Tuesday, 22 November 2016

A Newly-Discovered Species of Archaic Humans?

Two Vanuatu girls.
Photo credit: Graham Crumb
Source: Wikipedia
People from Melanesia may carry genetic evidence of a previously unknown extinct hominid species

It's hard to see how the Abrahamic religions can continue to hold on to the myth of a single ancestral couple for the whole of humanity in the face of the onslaught from scientific evidence that this model is nonsensical. The Catholic Church's attempt to subscribe to it as an essential part of their dogma whilst also accepting the scientific evidence for the evolution of humans from a common ancestor with other apes and through a series of archaic pre-modern hominids is becoming increasingly untenable.

For example, tentative evidence that the recent human evolutionary was more complicated than we think was presented to a the American Society of Human Genetics Annual Meeting recently by a team associated with the MD Anderson Cancer Center in Texas and the University of Utah. They have developed a model for analysing DNA and have applied it to the DNA of Melanesian people which suggests that, in addition to the introgression of Neanderthal and Denisovan DNA by interbreeding, there may have been a third, unidentified, source of DNA in the ancestry of these people.

The sequencing of complete Neanderthal and Denisovan genomes has provided several insights into human history. One important insight stems from the observation that modern non-Africans and archaic populations share more derived alleles than they should if there was no admixture between them. We now know that the ancestors of modern non-Africans met, and introgressed with, Neanderthals and Denisovans. The estimate of the quantity of shared derived alleles, the mixture proportion, rests on an assumption of no archaic admixture in African populations, and so African populations have been used as the “non-admixed” outgroup in prior analyses. We find that the story is likely more complex, that the history within Africa involves admixture with population(s) related to Neanderthal and Denisova, and that the mixture proportion estimates for non-African populations have been biased, particularly in Melanesia. Here, we present results from a composite likelihood estimator of archaic admixture, which allows multiple sources of archaic admixture. We apply the method to archaic introgression, but it can be used to estimate ancient admixture among any four populations where the modeled assumptions are met. This joint estimate of Neanderthal and Denisovan admixture avoids the biases of previous estimators in populations with admixture from both Neanderthal and Denisova. To correct for dependence in our data, we use a moving blocks bootstrap to calculate confidence intervals. With assumptions about population size and more recent population separation dates taken from the literature, we estimate the archaic-modern separation date at ~440,000 ± 300 years ago for all modern human populations. We also estimate the archaic-modern mixture proportion in the 1000 genomes, and the modern genomes sequenced with the high coverage Neanderthal and Denisovan genomes. We report those estimates here, support several prior findings, and provide evidence for a lower level of Denisovan admixture (0.0191 [0.0184, 0.0197]), relative to Neanderthal (0.0256 [0.0247, 0.0265]), in Melanesia. On the basis of an excess of shared derived alleles between San, Neanderthal, and Denisova we suggest that a third archaic population related more closely to Neanderthal and Denisova than to modern humans introgressed into the San genomes studied here.

PgmNr 73: A complex history of archaic admixture in modern humans.
R. Bohlender; Y. Yu; C. Huff; A. Rogers

It was only about a decade ago that we thought modern Homo sapiens had a single lineage going back to our emergence from H. erectus in Africa. We now, following advances in DNA recovery and sequencing techniques, that not only did non-African people in Eurasia interbreed with Neanderthals but that the ancestors of many Southeast Asian and Pacific Islander people interbred with a mysterious third hominid, the Denisovans, known only from DNA recovered from a finger bone found in the Denisova Cave in Siberia.

Now it seems there may have been a fourth species with which H. sapiens interbred. It's a matter of speculation just who these were, if indeed they existed, and how they fit in our family tree. They could have been H. erectus of a descendant species, as Neanderthals and Denisovans are believe to have been, but we have the tantalising prospect of an earlier migration out of Africa of a species which could have been the ancestor of the 'Hobbit' (H. floriensis).

This finding could shed some light on another Melanesian mystery: the Melanesian Islanders have black skin like Africans but a quarter of them have blond hair and it's not clear where the genes for this hair colour came from. Was it from this mysterious new species?

What is now very apparent from these discoveries is that the notion of even a single ancestral species for modern humans is wrong. Non-African people are the result of hybridisation between at least two species and maybe four or more. Not only is it nonsensical to try to fit the idea of a single ancestral couple into the model of modern humans evolving gradually and emerging by a slow process from archaic species, with never a founding couple, but it becomes even more ludicrous to try to force-fit this model into the picture of the added complication of hybridisation and humanity existing over much of its range and for a considerable period of time as an incompletely evolved ring species in the process of diversifying but not there yet.

Trying to maintain the notion that the science can live comfortably alongside a Bronze Age Middle-Eastern origin myth about a single ancestral couple is like trying to keep one foot on the riverbank and the other on a boat which is moving rapidly away. It's humorous to watch but ultimately disastrous.

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