Oldest Modern Human Genome Reconstructed Using DNA From 45,000-Year-Old Skull

Human Skull From Zlatý Kůň

This skull from Zlatý kůň cave near Prague belonged to the earliest known modern human in Europe. Credit: Marek Jantač

The fossil skull of a woman in Czechia has provided the oldest modern human genome yet reconstructed, representing a population that formed before the ancestors of present-day Europeans and Asians split apart.

In an article published in Nature Ecology & Evolution, an international team of researchers analyses the genome of an almost complete skull first discovered in Zlatý Kůň, Czechia in the early 1950s and now stored in the National Museum in Prague. The segments of Neanderthal DNA in its genome were longer than those of the Ust’-Ishim individual from Siberia, the previous oldest modern human sequenced, suggesting modern humans lived in the heart of Europe more than 45,000 years ago.

Zlatý Kůň Human Skull

Lateral view of the mostly-complete skull of Zlatý Kůň. Credit: Martin Frouz

Ancient DNA from Neandertals and early modern humans has recently shown that the groups likely interbred somewhere in the Near East after modern humans left Africa some 50,000 years ago. As a result, all people outside Africa carry around 2% to 3% Neandertal DNA. In modern human genomes, those Neandertal DNA segments became increasingly shorter over time and their length can be used to estimate when an individual lived. Archaeological data published last year furthermore suggests that modern humans were already present in southeastern Europe 47-43,000 years ago, but due to a scarcity of fairly complete human fossils and the lack of genomic DNA, there is little understanding of who these early human colonists were — or of their relationships to ancient and present-day human groups.

In a new study published in Nature Ecology & Evolution, an international team of researchers reports what is likely the oldest reconstructed modern human genome to date. First discovered in Czechia, the woman known to researchers as Zlatý kůň (golden horse in Czech) displayed longer stretches of Neanderthal DNA than the 45,000-year-old Ust’-Ishim individual from Siberia, the so-far oldest modern human genome. Analysis suggests that she was part of a population that formed before the populations that gave rise to present-day Europeans and Asians split apart.

A recent anthropological study based on the shape of Zlatý kůň’s skull showed similarities with people who lived in Europe before the Last Glacial Maximum — at least 30,000 years ago – but radiocarbon dating produced sporadic results, some as recent as 15,000 years ago. It wasn’t until Jaroslav Brůžek from the Faculty of Science, Prague and Petr Velemínský of Prague’s National Museum collaborated with the genetics laboratories of the Max Planck Institute for the Science of Human History that a clearer picture came into view.

Zlatý Kůň Skull

Initial attempts to date Zlatý Kůň based on the shape of her skull suggested she was at least 30,000 years old. Researchers now believe she lived more than 45,000 years ago. Credit: Martin Frouz

“We found evidence of cow DNA contamination in the analyzed bone, which suggests that a bovine-based glue used in the past to consolidate the skull was returning radiocarbon dates younger than the fossil’s true age,” says Cosimo Posth, co-lead author of the study. Posth was formerly a research group leader at the Max Planck Institute for the Science of Human History and is currently Professor of Archaeo- and Palaeogenetics at the University of Tübingen.

However, it was the Neandertal DNA that led the team to their major conclusions about the age of the fossil. Zlatý kůň carried about the same amount Neanderthal DNA in her genome, as Ust Ishim or other modern humans outside Africa, but the segments with Neanderthal ancestry were on average much longer.

“The results of our DNA analysis show that Zlatý kůň lived closer in time to the admixture event with Neanderthals,” says Kay Prüfer, co-lead author of the study.

The scientists were able to estimate that Zlatý kůň lived approximately 2,000 years after the last admixture. Based on these findings, the team argues that Zlatý kůň represents the oldest human genome to date, roughly the same age as — if not a few hundred years older than — Ust’-Ishim.

