillas.

Meganthropus would therefore weigh around 500 lbs (250 kg) and measure 8 feet tall (2.44 m).

He unearthed a jaw fragment, lost to the Japanese during Word War II, but a cast sent to Germany survived the war.

The lack of other physical evidence led most scientists to group it with Homo erectus, as a variant within that group.

This new paper however puts it in a separate species, distinct from H. erectus and the orangutans.

Could the Meganthropus have evolved into sentient beings? Could the small hominins (i.e. those found in Flores Island or the Philippines) be descendants of this ape?

Or are they related to Denisovans?

Now we know that they differ from Pongo (orangutans), Homo (us) and the Gigantopithecus.

Comparison: the jaw fragment of Meganthropus, an Orangutan jaw (right) and a reconstructed Homo erectus jaw (left) Credit: Senckenberg.

Wednesday, May 1, 2019

Archaic Ghost population admixed with Modern Humans in Africa

A paper published on April 26, 2019, Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations by Belen Lorente-Galdos et al. (Genome Biology201920:77 https://doi.org/10.1186/s13059-019-1684-5) looks into a "Ghost" archaic population (XAf) in Africa which admixed archaic genes into humans (AMH or anatomically modern humans) there.

The authors write:

"We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage."

These are quite high values. The authors continue:

"Our results suggest interbreeding of AMHs with an archaic ghost population that diverged from the AMH lineage at a temporal scale similar to the one between the Neanderthals and Denisovans.
This observation would indicate the presence of a deep archaic population substructure also in the African continent and contrasts with previous studies that suggested that a basal lineage had a major impact only on particular western African populations.
Furthermore, our analyses showed that the estimated proportion of Neanderthal ancestry in Eurasian populations is highly sensitive to the presence of XAf population, increasing by a threefold the amount of archaic introgression.
This result suggests that the amount of Neanderthal ancestry out of Africa that so far has been estimated could be an underestimation by not having considered events of archaic introgression in Africa in the tested models."

I find the last part very interesting, the paper is suggesting that we -non-Africans- may have even more Neanderthal genes than current studies suggest, because they have not considered this XAf admixture into the humans leaving Africa.

The paper downplays a possible "Into Africa" event where Neanderthal genes were passed on to Africans by Neanderthals and assume the source of those genes are more recent: Europeans or Asians. The authors write:

"Traces of Neanderthal introgression have been observed not only in North African populations, who are in fact historically and genetically different from sub-Saharan peoples, but also in other African populations, for instance in Yoruba genomes, although they were most likely introduced through recent Eurasian admixture."

They defined some timelines (we quote them below):

"The AMH lineage and the one from the archaic Eurasian populations diverged 603 kya" the CI is 495.85 to 796.86 kya

"The ghost XAf archaic population and the AMH lineage split 528 kya" (CI 230.16 to 700.06 kya)

"The Denisovan and Neanderthal lineages split 426 kya" (CI 332.77 to 538.37 kya)

Admixture of XAf was significant, considering that Neanderthal genes account for less than 2% of Eurasian genetic makeup. These are the African values of admixture:

3.8% (95% CI 1.7 to 4.8%) in Khoisan
3.9% (95% CI 1.3 to 4.9%) in Mbuti
5.8% (95% CI 0.7 to 0.97%) in West Africa

The paper found that there was high levels of inbreeding as they "observed that ... both Khoisan and Pygmies show higher levels of ROH that are closer to the ones found in North African or Eurasian populations". ROH or Runs of Homozygosity are are regions of the chromosomes where there are many consecutive homozygoous loci and are an indication of inbreeding.

So the supposedly ancient Khoshian are very similar in their ROH to the "more recent" Eurasians, which are supposed to have undergone bottlenecks and later inbreeding.

The issue of African diversity is not addressed clearly. Although they identify some introgression regions:

"Specific candidate introgressed regions have also been identified, for instance, a 20 kbp block found exclusively in sub-Saharan populations that covers the entire MUC7 gene, a protein abundantly expressed in saliva and associated with the composition of oral microbiome [40], or 265 loci spanning ~ 20 Mbp spread across the genome that were detected in two Western African Pygmy populations"

The impact of 4% archaic genes in the overall diversity of modern Africans must be significant, and that means that their diversity is not due to Africa being the cradle of mankind but to an admixture of archaic DNA.

High altitude dwelling Denisovans: Tibet 160K years ago

A paper published today in Nature (Chen, Fahu et al., A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau, doi 10.1038/s41586-019-1139-x ), identifies a lower jaw from a cave in Xiahe, China as belonging to a Densiovan, and dates it as 160,000 years old.

The abstract says:

"Denisovans are members of a hominin group who are currently only known directly from fragmentary fossils, the genomes of which have been studied from a single site, Denisova Cave in Siberia. They are also known indirectly from their genetic legacy through gene flow into several low-altitude East Asian populations and high-altitude modern Tibetans6. The lack of morphologically informative Denisovan fossils hinders our ability to connect geographically and temporally dispersed fossil hominins from Asia and to understand in a coherent manner their relation to recent Asian populations. This includes understanding the genetic adaptation of humans to the high-altitude Tibetan Plateau, which was inherited from the Denisovans. Here we report a Denisovan mandible, identified by ancient protein analysis, found on the Tibetan Plateau in Baishiya Karst Cave, Xiahe, Gansu, China. We determine the mandible to be at least 160 thousand years old through U-series dating of an adhering carbonate matrix. The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

This is significant for several reasons:

It is a second site with Denisovan fossils other than the original cave in the Altai mountains.
It puts the Denisovans in a high altitue environment: the Baishiya Karst Cave is set at 3,280 m (10,500 ft) in the Tibetan Plateau.
Present human populations in that area have inherited a Denisovan gene (found in the Altai cave remains), that gives them the ability to survive the lack of oxygen encountered at high altitudes. Now there is a Denisovan jaw bone in the right location: the Tibetan Plateau, where the Tibetans with this gene live (the Nepalese Sherpas also have it).

Denisovan Lower Jaw Bone. Dongju Zhang, Lanzhou University

The age is also interesting: 160,000 years old. This is in the same range as the age of the Altai cave: Denisovans were living in the Altai cave at least 200,000 years ago and continued living there until about 55,000 years ago. Neanderthals overlapped them, and lived in the cave between around 190,000-100,000 years ago.

The mandible was discovered in 1980, and only now has it been identificed through protein analysis as belonging to a Denisovan.

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