Origins of Modern Human Ancestry

Angela

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See:
https://www.nature.com/articles/s41586-021-03244-5
for a very interesting read.


  • Anders Bergström,
  • Chris Stringer,
  • Mateja Hajdinjak,
  • Eleanor M. L. Scerri &
  • Pontus Skoglund

"New finds in the palaeoanthropological and genomic records have changed our view of the origins of modern human ancestry. Here we review our current understanding of how the ancestry of modern humans around the globe can be traced into the deep past, and which ancestors it passes through during our journey back in time. We identify three key phases that are surrounded by major questions, and which will be at the frontiers of future research. The most recent phase comprises the worldwide expansion of modern humans between 40 and 60 thousand years ago (ka) and their last known contacts with archaic groups such as Neanderthals and Denisovans. The second phase is associated with a broadly construed African origin of modern human diversity between 60 and 300 ka. The oldest phase comprises the complex separation of modern human ancestors from archaic human groups from 0.3 to 1 million years ago. We argue that no specific point in time can currently be identified at which modern human ancestry was confined to a limited birthplace, and that patterns of the first appearance of anatomical or behavioural traits that are used to define Homo sapiens are consistent with a range of evolutionary histories."
 
Did Humans originate in an African-South Eurasian Central Zone?

South Asians have huge diversity in their relationship to early hominids (see stats below).
Africans look connected to Eurasians in two ways, a migration path from East Africa to NW India and also a migration path from SW Asia into Africa.
Evolution is much faster when populations move to new areas. Could Humans have evolved due to constant movement and migration around Northern Africa and South Eurasia in an anti-clockwise direction?
The d stat below shows the affinity of X to Y (Vindija Neanderthal) vs Z (Denisova). Everyone is closer to Vindija vs Denisova but the South Asians are not uniform at all and have huge variation in the d (result of the calc). In comparison the bolded shows how close Europeans are to each other.

WXYZdstdErrZ
Chimp.REFONG.SGVindija.DGDenisova.DG-0.1270.0124-10.2
Chimp.REFJattVindija.DGDenisova.DG-0.1260.0131-9.65
Chimp.REFPUN.SGVindija.DGDenisova.DG-0.1260.014-8.97
Chimp.REFGujaratiDVindija.DGDenisova.DG-0.1220.0117-10.4
Chimp.REFHanVindija.DGDenisova.DG-0.1220.0118-10.3
Chimp.REFControlVindija.DGDenisova.DG-0.1210.0127-9.52
Chimp.REFUBR.SGVindija.DGDenisova.DG-0.1210.0116-10.5
Chimp.REFGujaratiAVindija.DGDenisova.DG-0.120.0116-10.4
Chimp.REFITU.SGVindija.DGDenisova.DG-0.120.0114-10.5
Chimp.REFKalashVindija.DGDenisova.DG-0.1190.0114-10.4
Chimp.REFPJL.SGVindija.DGDenisova.DG-0.1190.0114-10.4
Chimp.REFBalochiVindija.DGDenisova.DG-0.1180.0112-10.5
Chimp.REFSindhi_PakistanVindija.DGDenisova.DG-0.1180.0114-10.4
Chimp.REFPathanVindija.DGDenisova.DG-0.1180.0114-10.3
Chimp.REFRorVindija.DGDenisova.DG-0.1180.012-9.8
Chimp.REFMongolVindija.DGDenisova.DG-0.1180.0116-10.1
Chimp.REFIranianVindija.DGDenisova.DG-0.1160.0114-10.1
Chimp.REFGujaratiBVindija.DGDenisova.DG-0.1150.0116-9.97
Chimp.REFEnglishVindija.DGDenisova.DG-0.1150.0116-9.89
Chimp.REFFrenchVindija.DGDenisova.DG-0.1150.0113-10.2
Chimp.REFRussianVindija.DGDenisova.DG-0.1150.0113-10.2
Chimp.REFRAJ.SGVindija.DGDenisova.DG-0.1140.0118-9.67
Chimp.REFGreekVindija.DGDenisova.DG-0.1130.0113-10
Chimp.REFSaudiVindija.DGDenisova.DG-0.1120.0115-9.74
Chimp.REFMbutiVindija.DGDenisova.DG-0.1110.011-10.1
Chimp.REFPapuanVindija.DGDenisova.DG-0.10.0122-8.22
Chimp.REFYorubaVindija.DGDenisova.DG-0.09950.011-9.07



The below f3(sample, Chimp; Gorilla) shows the shared drift between populations and Chimp, with Gorilla as a reference (outgroup). It shows Africans with the most, followed by South Asians, especially Gujaratis. Can this be read as a connection between Africa and Eurasia through East Africa and Gujarat in India with geneflow going South to North. I used Chimp here because Yoruba is skewed towards West Asia (due to back migrations?), see next section and this may also affect other Africans. I know this is 'weird' calculation but the results do seem credible and it does rank populations in a geographically meaningful way (Indian Gujaratis closest to Africans, with our most distant relative as an outgroup)