“It is quite intriguing that the earliest modern humans in Europe ultimately didn’t succeed! Just as with Ust’-Ishim and the so far oldest European skull from Oase 1, Zlatý kůň shows no genetic continuity with modern humans that lived in Europe after 40,000 years ago,” says Johannes Krause, senior author of the study and director at the Max Planck Institute for Evolutionary Anthropology.

One possible explanation for the discontinuity is the Campanian Ignimbrite volcanic eruption roughly 39,000 years ago, which severely affected climate in the northern hemisphere and may have reduced the survival chances of Neanderthals and early modern humans in large parts of Ice Age Europe.

Zlatý Kůň Skull Sampling

Micro-sampling the petrous bone of Zlatý Kůň from the base of the skull in the clean room at the Max Planck Institute for the Science of Human History, Jena. Credit: Cosimo Posth

As advances in ancient DNA reveal more about the story of our species, future genetic studies of other early European individuals will help to reconstruct the history and decline of the first modern humans to expand out of Africa and into Eurasia before the formation of modern-day non-African populations.

Reference: “A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia” by Kay Prüfer, Cosimo Posth, He Yu, Alexander Stoessel, Maria A. Spyrou, Thibaut Deviese, Marco Mattonai, Erika Ribechini, Thomas Higham, Petr Velemínský, Jaroslav Brůžek and Johannes Krause, 7 April 2021, Nature Ecology & Evolution.
DOI: 10.1038/s41559-021-01443-x

13 Comments on "Oldest Modern Human Genome Reconstructed Using DNA From 45,000-Year-Old Skull"

  1. If humans had a hard time of it 39000 years ago and failed in Europe at that time, to be followed by a second migration into Europe by another lot, then those who made it to PNG and Australia around 60-70000years ago………….?

  2. Sadly the account of creation provided by almighty God ,our creator is not considered in these discoveries. I am thankful for an accurate and complete history of human existence . The flood ,it appears ,may have altered the composition of discovered elements so that testing methods are not able to be accurately assessed by modern means. I pray Gods spirit convics you of the truth of all things …to your benefit.

  3. Human DNA science is hugely interesting. I love articles like this. What is also interesting is how we came into existence, theology is one idea, but I think we need to be open to the possibility that we may have to redefine who or what “God” is and that the true story of “God” may have to be redefined, as science evolves and redefines the human origin story.

  4. There is no place for the “creator”, cos he’s a fairytale. Only a buffoon would still believe in a god

  5. Hey yea Jeff, don’t bring religion into science. There’s a reason we learn science in schools and not religion.

  6. Jeff, why bother reading the article if you’ve made up your mind that the poem of the Jewish Bible is scientific? At least, that’s all I can assume you believe. Having had my ansestry done, I have a lot of Neanderthal dna and a history of long lived ancestors… Perhaps I myself am prehistoric in a sence…

  7. Iris kowalski | April 16, 2021 at 6:52 am | Reply

    There were are humans there are religion if there are no religion or no exist religion there are not or not exist humans..

  8. Iris kowalski | April 16, 2021 at 6:57 am | Reply

    There were are humans there are religion if there are no religion or no exist religion there are not or not exist humans..

  9. Only fake news

  10. BrendaLee Smith | April 16, 2021 at 11:10 am | Reply

    I really like articles like this on DNA and our origins. Hob brought up a good point in that we find more testable skeletons in Europe and Asia and less about the origins of the Australian and Pacific Islanders which is frustrating to me but …
    And Jeff, other than the dating what do you think of the DNA evidence? Who could the Neanderthals be? Where did they come from?

  11. I believe it’s highly likely aliens played with our DNA and created us. I can only imagine what our species would accomplish if we all believed in science and enlightenment. Instead of being hindered with religion, greed, and war. We could create more perfect bodies free of most sickness and rapid aging. Regrow every body part. No that’s playing God so we can’t do that. I can dream…

  12. Michael Friedmann | April 19, 2021 at 3:19 am | Reply

    What exactly does “no genetic continuity” mean? Zlaty kun’s X MtDNA was wiped out and didn’t survive? Or her Autosomal DNA doesn’t match anybody living today? Either way the possibility of contemporary descendants of this population can still exist just not on an X,Y, or Au, chromosome.

