31,000-year-old burial holds world's oldest known identical twins

Nov 12, 2020
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Given the time frame, is there any DNA or environmental evidence for a connection to Neanderthals and possibly their extinction?
 
Jan 3, 2020
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Given the time frame, is there any DNA or environmental evidence for a connection to Neanderthals and possibly their extinction?
Good question!

The article claims they got DNA, so any signs of Neanderthal introgression could potentially be found.

We were able to obtain
well-preserved endogenous DNA from a cranial vault fragment
of ind3, the results of which have already been published24.
In the case of ind1 and ind2, we sampled their petrous bones.
After enriching for 1,240,000 single-nucleotide polymorphisms
(SNPs), we obtained 722,470 SNPs on chromosomes 1–22
(1.772× average coverage) for ind1 by pooling data from two nonUDG-treated libraries (each SNP with a coverage of at least one
sequence) (Table 1 and Supplementary Data 1). We recovered
264,795 SNPs (0.282× coverage) for ind2 by pooling data from
four UDG-treated libraries (Table 1 and Supplementary Data 1).
Both individuals in Burial 1 were consistent with being genetic
males based on the ratio of sequenced reads aligning to the X
and Y chromosomes (Table 1). Low contamination estimates
(0–1.353%) and high deamination frequencies (ind1: 29.6%; ind2:
10.6%) support the authenticity of the recovered sequences
(Table 1).
To assess kinship and genetic affinities we carried out
population genetic analyses of the three individuals together
with previously published Eurasian Upper Palaeolithic and Mesolithic individuals. First, we analysed ind1 and ind2 using
f3- and f4-statistics. The individuals have genetic affinities similar
to those described by Fu et al. for ind3 (ref. 24). All three KremsWachtberg individuals share most alleles with each other, and
then with individuals from the Gravettian population cluster
named after the site of Dolní Věstonice (Czech Republic,
~100 km northeast)24 (Fig. 3a/b and Supplementary Data 2).
The Burial 1 boys share significantly more alleles with ind3 than
they do with any other Upper Palaeolithic/Mesolithic specimens
analysed, except for Věstonice13 for whom the signal is nonsignificant (Z = −1.477, Fig. 3a and Supplementary Data 2),
which points at close genetic ties between individuals from the
two contemporaneous sites.

Okay, so they didn't look at Neanderthal ancestry specifically (but you or any other interested are welcome to use their material). However, they did find a relation to the earlier individual 3 sequence, and that paper goes into Neanderthal ancestry [ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943878/ ].


From its abstract:

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. We analyze genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas the earliest modern humans in Europe did not contribute substantially to present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans.
The KremsWA3 individual in their paper was about 30,970 year old, had 203,986 useful SNPs, and an estimated 3.9% Neanderthal ancestry (95 % confidence interval 2.6% – 5.2%) [Extended Data Table 2] - it belonged to the "Vestonice" genetic cluster [Extended Data Table 1].

Next time someone does a larger population study along these lines, they can include the twins (and any other pertinent ancient genome material) and increase the precision and detail of such investigations.
 
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Excellent details regarding the DNA identification/analysis ...... Thanks. My speculative suspicion is that H. Sapiens brought measles and mumps into the H. Neanderthalis environment inducing recurrent pandemics, and critical skills population reductions which led eventually to the extinction of H. Neanderthalis. Both sub-species would have been affected. One marker of disease might/could be the loss of tooth enamel in H. Sapiens infants/children of that time period.
 
Jan 3, 2020
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Excellent details regarding the DNA identification/analysis ...... Thanks. My speculative suspicion is that H. Sapiens brought measles and mumps into the H. Neanderthalis environment inducing recurrent pandemics, and critical skills population reductions which led eventually to the extinction of H. Neanderthalis. Both sub-species would have been affected. One marker of disease might/could be the loss of tooth enamel in H. Sapiens infants/children of that time period.
The extinction of human populations is an interesting question where expert opinion differ.

On Neanderthals the population genetic numbers fit that they mixed more or less completely with migrating Africans so as the simplest hypothesis that is my preference. A recent paper put in a larger context however, and it could be that it was among 3 archaic humans that were more likely to go extinct from climate change [ https://www.sciencedaily.com/releases/2020/10/201015111729.htm ].

To shed light on past extinctions of Homo species including H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, and H. sapiens, the researchers relied on a high-resolution past climate emulator, which provides temperature, rainfall, and other data over the last 5 million years. They also looked to an extensive fossil database spanning more than 2,750 archaeological records to model the evolution of Homo species' climatic niche over time. The goal was to understand the climate preferences of those early humans and how they reacted to changes in climate.

Their studies offer robust evidence that three Homo species -- H. erectus, H. heidelbergensis, and H. neanderthalensis -- lost a significant portion of their climatic niche just before going extinct.
No doubt diseases (as well as food stress, re climate) have shaped human populations. Both Neanderthal and Denisovan alleles are adaptively selected for in modern humans [ https://www.sciencemag.org/news/2020/01/africans-carry-surprising-amount-neanderthal-dna , https://www.biorxiv.org/content/10.1101/2020.07.09.196444v1.full ]. There is also potentially a smidgen of Erectus that followed the other archaic genomes in at a proportionate frequency (e.g. today at ~ 0.1 % versus the few percent each of Neanderthal and Denisovan) but I think no one knows yet if it is selected for.

But it is as hard for me to tell if there was a pandemic [ https://en.wikipedia.org/wiki/Pandemic ] in different populations at the time as it is tell on the species/sub-species issue.

A pandemic (from Greek πᾶν, pan, "all" and δῆμος, demos, "people") is an epidemic of an infectious disease that has spread across a large region, for instance multiple continents or worldwide, affecting a substantial number of people. A widespread endemic disease with a stable number of infected people is not a pandemic. Widespread endemic diseases with a stable number of infected people such as recurrences of seasonal influenza are generally excluded as they occur simultaneously in large regions of the globe rather than being spread worldwide.
I'm not even sure if they had much of widespread epidemics at the time, since populations were so scattered.

Of your suggestions, measles is likely too young [ https://science.sciencemag.org/content/368/6497/1367 ].

We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.
In general the paramyxoviruses that measles and mumps belong to have a large range of hosts and a diverse evolutionary history [ https://www.nature.com/articles/s41598-017-02206-0 ]. I can't tell one way or the other about mumps before anyone has tried to locate its split date from related viruses.
 

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