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The Ancestry of Assassin’s Creed

- Written by Adha -

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A bit of background

Since the first game, the Assassin’s Creed franchise has relied on a very particular formula to give meaning to their games, and a big part of it is the Animus. As discussed already in dozens of videos, the Animus is a device that allows its user to explore the memories of their ancestor or someone else’s ancestors. This means that, together with the transmedia, we have many characters related to each other. This, of course, has also been the topic of many explanatory videos and articles about Assassin genealogy. Pictures and genealogy trees have been made about it. I will be using this knowledge to explain to you how the study of genealogy and ancestry works in the real world.

I must admit this is not an easy topic, so I’ll start explaining the basic concepts and progress bit by bit so you can understand what I’m talking about. Some information about this can be found in a video about the Animus on the YouTube channel of The Science of Assassin’s Creed. The most important things that must be known to understand this article are that: - The genome is the collective name for the set of DNA molecules in an organism, cell, DNA virus, or of RNA molecules in an RNA virus 1.

- A single DNA molecule is made of a nucleotide, which is made of a type of sugar, a nitrogen base and a phosphate group 1.

- Humans have two different DNAs, the nuclear one and a mitochondrial one. The nuclear is inherited from both parents and the mitochondrial is exclusively from the mother 1,2.

- DNA appears wrapped around proteins known as histone and non-histone proteins in the nuclei of our nucleated cells (also called eukaryotic cells). That packaging unit is called nucleosome, which can itself organise as chromatin when it’s packaged with other nucleosomes. This higher level of organisation is called chromatin 3.

- Chromatin can appear more or less loose in the nuclei as euchromatin and heterochromatin 3.

- Chromatin forms chromosomes, the most compact structure of DNA, when eukaryotic cells are preparing to divide. Each chromosome has two sister chromatids bound at the centromere 3.

- During the type of cell division called mitosis, chromosomes are duplicated before the two genetically identical daughter cells actually divide. Mitosis happens in all body tissues in what’s called diploid somatic cells (2n). This means all chromosomes appear in pairs. In humans, for example it’s 23 pairs of chromosomes (n=23; 2*23=46 chromosomes) 3.

- During the type of cell division called meiosis, two successive divisions give rise to four genetically different daughter cells. Chromosome duplication only happens once. To achieve this genetic diversity, during the first division two mechanisms are activated: independent assortment (where each pair of chromosomes bind, forming a bivalent and then two random chromatids are pulled from it; after the first division, the cells are still 2n) and recombination (where the pairs forming the bivalent exchange random segments of DNA at matching locations). After the first division, the daughter cells divide again, creating haploid sperm and egg cells (n), also called gametes. This type of division happens only in specialised germ-line cells in testis and ovary 3.

- An allele is one of two or more versions of a DNA sequence (a single base or a segment of bases) at a given genomic location 2.

- A haplotype is the combination of two alleles, each placed in a chromosome, each inherited from a parent. A mitotype is a mitochondrial haplotype 2.

- I’d like to point out that throughout the article, I assume Isu and human DNA are not separate genomes. They are combined in such a way that throughout the double helix of DNA, we can find small sequences of a triple helix.

What is ancestry?

Ancestry connects genetics and society in fundamental ways. For many people, it has cultural, religious or even political significance and can play a key role in shaping personal and public identities. Nonetheless, the term “ancestry” has been quite difficult to define. As used by the public, the terms ancestry and ancestors often indicate a general connection to people or things in the past. However, in a genetic context, they have a more specific meaning: your ancestors are the individuals from whom you are biologically descended, and ancestry is information about them and their genetic relationship to you.

Pedigree

There are two main ways in which ancestry can be understood, and that is via genealogy or genetics, as stated above. In the case of genealogy, we relate to our ancestors by labelling ourselves based on groups to which they belonged, be it culture, geography or some other aspect of an individual’s identity (e.g.: my grandfather was a Norseman and, therefore I’m one-fourth Norseman). This is what we call pedigree (Figure 1). In this case, knowing who your ancestors were is essential to assign categories. It’s a flawed system if you want all the information, of course, because it lacks the depth of genetic genealogy, with which the gaps created by unknown lineages can be filled by investigating DNA patterns shared across generations. It’s not an infallible field, though, as enough DNA material must be available and intact to perform tests on it 4.

Figure 1: The pedigree of a single individual. Circles are specific ancestors used to define ancestry categories such as culture or geographic region 4.

For the purpose of simplicity, in this text when referring to ancestry we’ll be talking about genetic ancestry.

Genetic ancestry

This kind of ancestry refers exclusively to the roads DNA took to create your personal genome. Because parents transmit only half their DNA to offspring each generation, an individual’s genetic ancestry involves only a small proportion of all their genealogical ancestors 5,6. At any given position in one of your chromosomes, your DNA is inherited through one of the many possible paths through your pedigree (Figure 2). This can be seen in plenty of the genetic ancestry trees seen in the Assassin’s Creed franchise. As an example, Figure 3 illustrates the inheritance of only one line to Desmond Miles.