  13. Why should science turn us away from God? Why is believing in a creator considered a  fairytale or why are billions of believers called bufoons ? Anyway Everybody is free to pick and choose and all have their own opinion and i respect that. So  heres a opinion of a believer ( me )  . I think Instead of denying a creator we should search our scriptures to see if one of them is scientifically accurate and i know if u do search with a pure  non predjuuce mind than God will guide u to the way .  We always here about the amazing pyramids on how or who built them and we are astonished at the different theorys but one thing is known, we do know they were built and did not come to exist on their own . Can a pyramid be compared to this vast universe and everything in it ? And can a design with a perfect order just be ? Can there be a construction without a constructer? And a grand design without a designer? How Will a atheist reply if i said my phone came by chance ? Or if i point towards a plane or ship and say theres no pilot or no captain or say its not controlled and give a bunch of reasons and explanations will they accept this theory? I assure you that Even a child will not accept this view and will question that if no captain exists than how can this plane or ship travel with no collisions ? Can earth from its rotation to its perfect position , the sun , and moon and everything around us from the water cycle to plants , animals and we humans have no maker ? There cannot be perfection from chance , for every effect there must be a cause its unacceptable to the human mind to believe that chance makes perfection ,  if two cars crash can u get a new truck ? The modern theory on how our universe came to existence is known as the big bang theory . Basically the big bang theory  describes how our universe was formed and how time , space and matter came to exist.  You  can either search for books or simply google search to learn more about the formation of the universe.  (Googled) ” did the universe have a beginning?”   ” The usual story of the Universe has a beginning, middle, and an end. It began with the Big Bang 13.8 billion years ago when the Universe was tiny, hot, and dense. When things finally cooled enough for the first hydrogen atoms to form, the Universe swiftly became transparent. ”
    Again science proves that there was a beginning, and their will be a end and if there was a beginning what was the cause ? Just a few things also taken from a scientific point of view from a book called “ Universe “ by collin A Ronan , (page 9) in which he says the universe began in a colossal explosion , in which energy, space, time and matter were created than goes on to say on (page 30) that the earliest moment was called planck time a brief interval of 10-43 seconds . He states that the entire universe today occupied a space 10 – 20 times smaller than a atomic nucleus and mentions that matter, energy, space, and time were CREATED in an inferno of particles and forces UNKNOWN in the modern universe “
    Although most scientist do admit there was a beginning and admit that everything was suddenly created but they do not further search who caused this to happen and they go on to say “Unknown forces”  About life he says ( page 158 ) that “ how life began on earth remains a mystery” than (page 154) says “ Life on earth is all – prevading but elusive. It can be found from ocean floor to mountain peak, yet cannot be made in a laboratory. New life can begin in a test tube with a human egg fertilized in vitro , but this cannot be nurtured to viable babyhood outside the womb  .” (my respect to the author) 
    you see how Science has no accurate explanation on how life formed and where it came from or why our planet has all the conditions just to support life . Furthermore (page 149) he says “ in our solar system only planet earth supports life , and in this sense our planet certainly is unique. Only here , it seems , are conditions suitable for the evolution , and existence of complex and intelligent life forms . “
