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#Post#: 431--------------------------------------------------
AI Finds Traces Of A Lost Species In Human DNA
DIR By: Satanica
Date: January 28, 2019, 11:27 am
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HTML https://www.gizmodo.com.au/2019/01/ai-finds-traces-of-a-lost-species-in-human-dna/
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>
> [....]
> New research published last week in Nature Communications
suggests a yet-to-be discovered hominid interbred with modern
humans tens of thousands of years ago. This mystery species
eventually went extinct, but an AI developed by researchers from
the Institute of Evolutionary Biology (IBE) and several other
European institutions found traces of its existence in the DNA
of present-day people with Asian ancestry.
>
> A press release issued by the Centre for Genomic Regulation
said it’s the first time deep learning has been used to explain
human history, “paving the way for this technology to be applied
in other questions in biology, genomics and evolution”.
>
> The mystery hominid is likely a hybrid species of Neanderthals
and Denisovans, according to the new research. Neanderthals, who
lived in Europe, and Denisovans, who spread to Siberia,
southeast Asia and Oceania, were a closely related group of
early humans, diverging from a common ancestor around 744,000
years ago.
>
> When anatomically modern humans (Homo sapiens) spilled into
Eurasia from Africa, they commingled and interbred with both
Neanderthals and Denisovans, which we know through genetic
research. In addition to the generous amount of DNA left behind
by the Neanderthals, scientists have extracted Denisovan DNA
from a well-preserved finger bone found in a Siberian cave.
>
> Today, we find traces of these extinct species in the DNA of
non-African humans, though only Asians retain genetic remnants
of the Denisovans.
>
> But as the new research suggests, modern humans, in addition
to interbreeding with Neanderthals and Denisovans, interbred
with a third, albeit unknown, species.
>
> This idea isn’t new. In 2016, a genetics study co-authored by
Mayukh Mondal from Tartu University and Jaume Bertranpetit from
Pompeu Fabra University — both of whom were involved in the new
study as well — offered evidence showing that indigenous
Australasian populations from South and Southeast Asia “harbour
a small proportion of ancestry from an unknown extinct hominin,
and this ancestry is absent from Europeans and East Asians”.
Their new study is an attempt to show where this “small
proportion of ancestry” came from.
>
> To that end, Mondal and Bertranpetit submitted evidence in the
form of a demographic analysis, one churned by deep learning and
sprinkled with some statistical analysis. Their algorithm
devised and compared numerous complex demographic models to make
predictions about the history of interbreeding events in
Eurasia.
>
> To do so, the researchers fed the algorithm a healthy diet of
whole genome sequences derived from both contemporary and
ancient DNA, enabling the neural network to create a large set
of possible demographic histories. A statistical analysis then
calculated which of these histories were the most probable.
>
> The team used deep learning to teach the algorithm to “predict
human demographics” through “hundreds of thousands of
simulations,” Òscar Lao, principal investigator at the Centro
Nacional de Análisis Genómico and a co-author of the new study,
said in a statement.
>
> “Whenever we run a simulation we are travelling along a
possible path in the history of humankind. Of all simulations,
deep learning allows us to observe what makes the ancestral
puzzle fit together.”
>
> The piecing together of this genetic jigsaw puzzle yielded the
proposed “third archaic introgression”, meaning a third
hybridisation event among ancient humans (the other two being
the genetic mixture between modern humans and Neanderthals and
modern humans with Denisovans). Modern humans interbred with an
unknown third species, and according to the models it’s either a
Neanderthal-Denisovan hybrid, or an early offshoot of the
Denisovan lineage.
>
> That Neanderthals and Denisovans, who share a common ancestor,
may have interbred is not an outrageous suggestion. Last year,
scientists discovered the 90,000-year-old remains of one such
hybrid individual — a girl with a Neanderthal mum and Denisovan
dad. Due to a lack of evidence, scientists aren’t sure if this
was a one-off thing, or if Neanderthals and Denisovans interbred
on the regular.
>
> The new study bolsters the suggestion that the two extinct
species bred often enough to produce a genetically
distinguishable hybrid population.
>
> Serena Tucci, an ecologist and evolutionary biologist from
Princeton University, said the new study reminded her of her own
research from last year, though the authors used a different
approach. Tucci and her colleagues used genetic evidence to show
that early modern humans mated with Denisovan populations on at
least two different historical occasions, which means the
lingering traces of Denisovan DNA embedded in the genomes of
Asian populations living today are derived from at least two
distinct Denisovan populations.
>
> As for claiming the existence of some unknown human species,
Tucci said the authors of the new study should refrain from
conjecturing beyond the available evidence.
>
> “While the study on the history of interaction between modern
humans and archaic hominin contemporaries remains fascinating, I
would be very cautious in making claims of admixture [genetic
mixing] from an ‘unknown’ extinct archaic hominin population or
speculate about the ‘discovery’ of a new hominin species,” Tucci
told Gizmodo.
>
> “As the authors noted, the exact relationship of this extinct
hominin population with the other known archaic populations
(i.e. Neanderthals and Denisovans) is not completely
disentangled — meaning that what the authors call an ‘unknown
hominin’ could likely be a Denisovan group. More work — and more
fossils — are needed to elucidate the history of archaic hominin
admixture.”
>
> No doubt, more evidence is needed. At the very least, however,
these latest studies should encourage archaeologists to be on
the lookout for more clues pointing to the existence of the
hypothesised species.
>
> As a final word, the use of AI in archaeogenetics is a very
cool development, and likely a sign of innovative research
methods to come.
>
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#Post#: 506--------------------------------------------------
Re: AI Finds Traces Of A Lost Species In Human DNA
DIR By: JinxyBean
Date: January 28, 2019, 9:56 pm
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Deep statistics are fascinating, but one wrong number in the
computation and we'll have a potted geranium among our
ancestors.
Neat to know! Thanks!
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