Figure 2: Genetic ancestry tree showing two converging DNA lines 4.

Figure 3: Genetic ancestry tree of the maternal line of Desmond Miles. Image by @ultimatezetya on Deviantart 7,8,9. The red lines indicate spouses and the blue indicate mark blood relatives.

Different positions in the genome may have different paths of inheritance, because parental chromosomes are shuffled together during meiotic recombination. Thus, the difference between genealogical and genetic ancestry can be summed up by the observation that full siblings have identical genealogical ancestry but differ in their genetic ancestry due to differences in the transmission of chromosomal segments from their parents 4. A good example of this would be the fact that Ezio Auditore, like his father Giovanni, had a much more natural Sixth Sense than his sister Claudia, who never really showed it as far as we know 8.

I would also like to point out here that due to the nature of the formation of gametes, the offspring only have access to genetic memories of their ancestors as seen in Assassin’s Creed 2. This is why Desmond cannot really follow Altair’s memories after Sef’s conception 8. Something similar happens with Haytham and Ratonhnhaké:tön 12.

Ancestral recombination graph

An even more detailed method that can be used to determine the origin of different parts of your DNA is a structure called an ancestral recombination graph (ARG). If we go back to the tree depicting an individual’s pedigree (Figure 1), the ARG is a subset of the pedigree representing the ancestry of the DNA inherited by that individual. It contains only those paths through which DNA has been inherited, and only those nodes corresponding to ancestors for which there was a recombination event 4. Recently, it was discovered, thanks to a new ARG inference approach, that only 1.5 to 7% of the human genome is unique. The rest of the lineages are shared with archaic hominins 10. The ARG, therefore, tells you which parts of your genome were inherited from which ancestors and represents all the ancestral information that can be obtained from genetic data alone (Figure 4). For example, your pedigree includes many ancestors from whom you inherited no genetic material. These ancestors are not included in the ARG, and your genome cannot provide any information about them 4. For instance, we know Callum Lynch inherited DNA from Arno Dorian 11. However, it could be very likely that he has no genetic material related to Arno’s great-grandmother, even though they are related by pedigree. The great-grandmother would then not be included in the ARG.

This type of representation is not included in any of the trees from the Assassin’s Creed franchise, so, in the future, the trees shown will be like the genetic ancestry tree represented in Figure 2.

Figure 4: Genetic ancestry in the form of the ARG for a single individual. The ARG is contained within the structure of the pedigree, with nodes corresponding to ancestors in which there was a recombination or coalescence event, and edges or lines between them representing paths of descent (through other ancestors which are not represented) for particular segments of DNA 4.

Isu ancestry

Now, in a more Assassin’s Creed-related topic, we have the Isu or Those Who Came Before, as we knew them in earlier games. These humanoids were a different species altogether from humans. They were incredibly advanced and dominated Earth for millennia until the Great Catastrophe 12. Already before the fall of their rule, some Isu had already cross-bred with humans. As an example, we have Phanes, the Isu scientist in charge of Project Anthropos or, in other words, the creation of humans. His daughter, a hybrid Isu-human named Eve, would become the official leader of the human rebellion against the Isu 13,14.

Interestingly, before the Great Catastrophe, there was another way to create an Isu-human hybrid. Elpis was a human that lived in Atlantis and the lover of Atlas, a son of Poseidon. She wanted to be with Atlas despite the restrictions on Isu-human relationships, so she tasked Kassandra (who appeared as the Dikastes in Aletheia’s simulation) to gather some adamant (pathorica as Abstergo Industries call it) to create an Isu device that would mix her human DNA with that of an Isu 13.

After the Great Catastrophe, the crossbreeding between Isu and humans became more common, first creating hybrids and later what we know as humans. That’s why Isu DNA can still be found in human DNA nowadays, albeit at a very low percentage of 0.0002-0.0005% 15. In some cases, like the one of Kassandra, Eivor and Desmond Miles, there are higher percentages than in your average person 16,17,18. Eivor is a special case, though, since she is what could be considered a Sage, a reincarnation of the Isu known as the Norse God Odin 17.

Humans with a high Isu DNA percentage

These humans have a very high percentage of Isu DNA and have natural access to the Sixth Sense or Eagle Vision in a more or less powerful way, but they are still affected by Pieces of Eden. An example could be, as mentioned before, Ezio Auditore, but other characters are Altaïr Ibn-La’Ahad, Desmond Miles, Edward and Haytham Kenway, etc 7,8,12,18.

Other characters show this affinity for Pieces of Eden and Eagle Vision to a lesser extent, such as Arno Dorian 15.