    Now after reading all of this I ask all readers :”Who made life suitable only on earth when before the big bang there was no beginning? Can a collision ( big bang ) work and perfect all the conditions to support life ? If the earth,  sun and moon were not in those exact locations would we all be here ? Why doesn’t the moon drift away from earth or all the planets just collide ? Who made the water cycle to where it forms clouds and rains in proportion ? Who governs all this system ? And why is it consistent? Why the consistency ? Why does the order of the planets and whole system not change or collapse ? Why does the sun keep rising and setting in the same direction? What about the complexity of the human body and the way the DNA works ? What made the conditions in the female body to nurish and carry a child with the utmost perfection ?  Those who deny God have no logical proof for their claim because everything in this existence is a proof of a maker and a intelligent designer . What I described are but little proofs using common sense , now i ask this what proof do atheists have for their claim ? Everything in this existence is a proof of a creator . Whats their biggest claim Other than God is unseen ? I ask them this can you see how a spirit ( life ) enters a womb of a pregnant mother in the embryo or when it  departs when a person dies ? If u put all your efforts to try to capture what a spirit ( life ) looks like or how it enters or departs all your efforts will fail and will suffer defeat because the nature of life is unseen !
    Than can not seeing it ( life ) deny that it exists ? Can you see the air you breathe? You cannot see it but you know it exists . What is life or air in comparison with the Almighty who has no likeness? He is far above to be seen , its the inner heart that perceives him . I can only say what was reported that the grandson of the Holy prophet of Islam Imam Hussein peace be upon him said in one of his prayers to the creator “ Blind is the eye that does not see you “ I agree whoever sees all that exists and denies a maker has a blind eye ( inner perception) i mean by the word “blind” the inner heart or perception not the actual physical eye….Now about evil its we who cause evil not God  thats why he sent messengers as representatives to guide and teach mankind but its us who denied them and played with most of his words.
    Can you not see everything in this existence submits its will to the creator without disobeying? From the sun , moon ,stars, plants , animals,and  water cycle.  Is it not only mankind thats disobeying the laws of creation ? Our free will and intellect is actually a test by our creator to examine us , our inner selves and desires to see who of us deserves reward and follows the guidance or who will cause evil and deserve his wrath or punishment . Who is the cause of evil we humans by following our desires and choosing evil or is  god the cause ? When a teacher instructs, explains , guides and warns and than gives a final exam at the end, isn’t it common sense that the students who tried and strived  pass and the ones who did not care and slacked off usually fail ? Why ? Who made them slack off and fail the teacher or there own free will ? The fact is God created us pure with desires and free will as a  test . Some things are beyond our will such as sickness , our lifespans exc.. Once we use our common sense and agree that there is  a creator than we will know that there must be a accurate scripture along with a  savior because there must be divine laws to govern mankind just like there is laws to all creation and there must be a afterlife ( heaven Nd hell ) where the evil doers and unjust get punished and the truthful the handicapped , sick , poor  and the faithful good  doers get rewarded .   …..Now about the old human remains or findings ,  that actually does not disapprove religion . Here is 2 hadiths ( quotes ) from imam jaafar al sadiq the 6th muslem shia imam who clearly says 1400 years ago that there were humans before prophet adam and they all became extinct.  book called “Khisal” narrated from Imam jaafar al Sadiq (pbuh) in which he says: “When Allah (God) created the earth, he created seven worlds in it (and made each one extinct); none of those worlds [generations] were of Prophet Adam’s generation. Allah created all of them from the earth’s crust and brought them one after another, and created a world for each one after the other, until He created Prophet Adam and ramified his generation from him.”