MbutiChimp.REFGorilla.REF170.37245.677332
YorubaChimp.REFGorilla.REF16.70.35546.989308
GujaratiBChimp.REFGorilla.REF16.30.34447.379192
GujaratiMuslimChimp.REFGorilla.REF16.30.37643.551980
KalashChimp.REFGorilla.REF16.20.34547.184255
IranianChimp.REFGorilla.REF16.20.3374888944
SaudiChimp.REFGorilla.REF16.20.34447.182632
JattChimp.REFGorilla.REF16.20.38142.451663
PathanChimp.REFGorilla.REF16.10.33947.587030
GujaratiDChimp.REFGorilla.REF16.10.34746.578459
EnglishChimp.REFGorilla.REF16.10.3447.483963
ITU.SGChimp.REFGorilla.REF160.33747.488704
HanChimp.REFGorilla.REF160.34546.484825
BIR.SGChimp.REFGorilla.REF15.80.35344.773392
ONG.SGChimp.REFGorilla.REF15.70.36343.362378


The below shows affinity to Yoruba. Saudi and Iran are much higher here than in the above, so it looks like there is a connection going from West Asia into Africa that is bringing Yoruba closer to Eurasians than Mbuti. Also, this is so pronounced that Yoruba is actually closer to Eurasians than to Mbuti (with Chimp as an outgroup).

ABCf3stderrZscorensnps
SaudiYorubaChimp.REF173.4690780.83467207.8397367
GujaratiBYorubaChimp.REF173.2560230.830172208.69997234
IranianYorubaChimp.REF173.2336720.812747213.14698169
EnglishYorubaChimp.REF173.1558910.8273209.30297808
PathanYorubaChimp.REF173.0613860.813003212.86797985
GujaratiDYorubaChimp.REF173.0577290.83851206.38797132
KalashYorubaChimp.REF172.9873360.822178210.40197720
ITU.SGYorubaChimp.REF172.8735790.808437213.83798141
HanYorubaChimp.REF172.6961530.823571209.69297706
JattYorubaChimp.REF172.4974260.907935189.98995283
BIR.SGYorubaChimp.REF172.4227460.845454203.94196617
GujaratiMuslimYorubaChimp.REF172.4058890.918324187.7495860
ONG.SGYorubaChimp.REF171.2366290.87319196.10596038
MbutiYorubaChimp.REF157.0579170.800474196.20695224


Finally, looking at affinity to ancient hominids, it seems the populations at the corners of the world have the most. Papuans have a lot, so do Northern Europeans apparantly, and Mbuti seems to have quite a bit too. South Asians seems to be most distant in general to ancient hominids. In the first calc above, we are comparing affinity to Denisova or Vindija, and everyone is closer to Vindija, meaning Vindija is closer to modern humans, so Denisova has more older DNA and Vindija shares more with modern humans which is newer DNA. So Mbuti and Papuans are very low on the list, so they share less DNA with the newer Vindija vs the older Denisova, compared to other modern humans, especially South Asians. Hence it looks like ancient hominid affinity is greatest in the most distant and isolated populations, and then at the outer parts (Europe and East Asia).
So taking everything together, does it make sense to say Humans could have evolved due to circular movements between African and Southern Eurasia? Ancient hominid affinity is then greatest in the outer parts, because ancient hominids leaving this central spiral can end up anywhere (East Asia, Siberia, Southern Africa, SE Asia) and then the centre continues to evolve towards modern humans. This explains why people like the Melasians have high Denisova and Neanderthal DNA, because they left the centre at an earlier stage, and so are missing the most recent drift shared by modern humans, also the Mbuti. Basically hominids may be all early humans who left the centre at an earlier stage, but who will also have localization. And humans may not have 'bred' with hominids but the amount of hominid dna in humans could be a result of leaving the centre earlier than others (or the AMH) and hence not sharing the most recent drift of AMH, so that part of the DNA matches hominid instead of AMH.

 
Not sure why the formatting is messed up, but I cant edit it, so just reposting the final paragraphs for readability. Still not great but the below is more readable.

Finally, looking at affinity to ancient hominids, it seems the populations at the corners of the world have the most. Papuans have a lot, so do Northern Europeans apparantly, and Mbuti seems to have quite a bit too. South Asians seems to be most distant in general to ancient hominids. In the first calc above, we are comparing affinity to Denisova or Vindija, and everyone is closer to Vindija, meaning Vindija is closer to modern humans, so Denisova has more older DNA and Vindija shares more with modern humans which is newer DNA. So Mbuti and Papuans are very low on the list, so they share less DNA with the newer Vindija vs the older Denisova, compared to other modern humans, especially South Asians. Hence it looks like ancient hominid affinity is greatest in the most distant and isolated populations, and then at the outer parts (Europe and East Asia).

So taking everything together, does it make sense to say Humans could have evolved due to circular movements between African and Southern Eurasia? Ancient hominid affinity is then greatest in the outer parts, because ancient hominids leaving this central spiral can end up anywhere (East Asia, Siberia, Southern Africa, SE Asia) and then the centre continues to evolve towards modern humans. This explains why people like the Melasians have high Denisova and Neanderthal DNA, because they left the centre at an earlier stage, and so are missing the most recent drift shared by modern humans, also the Mbuti. Basically hominids may be all early humans who left the centre at an earlier stage, but who will also have localization. And humans may not have 'bred' with hominids but the amount of hominid dna in humans could be a result of leaving the centre earlier than others (or the AMH) and hence not sharing the most recent drift of AMH, so that part of the DNA matches hominid instead of AMH.



 
we all come from apes. :)

Yes, and we are still apes today. Chimps are more closely related to humans than they are to gorillas, and gorillas are more closely related to humans than they are to orang utans. How then can modern humans (and all our ancestors of the past 25 million years) be classified as anything other than a branch of the ape family? The above paper ponders the details of the evolutionary history of one species of ape over the past few hundred thousand years and suggests the history may turn out to be more complex than previously thought.
 

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