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TanTin · 05-07-2024, 09:16 PM

There are many publications regarding Denisovan and Neanderthals.
We know lot about Neanderthals and we still know very little about Denisovans.

Now with the available genetic information we may do many additional tests and to check further what are the connections between current world populations and ancient Neanderthals and Denisova.

[Image: Neanderthal_at_AMNH.jpg]

TanTin · 05-07-2024, 09:31 PM

DOI: 10.1126/science.aao626

Denisova and Neanderthals are the first to diverge from the main tree.
But they don't break all the connections to human tree. There would be several interactions between Humans and Denisova/Neanderthals.

TanTin · 05-07-2024, 09:37 PM

Now let me try to show how connected are Humans and Neanderthals / Denisova.

Here is a list of 300 snips.

Show Content

Spoiler

"rs138814405, rs147858239, rs11152550, rs5982926, rs73632987, rs56314521, rs10522044, rs6641699, rs12557427, rs145731456, rs112669710, rs7474278, rs73178119, rs6567572, rs6641588, rs7391844, rs6641591, rs28720078, rs138065307, rs17139403, rs28654640, rs6639009, rs17139421, rs34626685, rs5916402, rs5916417, rs5915682, rs7892770, rs16997788, rs5916554, rs5962129, rs58226402, rs12688302, rs3843793, rs5961484, rs112504788, rs73435955, rs73435965, rs12008474, rs6638662, rs139936086, rs140935281, rs185032469, rs140364606, rs143744383, rs147256979, snp_23_4386709, rs114933932, rs5962182, rs10218421, rs12556581, rs5916639, rs5962195, rs73446101, rs16998794, rs12394654, rs16981043, rs5962216, rs5916676, rs5916678, rs12848207, rs5915797, rs5915798, rs5915799, rs5915800, rs5915801, rs5915803, rs2030907, rs5961529, rs4393058, rs5915856, rs112406998, rs5961584, rs950243, rs144693094, rs114405581, rs1562605, rs7058294, rs148775317, rs115944192, rs56214620, rs115552759, rs5961603, rs2166918, rs5915928, rs1448504, rs5915479, rs1448496, rs1900768, rs1381756, rs1381754, rs1462636, rs936506, rs113721242, rs5915500, rs7878812, rs5961300, rs5915507, rs1462641, rs62581440, rs6639373, rs5916024, rs7061867, rs16983621, rs7887423, rs16997184, rs67619687, rs6639417, rs12557249, rs4826772, rs7065048, rs67016307, rs67724431, rs7063649, rs73436834, rs112843241, rs200709153, rs7057989, rs73189740, rs73189742, rs7889175, rs67623600, rs7054190, rs73189758, rs113503100, snp_23_5329636, rs7052091, rs139449223, rs112298235, rs111463631, rs7064413, rs112221278, rs2068014, rs111807335, rs112846456, rs112004676, rs6529795, rs5915542, rs5916156, rs5961326, rs5915579, rs878251, rs878252, rs882145, rs2369265, rs5916208, rs5916210, rs13362940, rs727507, rs6639466, rs2128519, rs2887433, rs1032036, rs5029026, rs6418982, rs2054636, rs6529851, rs111363044, rs1482820, rs4484833, rs6529854, rs5915608, rs4826810, rs1482821, rs10482266, rs5961845, rs5961846, rs5961848, rs10127275, rs5961851, rs11094822, rs5961885, rs145917208, rs148220593, rs149276455, rs148060705, rs5916355, rs6529932, rs4826718, rs4826719, rs181555810, rs4826842, rs961541, rs1840485, rs7885458, rs73627065, rs5916385, rs12860153, rs4826725, rs5961431, rs73457165, rs73457167, rs112061379, rs28452036, rs12395835, rs1921513, rs7050055, rs16997949, rs1882294, rs7881203, rs7066353, rs6529956, rs113082124, rs7892324, rs5948754, rs141538599, rs12848526, rs2122442, rs185069223, rs72609559, rs12689156, rs72609565, rs72609581, rs4072230, rs12394747, rs150749953, rs143486573, snp_23_6844449, snp_23_6849743, rs5979866, rs5978220, rs57887844, rs5978851, rs7056478, rs4830396, rs7051403, rs3747390, rs1997185, rs5978888, rs112797417, snp_23_7297475, rs12391754, rs7878631, rs113015033, rs6639877, rs113116291, rs143097079, rs112592835, rs16992220, rs6530117, rs845122, rs7064392, rs5978807, rs7063537, snp_23_8174872, rs73627579, rs73627584, rs60154206, rs191288483, snp_23_8390721, rs1526868, rs1526866, rs1526864, rs5934417, rs7889430, rs6640144, rs6530178, rs57383076, rs808143, rs6640194, rs7887099, rs16985078, rs142025879, rs6530200, rs6638862, rs143490476, rs149088535, rs73479490, rs73184404, rs12009108, rs73184424, rs1232108, rs4830403, rs17307280, rs5934508, rs4830614, rs5978289, rs6640273, rs997483, rs73487528, rs61380464, rs6640292, rs73487545, rs184959843, rs4830618, rs10127199, rs7880467, rs1112644, rs4409579, rs5979043, rs12011932, rs6640323, rs5979056, rs6640325, snp_23_9210244, rs16985419, rs5979074, rs5934563, rs739663, rs11798141"

These are some snips from 23 CHR. (X-chr).

We do a simple count: how many of these snips are matching to Denisova3.

This will tell us in general who are the most Denisovan-related individuals.
And here are some results:

Show Content

TanTin · 05-07-2024, 09:44 PM

Now the same 300 snips can be visualized on the PCA.
I am adding a color to each individual, the color is matching to the number of snips that match the Denisova3.
We have the max number for Denisova. And you may see the other groups. The Neanderthals as we know share the most or the highest number of snips with Denisova. And then we have some surprises: there are many Africans who have the highest number of shared snips with Densiova/Neanderthals.

At the same time there are some Africans, who do not share such number of snips. Just the opposite: some Africans have a very low number of shared snips with Densisova/Neanderthals..
Here I am using some ESN.SG individuals for my test, but they are not the only one. There are also few other groups with low archaic number of snips.

TanTin · 05-07-2024, 09:51 PM

Here is the list of the individuals with the lowest number of shared snips compared to Denisova:
(less than 50 shared snips from 300 in total)

Show Content

TanTin · 05-07-2024, 10:20 PM

The existence of such low-Neanderthal low-Denisova africans is more or less contradicting to our expectations.
We do find such low-archaic Africans, but then we find lot higher archaic-mixed Europeans, Asians and Australians ?

All started from Africa, those in the root should have closer connection to the archaic hominoids. Unless if the mix was at later time.
But we don't see much proofs for such later mix. So other processes and explanations are also possible.

My suggestion , or attempt for explanation:
There could be some ancient African population which stayed isolated from the rest for many 10x thousands of years.
As a result of such isolation and as a result of some "selection" process , the archaic features were rejected during the selection process and these group became more distant from Neanderthal / Denisova .

Рespectively such group became the basic populations the base for the later Modern Humans.
At some later time this isolated group started to migrate and to mix with other groups in Africa and Ouside of Africa.

However we see also the existence of high Neanderthal/Denisova africans. bab001/ baa001 are also example for such high Neanderthal/Denisova Africans.

TanTin · 05-07-2024, 10:25 PM

example

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