    You see how he clearly says all those worlds or generations are all extinct and that they existed on earth !
    Again its narrated from the same Imam jaafar al Sadiq (as) in a book called Tawhid by sheikh sadouq in which the Imam jaafar peace be upon him explains: “You may assume that God has not created any humans other than you, but this is not true because he has created thousands of thousands of humans before you and you are the last generation of humans”. 

    Do these sayings disaprove these scientific findings ? No it actually agrees with these modern discoveries. So when you hear that remains from millions of years of humans are being discovered than a certain  religion has a answer to that. All beliefs are respected and i meant no disrespect but just wanted to clarify ..The holy quran is the final book sent to the final messenger confirming all previous scriptures and as a continuation and correction of the old testament and holy bible. It is the only scripture that is still intact every word by word and is the only scripture claiming to be the direct word of God and not sayings or by inspired individuals. It claims to be a miracle ( as all prophets  sent with different miracles to prove their claim ) its miracle is in its arabic form but the translation ( although not exact )  is also a  guidance.You can simply search “miracles of the quran ” and you will see wonders of accurate scientific phenomenons that were recently discovered and were written 1400 years ago from embryology all the way to the expansion of the universe . Actually heres a few verses of what i mentioned above and a few of the many verses of holy quran that  are all of scientific accuracy and have only recently been diacovered that were written more than 1400 years ago!  The development of the baby in the mothers womb  is mentioned in many places throughout the holy quran with the utmost accuracy .I really dont think there was technology or microscopes 1400 years ago .   Prophet adam was created directly from clay ( earth ) and heres the exact stages in the mothers womb . (Holy Quran 23:12-14)
    “And certainly did We create man from an extract of clay. ( 12 )
    Then We placed him as a sperm-drop in a firm lodging.(13)
    Then We made the sperm-drop into a clinging clot, and We made the clot into a lump [of flesh], and We made [from] the lump, bones, and We covered the bones with flesh; then We developed him into another creation. So blessed is Allah, the best of creators.”(14)

    ( when God says “we ” hes referring to his self thats a  form of elequence in arabic its a sign of greatness . )

    Expansion of Universe

    “The heavens, We have built them with power. And verily, We are expanding it”  (quran 51:47)

    The word is not heavens in arabic thats only the translation . Its referring to the ( samaa ) which is universe in that verse. Edwin hubble discovered the expansion of the universe  i believe in 1929 ! So how was it written in the Quran 1400 years back?

    (Quran 21:30) can this be the big bang theory?
    • Do not the Unbelievers see that the heavens and the earth were joined together (as one unit of creation), before we clove them asunder? We made from water every living thing. Will they not then believe?

    Below is a miraculous verse where God refers or inspires the female bee  …. in arabic grammer God is telling the  female bee  to make the honey . u can  simply google “are the worker bees , male or female” ? surprisingly  You will see that it says that all the worker bees are female ! now please is there a explanation  on how can anyone 1400 years ago know this unless these words are directly Gods words revealed to his last messenger .   These are a only a few of the many scientific phenomenons that are mentioned in this holy book.
    “Googlethe verse”
    (Quran 16:68-69)
    And your Lord (Allah) revealed to the bees: Build your hives in mountains, trees and in what they build. Then eat (to the female bee ) from every fruit and follow (to the female bee) your Lord’s enslaved paths, from its bellies  exits drink of different colors, in it healing for man. These are signs for those who contemplate.
    ( im not A expert to interpret these holy verses as theres scholars who are specialized in this fied ) but i am familiar with there scientific aspect . Anyway
    Dr  maurice Bucaille ( author of  ” the bible , the quran and science ) said :
    The Qur’an follows on from the two Revelations that preceded it and is not only free
    from contradictions in its narrations, the sign of the various human manipulations to
    be found in the Gospels, but provides a quality all of its own for those who examine it
    objectively and in the light of science i.e. its complete agreement with modern
    scientific data.”

    Back to the creation of previous humans   concerning the topic of our main discussion  (Holy Quran 2:30-33)
    Behold, thy Lord said to the angels: “I will create a vicegerent on earth.” They said: “Wilt Thou place therein one who will make mischief therein and shed blood?- whilst we do celebrate Thy praises and glorify Thy holy (name)?” He said: “I know what ye know not.”

    • And He taught Adam the names of all things; then He placed them before the angels, and said: “Tell me the names of these if ye are right.”

    • They (angels ) said: “Glory to Thee, of knowledge We have none, save what Thou Hast taught us: In truth it is Thou Who art perfect in knowledge and wisdom.”