Additionally, there are other characters from both the main games and transmedia that can use Eagle Vision by connecting with eagles of different species and seeing through their eyes, as well as controlling them, such as Bayek of Siwa with his Bonelli’s eagle called Senu and Io:nhiòte, Ratonhnhaké:ton’s daughter, with a random eagle that looks like an American Golden eagle 19,20.

These humans are people that, due to the convergence of different human lines and random chromosomal recombination, ended up with high Isu DNA content in their own DNA. The human with the highest recorded Isu DNA is Desmond, and his DNA content was 0.952%, 5 times lower than that found in Sages 15.

Tainted ones

These people have a much higher Isu DNA concentration than the previously discussed group. In this case, we’re talking about humans who are descended from Isu-human hybrids, whose hybrid line has been maintained more or less intact, and who possess special abilities aside from Eagle Vision. For example, they cannot be affected by Pieces of Eden. A good example of this is Kassandra of Sparta, who owned the broken spear of Leonidas, a powerful Piece of Eden. In addition to this, she was in contact with several Pieces of Eden such as those belonging to the Olympos Project and the Staff of Hermes Trismegistus, for her entire life without being negatively affected by them. Her biological father, Pythagoras, is also known to have carried the Staff for decades. This wasn’t the case for Layla Hassan, though. She was almost immediately corrupted by the staff’s power 16. Kassandra’s brother Alexios (also known as Deimos), Leonidas, Myrrine, Elpidios and a woman named Phila, who belonged to the Order of the Ancients, are the only known Tainted Ones so far 16,21.

To keep the purity of the hybrid line, people that knew to be part of one made sure they had children with other Tainted Ones or very likely with people with traits related to the Isu, such as the Sixth Sense. An example of this Tainted One relationship is that between Pythagoras and Myrrine 16.

A controversial topic of note is the fact that Amunet (Aya) didn’t inherit any Isu traits that we know of, and she definitely wasn’t a Tainted One. So, what happened? The most likely reason is that the DNA was heavily “diluted” during the 339 years that separate the births of Elpidios and Amunet. This could have happened if the way the Isu DNA has recombined with human DNA meaning the loss of triple helix fragments in the gametes and, also, if the people getting together with those with higher Isu DNA just didn’t have enough Isu DNA content in their genome resulting in an absence of significant Isu DNA in Amunet. This is actually quite interesting because if true, it reinforces the idea that Isu DNA is found exclusively in the nuclear genome (most likely non-coding) and not the mitochondrial, which is known to be more stable during inheritance, which is why it’s widely used in archaeology and evolution studies 22. An example of this is the presence of the same mitotypes in modern cats of the Levant and ancient cats mummified by Egyptians, even though the minimum time passed between these cats is 1800 years 23.

Sages

These are the ones that contain the highest (even more than the Tainted Ones) amount of Isu DNA, between 5-6% actually 15.

Previously, we were only aware of Sages that were reincarnations of the Isu Aita, Juno’s husband. Examples of Sagas were John Standish, François-Thomas Germain, Bartholomew Roberts and, more recently, Elijah, the son of Desmond Miles 15,18,24. With the release of AC Valhalla, we learned that (attention: major spoilers) other gods, specifically Norse gods, had found a way of reincarnating in humans millennia after their deaths 17. The way Aita and the Norse gods reincarnated are not the same, though. It seems like when Juno put Aita’s memories in the pool of human genomes, through probability and mathematics, she made possible his reincarnation several times in different people, which is not the case for the Norse gods as far as we know. The Sage Isu DNA is not inherited in the same way as human DNA since there aren’t known cases of Sages having children that were also Sages, although we don’t even know if Sages reproduced. Those we know of were obsessed with Juno or maddened by Aita’s memories, so they probably weren’t willing to have children. Another possibility is that Sages were infertile, although this may be a long shot.

A high presence of Isu DNA is not enough to be a Sage. The Isu DNA a Sage has must come from the same Isu individual, hence the term “reincarnation”, allowing them to access Isu memories with such intensity that at a certain point, the Sage might think they are the Isu, like in the case of Loki and Basim Ibn Ishaq, or Valka’s mother, Svala, who was the reincarnation of Freyja 17.

As explained by Darby McDevitt in October of 2022 ,the narrative director of Assassin’s Creed Valhalla, there aren’t two entities fighting for control of the body of the Sage. The Sage is generally unaware of their inherited Isu DNA until a traumatic event triggers the memories of the Isu they’re descended from. When that happens, the behaviour and mental health of the Sage are key variables that influence whether the Sage gives up their personality and lets the Isu memories, and personality take over, but not the Isu itself. When we see Sage-Isu interactions, for instance, between Eivor and Odin, we see a dramatised version of self-reflection by Eivor and not an actual conversation.

Hopefully, with Assassin’s Creed Mirage, we will get even more lore and answers about Sages. Or perhaps even more questions.

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