    • He said: “O Adam! Tell them their names.” When he (adam)had told them, Allah said: “Did I not tell you that I know the secrets of heaven and earth, and I know what ye reveal and what ye conceal?”

      The angels questioning the cause or reason for prophet Adams creation or the  creation of beings who will cause bloodshed  can actually be that the earth was previously  populated with   beings ( humans ) who shed eachothers blood and caused corruption which can indicate that there were creatures ( humans) before prophet adam who caused this corruption on earth then the almighty decided to create a being who can be a representative of the almighty on earth , moreover a prophet . This new being will be different than previous humanlike creations as he will be perfect in knowledge and intellect and conduct and will be a guide to mankind and will have prophets from his offspring such as ( noah , abraham, moses, jesus , mohamed peace be upon them all ) as guides or  representatives of God on earth. All humans today are from the offspring of prophet adam or the “modern man” and eve and as evolution is not my subject of debate ,  i dont deny science but confirm it ,   but what is known is that all humans today are directly from this last generation of humans and first perfect being ( prophet Adam ) we did not evolve from any other species but we were made as as a  special creation as prophet adam was created directly and did not evolve as i stated .As we know All previous human or humanlike species went extinct , Let us suppose we evolved why are homosapiens (humans ) the only creatures that evolved to this mental perfection ? Why don’t we see a gorilla or any other animal species making a invention or advancing in knowledge and technology? The fact is we ” modern upright ” or homosapiens or whatever we are called, DID not evolve , Why dont we think for one second on why is everything around us created with the utmost perfection? Is it made to support unintelligent , or intelligent beings  who can ponder on creation and appreciate the maker? The one who made this system and designed it with the utmost perfection must of made it and prepared it for intelligent beings who can learn and appreciate  the creator. Again Imam Husayn son of  ‘Ali (‘a) peace be upon them said: “Verily, Allah, ( God ) the Exalted, has not created human beings except for recognizing Him (God) and worshipping Him as (the consequence of) knowing Him; and when they worship Him they would lack the need of adoring any human being (or things) other than Him because of that worship.”
    (Safinat-ul-Bihar, vol. 2, p. 180)
    By the way the name “Allah” is Gods name in arabic and even our christian brothers use that holy name in arabic . Just clarifying so no one thinks the muslem God is different than the christian or jewish god. We the 3 abrahamic religions believe in the same God with slight differences,  He is the same creator that sent all the messengers with slightly different laws needed at those times at different periods. He sent prophets to every nation and culture preaching the same messege InTHEIR languages preaching, the divine laws and his oneness . Religion does not contridict scientific findings morever testifies to it because all modern homosapiens are different than all previous ancient human findings or remains as you all well know …. i advise anyone to read the (“Holy Quran”) which is the direct word of God brought down directly by arch angel gabriel to prophet mohamed peace be upon him and his family . All other books are not direct scriptures rather the work of man liks history books .  Another main book after this holy scripture  is  (“nahjul balaghaa” )which is a book of sermons from the prophets first successor imam Ali peace be upon him. These sermons are the jewels of knowledge after the holy Quran . Another book was actually made by a french committee contributing scientific knowledge to the 6th imam jaafar al sadiq and the book can be read online  (https://www.al-islam.org/articles/imam-jafar-al-sadiqs-contribution-sciences-hasnain-mohamedali. ) ..
    Imam Ali whom ( nahjul balaghaa ) belongs to was the first of the 12 imams or guides who carried on the messege after the holy prophet . He was the prophets son in law and The rest of the imams are from his lineage …The 12 imams or princes were prophesied in  the old Testament thousands of years before they were born ,God promises prophet abraham peace be upon him ( Genesis 17:20 )
    “And as for Ishmael, I have heard thee: Behold, I have blessed him, and will make him fruitful, and will multiply him exceedingly; twelve princes shall he beget, and I will make him a great nation.”

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